Kim Jaewon, Kim Minjun, Cho Eunjin, Lee Seung-Sook, Kim Seungchang, Jin Daehyeok, Lee Jun Heon
Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.
Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea.
J Anim Sci Technol. 2025 May;67(3):520-535. doi: 10.5187/jast.2024.e11. Epub 2025 May 31.
Runs of homozygosity (ROHs) are caused by identical haplotypes inherited from ancestors. ROHs provide useful information regarding the inbreeding rate, demographics, and selection history. The Yeonsan Ogye (YO) breed is an indigenous chicken in Korea that is characterized by a completely black body. In this study, we investigated ROH in the YO genome to determine ROH-based inbreeding coefficients and their correlations with other inbreeding estimators, then analyzed their genetic characteristics. Using 600K single nucleotide polymorphism (SNP) chip information for 189 chickens, we found 20,339 ROHs in the YO population. The average number of ROHs was 107, the total average ROH length was 165 Mb, and the average ROH length was 1.542 Mb. Most ROHs were short (< 8 Mb), suggesting a past population bottleneck. The average inbreeding coefficient ( ) calculated based on ROHs was 0.184 and this was correlated with other inbreeding coefficients estimated using allele frequencies. 17 ROH islands were detected and these regions exceeded the threshold of the top 1% of SNPs among SNPs present in ROHs. In the ROH islands, 152 genes were annotated, some of which were genes associated with meat production traits and hyperpigmentation in chickens. A comparison of overlapping regions between ROH islands and quantitative trait loci (QTLs) indicated that most QTLs were related to color traits. These results will help to optimize conservation strategies for the YO breed.
纯合子连续片段（ROHs）是由从祖先遗传而来的相同单倍型引起的。ROHs提供了有关近亲繁殖率、种群统计学和选择历史的有用信息。延山五黑鸡（YO）品种是韩国的本土鸡种，其特征是全身完全黑色。在本研究中，我们调查了YO基因组中的ROHs，以确定基于ROH的近亲繁殖系数及其与其他近亲繁殖估计值的相关性，然后分析它们的遗传特征。利用189只鸡的600K单核苷酸多态性（SNP）芯片信息，我们在YO群体中发现了20339个ROHs。ROHs的平均数量为107个，总平均ROH长度为165 Mb，平均ROH长度为1.542 Mb。大多数ROHs较短（<8 Mb），表明过去种群经历过瓶颈。基于ROHs计算的平均近亲繁殖系数（ ）为0.184，并且与使用等位基因频率估计的其他近亲繁殖系数相关。检测到17个ROH岛，这些区域超过了ROHs中SNP前1%的阈值。在ROH岛中，注释了152个基因，其中一些是与鸡的产肉性状和色素沉着相关的基因。ROH岛与数量性状位点（QTLs）重叠区域的比较表明，大多数QTLs与颜色性状相关。这些结果将有助于优化YO品种的保护策略。
