Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (and (L.) Millsp.) is the sixth most important food legume crop in the world. Pigeonpea cultivars contain about 20 to 23% protein from the total composition of seeds which also possess carbohydrates BINA (65 to 70%) and fiber. Pigeonpea Dal is a major source of dietary protein for more than a billion people in the developing world and a rich source of essential amino acids, like methionine, lysine and Rabbit polyclonal to ZNF394 tryptophan1C3. Globally pigeonpea is cultivated on 6.23 million ha (m ha) with an annual production of 4.74 million tons (mt). India is the primary pigeonpea growing country, where more than 85% of the BINA worlds pigeonpea production (3.29 mt, cultivated in 5.06?m ha area) and consumption takes place (http://faostat3.fao.org/home/, as of August 2016). Its productivity measured in experimental plots (~3700?kg/ha) could not be translated in farmers fields and average yield (<1000?kg/ha) remained stagnant during the last six decades3. This is mainly due to cultivation of pigeonpea with limited or no inputs in heavy diseases pressure by small-holder farmers. Fusarium wilt (FW) and sterility mosaic disease (SMD) are two epidemic diseases in pigeonpea that can cause complete yield losses in susceptible cultivars. FW caused by Butler has the global importance as it frequently occurs in both India and Africa, the major growing zones in the world. The annual losses due to FW have been reported to be US $ 71 million4 and 470, 000 t of grain in India and 30,000 t of grain in Africa5. As yield losses due to FW are significant, it is worthwhile to manage and further increase the disease resistance in pigeonpea cultivars. The most pragmatic, economical and environment-friendly approach for FW management is the utilization of genetic resistance6. FW resistance in pigeonpea has been found to be controlled by different gene actions while using different donor and suseptible BINA parents. The phenotypic data of segregating mapping populations revealed single to multiple genes with complementary to duplicate gene actions6, 7. Genomics-assisted breeding (GAB) provides strategies to combine indepth genome information with the trait phenotyping data for effective and efficient selection procedures8. For implementing GAB, it is essential to develop genetic maps and identify quantitative trait loci (QTLs) or genes associated with desired traits. Subsequently identified QTLs/genes could be deployed in breeding programs through marker-assisted selection (MAS) or some other molecular breeding approach9C11. In the case of pigeonpea, limited genetic diversity in cultivated gene pool coupled with inadequate genomic resources caused BINA serious impediments for applying GAB12. However, in recent past, ample genomic and genetic resources such as segregating populations (~20 mapping populations, including recombinant inbred lines; introgression lines, multi-parent advanced generation intercross (MAGIC) population and nested association mapping (NAM) population), molecular markers (>3,000, simple sequence repeat (SSR) markers; 15,360 diversity arrays technology (DArT arrays; 10,000 single nucleotide polymorphism (SNP) markers; 1,616 Kompetitive Allele Specific PCR (KASPar) assays; 48 SNPs- based Golden-Gate VeraCode assays and 60K SNPs- based Axiom?array), genetic maps (8 maps with SSRs, DArTs, SNPs), transcriptome assemblies (CcTA v1 and CcTA BINA v2), draft genome sequence etc. have been developed13, 14. Recently re-sequencing data through next generation sequencing (NGS) technologies have also been generated for identifying genome-wide variations in parental lines of mapping populations, segregating for economically important traits including FW resistance15. Additionally sequencing-based bulked segregant analysis (Seq-BSA) by using a few lines from the mapping population has been used to identify candidate SNPs for resistance to FW and SMD in pigeonpea16. In continuation to detect all possible minor and major affect loci contributing to FW resistance in pigeonpea genome, NGS based genetic mapping by employing the entire mapping population has been planned in the present study. NGS is also providing opportunities to develop high-density genetic maps by deploying high throughput genotyping approaches such as genotyping-by-sequencing (GBS). In fact, GBS has been extensively used in a number of crop species for analysing genetic diversity17, developing dense genetic maps18, 19, refining the target genomic regions20, establishing marker-trait associations21 as well as deploying in genomic selection22, 23. Therefore, in the present study, GBS based genetic maps for three intra-specific populations have been developed. Populations were phenotyped for one to two years at two to three locations. Subsequently detailed analyses of genotyping data together with phenotyping data have provided consistent genomic regions associated with FW resistance in pigeonpea. Results Mapping populations and phenotypic evaluation Three mapping populations including two pigeonpea.