02531nas a2200277 4500008004100000022001400041245009300055210006900148260008100217300001200298490000700310520153700317653002201854653001701876653002201893653002601915653003301941653002401974100002101998700002402019700002402043700002302067700001802090700002102108856012402129 2007 eng d a0268-914600aMitochondrial haplotypes reveal a strong genetic structure for three Indian sheep breeds0 aMitochondrial haplotypes reveal a strong genetic structure for t a9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLANDbBLACKWELL PUBLISHINGcOCT a460-4660 v383 a

This survey represents the first characterization of mitochondrial DNA diversity within three breeds of Indian sheep (two strains of the Deccani breed, as well as the Bannur and Garole breeds) from different geographic regions and with divergent phenotypic characteristics. A 1061-bp fragment of the mitochondrial genome spanning the control region, a portion of the 12S rRNA gene and the complete phenyl tRNA gene, was sequenced from 73 animals and compared with the corresponding published sequence from European and Asian breeds and the European Mouflon (Ovis musimon). Analysis of all 156 sequences revealed 73 haplotypes, 52 of which belonged to the Indian breeds. The three Indian breeds had no haplotypes in common, but one Indian haplotype was shared with European and other Asian breeds. The highest nucleotide and haplotype diversity was observed in the Bannur breed (0.00355 and 0.981 respectively), while the minimum was in the Sangamneri strain of the Deccani breed (0.00167 and 0.882 respectively). All 52 Indian haplotypes belonged to mitochondrial lineage A. Therefore, these Indian sheep are distinct from other Asian and European breeds studied so far. The relationships among the haplotypes showed strong breed structure and almost no introgression among these Indian breeds, consistent with Indian sheep husbandry, which discourages genetic exchange between breeds. These results have implications for the conservation of India's ovine biodiversity and suggest a common origin for the breeds investigated.

10aGenetic diversity10aIndian sheep10amitochondrial DNA10amitochondrial lineage10aphylogeographic distribution10asheep domestication1 aPardeshi, V., C.1 aKadoo, Narendra, Y.1 aSainani, Mohini, N.1 aMeadows, J., R. S.1 aKijas, J., W.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/mitochondrial-haplotypes-reveal-strong-genetic-structure-three-indian-sheep-breeds-001707nas a2200253 4500008004100000022001400041245005900055210005900114260007400173300001200247490000700259520089800266653002301164653001801187653002001205653002201225653001901247100002101266700001601287700002401303700001801327700001801345856009001363 2009 eng d a1380-374300aMolecular mapping of wilt resistance genes in chickpea0 aMolecular mapping of wilt resistance genes in chickpea aVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSbSPRINGERcSEP a177-1830 v243 a

Fusarium wilt is a widespread and serious chickpea disease caused by the soil-borne fungus Fusarium oxysporum f.sp. ciceri (Foc). We evaluated an F(9) recombinant inbred line population of chickpea for resistance to three Foc races (1, 2 and 3) in pot culture experiments and identified flanking and tightly linked DNA markers for the resistance genes. The simple sequence repeat markers H3A12 and TA110 flanked the Foc1 locus at 3.9 and 2.1 cM, respectively, while Foc2 was mapped 0.2 cM from TA96 and 2.7 cM from H3A12. The H1B06y and TA194 markers flanked the Foc3 locus at 0.2 and 0.7 cM, respectively. These markers were also validated using 16 diverse chickpea genotypes. Identification of tightly linked flanking markers for wilt resistance genes will be useful for their exploitation in breeding programs and to understand the mechanism of resistance and evolution of the genes.

10afusarium oxysporum10aFusarium wilt10aGenetic mapping10aMarker validation10aPathogen races1 aGowda, S., J. M.1 aRadhika, P.1 aKadoo, Narendra, Y.1 aMhase, L., B.1 aGupta, V., S. uhttps://library.ncl.res.in/content/molecular-mapping-wilt-resistance-genes-chickpea-002235nas a2200313 4500008004100000022001400041245010900055210006900164260009200233300001200325490000700337520115100344653003101495653001701526653001601543653002801559653001601587653002201603100001401625700001601639700001701655700001401672700002401686700003101710700002201741700002001763700001401783856012401797 2010 eng d a1234-198300aQTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.)0 aQTL mapping of 1000kernel weight kernel length and kernel width  aSTRZESZYNSKA 34, POZNAN, 60-479, POLANDbPOLISH ACAD SCIENCES, INST PLANT GENETICScDEC a421-4290 v513 a

Kernel size and morphology influence the market value and milling yield of bread wheat (Triticum aestivum L.). The objective of this study was to identify quantitative trait loci (QTLs) controlling kernel traits in hexaploid wheat. We recorded 1000-kernel weight, kernel length, and kernel width for 185 recombinant inbred lines from the cross Rye Selection 111 x Chinese Spring grown in 2 agro-climatic regions in India for many years. Composite interval mapping (CIM) was employed for QTL detection using a linkage map with 169 simple sequence repeat (SSR) markers. For 1000-kernel weight, 10 QTLs were identified on wheat chromosomes 1A, 1D, 2B, 2D, 4B, 5B, and 6B, whereas 6 QTLs for kernel length were detected on 1A, 2B, 2D, 5A, 5B and 5D. Chromosomes 1D, 2B, 2D, 4B, 53 and 5D had 9 QTLs for kernel width. Chromosomal regions with QTLs detected consistently for multiple year-location combinations were identified for each trait. Pleiotropic QTLs were found on chromosomes 2B, 2D, 4B, and 5B. The identified genomic regions controlling wheat kernel size and shape can be targeted during further studies for their genetic dissection.

10acomposite interval mapping10akernel shape10akernel size10aquantitative trait loci10aStable QTLs10aTriticum aestivum1 aRamya, P.1 aChaubal, A.1 aKulkarni, K.1 aGupta, L.1 aKadoo, Narendra, Y.1 aDhaliwal, Harcharan, Singh1 aChhuneja, Parveen1 aLagu, Meena, D.1 aGupta, V. uhttps://library.ncl.res.in/content/qtl-mapping-1000-kernel-weight-kernel-length-and-kernel-width-bread-wheat-triticum-002267nas a2200277 4500008004100000022001400041245011900055210006900174260007900243300001200322490000700334520126700341653000801608653002501616653002501641653001201666653001601678653002301694100002501717700002001742700002401762700002501786700002601811700002101837856013101858 2010 eng d a1073-608500aRelatedness of Indian flax genotypes (Linum usitatissimum L.): an inter-simple sequence repeat (ISSR) primer assay0 aRelatedness of Indian flax genotypes Linum usitatissimum L an in a999 RIVERVIEW DRIVE SUITE 208, TOTOWA, NJ 07512 USAbHUMANA PRESS INCcJUN a161-1700 v453 a

The objective of this study was to analyze the genetic relationships, using PCR-based ISSR markers, among 70 Indian flax (Linum usitatissimum L.) genotypes actively utilized in flax breeding programs. Twelve ISSR primers were used for the analysis yielding 136 loci, of which 87 were polymorphic. The average number of amplified loci and the average number of polymorphic loci per primer were 11.3 and 7.25, respectively, while the percent loci polymorphism ranged from 11.1 to 81.8 with an average of 63.9 across all the genotypes. The range of polymorphism information content scores was 0.03-0.49, with an average of 0.18. A dendrogram was generated based on the similarity matrix by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), wherein the flax genotypes were grouped in five clusters. The Jaccard's similarity coefficient among the genotypes ranged from 0.60 to 0.97. When the omega-3 alpha linolenic acid (ALA) contents of the individual genotypes were correlated with the clusters in the dendrogram, the high ALA containing genotypes were grouped in two clusters. This study identified SLS 50, Ayogi, and Sheetal to be the most diverse genotypes and suggested their use in breeding programs and for developing mapping populations.

10aALA10aAlpha linolenic acid10aDiversity assessment10aLinseed10aOil content10aOmega-3 fatty acid1 aRajwade, Ashwini, V.1 aArora, Ritu, S.1 aKadoo, Narendra, Y.1 aHarsulkar, Abhay, M.1 aGhorpade, Prakash, B.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/relatedness-indian-flax-genotypes-linum-usitatissimum-l-inter-simple-sequence-repeat-issr-001928nas a2200241 4500008004100000022001400041245010600055210006900161260007400230300001200304490000800316520107400324653000901398653002201407653001501429653001301444100001601457700002401473700002401497700002001521700001801541856012701559 2010 eng d a0016-670700aUnderstanding the genetic structure of symplocos laurina wall. populations using nuclear gene markers0 aUnderstanding the genetic structure of symplocos laurina wall po aVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSbSPRINGERcFEB a197-2100 v1383 a

To characterize the genetic diversity of present populations of Symplocos laurina, which grow in the montane forests in India, we analyzed the DNA sequences of a nuclear gene. Using the 881 bp sequence of cytosolic Glyceraldehyde-3-phosphate dehydrogenase gene, we detected 24 haplotypes among 195 individuals sampled from 14 populations. Two dominant haplotypes were distributed over the entire range of this species in India and several private haplotypes were found. Low genetic diversity within population, high differentiation, number of population specific haplotypes and deviation from neutral evolution characterized the present populations of S. laurina. An analysis of molecular variance indicated the presence of geographic structure within the haplotype distribution. The occurrence of S. laurina preglaciation in India is the most parsimonious explanation for the current geographic structure observed. The populations are presumably ancient and might have spread across its extant distribution range in India through a recent range expansion event.

10aGapC10aGenetic diversity10aGlaciation10aRefugium1 aBanu, Sofia1 aBhagwat, Rasika, M.1 aKadoo, Narendra, Y.1 aLagu, Meena, D.1 aGupta, V., S. uhttps://library.ncl.res.in/content/understanding-genetic-structure-symplocos-laurina-wall-populations-using-nuclear-gene-000857nas a2200229 4500008004100000245012900041210006900170260000800239300001200247490000700259100002200266700002400288700002100312700002300333700002500356700002500381700002900406700002100435700002200456700001700478856013200495 2011 eng d00aAuxin signaling and transport promote susceptibility to the root-infecting fungal pathogen fusarium oxysporum in arabidopsis0 aAuxin signaling and transport promote susceptibility to the root cJUN a733-7480 v241 aKidd, Brendan, N.1 aKadoo, Narendra, Y.1 aDombrecht, Bruno1 aTekeoglu, Muecella1 aGardiner, Donald, M.1 aThatcher, Louise, F.1 aAitken, Elizabeth, A. B.1 aSchenk, Peer, M.1 aManners, John, M.1 aKazan, Kemal uhttps://library.ncl.res.in/content/auxin-signaling-and-transport-promote-susceptibility-root-infecting-fungal-pathogen-fusarium02165nas a2200265 4500008004100000022001400041245006900055210006900124260008000193300000900273490000700282520128000289653002001569653001701589653003401606653002301640653001701663100002101680700001601701700001801717700002201735700001801757700002401775856010001799 2011 eng d a1234-198300aMapping of QTLs governing agronomic and yield traits in chickpea0 aMapping of QTLs governing agronomic and yield traits in chickpea aTIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANYbSPRINGER HEIDELBERGcFEB a9-210 v523 a

Chickpea is one of the most important leguminous cool season food crops, cultivated prevalently in South Asia and Middle East. The main objective of this study was to identify quantitative trait loci (QTLs) associated with seven agronomic and yield traits in two recombinant inbred line populations of chickpea derived from the crosses JG62xVijay (JV population) and VijayxICC4958 (VI population) from at least three environments. Single locus QTL analysis involved composite interval mapping (CIM) for individual traits and multiple-trait composite interval mapping (MCIM) for correlated traits to detect pleiotropic QTLs. Two-locus analysis was conducted to identify the main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL x environment interactions. Through CIM analysis, a total of 106 significant QTLs (41 in JV and 65 in VI populations) were identified for the seven traits, of which one QTL each for plant height and days to maturity was common in both the populations. Six pleiotropic QTLs that were consistent over the environments were also identified. LG2 in JV and LG1a in VI contained at least one QTL for each trait. Hence, concentrating on these LGs in molecular breeding programs is most likely to bring simultaneous improvement in these traits.

10aCicer arietinum10aQTL analysis10aQTL x environment interaction10aTwo-locus analysis10aYield traits1 aGowda, S., J. M.1 aRadhika, P.1 aMhase, L., B.1 aJamadagni, B., M.1 aGupta, V., S.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/mapping-qtls-governing-agronomic-and-yield-traits-chickpea-002469nas a2200253 4500008004100000022001400041245011400055210006900169260007400238300001200312490000700324520154700331653000901878653002901887653003101916653000801947100002101955700002501976700002402001700002602025700002102051700002102072856012202093 2012 eng d a1380-374300aDevelopment of genomic simple sequence repeat markers for linseed using next-generation sequencing technology0 aDevelopment of genomic simple sequence repeat markers for linsee aVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSbSPRINGERcJUN a597-6060 v303 a

Linseed (Linum usitatissimum L.) is regarded as a cash crop of tomorrow because of the presence of nutraceutically important alpha-linolenic acid (ALA) and lignan. However, only limited breeding progress has been made in this crop, mainly due to the lack of sufficient genetic and genomic resources. Among these, simple sequence repeats (SSR) are useful DNA markers for diversity analysis, genetic mapping and tagging traits because of their co-dominant and highly polymorphic nature. In order to develop SSR markers for linseed, we used three microsatellite isolation methods, viz., PCR Isolation of Microsatellite Arrays (PIMA), 5'-anchored PCR method, and Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO). The amplified products from these methods were pooled and sequenced using the 454 GS-FLX platform. A total of 36,332 reads were obtained, which assembled into 2,183 contigs and 2,509 singlets. The contigs and the singlets contained 1,842 microsatellite motifs, with dinucleotide motifs as the most abundant repeat type (54%) followed by trinucleotide motifs (44%). Based on this, 290 SSR markers were designed, 52 of which were evaluated using a panel of 27 diverse linseed genotypes. Among the three enrichment methods, the 5'-anchored PCR method was most efficient for isolation of microsatellites, while FIASCO was most efficient for developing SSR markers. We show the utility of next-generation sequencing technology for efficiently discovering a large number of microsatellite markers in non-model plants.

10aFlax10aMicrosatellite isolation10aNext-generation sequencing10aSSR1 aKale, Sandip, M.1 aPardeshi, Varsha, C.1 aKadoo, Narendra, Y.1 aGhorpade, Prakash, B.1 aJana, Murari, M.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/development-genomic-simple-sequence-repeat-markers-linseed-using-next-generation-002450nas a2200265 4500008004100000022001400041245015000055210006900205260009000274300001200364490000700376520141200383653001901795653004001814653002601854653001601880100002001896700002401916700002301940700001901963700003101982700002202013700001702035856013202052 2012 eng d a0733-521000aKernel morphometric traits in hexaploid wheat (Triticum aestivum L.) are modulated by intricate QTL x QTL and genotype x environment interactions0 aKernel morphometric traits in hexaploid wheat Triticum aestivum  a24-28 OVAL RD, LONDON NW1 7DX, ENGLANDbACADEMIC PRESS LTD- ELSEVIER SCIENCE LTDcSEP a432-4390 v563 a

Wheat kernel size and shape influence its flour yield and market price. A hexaploid wheat population of 185 recombinant inbred lines was evaluated for five kernel morphometric traits namely, 1000-kernel weight, kernel length, width, length width ratio and factor form density in two diverse agro-climatic regions in India in five to eight year location combinations. Additive main effects and multiplicative interaction analysis revealed significant contributions from genotype (G) and genotype x environment (G x E) effects for these traits. Quantitative trait locus (QTL) analysis by composite interval mapping (CIM) was performed using a linkage map of 251 SSR markers and 59 QTLs distributed on 16 chromosomes were identified. The majority of the QTLs were located on the D genome (44.07%) and the homeologous chromosomes of Group 2 (38.98%). Stable QTLs detected in three or more year location combinations were identified for four traits. Multi-trait CIM showed 10 chromosomal regions harboring putative pleiotropic loci. Complexity in the genetic effects was further revealed by QTL analysis based on mixed-linear model that indicated 19 QTLs with significant individual effects (main-effect QTLs) and 14 QTL x QTL interactions. Five of these - nineteen main-effect QTLs and one of the fourteen QTL x QTL interactions showed environmental influence. (c) 2012 Elsevier Ltd. All rights reserved.

10aEpistatic QTLs10aGenotype x environment interactions10aKernel size and shape10aStable QTLs1 aPrashant, Ramya1 aKadoo, Narendra, Y.1 aDesale, Charushila1 aKore, Prajakta1 aDhaliwal, Harcharan, Singh1 aChhuneja, Parveen1 aGupta, Vidya uhttps://library.ncl.res.in/content/kernel-morphometric-traits-hexaploid-wheat-triticum-aestivum-l-are-modulated-intricate-qtl-003222nas a2200193 4500008004100000022001400041245014400055210006900199260008100268300000800349490000700357520242200364100002502786700002502811700002102836700002402857700002102881856012602902 2012 eng d a1471-216400aPhylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns0 aPhylogenomic analysis of UDP glycosyltransferase 1 multigene fam a236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLANDbBIOMED CENTRAL LTDcMAY a1750 v133 a

Background: The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L.) is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT) genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches. Results: Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT) genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N). Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST), microarray data and reverse transcription quantitative real time PCR (RT-qPCR). Seventy-three per cent of these genes (100 out of 137) showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot genomes indicated that seven UGTs were flax diverged. Conclusions: Flax has a large number of UGT genes including few flax diverged ones. Phylogenetic analysis and expression profiles of these genes identified tissue and condition specific repertoire of UGT genes from this crop. This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions.

1 aBarvkar, Vitthal, T.1 aPardeshi, Varsha, C.1 aKale, Sandip, M.1 aKadoo, Narendra, Y.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/phylogenomic-analysis-udp-glycosyltransferase-1-multigene-family-linum-usitatissimum-002528nas a2200277 4500008004100000022001400041245014300055210006900198260007100267300001400338490000700352520148300359653002501842653001601867653003201883653002601915653000801941653003701949100002501986700002502011700002102036700002402057700002002081700002102101856012802122 2012 eng d a1535-389300aProteome profiling of flax (linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development0 aProteome profiling of flax linum usitatissimum seed characteriza a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcDEC a6264-62760 v113 a

Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of ID-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.

10aalpha-linolenic acid10acarbon flux10aDigital expression analysis10aflax seed development10aMSE10asecoisolariciresinol diglucoside1 aBarvkar, Vitthal, T.1 aPardeshi, Varsha, C.1 aKale, Sandip, M.1 aKadoo, Narendra, Y.1 aGiri, Ashok, P.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/proteome-profiling-flax-linum-usitatissimum-seed-characterization-functional-metabolic-002427nas a2200301 4500008004100000022001400041245011800055210006900173260005700242300001400299490000800313520138600321653003201707653001701739653001201756653001001768653002801778653002201806100002501828700002501853700002101878700001701899700002101916700001601937700002101953700002401974856012701998 2013 eng d a0032-093500aGenome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum)0 aGenomewide identification and characterization of microRNA genes a233 SPRING ST, NEW YORK, NY 10013 USAbSPRINGERcAPR a1149-11610 v2373 a

MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.

10aDigital expression analysis10aGene cluster10aLinseed10amiRNA10aMiRNA target transcript10aPromoter analysis1 aBarvkar, Vitthal, T.1 aPardeshi, Varsha, C.1 aKale, Sandip, M.1 aQiu, Shuqing1 aRollins, Meaghen1 aDatla, Raju1 aGupta, Vidya, S.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/genome-wide-identification-and-characterization-microrna-genes-and-their-targets-flax-002468nas a2200265 4500008004100000022001400041245015900055210006900214260012000283300001000403490000700413520142200420653000901842653003001851653001901881653001201900653002601912653002201938100002101960700002501981700002502006700002102031700002402052856012602076 2013 eng d a0831-279600aGenome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure0 aGenomewide identification and characterization of nucleotide bin a1200 MONTREAL ROAD, BUILDING M-55, OTTAWA, ON K1A 0R6, CANADAbCANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESScFEB a91-990 v563 a

Plants employ different disease-resistance genes to detect pathogens and to induce defense responses. The largest class of these genes encodes proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains. To identify the putative NBS-LRR encoding genes from linseed, we analyzed the recently published linseed genome sequence and identified 147 NBS-LRR genes. The NBS domain was used for phylogeny construction and these genes were classified into two well-known families, non-TIR (CNL) and TIR related (TNL), and formed eight clades in the neighbor-joining bootstrap tree. Eight different gene structures were observed among these genes. An unusual domain arrangement was observed in the TNL family members, predominantly in the TNL-5 clade members belonging to class D. About 12% of the genes observed were linseed specific. The study indicated that the linseed genes probably have an ancient origin with few progenitor genes. Quantitative expression analysis of five genes showed inducible expression. The in silico expression evidence was obtained for a few of these genes, and the expression was not correlated with the presence of any particular regulatory element or with unusual domain arrangement in those genes. This study will help in understanding the evolution of these genes, the development of disease resistant varieties, and the mechanism of disease resistance in linseed.

10aFlax10ain silico gene expression10amotif analysis10aNBS-LRR10aPhylogenetic analysis10aPromoter analysis1 aKale, Sandip, M.1 aPardeshi, Varsha, C.1 aBarvkar, Vitthal, T.1 aGupta, Vidya, S.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/genome-wide-identification-and-characterization-nucleotide-binding-site-leucine-rich-002740nas a2200277 4500008004100000022001400041245017800055210006900233260010600302300001000408490000700418520166900425653000802094653002702102653001602129653000902145653002002154653001202174100002502186700002402211700002402235700002502259700002602284700002102310856013102331 2014 eng d a0031-942200aDifferential transcriptional activity of SAD, FAD2 and FAD3 desaturase genes in developing seeds of linseed contributes to varietal variation in alpha-linolenic acid content0 aDifferential transcriptional activity of SAD FAD2 and FAD3 desat aTHE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLANDbPERGAMON-ELSEVIER SCIENCE LTDcFEB a41-530 v983 a

Linseed or flax (Linum usitatissimum L.) varieties differ markedly in their seed a-linolenic acid (ALA) levels. Fatty acid desaturases play a key role in accumulating ALA in seed. We performed fatty acid (FA) profiling of various seed developmental stages of ten Indian linseed varieties including one mutant variety. Depending on their ALA contents, these varieties were grouped under high ALA and low ALA groups. Transcript profiling of six microsomal desaturase genes (SAD1, SAD2, FAD2, FAD2-2, FAD3A and FAD3B), which act sequentially in the fatty acid desaturation pathway, was performed using real-time PCR. We observed gene specific as well as temporal expression pattern for all the desaturases and their differential expression profiles corresponded well with the variation in FA accumulation in the two groups. Our study points to efficient conversion of intermediate FAs [stearic (SA), oleic (OA) and linoleic acids (LA)] to the final product, ALA, due to efficient action of all the desaturases in high ALA group. While in the low ALA group, even though the initial conversion up to OA was efficient, later conversions up to ALA seemed to be inefficient, leading to higher accumulation of OA and LA instead of ALA. We sequenced the six desaturase genes from the ten varieties and observed that variation in the amino acid (AA) sequences of desaturases was not responsible for differential ALA accumulation, except in the mutant variety TL23 with very low (<2%) ALA content. In TL23, a point mutation in the FAD3A gene resulted into a premature stop codon generating a truncated protein with 291 AA. (C) 2013 Elsevier Ltd. All rights reserved.

10aALA10aFatty acid desaturases10aFatty acids10aFlax10aGene expression10aLinseed1 aRajwade, Ashwini, V.1 aKadoo, Narendra, Y.1 aBorikar, Sanjay, P.1 aHarsulkar, Abhay, M.1 aGhorpade, Prakash, B.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/differential-transcriptional-activity-sad-fad2-and-fad3-desaturase-genes-developing-seeds-002454nas a2200265 4500008004100000022001400041245010500055210006900160260007400229300001400303490000800317520151000325653002601835653002201861653000901883653001601892653002201908100002401930700001601954700002601970700002401996700002002020700002102040856012702061 2014 eng d a0378-269700aEvaluation of genetic variability in Symplocos laurina Wall. from two biodiversity hotspots of India0 aEvaluation of genetic variability in Symplocos laurina Wall from aSACHSENPLATZ 4-6, PO BOX 89, A-1201 WIEN, AUSTRIAbSPRINGER WIENcDEC a2239-22470 v3003 a

Symplocos laurina Wall., an important medicinal tree species, is one of the pioneering plants for establishment of shola forest ecosystem. We analyzed 208 accessions of S. laurina from 13 populations belonging to three ecoregions in India namely, Western Ghats, Eastern Ghats and Northeast India, to comment on the genetic diversity and population structure of the species. Of the 100 inter simple sequence repeat primers screened, eight were selected based on their clear and reproducible polymorphic patterns. These eight ISSR primers produced on an average 1,014 bands from 208 accessions, of which 6.58 % were rare bands, 55.96 % were shared bands and 37.46 % were similar bands. The primers, UBC835 and UBC880, amplified the highest number of polymorphic loci (16), while the primer UBC852 amplified the least number of amplicons (9). The values for total genetic diversity (H-T) and the average heterozygosity (H-S) were 0.3407 and 0.2263, respectively; while the coefficient of genetic differentiation (G(ST)) was 0.3358. Within-population variance was higher (68 %) than among-population variance (17 %), indicating high intra-population genetic diversity. These populations were grouped according to their geographical location in cluster analysis. Mantel test also showed significant positive correlation between genetic and geographical distances. The present study revealed the importance of the Palghat gap in South India in shaping the distribution of genetic diversity in S. laurina.

10aBiodiversity hotspots10aGenetic diversity10aISSR10aPalghat gap10aSymplocos laurina1 aBhagwat, Rasika, M.1 aBanu, Sofia1 aDholakia, Bhushan, B.1 aKadoo, Narendra, Y.1 aLagu, Meena, D.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/evaluation-genetic-variability-symplocos-laurina-wall-two-biodiversity-hotspots-india-000693nas a2200181 4500008004100000245011800041210006900159260000800228300001000236490000800246100001600254700002100270700002400291700001900315700002100334700002400355856013200379 2015 eng d00aAnalysis of genetic variability in Aquilaria malaccensis from Bramhaputra valley, Assam, India using ISSR markers0 aAnalysis of genetic variability in Aquilaria malaccensis from Br cNOV a24-320 v2171 aBanu, Sofia1 aBaruah, Darshana1 aBhagwat, Rasika, M.1 aSarkar, Purabi1 aBhowmick, Ananya1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/analysis-genetic-variability-aquilaria-malaccensis-bramhaputra-valley-assam-india-using-issr02219nas a2200217 4500008004100000022001400041245014700055210006900202260011500271300001200386490000700398520132900405653002501734653001901759100001701778700001601795700001801811700002401829700001801853856013001871 2015 eng d a0006-313400aExpression of stable reference genes and SPINDLY gene in response to gibberellic acid application at different stages of grapevine development0 aExpression of stable reference genes and SPINDLY gene in respons aROZVOJOVA 263, PRAHA 6, CZ-165 02, CZECH REPUBLICbACAD SCIENCES CZECH REPUBLIC, INST EXPERIMENTAL BOTANYcSEP a436-4440 v593 a

Gibberellic acid (GA(3)) is widely used at different stages of berry development, and to understand the molecular mechanism of its action requires identification of stable reference genes. We sprayed grapevine (Vitis vinifera L.) cv. Thompson Seedless with GA(3) at rachis stage for rachis elongation, at flower cluster stage for flower thinning, and at 3 - 4 mm berry stage for berry elongation. Tissue samples were collected at different time points after GA(3) application. The expression of 10 candidate reference genes was analyzed using 4 different algorithms to assess their suitability for real time-PCR data normalization. Based on the overall ranking, PP2A, Sutra, and SAND were identified as the most stably expressed genes across all samples. With regard to different stages, tubulin, EF1 alpha, and UBC were the most stable genes during rachis elongation; PP2A, SAND, and Sutra were the most suitable at the flower cluster and berry stages. The expression of GA signaling gene SPINDLY (VvSpy) was analyzed to validate the stable reference genes. After the GA(3) application, the expression of VvSpy was reduced at the rachis stage but did not change at the flower cluster and berry stages. The expression profile of VvSpy was comparable when two or three reference genes were used for data normalization.

10adevelopmental stages10aVitis vinifera1 aUpadhyay, A.1 aJogaiah, S.1 aMaske, S., R.1 aKadoo, Narendra, Y.1 aGupta, V., S. uhttps://library.ncl.res.in/content/expression-stable-reference-genes-and-spindly-gene-response-gibberellic-acid-application-002394nas a2200301 4500008004100000022001400041245011400055210006900169260009000238300001000328490000700338520136900345653001801714653001901732653001401751653000801765100002001773700002001793700001501813700001801828700001801846700002601864700001501890700001901905700002401924700001701948856012701965 2015 eng d a0733-521000aGenotype x environment interactions and QTL clusters underlying dough rheology traits in triticum aestivum L.0 aGenotype x environment interactions and QTL clusters underlying  a24-28 OVAL RD, LONDON NW1 7DX, ENGLANDbACADEMIC PRESS LTD- ELSEVIER SCIENCE LTDcJUL a82-910 v643 a

Genetic dissection of dough rheology traits (DRT) in hexaploid wheat was carried out using nine mixograph characters evaluated in two consecutive years in three agro-climatic zones in India in an RIL population (HI977 x HD2329). Pearson correlations determined in each year-location indicated 15 stable trait inter-relationships among them but inconsistent correlations with loaf volume (LV) were observed. Using AMMI analysis we derived patterns in G x E interactions (GEI) indicating 6-47% contribution for the DRT. Composite interval mapping using a linkage map of 202 SSR markers identified 144 DRT QTLs of which, 96 were detected in single- and the rest in two to five year-locations. Sixteen QTL clusters located on ten chromosomes were identified and only three of them on chromosomes 1B, 5B and 6D involved LV QTLs. For each trait, majority of the DRT QTLs detected in single as well as multiple environments showed location-specificity and suggested that owing to GEI, breeding for wheat dough quality might need careful selection of QTLs targeted for individual agro-climatic zones. The inconsistent correlations of DRT and LV and differential locations of their QTLs in this population corroborated that using dough rheological traits alone to predict LV might pose challenges during wheat improvement. (C) 2015 Elsevier Ltd. All rights reserved.

10aAMMI analysis10aDough rheology10aMixograph10aQTL1 aPrashant, Ramya1 aMani, Elangovan1 aRai, Richa1 aGupta, R., K.1 aTiwari, Ratan1 aDholakia, Bhushan, B.1 aOak, Manoj1 aRoeder, Marion1 aKadoo, Narendra, Y.1 aGupta, Vidya uhttps://library.ncl.res.in/content/genotype-x-environment-interactions-and-qtl-clusters-underlying-dough-rheology-traits-002495nas a2200277 4500008004100000022001400041245012300055210006900178260010600247300001200353490000800365520149500373653001301868653001801881653001001899653001701909653001201926653001601938100002001954700002601974700002602000700002402026700002002050700002102070856012602091 2015 eng d a0031-942200aMetabolic profiling of chickpea-Fusarium interaction identifies differential modulation of disease resistance pathways0 aMetabolic profiling of chickpeaFusarium interaction identifies d aTHE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLANDbPERGAMON-ELSEVIER SCIENCE LTDcAUG a120-1290 v1163 a

Chickpea is the third most widely grown legume in the world and mainly used as a vegetarian source of human dietary protein. Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceri (Foc), is one of the major threats to global chickpea production. Host resistance is the best way to protect crops from diseases; however, in spite of using various approaches, the mechanism of Foc resistance in chickpea remains largely obscure. In the present study, non-targeted metabolic profiling at several time points of resistant and susceptible chickpea cultivars using high-resolution liquid chromatography-mass spectrometry was applied to better understand the mechanistic basis of wilt resistance or susceptibility. Multivariate analysis of the data (OPLS-DA) revealed discriminating metabolites in chickpea root tissue after Foc inoculation such as flavonoids, isoflavonoids, alkaloids, amino acids and sugars. Foc inoculated resistant plants had more flavonoids and isoflavonoids along with their malonyl conjugates. Many antifungal metabolites that were induced after Foc infection viz, aurantion-obstine beta-glucosides and querecitin were elevated in resistant cultivar. Overall, diverse genetic and biochemical mechanisms were operational in the resistant cultivar for Foc defense as compared to the susceptible plant. The resistant chickpea plants employed the above-mentioned metabolic pathways as potential defense strategy against Foc. (C) 2015 Elsevier Ltd. All rights reserved.

10aChickpea10aFusarium wilt10aLC-MS10aMetabolomics10aOPLS-DA10aPhytoalexin1 aKumar, Yashwant1 aDholakia, Bhushan, B.1 aPanigrahi, Priyabrata1 aKadoo, Narendra, Y.1 aGiri, Ashok, P.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/metabolic-profiling-chickpea-fusarium-interaction-identifies-differential-modulation-002376nas a2200193 4500008004100000022001400041245006500055210006500120260009100185300002900276490000700305520165500312100002401967700002601991700002402017700002102041700002102062856009902083 2015 eng d a1932-620300aTwo new potential barcodes to discriminate dalbergia species0 aTwo new potential barcodes to discriminate dalbergia species a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcNOV aArticle Number: e01429650 v103 a

DNA barcoding enables precise identification of species from analysis of unique DNA sequence of a target gene. The present study was undertaken to develop barcodes for different species of the genus Dalbergia, an economically important timber plant and is widely distributed in the tropics. Ten Dalbergia species selected from the Western Ghats of India were evaluated using three regions in the plastid genome (matK, rbcL, trnH-psbA), a nuclear transcribed spacer (nrITS) and their combinations, in order to discriminate them at species level. Five criteria: (i) inter and intraspecific distances, (ii) Neighbor Joining (NJ) trees, (iii) Best Match (BM) and Best Close Match (BCM), (iv) character based rank test and (v) Wilcoxon signed rank test were used for species discrimination. Among the evaluated loci, rbcL had the highest success rate for amplification and sequencing (97.6%), followed by matK (97.0%), trnH-psbA (94.7%) and nrITS (80.5%). The inter and intraspecific distances, along with Wilcoxon signed rank test, indicated a higher divergence for nrITS. The BM and BCM approaches revealed the highest rate of correct species identification (100%) with matK, matK+rbcL and matK+trnH-psb loci. These three loci, along with nrITS, were further supported by character based identification method. Considering the overall performance of these loci and their ranking with different approaches, we suggest matK and matK+rbcL as the most suitable barcodes to unambiguously differentiate Dalbergia species. These findings will potentially be helpful in delineating the various species of Dalbergia genus, as well as other related genera.

1 aBhagwat, Rasika, M.1 aDholakia, Bhushan, B.1 aKadoo, Narendra, Y.1 aBalasundaran, M.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/two-new-potential-barcodes-discriminate-dalbergia-species-102563nas a2200229 4500008004100000245012400041210006900165260000800234300001400242490000700256520177300263100002602036700001702062700001702079700001502096700001702111700001902128700001702147700002402164700001702188856012802205 2016 eng d00aBiosynthesis of anti-proliferative gold using endophytic fusarium oxysporum strain isolated from neem (A-indica) leaves0 aBiosynthesis of antiproliferative gold using endophytic fusarium cJAN a2036-20420 v163 a

Here we report a simple, rapid, environment friendly approach for the synthesis of gold nanoparticles using neem (Azadirachta indica A. Juss.) fungal endophyte, which based upon morphological and cultural characteristics was eventually identified as Fusarium oxysporum. The aqueous precursor (HAuCl4) solution when reacted with endophytic fungus resulted in the biosynthesis of abundant amounts of well dispersed gold nanoparticles of 10-40 nm with an average size of 22nm. These biosynthesized gold nanoparticles were then characterized by standard analytical techniques such as UV-Visible spectroscopy, X-ray diffraction, Transmission Electron Microscopy and Fourier Transform Infrared Spectroscopy. Cytotoxic activity of these nanoparticles was checked against three different cell types including breast cancer (ZR-75-1), Daudi (Human Burkitt's lymphoma cancer) and normal human peripheral blood mononuclear cells (PBMC), where it was found that our gold nanoparticles are anti-proliferative against cancer cells but completely safe toward normal cells. In addition to this, assessment of toxicity toward human RBC revealed less than 0.1 % hemolysis as compared to Triton X-100 suggesting safe nature of our biosynthesized gold nanoparticles on human cells. Also, our nanoparticles exhibited no anti-fungal (against Aspergillus niger) or anti-bacterial [against Gram positive (Bacillus subtilis & Staphylococcus aureus) and Gram negative (Escherichia coli & Pseudomonas aeruginosa) bacteria] activity thus suggesting their non-toxic, biocompatible nature. The present investigation opens up avenues for eco-friendly, biocompatible nanomaterials to be used in a wide variety of application such as drug delivery, therapeutics, theranostics and so on.

1 aSiddiqui, Ejaz, Ahmad1 aAhmad, Absar1 aJulius, Anju1 aSyed, Asad1 aKhan, Shadab1 aKharat, Mahesh1 aPai, Kalpana1 aKadoo, Narendra, Y.1 aGupta, Vidya uhttps://library.ncl.res.in/content/biosynthesis-anti-proliferative-gold-using-endophytic-fusarium-oxysporum-strain-isolated02052nas a2200181 4500008004100000022001400041245015900055210006900214260009100283300002900374490000700403520124100410100002301651700002401674700002401698700002101722856012701743 2016 eng d a1932-620300aDynamics of colonization and expression of pathogenicity related genes in fusarium oxysporum f.sp ciceri during chickpea vascular wilt disease progression0 aDynamics of colonization and expression of pathogenicity related a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcMAY aArticle Number: e01564900 v113 a

Fusarium wilt caused by Fusarium oxysporum f.sp. ciceri (Foc) is a constant threat to chickpea productivity in several parts of the world. Understanding the molecular basis of chickpea-Foc interaction is necessary to improve chickpea resistance to Foc and thereby the productivity of chickpea. We transformed Foc race 2 using green fluorescent protein (GFP) gene and used it to characterize pathogen progression and colonization in wilt-susceptible (JG62) and wilt-resistant (Digvijay) chickpea cultivars using confocal microscopy. We also employed quantitative PCR (qPCR) to estimate the pathogen load and progression across various tissues of both the chickpea cultivars during the course of the disease. Additionally, the expression of several candidate pathogen virulence genes was analyzed using quantitative reverse transcriptase PCR (qRT-PCR), which showed their characteristic expression in wilt-susceptible and resistant chickpea cultivars. Our results suggest that the pathogen colonizes the susceptible cultivar defeating its defense; however, albeit its entry in the resistant plant, further proliferation is severely restricted providing an evidence of efficient defense mechanism in the resistant chickpea cultivar.

1 aUpasani, Medha, L.1 aGurjar, Gayatri, S.1 aKadoo, Narendra, Y.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/dynamics-colonization-and-expression-pathogenicity-related-genes-fusarium-oxysporum-fsp02652nas a2200373 4500008004100000022001400041245014200055210006900197260006700266300001400333490000700347520139300354653001301747653002301760653001701783653000801800653003101808653001501839100002001854700001701874700002601891700002601917700002001943700002301963700002501986700001602011700001302027700003402040700002402074700002002098700001602118700002102134856012302155 2016 eng d a1467-764400aFusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics0 aFusarium oxysporum mediates systems metabolic reprogramming of c a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcJUL a1589-16030 v143 a

Molecular changes elicited by plants in response to fungal attack and how this affects plant-pathogen interaction, including susceptibility or resistance, remain elusive. We studied the dynamics in root metabolism during compatible and incompatible interactions between chickpea and Fusarium oxysporum f. sp. ciceri (Foc), using quantitative label-free proteomics and NMR-based metabolomics. Results demonstrated differential expression of proteins and metabolites upon Foc inoculations in the resistant plants compared with the susceptible ones. Additionally, expression analysis of candidate genes supported the proteomic and metabolic variations in the chickpea roots upon Foc inoculation. In particular, we found that the resistant plants revealed significant increase in the carbon and nitrogen metabolism; generation of reactive oxygen species (ROS), lignification and phytoalexins. The levels of some of the pathogenesis-related proteins were significantly higher upon Foc inoculation in the resistant plant. Interestingly, results also exhibited the crucial role of altered Yang cycle, which contributed in different methylation reactions and unfolded protein response in the chickpea roots against Foc. Overall, the observed modulations in the metabolic flux as outcome of several orchestrated molecular events are determinant of plant's role in chickpea-Foc interactions.

10aChickpea10afusarium oxysporum10aMetabolomics10aNMR10aplant-pathogen interaction10aproteomics1 aKumar, Yashwant1 aZhang, Limin1 aPanigrahi, Priyabrata1 aDholakia, Bhushan, B.1 aDewangan, Veena1 aChavan, Sachin, G.1 aKunjir, Shrikant, M.1 aWu, Xiangyu1 aLi, Ning1 aRajmohanan, Pattuparambil, R.1 aKadoo, Narendra, Y.1 aGiri, Ashok, P.1 aTang, Huiru1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/fusarium-oxysporum-mediates-systems-metabolic-reprogramming-chickpea-roots-revealed02113nas a2200169 4500008004100000245015300041210006900194260000800263300001400271490000700285520143100292100002501723700002201748700002401770700002101794856012801815 2016 eng d00aSequence characterization and in silico structure prediction of fatty acid desaturases in linseed varieties with differential fatty acid composition0 aSequence characterization and in silico structure prediction of  cDEC a4896-49060 v963 a

BACKGROUND: Linseed is the richest agricultural source of alpha-linolenic acid (ALA), an omega-3 fatty acid (FA) that offers several nutritional benefits. In the present study, sequence characterization of six desaturase genes (SAD1, SAD2, FAD2, FAD2-2, FAD3A and FAD3B) and 3D structure prediction of their proteins from ten Indian linseed varieties differing in ALA content were performed to determine whether the nucleotide and amino acid (AA) sequence variants have any functional implications in differential accumulation of ALA or other FAs in linseed. RESULTS: The SAD and FAD2 genes exhibited few sequence variations among the ten varieties, forming only one or two protein isoforms. In contrast, the FAD3A and FAD3B genes showed more sequence variations and three or four protein isoforms. Interestingly, the two high-ALA varieties NL260 and Padmini had the same FAD3B nucleotide and protein isoforms, which differed from all other varieties. Surprisingly, no AA changes altered the 3D structures of the desaturase proteins. CONCLUSION: Several nucleotide and AA sequence variations in desaturase genes were observed; however, they did not alter the 3D structure of any desaturase protein and were not correlated with FA levels among the ten linseed varieties, which had different ALA contents. This suggests a complex regulatory process of biosynthesis of FAs in linseed. (C) 2016 Society of Chemical Industry

1 aRajwade, Ashwini, V.1 aJoshi, Rakesh, S.1 aKadoo, Narendra, Y.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/sequence-characterization-and-silico-structure-prediction-fatty-acid-desaturases-linseed02042nas a2200193 4500008004100000245011800041210006900159260000800228490000600236520130800242100002301550700002301573700002401596700002801620700002401648700002401672700002101696856013101717 2017 eng d00aChickpea-fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies0 aChickpeafusarium oxysporum interaction transcriptome reveals dif cAUG0 v73 aFusarium wilt is one of the major biotic stresses reducing chickpea productivity. The use of wilt-resistant cultivars is the most appropriate means to combat the disease and secure productivity. As a step towards understanding the molecular basis of wilt resistance in chickpea, we investigated the transcriptomes of wilt-susceptible and wilt-resistant cultivars under both Fusarium oxysporum f.sp. ciceri (Foc) challenged and unchallenged conditions. Transcriptome profiling using LongSAGE provided a valuable insight into the molecular interactions between chickpea and Foc, which revealed several known as well as novel genes with differential or unique expression patterns in chickpea contributing to lignification, hormonal homeostasis, plant defense signaling, ROS homeostasis, R-gene mediated defense, etc. Similarly, several Foc genes characteristically required for survival and growth of the pathogen were expressed only in the susceptible cultivar with null expression of most of these genes in the resistant cultivar. This study provides a rich resource for functional characterization of the genes involved in resistance mechanism and their use in breeding for sustainable wilt-resistance. Additionally, it provides pathogen targets facilitating the development of novel control strategies.1 aUpasani, Medha, L.1 aLimaye, Bhakti, M.1 aGurjar, Gayatri, S.1 aKasibhatla, Sunitha, M.1 aJoshi, Rajendra, R.1 aKadoo, Narendra, Y.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/chickpea-fusarium-oxysporum-interaction-transcriptome-reveals-differential-modulation-plant02190nas a2200217 4500008004100000245016800041210006900209260000800278490000600286520134900292100002601641700002401667700001601691700002501707700002201732700002401754700002301778700002001801700002101821856013001842 2017 eng d00aTranscriptional transitions in alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics0 aTranscriptional transitions in alphonso mango Mangifera indica L cAUG0 v73 aAlphonso is known as the "King of mangos" due to its unique flavor, attractive color, low fiber pulp and long shelf life. We analyzed the transcriptome of Alphonso mango through Illumina sequencing from seven stages of fruit development and ripening as well as flower. Total transcriptome data from these stages ranged between 65 and 143 Mb. Importantly, 20,755 unique transcripts were annotated and 4,611 were assigned enzyme commission numbers, which encoded 142 biological pathways. These included ethylene and flavor related secondary metabolite biosynthesis pathways, as well as those involved in metabolism of starch, sucrose, amino acids and fatty acids. Differential regulation ( p-value <= 0.05) of thousands of transcripts was evident in various stages of fruit development and ripening. Novel transcripts for biosynthesis of mono-terpenes, sesqui-terpenes, di-terpenes, lactones and furanones involved in flavor formation were identified. Large number of transcripts encoding cell wall modifying enzymes was found to be steady in their expression, while few were differentially regulated through these stages. Novel 79 transcripts of inhibitors of cell wall modifying enzymes were simultaneously detected throughout Alphonso fruit development and ripening, suggesting controlled activity of these enzymes involved in fruit softening.1 aDeshpande, Ashish, B.1 aAnamika, Krishanpal1 aJha, Vineet1 aChidley, Hemangi, G.1 aOak, Pranjali, S.1 aKadoo, Narendra, Y.1 aPujari, Keshav, H.1 aGiri, Ashok, P.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/transcriptional-transitions-alphonso-mango-mangifera-indica-l-during-fruit-development-and02986nas a2200265 4500008004100000022001400041245019100055210006900246260000800315300001400323490000700337520201800344653002302362653001702385653002702402653001202429653002602441653001902467100002302486700001702509700002102526700002402547700002102571856012802592 2018 eng d a1438-793X00aGA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis0 aGA3 application in grapes Vitis vinifera L modulates different s cJUL a439–4550 v183 aIn grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3–4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA3-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA3 application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA3 application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA3. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA3 response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.10aBunch architecture10aGA3 response10aMicrosatellite markers10aRNA seq10aTranscription factors10aVitis vinifera1 aUpadhyay, Anuradha1 aMaske, Smita1 aJogaiah, Satisha1 aKadoo, Narendra, Y.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/ga3-application-grapes-vitis-vinifera-l-modulates-different-sets-genes-cluster-emergence02530nas a2200169 4500008004100000245012000041210006900161260000900230490000700239520187400246100002302120700002002143700002402163700002302187700002102210856012902231 2019 eng d00aGlobal study of MFS superfamily transporters in arabidopsis and grapes reveals their functional diversity in plants0 aGlobal study of MFS superfamily transporters in arabidopsis and  cJUN 0 v183 aThe Major Facilitator Superfamily (MFS) is the largest superfamily of secondary transporters present in all organisms, from prokaryotes to higher eukaryotes, that facilitates transport of diverse molecules like sugars, vitamins, amino-acids, hormones, etc. across cell membranes. The superfamily was further expanded to MFS Superfamily (MFSS) to integrate MFS with nine more families. The present study revealed their land plant specific diversity through identification across six species from unicellular alga to higher flowering plants. We identified 71, 131, 254, 260, 213 and 203 MFSS transporters in Chlamydomonas reinhardtii, Physcomitrella patens, Selaginella moellendorffii, Oryza sativa (var. Japonica), Arabidopsis thaliana and Vitis vinifera, respectively and classified them into MFSS families and subfamilies based on their transporter classification identifiers (TCIDs). Detailed analysis of 20 land plant specific subfamilies was conducted in A. thaliana and V. vinifera. Phylogenetic and gene duplication studies revealed the expansion of sugar porter and proton dependent oligopeptide transporter families in Arabidopsis and grape. The subcellular localization of the majority of the transporters was predicted to be in the plasma membrane. Furthermore, the microarray expression analysis of MFSS transporters from Arabidopsis and grapes revealed their multi-tissue-specificity and differential regulation under biotic and abiotic stress conditions. Studies of the transmembrane topology highlighted the presence of central cytoplasmic loop along with family specific topological variations that were evident from phylogenetic analysis. Overall, this study adds to the knowledge of functional and structural diversity and evolution of MFSS transporters in plants and opens the scope for detailed physiological and functional studies on these proteins.1 aPatil, Sucheta, S.1 aPrashant, Ramya1 aKadoo, Narendra, Y.1 aUpadhyay, Anuradha1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/global-study-mfs-superfamily-transporters-arabidopsis-and-grapes-reveals-their-functional02127nas a2200193 4500008004100000022001400041245013300055210006900188260000900257300002400266490000600290520140700296100001601703700002501719700002301744700002001767700002401787856012201811 2019 eng d a2045-232200aIntegrative omics analysis in Pandanus odorifer (Forssk.) Kuntze reveals the role of Asparagine synthetase in salinity tolerance0 aIntegrative omics analysis in Pandanus odorifer Forssk Kuntze re cJAN  aArticle Number: 9320 v93 a

Pandanus odorifer (Forssk) Kuntze grows naturally along the coastal regions and withstands salt-sprays as well as strong winds. A combination of omics approaches and enzyme activity studies was employed to comprehend the mechanistic basis of high salinity tolerance in P. odorifer. The young seedlings of P. odorifer were exposed to 1 M salt stress for up to three weeks and analyzed using RNAsequencing (RNAseq) and LC-MS. Integrative omics analysis revealed high expression of the Asparagine synthetase (AS) (EC 6.3.5.4) (8.95 fold) and remarkable levels of Asparagine (Asn) (28.5 fold). This indicated that salt stress promoted Asn accumulation in P. odorifer. To understand this further, the Asn biosynthesis pathway was traced out in P. odorifer. It was noticed that seven genes involved in Asn bisynthetic pathway namely glutamine synthetase (GS) (EC 6.3.1.2) glutamate synthase (GOGAT) (EC 1.4.1.14), aspartate kinase (EC 2.7.2.4), pyruvate kinase (EC 2.7.1.40), aspartate aminotransferase (AspAT) (EC 2.6.1.1), phosphoenolpyruvate carboxylase (PEPC) (EC 4.1.1.31) and AS were up-regulated under salt stress. AS transcripts were most abundant thereby showed its highest activity and thus were generating maximal Asn under salt stress. Also, an up-regulated Na+/H+ antiporter (NHX1) facilitated compartmentalization of Na+ into vacuoles, suggesting P. odorifer as salt accumulator species.

1 aRashmi, Deo1 aBarvkar, Vitthal, T.1 aNadaf, Altafhusain1 aMundhe, Swapnil1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/integrative-omics-analysis-pandanus-odorifer-forssk-kuntze-reveals-role-asparagine02574nas a2200253 4500008004100000022001400041245013200055210006900187260000800256300001200264490000700276520169200283653002601975653002502001653002502026653001802051653001202069653002902081100002002110700001802130700002002148700002402168856012802192 2019 eng d a1438-793X00aTranscriptomics analysis of propiconazole-treated Cochliobolus sativus reveals new putative azole targets in the plant pathogen0 aTranscriptomics analysis of propiconazoletreated Cochliobolus sa cMAY a453-4650 v193 a

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is a filamentous fungus from the class Dothideomycetes. It is a pathogen of cereals including wheat and barley, and causes foliar spot blotch, root rot, black point on grains, head blight, leaf blight, and seedling blight diseases. Annual yields of these economically important cereals are severely reduced due to this pathogen attack. Evolution of fungicide resistant pathogen strains, availability of a limited number of potent antifungal compounds, and their efficacy are the acute issues in field management of phytopathogenic fungi. Propiconazole is a widely used azole fungicide to control the disease in fields. The known targets of azoles are the demethylase enzymes involved in ergosterol biosynthesis. Nonetheless, azoles have multiple modes of action, some of which have not been explored yet. Identifying the off-target effects of fungicides by dissecting gene expression profiles in response to them can provide insights into their modes of action and possible mechanisms of fungicide resistance. Moreover it can also reveal additional targets for development of new fungicides. Hence, we analyzed the global gene expression profile of C. sativus on exposure to sub-lethal doses of propiconazole in a time series. The gene expression patterns were confirmed using quantitative reverse transcriptase PCR (qRT-PCR). This study revealed overexpression of target genes from the sterol biosynthesis pathway supporting the reported mode of resistance against azoles. In addition, some new potential targets have also been identified, which could be explored to develop new fungicides and plant protection strategies.

10aBipolaris sorokiniana10aCochliobolus sativus10aFungicide resistance10aPropiconazole10aRNA-seq10aTranscriptomics analysis1 aSomani, Deepika1 aAdhav, Ragini1 aPrashant, Ramya1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/transcriptomics-analysis-propiconazole-treated-cochliobolus-sativus-reveals-new-putative02302nas a2200241 4500008004100000022001400041245011100055210006900166260000800235520145800243653002301701653002101724653001301745653002201758653001901780100001701799700002301816700002101839700002301860700002401883700002101907856013201928 2019 eng d a0721-759500aWhole proteome analysis of GA(3) response at panicle stage in Grape (Vitis vinifera) CV. Thompson seedless0 aWhole proteome analysis of GA3 response at panicle stage in Grap cOCT3 a

Rachis elongation is a crucial process in producing good quality table grapes. In compact clustered grape variety like Thompson Seedless, treating the flower panicles with a mild dose of GA(3) results in loose clusters. We sprayed GA(3) on Thompson Seedless panicles immediately after emergence, and the samples were collected at 6 h and 24 h after application. Whole proteome analysis revealed significant differential expression of 530 proteins of the total 1288 expressed proteins at two time-points. GO term enrichment analysis revealed enrichment of GO terms related to translation, biosynthetic processes, and photosynthesis in GA(3)-treated samples. As the process of rachis elongation requires enhanced carbon metabolism and accumulation of sugars through the expansion of phloem area, we attribute this to the overexpression of several proteins involved in these processes. Significantly highly expressed proteins also belonged to biological processes like the generation of precursor metabolites, cellular protein metabolic processes, response to abiotic stimulus, and protein metabolic processes. This study might be the first of its kind in deciphering the contribution of a different group of proteins during rachis elongation as an early response to GA(3) application in seedless grapes. These results provide quality information on various physiological and biochemical changes occurring during early stages of rachis elongation.

10aBunch architecture10aGibberellic acid10aProteome10aRachis elongation10aVitis vinifera1 aMaske, Smita1 aUpadhyay, Anuradha1 aJogaiha, Satisha1 aPatil, Sucheta, S.1 aKadoo, Narendra, Y.1 aGupta, Vidya, S. uhttps://library.ncl.res.in/content/whole-proteome-analysis-ga3-response-panicle-stage-grape-vitis-vinifera-cv-thompson-seedless02045nas a2200229 4500008004100000022001400041245006700055210006600122260000800188300001400196490000700210520132400217653002501541653001701566653002601583653002301609653001401632100002201646700002401668700002401692856009901716 2020 eng d a0006-308800aInsights of Bipolaris sorokinianasecretome-anin silicoapproach0 aInsights of Bipolaris sorokinianasecretomeanin silicoapproach cDEC a2367-23810 v753 a

The plant pathogen,Bipolaris sorokiniana(teleomorph:Cochliobolus sativus), is of global concern as it attacks many economically important cereals and grasses. During the infection process, phytopathogenic fungi are known to secrete a variety of proteins collectively known as the secretome, analyzing which can help in deciphering the mechanism of fungal pathogenesis. In this study, we performedin silicosecretome analysis ofC. sativusstrain ND90Pr using established secretome prediction pipeline involving software tools such as SignalP, TargetP, TMHMM, big-PI Fungal Predictor, ProtComp, and WoLF PSORT. Using these software and other prediction criteria, we identified 196 probable secretory proteins from theB. sorokinianaproteome. Characterization of the predicted secretome revealed proteins that may have probable functions in degradation of the plant cell wall, lipids, proteins, and nucleic acids, as well as in pathogenesis and metabolism. Further, the PHI-base analysis identified 38 proteins having a possible role in pathogenicity and virulence. This study helped to predict the composition of the secretome ofB. sorokinianaand extrapolate its role in plant infection and pathogen survival. It may provide clues for developing new control strategies targeting the vital fungal secretory proteins.

10aCochliobolus sativus10apathogenesis10aPhytopathogenic fungi10aSecretory proteins10aVirulence1 aPathak, Gauri, M.1 aGurjar, Gayatri, S.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/insights-bipolaris-sorokinianasecretome-anin-silicoapproach02172nas a2200277 4500008004100000022001400041245012700055210006900182260000800251300001200259490000700271520123000278653002601508653001901534653002001553653001901573653002801592100001601620700002001636700002001656700002101676700002301697700002101720700002401741856012901765 2021 eng d a0721-759500aGibberellic acid induces unique molecular responses in `thompson seedless' grapes as revealed by non-targeted metabolomics0 aGibberellic acid induces unique molecular responses in thompson  cFEB a293-3040 v403 a

Compact clusters and small berry size are the major problems associated with the commercialization of table grapes. The application of gibberellic acid 3 (GA(3)) has been a long-followed practice to overcome these issues. To analyze the molecular response of `Thompson Seedless' grapes to GA(3) treatment, we investigated the metabolomes of its rachises, clusters, and berries, 6 h and 24 h after the treatment. Metabolite profiling using non-targeted metabolomics approach revealed several metabolites, including arginine, proline, tyrosine, kaempferol, resveratrol, catechin, and so on as possible biomarkers of GA(3) treatment in grapes. GA(3) treatment greatly impacted the alanine, aspartate, and glutamate metabolism pathways, and the GA(3)-mediated alterations in the levels of certain plant growth regulators and primary metabolites were in accordance with important growth and developmental processes in grapes. This study highlights the effect of GA(3) on the profiles of certain polyphenols impacting the flavone and flavonol biosynthesis pathways and hence the nutritional aspect of grapes. The results of this study would be useful to develop self-elongating varieties simplifying the grape cultivation.

10aBiosynthetic pathways10aGA(3) response10aGA(3) signaling10aSultana grapes10aUntargeted metabolomics1 aJadhav, Uma1 aMundhe, Swapnil1 aKumar, Yashwant1 aJogaiah, Satisha1 aUpadhyay, Anuradha1 aGupta, Vidya, S.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/gibberellic-acid-induces-unique-molecular-responses-thompson-seedless-grapes-revealed-non02009nas a2200217 4500008004100000020001400041245013100055210006900186260000800255300001400263490000700277520121500284100001601499700002001515700002001535700002101555700002301576700002101599700002401620856014701644 2021 eng d a1435-810700aGibberellic acid induces unique molecular responses in ‘thompson seedless’ grapes as revealed by non-targeted metabolomics0 aGibberellic acid induces unique molecular responses in thompson  cFEB a293 - 3040 v403 aCompact clusters and small berry size are the major problems associated with the commercialization of table grapes. The application of gibberellic acid 3 (GA3) has been a long-followed practice to overcome these issues. To analyze the molecular response of ‘Thompson Seedless’ grapes to GA3 treatment, we investigated the metabolomes of its rachises, clusters, and berries, 6 h and 24 h after the treatment. Metabolite profiling using non-targeted metabolomics approach revealed several metabolites, including arginine, proline, tyrosine, kaempferol, resveratrol, catechin, and so on as possible biomarkers of GA3 treatment in grapes. GA3 treatment greatly impacted the alanine, aspartate, and glutamate metabolism pathways, and the GA3-mediated alterations in the levels of certain plant growth regulators and primary metabolites were in accordance with important growth and developmental processes in grapes. This study highlights the effect of GA3 on the profiles of certain polyphenols impacting the flavone and flavonol biosynthesis pathways and hence the nutritional aspect of grapes. The results of this study would be useful to develop self-elongating varieties simplifying the grape cultivation.1 aJadhav, Uma1 aMundhe, Swapnil1 aKumar, Yashwant1 aJogaiah, Satisha1 aUpadhyay, Anuradha1 aGupta, Vidya, S.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/gibberellic-acid-induces-unique-molecular-responses-%E2%80%98thompson-seedless%E2%80%99-grapes-revealed-non02641nas a2200289 4500008004100000245015100041210006900192260000800261300001100269490000700280520161900287653001501906653002201921653002101943653002501964653002801989653001802017100002402035700002702059700002202086700002102108700002402129700002302153700002402176700002302200856012802223 2022 eng d00aDiversity assessment of Gloriosa superba accessions from Western Ghats of India based on morphological traits, ISSR markers and metabolite content0 aDiversity assessment of Gloriosa superba accessions from Western cSEP a1003880 v303 a

Gloriosa superba L. (glory lily) is a medicinally and horticulturally important plant used as a commercial source of the alkaloid colchicine. The Western Ghats in India is mostly unexplored for the morphological, genetic, and metabolite diversity of the species. In the current study, three methodologies were employed to assess the diversity among 50 established accessions of G. superba collected from several locations in the Western Ghats. The morphological analysis revealed that, among the studied traits, seed yield per vine and dry seed weight per 100 seeds for the established accessions were the most diverse traits. The former exhibited a significantly positive correlation with four vegetative and five yield traits. The first three principal components showed nine traits contributing to the variation. Intra-specific molecular variation based on inter simple sequence repeat markers distributed the accessions in three clusters with high polymorphism and low genetic diversity indices. Liquid chromatography high-resolution mass spectrometry analysis revealed significant variation among the screened accessions for colchicine content in tuber and seed tissue. Interestingly, an unexplored tissue, pod shell, was found to contain significantly high colchicine, which could be explored for commercial colchicine extraction. The morphogenetic and metabolite variation revealed by the study would be useful to develop elite varieties to expand the cultivation of glory lily across the country, fulfilling the increasing demand for colchicine and providing remunerative income to the farmers.

10aColchicine10aGenetic diversity10aGloriosa superba10aMetabolite diversity10aMorphological diversity10aWestern Ghats1 aMahajan, Yogesh, A.1 aShinde, Balkrishna, A.1 aMulani, Fayaj, A.1 aGade, Akshay, B.1 aKasodekar, Amol, K.1 aThulasiram, H., V.1 aKadoo, Narendra, Y.1 aNikam, Tukaram, D. uhttps://library.ncl.res.in/content/diversity-assessment-gloriosa-superba-accessions-western-ghats-india-based-morphological02526nas a2200277 4500008004100000022001400041245010300055210006900158260000800227300000700235490000700242520162300249653001801872653001301890653001301903653002301916653002001939653002701959100001601986700002302002700002402025700002502049700002102074700002702095856012602122 2023 eng d a0137-588100aRole of ions and their transporters in combating salt stress in Pandanus odorifer (Forssk.) Kuntze0 aRole of ions and their transporters in combating salt stress in  cMAY a660 v453 a

Soil salinity is a major environmental constraint causing huge losses in crop production. Pandanus odorifer (Forssk.) Kuntze is an aromatic monocot plant species belonging to the family Pandanaceae, which grows naturally on the saline soils along the coasts of Asia, Southeast Asia, and Polynesia. The plants are dioecious and highly fertile, and the consistent saline sprays, strong winds, and severe soil salinity hardly affect their growth and fertility. Hence, understanding the mechanism of high salinity tolerance in P. odorifer could provide major advances in overcoming salinity stress in crop plants. In the present study, we analyzed control (0 M NaCl) and treated (1 M NaCl treatment for 3 weeks) plants of P. odorifer to understand the role of ion distribution, ion transport, and related mechanisms under salt stress. Using a combination of ionomics and transcriptomics approaches, we identified the molecular mechanisms contributing to the high salinity stress in P. odorifer. Under NaCl stress, there was a significant increase in Na, Cl, and other ions in leaves, while the concentrations of Si, Fe, Ni, and Ti decreased. Similarly, in roots, the levels of Na, Mg, Cd, and Cr were significantly high, while the levels of other ions decreased. Most of the genes related to ion transport and homeostasis, such as NHX1, CLC-C, SOS1, HAK, and ABC transporters, were upregulated in 1 M NaCl stress conditions. This study revealed that vacuolar sequestration of Na+ and the distribution of ions in the roots and shoots play significant roles in the salt-stress tolerance mechanism of P. odorifer.

10aIon transport10aIonomics10aPandanus10aSalinity tolerance10aTranscriptomics10aVacuolar sequestration1 aRashmi, Deo1 aAnsari, Waquar, A.1 aKadoo, Narendra, Y.1 aBarvkar, Vitthal, T.1 aDeshmukh, Rupesh1 aNadaf, Altafhusain, B. uhttps://library.ncl.res.in/content/role-ions-and-their-transporters-combating-salt-stress-pandanus-odorifer-forssk-kuntze02611nas a2200241 4500008004100000245014200041210006900183260000800252300001100260490000700271520174900278653002202027653002402049653002102073653001802094653001602112100002802128700002102156700001702177700002402194700002402218856012702242 2023 eng d00aSeasonal dynamics and tree foliar habit drive the rhizobacterial diversity in congeneric Ficus species from Northern Western Ghats, India0 aSeasonal dynamics and tree foliar habit drive the rhizobacterial cDEC a1007900 v283 a

Tree species, annual climatic cycle, and geochemical properties influence the tree rhizospheric microbiome. However, its understanding in the moist deciduous forest of Northern Western Ghats (NWG), India, is limited. Moreover, the effects of foliar habits of trees and seasonal variations on rhizobacterial communities across congeneric tree species are unexplored. Hence, we employed high throughput 16 S rRNA gene sequencing to examine the effects of foliar habits of congeneric tree species and seasonal influences on the rhizobacterial community. For this study, rhizospheric soil from Ficus arnottiana (deciduous) and Ficus talboti (evergreen) trees from NWG, India, was collected during three seasons (summer, monsoon, and winter) and subjected to high throughput sequencing. A total of 3031 amplicon sequence variants (ASV) were observed, of which 1257 and 1181 ASV were unique to F. arnottiana and F. talboti, respectively, and 593 ASV were common to both species. The phyla Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi were ubiquitous and contributed >90% to the rhizobacterial community. Some bacterial phyla were exclusively associated with either of the tree species and seasons. Different bacterial phyla performed similar functions in different seasons, indicating their functional redundancy and emphasizing their resilience and adaptability across seasons. It was observed that seasonal dynamics mainly drove the rhizobacterial diversity; however, it was also influenced by the foliar habits of the trees and geochemical properties. The study enhances the understanding of congeneric tree microbiomes and offers valuable insights into their potential applications through microbiome engineering.

10aAmplicon variants10aBacterial diversity10aFicus arnottiana10aFicus talboti10aRhizosphere1 aSalunkhe, Vaishnavi, H.1 aKunte, Pooja, S.1 aPaul, Dhiraj1 aKasodekar, Amol, K.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/seasonal-dynamics-and-tree-foliar-habit-drive-rhizobacterial-diversity-congeneric-ficus02422nas a2200301 4500008004100000022001400041245011200055210006900167260000800236300001100244490000800255520141300263653002501676653001501701653002201716653001501738653002701753653002101780100002401801700002701825700002401852700002001876700002701896700002401923700002401947700002301971856012601994 2024 eng d a0926-669000aUnlocking the genetic and biotechnological potential of Gloriosa superba to enhance its alkaloid production0 aUnlocking the genetic and biotechnological potential of Gloriosa cMAY a1181440 v2113 a

Gloriosa superba is a medicinally important plant that produces the pharmaceutically precious colchicine molecule. Colchicine is being used for treating gout, for enhancing the production of interleukin-8 (inhibits human pancreatic cancer) and many other human ailments. Since its seeds and rhizomes (tuberous roots) are the chief sources of colchicine, pharmaceutical industries exploit the natural sources, thus demolishing its habitat. Chemo- and genetic diversity among the G. superba populations exist, but has not been exploited profitably. Scope exists for generating mutants using the chemical mutagens and also via breeding methods to generate superior varieties for commercial cultivation. Innovative methods for breaking seed dormancy and superior colchicine extraction, besides biotechnological interventions are imperative to save the biodiversity and to produce colchicine on a large scale. Biorhizomes produced in vitro hold great promise for biomanufacturing colchicine in bioreactors commercially. Since the biosynthetic pathway of colchicine is now known, isolation of the pathway genes and their heterologous overexpression or the application of synthetic biology methods needs to be explored in future for industrial manufacturing of colchicine. Advances made in the recent past in these fields of colchicine production from G. superba are critically evaluated in this review.

10aBiosynthetic pathway10aColchicine10aGenetic diversity10aGlory lily10aMetabolite elicitation10aOmics approaches1 aMahajan, Yogesh, A.1 aShinde, Balkrishna, A.1 aShirke, Harshad, A.1 aGandra, Jawahar1 aSuravajhala, Prashanth1 aKishor, P., B. Kavi1 aKadoo, Narendra, Y.1 aNikam, Tukaram, D. uhttps://library.ncl.res.in/content/unlocking-genetic-and-biotechnological-potential-gloriosa-superba-enhance-its-alkaloid02558nas a2200253 4500008004100000022001400041245009000055210006900145260000800214300001200222490000700234520173800241653001901979653001301998653001802011653002302029653001602052653002602068100001602094700002502110700002702135700002402162856011802186 2025 eng d a0971-781100aHarnessing microRNAs and their targets for salt stress tolerance in Pandanus odorifer0 aHarnessing microRNAs and their targets for salt stress tolerance cSEP a714-7300 v343 a

Salinity poses a formidable challenge to agriculture, detrimentally impacting plant growth and the yield of several crops globally. Pandanus odorifer (Forssk.) Kuntze is a highly salt-stress resilient plant that grows naturally along the coastal regions of Asia, Southeast Asia, and Polynesia. It is frequently found as a frontier species along the sandy shores receiving constant salt sprays. MicroRNAs (miRNAs) play essential regulatory roles in growth, development, and combating various biotic and abiotic stresses. Thus, characterizing miRNAs and their targets is critical to understanding their roles in salt stress tolerance. Through a rigorous analysis based on homology, secondary structure and signatures of other miRNA genes, we identified 52 conserved nonredundant miRNAs from the P. odorifer transcriptome data. These miRNAs were diverse and belonged to 23 miRNA phylogenetic families. Several miRNAs, including pod-MIR156a, pod-MIR164d, and pod-MIR535d, demonstrated distinct expression patterns in response to salt stress. Their target genes exhibited opposing expression trends, corroborating the intricate miRNA-target relationship. Delving deeper into their influence, we discovered that these miRNAs mainly targeted transcription factors that are known for their pivotal roles in stress responses. We also detected four miRNA-star (miRNA*) sequences (the complementary strands of functional mature miRNAs), which supports the authenticity of the identified miRNAs. This study unveils the intricate regulatory mechanism through which miRNAs may reinforce salt stress tolerance in P. odorifer, providing a promising avenue for enhancing crop resilience to various stresses through miRNA-based strategies.

10aAbiotic stress10amicroRNA10amiRNA targets10aSalinity tolerance10asalt stress10aTranscription factors1 aRashmi, Deo1 aBarvkar, Vitthal, T.1 aNadaf, Altafhusain, B.1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/harnessing-micrornas-and-their-targets-salt-stress-tolerance-pandanus-odorifer02891nas a2200229 4500008004100000022001400041245011200055210006900167260000800236300000800244490000800252520211300260653000902373653001202382653002002394653001802414653003302432653002002465100002002485700002402505856013202529 2025 eng d a0032-093500aIntegrative multi-omics and computer-aided biofungicide design approach to combat fusarium wilt of chickpea0 aIntegrative multiomics and computeraided biofungicide design app cSEP a1070 v2623 a

Main conclusionIntegrating multi-omics and computer-aided drug discovery approaches can overcome the limitations of traditional methods and help develop highly effective, specific, and environmentally safe biofungicides to control crop diseases.AbstractChickpea is a valuable legume crop in terms of nutrition, food security, economic sustainability, and environmental benefits. Fusarium wilt caused by the soil-borne fungus Fusarium oxysporum f.sp. ciceri is one of the most important diseases affecting chickpea. Several disease management methods, including crop rotation, soil fumigation with chemical fungicides, soil solarization, etc., are practiced to manage the disease. However, these methods have various limitations and cannot completely control the disease. Moreover, chemical fungicides indiscriminately kill even the beneficial soil microbes, pollute groundwater, and enter the food chain. Hence, modern approaches emphasizing innovative strategies and technologies need to be explored to manage the disease effectively. In this review, we propose integrating multi-omics (genomics, proteomics, metabolomics, etc.) and computer-aided drug discovery (CADD) approaches to develop biofungicides targeting vital pathogen proteins. Multi-omics approaches can delve deeper into the plant-pathogen interaction and reveal essential pathogen genes or proteins. These proteins could be targeted using CADD to identify phytochemical-based potential biofungicides, either using structure- or ligand-based drug design approaches. The potential biofungicides can be subjected to the prediction of carcinogenicity, hepatotoxicity, mutagenicity, etc., to identify biofungicides that are safe to use and are highly specific to the target pathogen. In vivo and in vitro validation studies can be followed to establish the efficacy and safety of the identified biofungicides for their practical application. This integrated approach can reduce the time and cost compared to the traditional methods and accelerate the discovery of highly effective biofungicides to protect crops from various diseases.

10aCADD10adocking10aFungal diseases10aMD Simulation10aProtein structure prediction10aTranscriptomics1 aSahoo, Rosaleen1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/integrative-multi-omics-and-computer-aided-biofungicide-design-approach-combat-fusarium-wilt02482nas a2200277 4500008004100000022001400041245011000055210006900165260000800234300001200242490000700254520152400261653001801785653003101803653001301834653002601847653002001873100002301893700002401916700002001940700002701960700002901987700003302016700002402049856013102073 2025 eng d a0971-589400aTranscriptome analyses reveal TaWRKY41 as a potential candidate governing spot blotch resistance in wheat0 aTranscriptome analyses reveal TaWRKY41 as a potential candidate  cAPR a591-6080 v313 a

Spot blotch disease caused by Bipolaris sorokiniana poses a significant threat to wheat production. Cultivation of disease-resistant wheat genotypes appears to be the most practical approach to mitigate the impact of this devastating disease. However, the molecular responses of wheat plants during spot blotch disease progression remain poorly understood. This study employed RNA-sequencing to unravel the spatiotemporal molecular events underlying the resistance mechanism in the spot blotch susceptible and resistant wheat genotypes. This study further provides a comprehensive overview of differentially expressed transcripts through functional analysis and transcription factor identification, elucidating the biological mechanisms governing wheat-B. sorokiniana interaction. In the resistant genotype, the expression of one of the key transcription factors, TaWRKY41, was significantly induced upon pathogen inoculation. Computational studies, electrophoretic-mobility shift assay, and yeast one-hybrid assay confirmed the interaction of the recombinant TaWRKY41 protein with W-box elements present in the promoters of plant defense-related genes. Furthermore, co-expression network analyses identified downstream genes positively correlated with TaWRKY41, providing insights into their probable involvement in the defense response. Overall, our investigation suggests that TaWRKY41 contributes to spot blotch resistance in wheat. This knowledge can help develop new disease-resistant wheat varieties.

10aPlant defense10aplant-pathogen interaction10aTaWRKY4110aTranscription factors10aTranscriptomics1 aDayama, Bhakti, R.1 aMahadik, Varsha, A.1 aSomani, Deepika1 aShinde, Balkrishna, A.1 aKondhare, Kirtikumar, R.1 aKarthikeyan, Muthukumarasamy1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/transcriptome-analyses-reveal-tawrky41-potential-candidate-governing-spot-blotch-resistance