Genetic dissection of two elite japonica varieties reveals founder transmission and selection in breeding

文献类型： 外文期刊

第一作者： Ye, Junhua

作者： Ye, Junhua;Yan, Ying;Zhang, Lixia;Wang, Kai;Yang, Hang;Shi, Zhenying;Hu, Zejun;Cao, Liming;Wu, Shujun;Ye, Junhua;Yan, Ying;Cao, Liming

作者机构：

关键词： Pedigree analysis; Breeding; Founder parent; Rice

期刊名称：GENOMICS （ 影响因子：3.0； 五年影响因子：3.3 ）

ISSN： 0888-7543

年卷期： 2025 年 117 卷 5 期

页码：

收录情况： SCI

摘要： Understanding the genetic basis of elite rice varieties is conducive to the strategic utilization of genetic resources in modern breeding programs. To elucidate the genetic component and transmission across pedigrees, we investigated two elite inbred japonica varieties, Huruan1212 (HR1212) and Hugeng137 (HG137), through whole-genome sequencing with an average depth of 38.2x and pedigree analysis. We identified specific SNPs and enriched pathways underlying HR1212's excellent eating and cooking quality and HG137's stress resistance. Genomic scans traced the contributions of founder parents Xiushui04 and Wuyugeng3, revealing transmission patterns of favorable alleles across generations. Notably, the shared identity-by-descent (sIBD) segments of the two pedigrees overlapped by 74 Mb, total formed 118.42 Mb of conserved genetic segments, with validation in other founder-derived lines. This research provides valuable insights for utilizing founder parents and elite varieties and highlights the critical need to implement genome-informed breeding strategies in future breeding practice.

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