Yussif Illyass, Kugonza Donald Rugira, Masembe Charles
College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda.
College of Natural Resources, Makerere University, Kampala, Uganda.
Front Genet. 2024 Mar 7;15:1325569. doi: 10.3389/fgene.2024.1325569. eCollection 2024.
The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity () was 0.437, with a nucleotide diversity () of 0.0169, while the average number of nucleotide differences () was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima's D (-2.320) and Fu's Fs (-51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.
乌干达本土鸡占该国鸡资源的80%以上，但其遗传多样性在很大程度上尚未因其遗传贡献得到充分表征。本研究评估了乌干达本土鸡群体的遗传多样性和种群结构，作为改良和保护策略的重要组成部分。对乌干达12个鸡群体中的344个线粒体DNA（mtDNA）D环序列进行了评估。28个多态性位点，占658 bp总分析位点的4.26%，定义了32个单倍型。单倍型多样性（）为0.437，核苷酸多样性（）为0.0169，而核苷酸差异平均数（）为0.576，表明该群体具有中等程度的遗传多样性。分子方差分析发现，群体内鸡单倍型间的总序列变异占98.39%（ρ<0.01），群体间占1.08%（ρ<0.05），区域内群体间占0.75%（ρ>0.05）。这揭示了群体间细微的遗传分化，这似乎受到种群碎片化的影响，可能是由于中性突变、随机遗传漂变和/或平衡选择。所有单倍型均仅与E单倍群mtDNA系统发育树具有亲缘关系，单倍型UGA01表明是乌干达的一个祖先单倍型。中性检验Tajima's D（-2.320）和Fu's Fs（-51.369），结合错配分布来衡量近期历史人口事件的特征，支持了整个鸡群体的种群扩张。结果表明，乌干达鸡有一个母系祖先，来自一个起源于印度次大陆并遍布全球的谱系。缺乏系统地理学信号与近期的扩张事件一致，单倍型在国内广泛进行遗传混合。因此，鉴于较高的遗传多样性来自鸡群体内部，本研究的结果有可能指导乌干达的保护策略和育种计划。
