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

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics Pub Date : 2025-08-08 DOI:10.1016/j.ygeno.2025.111096

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

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引用次数: 0

Abstract

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 38.2× 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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两个粳稻优良品种的遗传剖析揭示了育种中的奠基遗传和选择。

了解水稻优良品种的遗传基础，有助于在现代育种中战略性地利用遗传资源。为阐明其遗传成分及其家系间的遗传传递，本研究采用平均38.2 x深度的全基因组测序和家系分析方法，对2个优良自交系粳稻品种“沪卷1212”（HR1212）和“沪更137”（HG137）进行了研究。我们发现了HR1212优良的食用和烹饪品质以及HG137的抗逆性背后的特定snp和富集途径。基因组扫描追踪了创始人父母秀水04和武玉根3的贡献，揭示了有利等位基因在代际间的传播模式。值得注意的是，两个家系的共同血统认同（sIBD）片段重叠74 Mb，共形成118.42 Mb的保守遗传片段，在其他创始人衍生系中也得到了验证。该研究为利用始祖亲本和优良品种提供了有价值的见解，并强调了在未来育种实践中实施基因组信息育种策略的关键必要性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

期刊介绍： Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.