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.)

Luo, H and Ren, X and Li, Z and Xu, Z and Li, X and Huang, L and Zhou, X and Chen, Y and Chen, W and Lei, Y and Liao, B and Pandey, M K and Varshney, R K and Guo, B and Jiang, X and Liu, F and 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). pp. 1-12. ISSN 1471-2164

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Background 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. Results 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) 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. Conclusions 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.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Peanut, QTL, Pod length, Pod width, Hundred-pod weight, Yield, Quantitative trait loci, QTL analysis
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 31 Mar 2017 09:06
Last Modified: 18 Apr 2017 05:58
Official URL: http://10.2135/10.1186/s12864-016-3456-x
Acknowledgement: This study was supported by the National Natural Science Foundations of China (31271764, 31371662, 31471534 and 31461143022), the China Agriculture Research System (CARS-14), and the Crop Germplasm Resources Project of China (NB2012-2130135-28). The work reported in this article was undertaken as a part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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