Marker-trait associations for ideotypic traits in pigeonpea (Cajanus cajan L.)

Pigeonpea is an important legume crop, serving as a major source of dietary protein for the predominant vegetarian Indian population. Breeding for short duation and higher yield remains a key focus of pigeonpea improvement programs in the country. Identifying QTLs and genes governing key plant ideotype traits is crucial for accelerating genetic gain through marker-assisted selection, genomic selection and systematic breeding programs. In this study, association analysis was performed using 93 diverse pigeonpea genotypes evaluated over two years (2016-17 and 2017-18) for phenotypic data and genotyped with 63 pigeonpea-specific polymorphic simple sequence repeat (SSR) markers.

The mapping panel was screened for various plant ideotypic traits over two consecutive years, and the panel was genotyped with 63 polymorphic SSR markers. The genotypic data were utilized to study the population structure following the admixture model. Phenotypic and genotypic data, along with population structure information, were used to identify marker-trait associations (MTAs) using both the GLM and MLM methods. Candidate genes were then searched in the genome near the positions of the associated markers.

A total of 11 and 22 MTAs were identified using GLM (with Q) and MLM (with Q + K) models, respectively, for six traits viz., days to initial flowering (IFL), days to 50% flowering (DFF), days to maturity (DM), plant height (PH), no. of primany branches (PB), and seeds per pod (SPP) at a corrected p-value of < 0.05. The phenotypic variation explained by these MTAs ranged upto 30.76%. Among these, markers HASSR28, HASSR30, and HASSR199 were consistently associated with IFL, accounting for > 12%, > 16%, and > 4.9% of the phenotypic variation, respectively. In addition, flowering traits related candidate genes, such as Glycosyltransferase, cold-responsive protein kinase 1, NRT1/PTR family 5.4, and Root phototropism protein 2, were identified in the vicinity of significant markers.

The present study identified MTAs for flowering time, days to maturity, and plant height, and also revealed few potential candidate genes linked to these traits. Validation of MTAs and understanding the functions of candidate genes will pave the way for the development of short-duration, and high-yielding pigeonpea cultivars.