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Application of Next Generation Sequencing and Genotyping Technologies to Develop Large‐Scale Genomic Resources in SAT Legume Crops

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Relation http://oar.icrisat.org/5489/
 
Title Application of Next Generation Sequencing and Genotyping Technologies to Develop Large‐Scale Genomic Resources in SAT Legume Crops
 
Creator Varshney, R K
 
Subject Chickpea
Pigeonpea
Groundnut
 
Description Molecular markers and genetic maps are the pre‐requisites for trait mapping and genomics‐assisted crop
improvement. However, very limited genomic resources were available until recently for the legume crops important
in the semi‐arid tropics (SAT). As a part of several initiatives, species‐specific genomic resources are now being
developed in most of these legume crops. For instance, using simple sequence repeat (SSR)‐enriched libraries and
bacterial artificial chromosome (BAC)‐end sequence mining approaches, nearly 1,500‐ 3,000 novel SSR markers
have been developed for chickpea, pigeonpea and groundnut. In addition, next generation sequencing technologies
like Roche 454/FLX and Illumina/Solexa, in addition to Sanger sequencing, are being used to sequence the
transcriptomes of reference or parental genotypes of mapping populations of chickpea and pigeonpea to access the
gene space and develop functional markers. Based on Sanger and 454/FLX transcript reads, transcriptome
assemblies have been developed for chickpea (103,215 tentative unique sequences, TUSs) and pigeonpea (127,754
TUSs) that are being characterized using genome sequence data of Medicago and soybean. In parallel, RNA of four
chickpea and twelve pigeonpea genotypes, that represent parents of different mapping populations, have been
sequenced by using Illumina/Solexa sequencing approach that has resulted ca. 120 million reads for chickpea and 20
million reads for pigeonpea. Alignment of these Illumina/Solexa reads of these genotypes with transcriptome
assembly of the respective species has provided a large number (tens of thousands) of SNPs. Selected set of SNPs are
being used to develop large‐scale SNP genotyping platform in chickpea and pigeonpea. By using the existing
resource of SSR, SNP and DArT markers, high‐density genetic maps are being developed in these species for trait
mapping and molecular breeding. It is anticipated that molecular breeding practice may be routine and part of
breeding activities in the SAT legumes in coming future
 
Date 2011
 
Type Conference or Workshop Item
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/5489/1/GenomicsandCropImprovementRelevanceandReservations_2010.pdf
Varshney, R K (2011) Application of Next Generation Sequencing and Genotyping Technologies to Develop Large‐Scale Genomic Resources in SAT Legume Crops. In: National Symposium on Genomics and Crop Improvement: Relevance and Reservations , February 25 - 27, 2010, Acharya N G Ranga Agricultural University, Rajendranagar, Hyd.