Genome-wide association analysis identifies a candidate gene controlling seed size and yield in Xanthoceras sorbifolium Bunge

Abstract

Yellow horn (Xanthoceras sorbifolium Bunge) is a woody oilseed tree species whose seed oil is rich in unsaturated fatty acids and rare neuronic acids, and can be used as a high-grade edible oil or as a feedstock for biodiesel production. However, the genetic mechanisms related to seed yield in yellow horn are not well elucidated. This study identified 2 164 863 SNP loci based on 222 genome-wide resequencing data of yellow horn germplasm. We conducted genome-wide association study (GWAS) analysis on three core traits (hundred-grain weight, single-fruit seed mass, and single-fruit seed number) that influence seed yield for the years 2022 and 2020, and identified 399 significant SNP loci. Among these loci, the Chr10_24013014 and Chr10_24012613 loci caught our attention due to their consistent associations across multiple analyses. Through Sanger sequencing, we validated the genotypes of these two loci across 16 germplasms, confirming their consistency with the GWAS analysis results. Downstream of these two significant loci, we identified a candidate gene encoding an AP2 transcription factor protein, which we named XsAP2. RT-qPCR analysis revealed high expression of the XsAP2 gene in seeds, and a significant negative correlation between its expression levels and seed hundred-grain weight, as well as single-fruit seed mass, suggesting its potential role in the normal seed development process. Transgenic Arabidopsis lines with the overexpressed XsAP2 gene exhibited varying degrees of reduction in seed size, number of seeds per silique, and number of siliques per plant compared with wild-type Arabidopsis. Combining these results, we hypothesize that the XsAP2 gene may have a negative regulatory effect on seed yield of yellow horn. These results provide a reference for the molecular breeding of high-yielding yellow horn.

Acknowledgements

This work was financially supported by the Youth Top Talent Project of the Ten Thousand Talents Program of the State and Natural Science Foundation of China (31870594).

Author contributions

Z.Z., H.Y., and L.W. designed the research. Z.Z. performed data collection and analysis and the field experiments, and wrote the manuscript. C.L. and W.Z. provided experimental materials and supplemented the experimental protocol. Y.Y. and Z.Z. com-pleted the phenotyping. Q.B. provided resequencing data. H.Y. and L.W. helped to solve the experimental problems, reviewed the manuscript, and provided constructive comments.

Data availability

The data underlying this article are available in the NCBI database at https://www.ncbi.nlm.nih.gov/sra, and can be accessed with PRJNA1031336. The detailed run code and parameters for the GWAS analysis are available on GitHub (https://github.com/ziquanzhao/Python_GX/tree/master/Python_apply/EasyGWAS).

Conflict of interest

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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