Luo Jing, Min Qi, Sun Xueliang, Guo Xinyu, Song Meijun, Zeng Xuehui, Guo Jiazhong, Zhang Hongping, Han Yanguo, Li Li
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
Animals (Basel). 2024 Dec 15;14(24):3616. doi: 10.3390/ani14243616.
Natural selection and artificial breeding are crucial methods for developing new animal groups. The Baiyu black goats and Chuanzhong black goats are indigenous goat breeds from distinct ecological regions in Sichuan Province, with dramatically different growth and reproductivity. This study aimed to systematically elucidate the differences in production performance and genetic traits between Baiyu black goats and Chuanzhong black goats. We quantified growth and reproductive attributes for both breeds. Furthermore, we conducted a comprehensive analysis of genetic diversity, population structure, and selection signatures using whole-genome resequencing data. This dataset included 30 individuals from the Baiyu black goat breed, 41 from the Chuanzhong black goat breed, and an additional 59 individuals representing Chengdu grey goats, Tibetan cashmere goats, and Jianchang black goats, totaling 130 individuals across five goat breeds. The comparative analysis of production performance revealed that the weight and body size of Chuanzhong black goats were significantly higher than those of Baiyu black goats ( < 0.01). At the same time, the average kidding rate and kid-weaning survival rate of Chuanzhong black goats were also notably superior to those of Baiyu black goats ( < 0.01). The Baiyu black goats exhibited a more abundant genetic diversity and distinct genetic differences compared to the Chuanzhong black goat, according to an analysis grounded on genomic variation. The Baiyu black goats are more closely related to Tibetan cashmere goats, whereas Chuanzhong black goats share a closer genetic relationship with Chengdu grey goats. Additionally, we employed the π, Fst, and XP-EHH methodologies to identify genes related to immunity (, , , and ), neurodevelopment (, , , , , and ), reproduction ( and ), body size (, , and ), and meat quality traits ( and ). These results provide a theoretical basis for further resource conservation and breeding improvement of the Baiyu black goat and Chuanzhong black goat.
自然选择和人工选育是培育新动物群体的关键方法。白玉黑山羊和川中黑山羊是四川省不同生态区域的本地山羊品种，其生长和繁殖性能差异显著。本研究旨在系统阐明白玉黑山羊和川中黑山羊在生产性能和遗传特性上的差异。我们对两个品种的生长和繁殖属性进行了量化。此外，我们利用全基因组重测序数据对遗传多样性、群体结构和选择印记进行了全面分析。该数据集包括30只白玉黑山羊、41只川中黑山羊，以及另外59只代表成都麻羊、藏山羊和建昌黑山羊的个体，五个山羊品种共计130只个体。生产性能的比较分析表明，川中黑山羊的体重和体尺显著高于白玉黑山羊（<0.01）。同时，川中黑山羊的平均产羔率和羔羊断奶成活率也明显优于白玉黑山羊（<0.01）。基于基因组变异的分析表明，与川中黑山羊相比，白玉黑山羊表现出更丰富的遗传多样性和明显的遗传差异。白玉黑山羊与藏山羊的亲缘关系更近，而川中黑山羊与成都麻羊的遗传关系更近。此外，我们采用π、Fst和XP-EHH方法鉴定了与免疫（、、、和）、神经发育（、、、、和）、繁殖（和）、体尺（、和）以及肉质性状（和）相关的基因。这些结果为进一步保护白玉黑山羊和川中黑山羊资源以及改良育种提供了理论依据。
