Application of Next Generation Sequencing and Genotyping Technologies to Develop Large‐Scale Genomic Resources in SAT Legume CropsR KVarshneyauthorMolecular 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 futureChickpeaPigeonpeaGroundnut2011Conference or Workshop Item