02468nas a2200253 4500008004100000022001400041245011400055210006900169260007400238300001200312490000700324520154700331653000901878653002901887653003101916653000801947100002101955700002501976700002402001700002602025700002102051700002102072856012102093 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. uhttp://library.ncl.res.in/content/development-genomic-simple-sequence-repeat-markers-linseed-using-next-generation-002467nas a2200265 4500008004100000022001400041245015900055210006900214260012000283300001000403490000700413520142200420653000901842653003001851653001901881653001201900653002601912653002201938100002101960700002501981700002502006700002102031700002402052856012502076 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. uhttp://library.ncl.res.in/content/genome-wide-identification-and-characterization-nucleotide-binding-site-leucine-rich-002739nas a2200277 4500008004100000022001400041245017800055210006900233260010600302300001000408490000700418520166900425653000802094653002702102653001602129653000902145653002002154653001202174100002502186700002402211700002402235700002502259700002602284700002102310856013002331 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. uhttp://library.ncl.res.in/content/differential-transcriptional-activity-sad-fad2-and-fad3-desaturase-genes-developing-seeds-0