@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 = {<p>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.</p>},
	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:000316557400002,
	title = {Genome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure},
	journal = {Genome},
	volume = {56},
	number = {2},
	year = {2013},
	month = {FEB},
	pages = {91-99},
	publisher = {CANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESS},
	address = {1200 MONTREAL ROAD, BUILDING M-55, OTTAWA, ON K1A 0R6, CANADA},
	abstract = {<p>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.</p>},
	keywords = {Flax, in silico gene expression, motif analysis, NBS-LRR, Phylogenetic analysis, Promoter analysis},
	issn = {0831-2796},
	doi = {10.1139/gen-2012-0135},
	author = {Kale, Sandip M. and Pardeshi, Varsha C. and Barvkar, Vitthal T. and Gupta, Vidya S. and Kadoo, Narendra Y.}
}
