College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences and Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
BMC Genomics. 2024 Aug 2;25(1):754. doi: 10.1186/s12864-024-10671-x.
Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl.
In total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie.
Our study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts.
丝毛鸡是中国传统的鸡种，具有独特的专门形态特征组合。虽然之前的研究集中在这些特征的遗传基础上，但丝毛鸡品种的整体基因组特征仍在很大程度上未被探索。在这项研究中，我们通过与其他七个中国本土品种（IDGBs）、一个商业品种和野生祖先红原鸡的比较分析，利用全基因组重测序数据来研究丝毛鸡品种的遗传多样性、选择信号和种群历史。
总共获得了 2080 万个高质量的单核苷酸多态性和 86 个大的结构变异。我们发现，丝毛鸡表现出相对较高的近亲繁殖水平，并且在遗传上与其他 IDGBs 不同。此外，我们的分析表明，与其他 IDGBs 相比，丝毛鸡经历了更强的历史种群瓶颈和更小的有效种群规模。我们鉴定了 45 个可能在黑色素生成途径中受到选择的基因，这些基因可能与羽毛颜色有关。在这些基因中，LMBR1 和 PDSS2 分别与额外的脚趾和无钩羽毛有关。其中 6 个被选择的基因（KITLG、GSK3B、SOBP、CTBP1、ELMO2、SNRPN）已知与人类的神经发育和精神疾病有关，可能与丝毛鸡独特的行为有关。我们进一步鉴定了丝毛鸡的结构变异，并发现了先前报道的与过度色素沉着（END3）、 muff 和 beard（HOXB8）和玫瑰冠 phenotype（MNR2）相关的变异。此外，我们发现了一个重叠 GMDS 基因的 0.61Mb 倒位，该倒位先前与斑马鱼和人类的神经发育缺陷有关。这也可能与丝毛鸡行为的独特性有关。
我们的研究表明，与其他 IDGB 鸡群相比，丝毛鸡在遗传上是独特的，并且相对近亲繁殖程度较高，这可能归因于更长时间的种群瓶颈和选择性繁殖实践。这些结果增强了我们对驯化和选择性繁殖如何塑造丝毛鸡基因组的理解。这些发现为驯化和禽类基因组学的更广泛领域做出了贡献，并对未来的保护和繁殖努力具有意义。
