Grapevine pangenome facilitates trait genetics and genomic breeding DOI Creative Commons
Zhongjie Liu, Nan Wang, Ying Su

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 4, 2024

Grapevine breeding is hindered by a limited understanding of the genetic basis complex agronomic traits. This study constructs 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 variation map with 9,105,787 short variations 236,449 structural (SVs) resequencing data 466 grapevine cultivars. Integrating SVs into genome-wide association study, 148 quantitative trait loci for 29 traits (50.7% identified), 12 significantly contributed SVs. The estimated heritability improves 22.78% on average when including We discovered locus regions under divergent artificial selection in metabolism berry development between wine table grapes, respectively. Moreover, significant correlations were detected among Under polygenic model, conducted genomic predictions each trait. In general, our facilitates superior cultivars via multiple By constructing incorporating phenotypic maps, investigates traits, empowering breeding.

Language: Английский

Grapevine pangenome facilitates trait genetics and genomic breeding DOI Creative Commons
Zhongjie Liu, Nan Wang, Ying Su

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 4, 2024

Grapevine breeding is hindered by a limited understanding of the genetic basis complex agronomic traits. This study constructs 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 variation map with 9,105,787 short variations 236,449 structural (SVs) resequencing data 466 grapevine cultivars. Integrating SVs into genome-wide association study, 148 quantitative trait loci for 29 traits (50.7% identified), 12 significantly contributed SVs. The estimated heritability improves 22.78% on average when including We discovered locus regions under divergent artificial selection in metabolism berry development between wine table grapes, respectively. Moreover, significant correlations were detected among Under polygenic model, conducted genomic predictions each trait. In general, our facilitates superior cultivars via multiple By constructing incorporating phenotypic maps, investigates traits, empowering breeding.

Language: Английский

Citations

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