Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq

Zhenghao Lv; Guohu Lan; Baiyi Bai; Penghao Yu; Chuantang Wang; He Zhang; Chao Zhong; Xinhua Zhao; Haiqiu Yu

doi:10.1016/j.ygeno.2024.110835

Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq

Genomics. 2024 Mar 22;116(3):110835. doi: 10.1016/j.ygeno.2024.110835. Online ahead of print.

Authors

Zhenghao Lv¹, Guohu Lan¹, Baiyi Bai², Penghao Yu¹, Chuantang Wang³, He Zhang¹, Chao Zhong¹, Xinhua Zhao¹, Haiqiu Yu⁴

Affiliations

¹ Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China.
² College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China.
³ Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Shandong Peanut Research Institute, Qingdao 266100, China.
⁴ Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China. Electronic address: yuhaiqiu@syau.edu.cn.

PMID: 38521201
DOI: 10.1016/j.ygeno.2024.110835

Abstract

Pod length (PL) is one of the major traits determining pod size and yield of peanut. Discovering the quantitative trait loci (QTL) and identifying candidate genes associated with PL are essential for breeding high-yield peanut. In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F₂ population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which Arahy.PF2L6F (AhCDC48) and Arahy.P4LK2T (AhTAA1) were speculated to be PL-related candidate genes. These results were informative for the elucidation of the underlying regulatory mechanism in peanut pod length and would facilitate further identification of valuable target genes.

Keywords: Candidate genes; Peanut; Pod length; QTL-seq; RNA-seq.