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

IF 7.6 Q1 GENETICS & HEREDITY 园艺研究(英文) Pub Date : 2023-11-22 eCollection Date: 2024-01-01 DOI:10.1093/hr/uhad243
Ziquan Zhao, Chongjun Liang, Wei Zhang, Yingying Yang, Quanxin Bi, Haiyan Yu, Libing Wang
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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.

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全基因组关联分析确定了控制 Xanthoceras sorbifolium Bunge 种子大小和产量的候选基因。
黄角(Xanthoceras sorbifolium Bunge)是一种木本油料树种,其种子油富含不饱和脂肪酸和稀有神经酸,可用作高级食用油或生物柴油生产的原料。然而,与黄角树种子产量有关的遗传机制尚未得到很好的阐明。本研究基于黄角种质的 222 个全基因组重测序数据,确定了 2 164 863 个 SNP 位点。我们对 2022 年和 2020 年影响种子产量的三个核心性状(百粒重、单果种子量和单果种子数)进行了全基因组关联研究(GWAS)分析,发现了 399 个显著的 SNP 位点。在这些位点中,Chr10_24013014 和 Chr10_24012613 位点因其在多项分析中的一致性而引起了我们的注意。通过 Sanger 测序,我们验证了这两个位点在 16 个种质中的基因型,证实了它们与 GWAS 分析结果的一致性。在这两个重要位点的下游,我们发现了一个编码 AP2 转录因子蛋白的候选基因,并将其命名为 XsAP2。RT-qPCR 分析表明,XsAP2 基因在种子中的表达量很高,其表达水平与种子百粒重以及单果种子质量呈显著负相关,表明它在种子的正常发育过程中可能发挥作用。与野生型拟南芥相比,过表达 XsAP2 基因的转基因拟南芥品系在种子大小、每粒颖果种子数和每株颖果数方面都有不同程度的减少。综合这些结果,我们推测 XsAP2 基因可能对黄角种子产量有负面调控作用。这些结果为高产黄角的分子育种提供了参考。
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