数字农科院2.0

Comprehensive comparison between structural variants and singlenucleotide polymorphism in genomic selection of rice (Oryza sativa L.)

文献类型： 外文期刊

作者： 梁伦平;;张超普;;余林俊;;盛婷婷;;郑舒月;;李士娇;;周姝然;;冯庭;;张帆;;黎志康;;崔彦茹;;王文生;;黎珉

关键词： Structural variation QTL SNP Predictive ability

期刊名称： Crop Journal

ISSN： 2095-5421

年卷期： 2025 年

页码：

收录情况： SCIE（2025版） ; ; CSCD（2025-2026年度） ; ; 科技核心（2024版） ; ; 农林核心（2024版）

摘要： Recent genomic research on plant populations has revealed abundant structural variations (SVs) of > 50 bp within and among genotypes of major crop species, but the application of SVs as a unique type of molecular marker in genetic research and breeding remains limited. In this study, we used a panel of 305 rice accessions from the 3000 Rice Genome Project to compare 26,000 + SVs (> 90 % deletions and translocations) and 180,000 + high-quality SNPs in predicting the field performance of 20 traits using nine commonly used genomic selection models. We demonstrated that SVs had slightly lower prediction accuracies (PA) across 20 different traits than SNPs, but saved 53.8 %–77.8 % of computation time toachieve reasonably high PA. The major advantage of SVs as valuable markers in obtaining reliable genomic estimated breeding values (GEBVs) in GS experiments resulted primarily from their greater phenotypic effects on high heritability traits. Our results suggested that P0.01 was an appropriate threshold for marker filtering of both SVs and SNPs to achieve high PA in genomic selection experiments. A dataset containing all identified SVs from this study has been deposited at the China National Center forBioinformation under BioProject: PRJCA038102, a publicly accessible molecular marker resource,enabling broad applications in rice research including gene/QTL discovery, allelic mining, and genomic selection experiments

分类号：

  • 相关文献
作者其他论文 更多>>