Development of genomic resources in pigeonpea (Cajanus cajan L.Millspaugh)

Abstract

This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan crop species' of the semi-arid tropic regions. A set of 88.860 BAC (bacterial anificial chromosomes)-end sequences (BESs) were generated after constructing two BAC libraries by using Hindlll (34.560 clones) and BamHl (34.560 clones) restriction enzymes. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on two parental genotypes (ICP 28 and ICPW 94). In addition. Roche FLXl454 sequencing was carried out on a normalized cDNA pool prepared from 31 tissues and produced 494.353 shon transcript reads (STRs). Cluster analysis of these STRs. together with 10.817 Sanger ESTs, resulted in 127.754 pigeonpea transcript assemblies (CcTAs). Additionally. Illurnina 1G sequencing was performed on four parental genotypes of two mapping populations and a set of 7.453 SNPs were identified. Based on BES-SSR markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. In summary. while BAC libraries, BESs and CcTAs should be useful for genomics studies. BES-SSR. SNP markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea