Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits

Abstract

Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea.

Adapting legume crops to climate change using genomic approaches

“…GWAS has also proven to be successful in identifying candidate genes for ascochyta blight resistance (Li et al, ) and heat and drought tolerant loci in chickpea (Thudi, Upadhyaya, et al, ), and Aphanomyces euteiches resistance in Medicago truncatula (Bonhomme et al, ). Applying GWAS in a population comprising 292 pigeonpea accessions using data over several years enabled identification of association between candidate genes and traits, including 100‐seed weight, days to 50% flowering, and plant height (Varshney et al, ). Hoyos‐Villegas, Song, and Kelly () investigated the genetic basis of variation for drought tolerance and related traits in a diversity panel including 96 Middle American genotypes of common bean, and the GWAS analysis allowed identification of significant marker‐trait associations for traits related to drought tolerance and candidate genes associated with wilting.…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…Several million structural variations that aid in trait mapping and trait improvement were reported (Kumar et al, 2016;Thudi et al, 2016b). In addition, genome-wide single nucleotide polymorphisms (SNPs) were also used to identify significant marker trait associations for economically important traits (Zhou et al, 2015a;Varshney et al, 2017). Resequencing germplasm lines also enabled us to understand the spatial and temporal trends in diversity in released varieties of chickpea (Thudi et al, 2016a), cultivated and wild accessions of soybean (Lam et al, 2010;Zhou et al, 2015a), and a reference set of pigeonpea Table 1).…”

Origin of early maturing pigeonpea germplasm and its impact on adaptation and cropping systems

“…Various taxonomical, cytological and genomics evidences related to the origin of pigeonpea have confirmed that the cultivated form of pigeonpea originated in central India from a wild species known as Cajanus cajanifolius through various natural mutational and selection events (Pundir & Singh, ; van der Maesen, ; Varshney et al, ). This wild species is non‐determinate and photosensitive which flowers in about 120 days and matures in 170–180 days (Remanandan, Sastry, & Mengesha, ).…”