High resolution mapping of restoration of fertility (Rf) by combining large population and high density genetic map in pigeonpea [Cajanus cajan (L.) Millsp]

Abstract

Background: Restoration of fertility (Rf) is an important trait for pigeonpea hybrid breeding. Few coarse quantitative trait locus (QTL) studies conducted in the past identified QTLs with large confidence intervals on the genetic map and could not provide any information on possible genes responsible for Rf in pigeonpea. Therefore, a larger population comprising of 369 F 2 s derived from ICPA 2039 × ICPL 87119 was genotyped with high density Axiom Cajanus SNP Array with 56 K single nucleotide polymorphism (SNPs) for high resolution mapping of Rf. Results: A genetic map with 4867 markers was developed and a total of four QTLs for Rf were identified. While one major effect QTL (qRf8.1) was co-localized with the QTL identified in two previous studies and its size was refined from 1.2 Mb to 0.41 Mb. Further analysis of qRf8.1 QTL with genome sequence provided 20 genes including two genes namely flowering locus protein T and 2-oxoglutarate/Fe (II)-dependent dioxygenases (2-ODDs) superfamily protein with known function in the restoration of fertility. Conclusion: The qRf8.1 QTL and the potential candidate genes present in this QTL will be valuable for genomicsassisted breeding and identification of causal genes/nucleotides for the restoration of fertility in the hybrid breeding program of pigeonpea.

Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

“…An F 2 mapping population derived by crossing ICPA 2039 × ICPL 87119 was used for high-density linkage map construction in the present study. A total of 336 progenies, along with parental lines, were genotyped using the “Axiom Cajanus SNP Array”, which resulted in the identification of 11,697 polymorphic markers [49] . The R/qtl package [50] from the R environment was used for linkage map construction.…”

Meta‐analysis of the quantitative trait loci associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits in pigeonpea (Cajanus cajan L.)

“…Additionally, because of the accessibility of NGS‐based high‐throughput marker systems, advancements in QTL mapping methodologies, and a rise in geneticists’ interest in genetic dissection studies, linkage‐based QTL mapping studies have recently become widespread. Just to exemplify, during the final writing of this paper, three linkage‐based QTL mapping studies were published (Saxena, Kale, et al., 2020; Saxena, Molla, et al., 2020; Singh, Sinha, et al., 2022), which reported the identification of several QTLs for fertility restoration, days to flowering, and yield‐related traits. Comparison of the physical positions of these QTLs with the physical coordinates of MQTLs revealed the co‐localization of five of these QTLs with three MQTLs (viz., CC_MQTL7.2, CC_MQTL8.2, and CC_MQTL8.4) identified during the present study.…”