@article { ISI:000304646100048, title = {Development of genomic simple sequence repeat markers for linseed using next-generation sequencing technology}, journal = {Molecular Breeding}, volume = {30}, number = {1}, year = {2012}, month = {JUN}, pages = {597-606}, publisher = {SPRINGER}, address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, abstract = {

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{\textquoteright}-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{\textquoteright}-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.

}, keywords = {Flax, Microsatellite isolation, Next-generation sequencing, SSR}, issn = {1380-3743}, doi = {10.1007/s11032-011-9648-9}, author = {Kale, Sandip M. and Pardeshi, Varsha C. and Kadoo, Narendra Y. and Ghorpade, Prakash B. and Jana, Murari M. and Gupta, Vidya S.} } @article { ISI:000331020000004, title = {Differential transcriptional activity of SAD, FAD2 and FAD3 desaturase genes in developing seeds of linseed contributes to varietal variation in alpha-linolenic acid content}, journal = {Phytochemistry}, volume = {98}, year = {2014}, month = {FEB}, pages = {41-53}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, type = {Article}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

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.

}, keywords = {ALA, Fatty acid desaturases, Fatty acids, Flax, Gene expression, Linseed}, issn = {0031-9422}, doi = {10.1016/j.phytochem.2013.12.002}, author = {Rajwade, Ashwini V. and Kadoo, Narendra Y. and Borikar, Sanjay P. and Harsulkar, Abhay M. and Ghorpade, Prakash B. and Gupta, Vidya S.} } @article { ISI:000376882500147, title = {Dynamics of colonization and expression of pathogenicity related genes in fusarium oxysporum f.sp ciceri during chickpea vascular wilt disease progression}, journal = {Plos One}, volume = {11}, number = {5}, year = {2016}, month = {MAY}, pages = {Article Number: e0156490}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {

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.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0156490}, author = {Upasani, Medha L. and Gurjar, Gayatri S. and Kadoo, Narendra Y. and Gupta, Vidya S.} } @article {48194, title = {Diversity assessment of Gloriosa superba accessions from Western Ghats of India based on morphological traits, ISSR markers and metabolite content}, journal = {Journal of Applied Research on Medicinal and Aromatic Plants}, volume = {30}, year = {2022}, month = {SEP}, pages = {100388}, type = {Article}, abstract = {

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.

}, keywords = {Colchicine, Genetic diversity, Gloriosa superba, Metabolite diversity, Morphological diversity, Western Ghats}, doi = {10.1016/j.jarmap.2022.100388}, author = {Mahajan, Yogesh A. and Shinde, Balkrishna A. and Mulani, Fayaj A. and Gade, Akshay B. and Kasodekar, Amol K. and Thulasiram, H. V. and Kadoo, Narendra Y. and Nikam, Tukaram D.} }