Co-localization of major quantitative trait loci for pod size and weight to a 3.7\xa0cM interval on chromosome A05 in cultivated peanut (Arachis hypogaea L.)

Yuning Chen,Fei Liu,Huifang Jiang,Xiangguo Jiang,Zhendong Li,Boshou Liao,Baozhu Guo,Manish K. Pandey,Weigang Chen,Zhijun Xu,Xinping Li,Li Huang,Xiaojing Zhou,Huaiyong Luo,Yong Lei,Xiaoping Ren,Rajeev K. Varshney

doi:10.1186/s12864-016-3456-x

Abstract

BackgroundCultivated peanut (Arachis hypogaea L.), an important source of edible oil and protein, is widely grown in tropical and subtropical areas of the world. Genetic improvement of yield-related traits is essential for improving yield potential of new peanut varieties. Genomics-assisted breeding (GAB) can accelerate the process of genetic improvement but requires linked markers for the traits of interest. In this context, we developed a recombinant inbred line (RIL) mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 individuals and used to map quantitative trait loci (QTLs) associated with three important pod features, namely pod length, pod width and hundred-pod weight.ResultsQTL analysis using the phenotyping data generated across four environments in two locations and genotyping data on 743 mapped loci identified 15 QTLs for pod length, 11 QTLs for pod width and 16 QTLs for hundred-pod weight. The phenotypic variation explained (PVE) ranged from 3.68 to 27.84%. Thirteen QTLs were consistently detected in at least two environments and three QTLs (qPLA05.7, qPLA09.3 and qHPWA05.6) were detected in all four environments indicating their consistent and stable expression. Three major QTLs, detected in at least three environments, were found to be co-localized to a 3.7 cM interval on chromosome A05, and they were qPLA05.7 for pod length (16.89–27.84% PVE), qPWA05.5 for pod width (13.73–14.12% PVE), and qHPWA05.6 for hundred-pod weight (13.75–26.82% PVE). This 3.7 cM linkage interval corresponds to ~2.47 Mb genomic region of the pseudomolecule A05 of A. duranensis, including 114 annotated genes related to catalytic activity and metabolic process.ConclusionsThis study identified three major consistent and stable QTLs for pod size and weight which were co-localized in a 3.7 cM interval on chromosome A05. These QTL regions not only offer further investigation for gene discovery and development of functional markers but also provide opportunity for deployment of these QTLs in GAB for improving yield in peanut.

Highlights

Cultivated peanut (Arachis hypogaea L.), an important source of edible oil and protein, is widely grown in tropical and subtropical areas of the world
The normality test indicated that the phenotypic data were normally distributed for pod-related traits (PRTs), except pod weight (PW) in WH2013 trial, pod length (PL) in WH2015 trial and hundred-pod weight (HPW) in XY2015 trial (Table 1, Fig. 1)
The present study identified 15 Quantitative trait loci (QTLs) for pod length, 11 QTLs for pod width and 16 QTLs for hundred-pod weight using a recombinant inbred lines (RILs) population across four environments in two locations

Summary

Introduction

Cultivated peanut (Arachis hypogaea L.), an important source of edible oil and protein, is widely grown in tropical and subtropical areas of the world. Genomics-assisted breeding (GAB) can accelerate the process of genetic improvement but requires linked markers for the traits of interest. In this context, we developed a recombinant inbred line (RIL) mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 individuals and used to map quantitative trait loci (QTLs) associated with three important pod features, namely pod length, pod width and hundred-pod weight. Genomics-assisted breeding (GAB) has potential to accelerate the process of achieving higher genetic gain in less time and with minimum resources using molecular markers [4, 5]. In order to deploy GAB, linked markers for PRTs is essential for developing high yielding peanut varieties

Methods

Results

Discussion

Conclusion