背景:Silkie是一种传统的中国鸡品种,其特征是其独特的特殊形态性状组合。虽然以前的研究集中在这些性状的遗传基础上,Silkie品种的整体基因组特征仍未被探索。在这项研究中,我们使用全基因组重测序数据来检查遗传多样性,通过与其他七个中国本土品种(IDGB)的比较分析,Silkie品种的选择性信号和人口统计学历史,商业品种,和野生祖先红丛林禽。
结果:总计,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Silkie表现出相对较高的近亲繁殖水平,并且在遗传上与其他IDGB不同。此外,我们的分析表明,与其他IDGB相比,Silkie经历了更强的历史人口瓶颈,有效人口规模较小。我们确定了45个推定选择的基因,这些基因富集在黑素生成途径中,这可能与羽毛的颜色有关。在这些基因中,LMBR1和PDSS2以前曾与多余的脚趾和无钩羽毛相关联,分别。选定的六个基因(KITLG,GSK3B,SOBP,CTBP1,ELMO2,SNRPN)已知与人类的神经发育和精神疾病有关,并且可能与Silkie的独特行为有关。我们进一步确定了Silkie的结构变异,并发现了先前报道的与色素沉着过度有关的变异(END3),muff和胡须(HOXB8),和玫瑰梳表型(MNR2)。此外,我们发现与GMDS基因重叠的0.61Mb反转,这与斑马鱼和人类的神经发育缺陷有关。这也可能与Silkie的行为独特性有关。
结论:我们的研究表明,与其他IDGB鸡种群相比,Silkie在遗传上是不同的,并且是相对较高的近交。可能归因于更长时间的种群瓶颈和选择性育种实践。这些结果增强了我们对驯化和选择性育种如何塑造Silkie基因组的理解。这些发现有助于更广泛的驯化和鸟类基因组学领域,并对未来的保护和育种工作产生影响。
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.