Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq

IF 2 3区 农林科学 Q2 AGRONOMY Crop Science Pub Date : 2024-11-05 DOI:10.1002/csc2.21395
Arnaud Comlan Gouda, Jean Rodrigue Sangare, Karlin Gnikoua, Peterson Wambugu, Trevis D. Huggins, Marie Noelle Ndjiondjop
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Abstract

Utilizing the full potential of rice collections mainly depends on an in‐depth exploration and understanding of the vast diversity in its germplasm. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. In the present study, we comprehensively characterized a collection of 9013 accessions, including Oryza barthii A. Chev., Oryza glaberrima Steud., Oryza longistaminata A. Chev. & Roehr., Oryza sativa L. ssp. indica, and Oryza sativa L. ssp. japonica, for genetic diversity and population structure using genotyping‐by‐sequencing through DArTseq analysis. We identified 27,718 high‐quality single nucleotide polymorphism markers after the genotypic data were filtered. Based on the analyses, the collection has extensive genetic diversity, and the average genetic distance of the entire set was 0.267 (range 0.001–0.469), with 45.1% of pairs of accessions being highly distant and 40.1% moderately distant from each other. Neighbor‐joining tree, principal component, and Bayesian population structure analyses clustered the 9013 accessions into six groups, based roughly on their taxonomic and biological status. The first, second, and third groups consisted of accessions belonging to O. glaberrima, O. barthii, and O. longistaminata, respectively. The fourth, fifth, and sixth groups were improved‐indica, japonica, and traditional‐indica accessions, respectively. The highest value of genetic variance proportion (PhiPT) was found in the species group followed by groups based on cluster analysis and on Bayesian population structure at K = 6. These results allow us to better understand the genetic diversity present in 9013 rice accessions maintained in the AfricaRice genebank and offer a valuable tool for pre breeding, breeding, and further genetic applications.
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利用 DArTseq 分析非洲水稻基因库中水稻品种的遗传变异和种群结构
要充分发挥水稻藏品的潜力,主要取决于深入探索和了解其种质的巨大多样性。非洲水稻基因库(AfricaRice genebank)拥有非洲大陆最大的水稻种质资源库。在本研究中,我们通过 DArTseq 分析,利用基因分型测序技术,对 9013 份材料进行了全面鉴定,包括 Oryza barthii A. Chev.、Oryza glaberrima Steud.、Oryza longistaminata A. Chev.在对基因型数据进行筛选后,我们确定了 27,718 个高质量的单核苷酸多态性标记。根据分析结果,该收集具有广泛的遗传多样性,整个收集的平均遗传距离为 0.267(范围为 0.001-0.469),其中 45.1%的配对种间距离很远,40.1%的配对种间距离中等。通过邻接树、主成分和贝叶斯种群结构分析,大致根据分类学和生物学地位将 9013 个登录物种分为六组。第一组、第二组和第三组分别由属于 O. glaberrima、O. barthii 和 O. longistaminata 的加入者组成。第四、第五和第六组分别为改良籼型、粳型和传统籼型。在 K = 6 时,物种组的遗传变异比例(PhiPT)值最高,其次是基于聚类分析和贝叶斯种群结构的组。这些结果使我们能够更好地了解非洲水稻基因库中保存的 9013 个水稻品种的遗传多样性,并为预育种、育种和进一步的遗传应用提供了宝贵的工具。
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来源期刊
Crop Science
Crop Science 农林科学-农艺学
CiteScore
4.50
自引率
8.70%
发文量
197
审稿时长
3 months
期刊介绍: Articles in Crop Science are of interest to researchers, policy makers, educators, and practitioners. The scope of articles in Crop Science includes crop breeding and genetics; crop physiology and metabolism; crop ecology, production, and management; seed physiology, production, and technology; turfgrass science; forage and grazing land ecology and management; genomics, molecular genetics, and biotechnology; germplasm collections and their use; and biomedical, health beneficial, and nutritionally enhanced plants. Crop Science publishes thematic collections of articles across its scope and includes topical Review and Interpretation, and Perspectives articles.
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