中国农业科学院周永锋研究小组取得一项新突破。他们的研究发现葡萄泛基因组有利于性状遗传和基因组育种。这一研究成果发表在2024年11月4日出版的国际学术期刊《自然—遗传学》上。

研究人员表示，葡萄育种受到对复杂农艺性状遗传基础的有限理解的阻碍。本研究从18个新生成的端粒到端粒的阶段性组装体，和11个已发表的组装体构建了基于图的泛基因组参考（Grapepan v.1.0）。

利用Grapepan v.1.0和466个葡萄品种的重测序数据，研究人员构建了包含9105787个短变异和236449个结构变异的变异图谱。将sv整合到全基因组关联研究中，研究人员绘制了29个农艺性状的148个数量性状位点（新鉴定的50.7%），其中12个性状由sv显著贡献。

当包括sv时，估计遗传力平均提高22.78%。该研究团队发现，酿酒葡萄和鲜食葡萄在代谢和果实发育上，存在不同人工选择的数量性状定位区域。

此外，研究人员还发现29个性状间存在显著的遗传相关。在多基因模型下，研究人员对每个性状进行了基因组预测。总的来说，他们的研究通过多性状的基因组选择促进了优良品种的选育。

附：英文原文

Title: Grapevine pangenome facilitates trait genetics and genomic breeding

Author: Liu, Zhongjie, Wang, Nan, Su, Ying, Long, Qiming, Peng, Yanling, Shangguan, Lingfei, Zhang, Fan, Cao, Shuo, Wang, Xu, Ge, Mengqing, Xue, Hui, Ma, Zhiyao, Liu, Wenwen, Xu, Xiaodong, Li, Chaochao, Cao, Xuejing, Ahmad, Bilal, Su, Xiangnian, Liu, Yuting, Huang, Guizhou, Du, Mengrui, Liu, Zhenya, Gan, Yu, Sun, Lei, Fan, Xiucai, Zhang, Chuan, Zhong, Haixia, Leng, Xiangpeng, Ren, Yanhua, Dong, Tianyu, Pei, Dan, Wu, Xinyu, Jin, Zhongxin, Wang, Yiwen, Liu, Chonghuai, Chen, Jinfeng, Gaut, Brandon, Huang, Sanwen, Fang, Jinggui, Xiao, Hua, Zhou, Yongfeng

Issue&Volume: 2024-11-04

Abstract: Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits.

DOI: 10.1038/s41588-024-01967-5

Source: https://www.nature.com/articles/s41588-024-01967-5