Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing

Xin Zhang; Xiaoji Zhang; Luhuan Wang; Qimei Liu; Yuying Liang; Jiayu Zhang; Yunyun Xue; Yuexia Tian; Huiqi Zhang; Na Li; Cong Sheng; Pingping Nie; Suping Feng; Boshou Liao; Dongmei Bai

doi:10.3389/fpls.2023.1153293

Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing

Front Plant Sci. 2023 May 8:14:1153293. doi: 10.3389/fpls.2023.1153293. eCollection 2023.

Authors

Xin Zhang^{1

2}, Xiaoji Zhang³, Luhuan Wang³, Qimei Liu⁴, Yuying Liang³, Jiayu Zhang³, Yunyun Xue¹, Yuexia Tian¹, Huiqi Zhang¹, Na Li¹, Cong Sheng⁵, Pingping Nie⁶, Suping Feng⁷, Boshou Liao⁸, Dongmei Bai¹

Affiliations

¹ Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China.
² State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, China.
³ College of Agronomy, Shanxi Agricultural University, Taigu, China.
⁴ College of Plant Protection, Shanxi Agricultural University, Taigu, China.
⁵ Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
⁶ College of Life Sciences, Zaozhuang University, Zaozhuang, China.
⁷ College of Food Science and Engineering, Hainan Tropical Ocean College, Hainan, China.
⁸ The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.

Abstract

Low temperatures significantly affect the growth and yield of peanuts. Temperatures lower than 12 °C are generally detrimental for the germination of peanuts. To date, there has been no report on precise information on the quantitative trait loci (QTL) for cold tolerance during the germination in peanuts. In this study, we developed a recombinant inbred line (RIL) population comprising 807 RILs by tolerant and sensitive parents. Phenotypic frequencies of germination rate low-temperature conditions among RIL population showed normally distributed in five environments. Then, we constructed a high density SNP-based genetic linkage map through whole genome re-sequencing (WGRS) technique and identified a major quantitative trait locus (QTL), qRGRB09, on chromosome B09. The cold tolerance-related QTLs were repeatedly detected in all five environments, and the genetic distance was 6.01 cM (46.74 cM - 61.75 cM) after taking a union set. To further confirm that qRGRB09 was located on chromosome B09, we developed Kompetitive Allele Specific PCR (KASP) markers for the corresponding QTL regions. A regional QTL mapping analysis, which was conducted after taking the intersection of QTL intervals of all environments into account, confirmed that qRGRB09 was between the KASP markers, G22096 and G220967 (chrB09:155637831-155854093), and this region was 216.26 kb in size, wherein a total of 15 annotated genes were detected. This study illustrates the relevance of WGRS-based genetic maps for QTL mapping and KASP genotyping that facilitated QTL fine mapping of peanuts. The results of our study also provided useful information on the genetic architecture underlying cold tolerance during germination in peanuts, which in turn may be useful for those engaged in molecular studies as well as crop improvement in the cold-stressed environment.

Keywords: QTL; candidate genes; cold tolerance; germination; peanut; whole genome re-sequencing.

Grants and funding

This work was supported by the National Natural Science Foundation of China (31871662), the National Peanut Industry Technology System Construction (CARS-13), the Open Project of Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P. R. China (KF2021004), the Fundamental Research Program of Shanxi Province (202203021221178), the Science and Technology Major Project of Shanxi Province (202201140601025), the Research Program Sponsored by the State Key Laboratory of Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University (202105D121008), the earmarked fund for Modern Agro-industry Technology Research System (2023CYJSTX05), and the Key Research and Development Program of Hainan Province (ZDYF2022XDNY217).