Grapevine pangenome facilitates trait genetics and genomic breeding
Zhongjie Liu1, Nan Wang1, Ying Su1
1National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Nature Genetics
|November 4, 2024
Summary
This study introduces Grapepan v.1.0, a pangenome reference that improves understanding of grapevine genetic traits. Integrating structural variations enhances genomic prediction for superior cultivar breeding.
Area of Science:
- Genomics
- Plant Breeding
- Bioinformatics
Background:
- Grapevine breeding is limited by poor understanding of complex agronomic traits.
- A comprehensive genetic reference is needed to improve breeding efficiency.
Purpose of the Study:
- To construct a graph-based pangenome reference for grapevines.
- To identify genetic variations influencing agronomic traits.
- To enhance genomic prediction models for grapevine breeding.
Main Methods:
- Construction of Grapepan v.1.0 using 29 grapevine assemblies.
- Generation of a variation map including short and structural variations (SVs) from 466 cultivars.
- Integration of SVs into genome-wide association studies and genomic prediction.
Main Results:
- A pangenome reference (Grapepan v.1.0) and a variation map of over 9 million short and 236,000 SVs were created.
- 148 quantitative trait loci for 29 agronomic traits were mapped, with 12 significantly influenced by SVs.
- Heritability estimates improved by 22.78% on average with SV inclusion; divergent selection and genetic correlations were identified.
Conclusions:
- The study provides a valuable resource for grapevine genomics and breeding.
- Structural variations play a significant role in agronomic traits and heritability.
- Enhanced genomic selection using the pangenome reference can accelerate the development of superior grapevine cultivars.
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