Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe

Fine mapping of a “QTL-hotspot” for drought tolerance in chickpea (Cicer arietinum L.)

To understand the genetic complexity and mechanism of drought tolerance in chickpea, a genomic region (~35 cM) harboring QTL for drought tolerance traits was identified on linkage group 04 (CaLG04) using a linkage mapping based approach. To enhance marker density in this region, two approaches were adopted: (i) genotyping-by-sequencing (GBS) and (ii) re sequencing at low coverage referred to as Skim sequencing. The GBS approach, with 5X and 0.2X coverage on parental lines and 232 RILs, respectively, provided 828 single nucleotide polymorphism (SNP) markers. A total of 49 SNPs were integrated in the “QTL-hotspot” region that narrowed the QTL interval from 35cM to 14 cM (~7 Mb on the physical map). The Skim sequencing approach, with 7-8X and 0.72X coverage on parental lines and 232 RILs respectively, identified 53,175 high quality SNPs utilized to construct a bin map with 1,610 recombination bins. QTL analysis using the bin map and precise phenotyping data split the ~7 Mb QTL into four regions: (i) 13.16-13.23 Mb region harboring 8 candidate genes and QTL for 5 drought tolerance traits; (ii) 13.39-13.54 Mb region harboring 11 candidate genes and QTL for 4 drought tolerance traits (iii) 14.15-14.27 Mb region harboring 11 candidate genes and QTL for pod number (POD) (iv) 14.99-15.08 Mb region harboring 9 candidate genes and QTL for POD. In addition to an approach that will enable further fine mapping of the QTL regions identified, candidate genes ware being characterized for potential to improve drought tolerance in chickpea