Velasco Vanessa V, Tsudzuki Masaoki, Hashimoto Norikazu, Goto Naoki, Ishikawa Akira
Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
Laboratory of Animal Breeding and Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8525, Japan.
Animals (Basel). 2024 Nov 20;14(22):3341. doi: 10.3390/ani14223341.
Understanding genetic diversity, runs of homozygosity (ROH), and selection signatures is critical for the conservation and breeding management of native Japanese chickens. In this study, genetic diversity, ROH, and selection signatures in 11 populations of seven native Japanese breeds and three foreign breeds with different genetic and behavioral backgrounds were investigated using 11,493 SNPs identified through restriction-site-associated DNA sequencing. The Oh-Shamo (OSM), an aggressive cockfighting breed, exhibited the highest genetic diversity. Six native Japanese breeds, Ingie (IG), Ryujin-Jidori (RYU), Tosa-Jidori (TJI), Tosa-Kukin (TKU), Nagoya (NAG), and Ukkokei (UK), showed intermediate levels of genetic diversity and ROH. Population analyses grouped the 11 populations into four distinct clusters: (1) five populations comprising three foreign breeds (the Fayoumi inbred line, closed-colony G line of White Leghorn, commercial T line of WL, and White Plymouth Rock) and the IG Japanese breed; (2) OSM and two old Jidori breeds (RYU and TJI); (3) TKU and UK; and (4) the meat-type Nagoya breed. ROH and Fst analyses identified seven SNPs on chromosomes 13, 17, 20, 24, and 26, five of which were candidate genetic variants for fear-related behavior. These findings provide insights into genetic diversity and conserved genomic segments valuable for breeding and conservation in Japanese chicken breeds.
了解遗传多样性、纯合子连续区域（ROH）和选择信号对于日本本土鸡的保护和育种管理至关重要。在本研究中，利用通过限制性位点相关DNA测序鉴定的11493个单核苷酸多态性（SNP），对7个具有不同遗传和行为背景的日本本土品种和3个外国品种的11个群体的遗传多样性、ROH和选择信号进行了调查。具有攻击性的斗鸡品种大斗鸡（OSM）表现出最高的遗传多样性。6个日本本土品种，印地鸡（IG）、龙神地鸡（RYU）、土佐地鸡（TJI）、土佐九斤鸡（TKU）、名古屋鸡（NAG）和乌骨鸡（UK），显示出中等水平的遗传多样性和ROH。群体分析将11个群体分为四个不同的聚类：（1）由3个外国品种（法尤米近交系、白来航封闭群体G系、白来航商业T系和白普利茅斯岩鸡）和IG日本品种组成的5个群体；（2）大斗鸡和2个古老的地鸡品种（龙神地鸡和土佐地鸡）；（3）土佐九斤鸡和乌骨鸡；（4）肉用型名古屋鸡品种。ROH和Fst分析在13号、17号、20号、24号和26号染色体上鉴定出7个SNP，其中5个是与恐惧相关行为的候选遗传变异。这些发现为日本鸡品种的遗传多样性和对育种及保护有价值的保守基因组区域提供了见解。
