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利用DArTseq SNP技术分析布热塞拉和鲁瓦马加纳本地鸡种群与萨索鸡的遗传多样性及亲缘关系。

Genetic diversity and relationship of Bugesera and Rwamagana indigenous chicken populations with SASSO chickens using DArTseq SNPs.

作者信息

Mujyambere Valentin, Adomako Kwaku, Ntawubizi Martin, Nyinawamwiza Laetitia, Uwihirwe Judith, Kena Alexander Wireko

机构信息

Department of Animal Production, University of Rwanda, Nyagatare, Rwanda.

Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.

出版信息

PLoS One. 2025 Sep 12;20(9):e0331316. doi: 10.1371/journal.pone.0331316. eCollection 2025.

DOI:10.1371/journal.pone.0331316
PMID:40938903
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12431124/
Abstract

The genetic improvement of Rwandan indigenous chickens (IC) is becoming a priority and requires genetic characterization as the foundation for genetic improvement. The aim was to study the genetic diversity and relationship of IC from Bugesera and Rwamagana districts with SASSO chickens in Rwanda. Eighty-seven DNA samples were genotyped using Diversity Array Technology and generated 45,677 DArTseq SNPs. After the quality control, the genetic diversity and relationship were analyzed with dartR package, STRUCTURE and STRUCTURE Harvester. Only 8087 markers and 86 samples were remained for analysis. The high and low expected heterozygosity (He) were observed in Rwamagana (0.405) and SASSO (0.388) populations, respectively. The lowest difference was observed between SASSO and Rwamagana populations (0.018). The structure analysis separated IC (Cluster 1) from SASSO chickens (Cluster 2). Chickens from Rwamagana population were genetically related to SASSO indicating the uncontrolled crossbreeding. DArTseq SNPs were efficient and can be recommended for genomic studies in chickens.

摘要

卢旺达本土鸡的遗传改良正成为一项优先任务，且需要进行遗传特征分析作为遗传改良的基础。目的是研究来自布热塞拉和鲁瓦马加纳地区的卢旺达本土鸡与卢旺达萨索鸡的遗传多样性及亲缘关系。使用多样性阵列技术对87个DNA样本进行基因分型，产生了45,677个DArTseq单核苷酸多态性（SNP）。经过质量控制后，使用dartR软件包、STRUCTURE软件和STRUCTURE Harvester软件对遗传多样性和亲缘关系进行分析。最终仅保留8087个标记和86个样本用于分析。分别在鲁瓦马加纳群体（0.405）和萨索群体（0.388）中观察到高和低的期望杂合度（He）。在萨索群体和鲁瓦马加纳群体之间观察到最小差异（0.018）。结构分析将本土鸡（聚类1）与萨索鸡（聚类2）区分开来。来自鲁瓦马加纳群体的鸡与萨索鸡存在遗传关联，表明存在不受控制的杂交情况。DArTseq SNP是有效的，可推荐用于鸡的基因组研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/252905f62dfd/pone.0331316.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/18b83a3d894a/pone.0331316.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/93b52e73a2f1/pone.0331316.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/da4effe83823/pone.0331316.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/033bcd0d6b1e/pone.0331316.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/12f4269e0a34/pone.0331316.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/54de54d12972/pone.0331316.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/252905f62dfd/pone.0331316.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/18b83a3d894a/pone.0331316.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/93b52e73a2f1/pone.0331316.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/da4effe83823/pone.0331316.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/033bcd0d6b1e/pone.0331316.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/12f4269e0a34/pone.0331316.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/54de54d12972/pone.0331316.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/938a/12431124/252905f62dfd/pone.0331316.g007.jpg

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本文引用的文献

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PLoS One. 2022 Aug 22;17(8):e0267464. doi: 10.1371/journal.pone.0267464. eCollection 2022.
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NGS allele counts versus called genotypes for testing genetic association.
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Comput Struct Biotechnol J. 2022 Jul 11;20:3729-3733. doi: 10.1016/j.csbj.2022.07.016. eCollection 2022.
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