Development of genomic simple sequence repeat markers for linseed using next-generation sequencing technology

TitleDevelopment of genomic simple sequence repeat markers for linseed using next-generation sequencing technology
Publication TypeJournal Article
Year of Publication2012
AuthorsKale, SM, Pardeshi, VC, Kadoo, NY, Ghorpade, PB, Jana, MM, Gupta, VS
JournalMolecular Breeding
Volume30
Issue1
Pagination597-606
Date PublishedJUN
ISSN1380-3743
KeywordsFlax, Microsatellite isolation, Next-generation sequencing, SSR
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'-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.

DOI10.1007/s11032-011-9648-9
Type of Journal (Indian or Foreign)Foreign
Impact Factor (IF)3.251
Divison category: 
Biochemical Sciences