Zhang Kai, Wang Guozhi, Wang Lihuan, Wen Bin, Fu Xiangchao, Liu Ning, Yu Zhiju, Jian Wensu, Guo Xiaolin, Liu Hanzhong, Chen Shi-Yi
Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China.
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China.
Front Vet Sci. 2023 Aug 16;10:1184764. doi: 10.3389/fvets.2023.1184764. eCollection 2023.
Coat color is an important phenotypic characteristic of the domestic rabbit () and has specific economic importance in the Rex rabbit industry. Coat color varies considerably among different populations of rabbits, and several causal genes for this variation have been thoroughly studied. Nevertheless, the candidate genes affecting coat color variation in Chinese Rex rabbits remained to be investigated. In this study, we collected blood samples from 250 Chinese Rex rabbits with six different coat colors. We performed genome sequencing using a restriction site-associated DNA sequencing approach. A total of 91,546 single nucleotide polymorphisms (SNPs), evenly distributed among 21 autosomes, were identified. Genome-wide association studies (GWAS) were performed using a mixed linear model, in which the individual polygenic effect was fitted as a random effect. We detected a total of 24 significant SNPs that were located within a genomic region on chromosome 4 (OCU4). After re-fitting the most significant SNP (OCU4:13,434,448, = 1.31e-12) as a covariate, another near-significant SNP (OCU4:11,344,946, = 7.03e-07) was still present. Hence, we conclude that the 2.1-Mb genomic region located between these two significant SNPs is significantly associated with coat color in Chinese Rex rabbits. The well-studied coat-color-associated agouti signaling protein () gene is located within this region. Furthermore, low genetic differentiation was also observed among the six coat color varieties. In conclusion, our results confirmed that is a putative causal gene affecting coat color variation in Chinese Rex rabbits.
毛色是家兔重要的表型特征，在獭兔产业中具有特定的经济重要性。不同兔群之间毛色差异很大，且已对造成这种差异的几个因果基因进行了深入研究。然而，影响中国獭兔毛色变异的候选基因仍有待研究。在本研究中，我们采集了250只具有六种不同毛色的中国獭兔的血样。我们使用限制性位点相关DNA测序方法进行了基因组测序。共鉴定出91546个单核苷酸多态性（SNP），它们均匀分布在21条常染色体上。使用混合线性模型进行全基因组关联研究（GWAS），其中个体多基因效应被拟合为随机效应。我们总共检测到24个位于4号染色体（OCU4）上一个基因组区域内的显著SNP。在将最显著的SNP（OCU4:13434448，P = 1.31e - 12）重新拟合为协变量后，另一个接近显著的SNP（OCU4:11344946，P = 7.03e - 07）仍然存在。因此，我们得出结论，这两个显著SNP之间的2.1 Mb基因组区域与中国獭兔的毛色显著相关。经过充分研究的与毛色相关的刺鼠信号蛋白（）基因位于该区域内。此外，在六个毛色品种之间也观察到低遗传分化。总之，我们的结果证实 是影响中国獭兔毛色变异的一个推定因果基因。
