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

Authors: LUO, HUAIYONG - Chinese Academy Of Agricultural Sciences; REN, XIAOPING - Chinese Academy Of Agricultural Sciences; LI, ZHENDONG - Chinese Academy Of Agricultural Sciences; XU, ZHIJUN - Chinese Academy Of Agricultural Sciences; LI, XINPING - Chinese Academy Of Agricultural Sciences; HUANG, LI - Chinese Academy Of Agricultural Sciences; ZHOU, XIAOJING - Chinese Academy Of Agricultural Sciences; CHEN, YUNING - Chinese Academy Of Agricultural Sciences; CHEN, WEIGANG - Chinese Academy Of Agricultural Sciences; LEI, YONG - Chinese Academy Of Agricultural Sciences; LIAO, BOSHOU - Chinese Academy Of Agricultural Sciences; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Guo, Baozhu; JIANG, XIANGGUO - Chinese Academy Of Agricultural Sciences; LIU, FEI - Chinese Academy Of Agricultural Sciences; JIANG, HUIFANG - Chinese Academy Of Agricultural Sciences

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2017
Publication Date: 5/10/2017
Citation: Luo, H., Ren, X., Li, Z., Xu, Z., Li, X., Huang, L., Zhou, X., Chen, Y., Chen, W., Lei, Y., Liao, B., Pandey, M.K., Varshney, R.K., Guo, B., Jiang, X., Liu, F., Jiang, H. 2017. Co-localization of major quantitative trait loci for pod size and weight to a 3.7 cM interval on chromosome A05 in cultivated peanut (Arachis hypogaea L.). BMC Genomics. 18:58. doi:10.1186/s12864-016-3456-x.

Interpretive Summary: Improving yield has been one of the major objectives in peanut breeding programs, which is directly influenced by pod-related traits (PRTs). In order to select a promising line for varietal release, breeders need to assess its potential in multiple environments to check its stable performance to achieve higher adoption in the farmers’ field. 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. In this study, a population was developed from the cross between Yuanza 9102 and Xuzhou 68-4 and used to identify QTLs controlling yield-related traits such as pod length (PL), pod width (PW), and hundred pod weight (HPW) across four environments. The variety Yuanza 9102 is a small-pod with low pod weight while the variety Xuzhou 68-4 has large pods and higher pod weight. 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, qPWA05.5 for pod width, and qHPWA05.6 for hundred-pod weight. This 3.7 cM linkage interval corresponds to ~2.47 Mb genomic region of the pseudomolecule A05 of A. duranensis. These three major QTLs associated with pod yield, in a 3.7 cM interval on chromosome A05, will offer further investigation for gene discovery and development of functional markers for deployment of these QTLs in GAB for improving yield in peanut breeding programs.

Technical Abstract: Cultivated 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. The QTL 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) 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. This 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.