Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits

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 IbMYB1, IbZEP1, 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.

Acknowledgements

This work was supported by the National Key Research & Development Program of China (2018YFD1000705/2018YFD1000700), the Natural Science Foundation of Jiangsu Province of China (BK20221213), and the China Agriculture Research System (CARS-10-GW01). We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

Author contributions

Q.C. and S.X. designed the study. S.X. conducted the data analysis and wrote the manuscript. X.D. prepared materials for genome resequencing and investigated aboveground agronomic traits. Li.Z. measured most physiological traits. Lu.Z. verified the molecular markers by electrophoresis. Z.Z., B.G., A.Z., D.Z., R.Y., J.W., Y.W., and Q.L. participated in the planting, phenotyping, reaping, storage, and transport of plant materials. P.X. assisted with data analysis. Q.C. supervised the research and the manuscript. All authors read and approved the manuscript.

Data availability

The sequence read archives of 314 samples were deposited in the NCBI database (Accession No. PRJNA857483). The SNP dataset and the phenotype data were deposited in a publicly available database (https://zenodo.org/) and can be accessed via the DOI number (10.5281/zenodo.7184909).

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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