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Article|19 Oct 2022|OPEN
Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits
Shizhuo Xiao1 ,† , Xibin Dai1 ,† , Lingxiao Zhao1 ,† , Zhilin Zhou1 , Lukuan Zhao1 , Pan Xu2 , Bingqian Gao1 , An Zhang1 , Donglan Zhao1 , Rui Yuan1 , Yao Wang1 , Jie Wang1 , Qinglian Li1 and Qinghe Cao,1 ,
1Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
2College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
*Corresponding author. E-mail: caoqinghe@jaas.ac.cn
Shizhuo Xiao,Xibin Dai and Lingxiao Zhao contributed equally to the study.

Horticulture Research 10,
Article number: uhac234 (2023)
doi: https://doi.org/10.1093/hr/uhac234
Views: 433

Received: 25 May 2022
Accepted: 13 Oct 2022
Published online: 19 Oct 2022

Abstract

Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity, which limits gene mining for important agronomic traits. Here, 314 sweetpotato germplasm resources were deeply resequenced, and 4 599 509 SNPs and 846 654 InDels were generated, among which 196 124 SNPs were nonsynonymous and 9690 InDels were frameshifted. Based on the Indels, genome-wide marker primers were designed, and 3219 of 40 366 primer pairs were selected to construct the core InDel marker set. The molecular ID of 104 sweetpotato samples verified the availability of these primers. The sweetpotato population structures were then assessed through multiple approaches using SNPs, and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources. As many as 20 important agronomic traits were evaluated, and a genome-wide association study was conducted on these traits. A total of 19 high-confidence loci were detected in both models. These loci included several candidate genes, such as IbMYB1IbZEP1, and IbYABBY1, which might be involved in anthocyanin metabolism, carotenoid metabolism, and leaf morphogenesis, respectively. Among them, IbZEP1 and IbYABBY1 were first reported in sweetpotato. The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with flesh color (orange or not orange) in sweetpotato. The expression levels of IbYABBY1 were also correlated with leaf shape. These results will assist in genetic and breeding studies in sweetpotato.