Genetic structure, KASP markers, and core germplasm resources of rice landraces from the Taihu Lake Basin

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics Pub Date : 2025-06-10 DOI:10.1016/j.ygeno.2025.111069

Zijie Shen , Naiwei Li , Zhengbin Zhu , Xin Zou , Xiaoqin Sun , Jia Liu , Ruisen Lu

{"title":"Genetic structure, KASP markers, and core germplasm resources of rice landraces from the Taihu Lake Basin","authors":"Zijie Shen , Naiwei Li , Zhengbin Zhu , Xin Zou , Xiaoqin Sun , Jia Liu , Ruisen Lu","doi":"10.1016/j.ygeno.2025.111069","DOIUrl":null,"url":null,"abstract":"<div><div>Rice (<em>Oryza sativa</em> L.), a global staple crop, is crucial to food security, particularly in Asia. The Taihu Lake Basin, located in the middle and lower reaches of the Yangtze River, is a secondary origin center for rice, with a cultivation history dating back over 8000 years. However, the genetic diversity of traditional rice landraces in this region faces significant threats due to the widespread adoption of high-yielding cultivars. This study aimed to characterize the genetic structure of rice landraces from the Taihu Lake Basin, develop KASP markers for precise identification, and establish a core germplasm collection, using high-throughput resequencing technologies. A total of 114 rice landrace accessions from the Taihu Lake Basin were sampled and analyzed. Population genetic structure analysis revealed seven distinct genetic groups. Utilizing this dataset, a set of 27 kompetitive allele specific PCR (KASP) markers were developed, enabling accurate genotyping and efficient landrace identification. Furthermore, a core germplasm collection was established, representing 99 % of the genetic diversity of the original collection. Overall, this study provides a valuable resource for the conservation and sustainable utilization of rice landraces in the Taihu Lake Basin, supporting future rice breeding programs and ensuring the preservation of genetic resources crucial for crop improvement.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 4","pages":"Article 111069"},"PeriodicalIF":3.4000,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0888754325000850","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Rice (Oryza sativa L.), a global staple crop, is crucial to food security, particularly in Asia. The Taihu Lake Basin, located in the middle and lower reaches of the Yangtze River, is a secondary origin center for rice, with a cultivation history dating back over 8000 years. However, the genetic diversity of traditional rice landraces in this region faces significant threats due to the widespread adoption of high-yielding cultivars. This study aimed to characterize the genetic structure of rice landraces from the Taihu Lake Basin, develop KASP markers for precise identification, and establish a core germplasm collection, using high-throughput resequencing technologies. A total of 114 rice landrace accessions from the Taihu Lake Basin were sampled and analyzed. Population genetic structure analysis revealed seven distinct genetic groups. Utilizing this dataset, a set of 27 kompetitive allele specific PCR (KASP) markers were developed, enabling accurate genotyping and efficient landrace identification. Furthermore, a core germplasm collection was established, representing 99 % of the genetic diversity of the original collection. Overall, this study provides a valuable resource for the conservation and sustainable utilization of rice landraces in the Taihu Lake Basin, supporting future rice breeding programs and ensuring the preservation of genetic resources crucial for crop improvement.

查看原文本刊更多论文

太湖流域地方水稻品种遗传结构、KASP标记及核心种质资源

水稻（Oryza sativa L.）是一种全球主要作物，对粮食安全至关重要，尤其是在亚洲。太湖流域位于长江中下游，是水稻的第二产地，有8000多年的种植历史。然而，由于高产品种的广泛采用，该地区传统水稻地方品种的遗传多样性面临严重威胁。本研究旨在利用高通量重测序技术，对太湖流域水稻地方品种的遗传结构进行表征，开发KASP标记进行精确鉴定，并建立核心种质资源库。对太湖流域114份地方水稻材料进行了抽样分析。群体遗传结构分析显示出7个不同的遗传群。利用该数据集，开发了一套27个竞争性等位基因特异性PCR （KASP）标记，实现了准确的基因分型和高效的地方品种鉴定。此外，还建立了一个核心种质，代表了原始种质99%的遗传多样性。总之，本研究为太湖流域水稻地方品种的保护和可持续利用提供了宝贵的资源，为未来的水稻育种计划提供了支持，并确保了对作物改良至关重要的遗传资源的保存。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

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.