Table_4_Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus).XLS

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14–20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion–deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide FST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.崇明白山羊（Chongming white goat, CM）是一种本土山羊品种，具备适应本地环境与人工选育的独特性状。本研究通过全基因组重测序（whole-genome re-sequencing）技术，对10个家山羊品种开展了14~20倍覆盖度的测序，以探究崇明白山羊的基因组特征与选择印记。在完成读段比对与变异检测后，我们共鉴定到23,508,551个单核苷酸多态性（single-nucleotide polymorphisms, SNPs）与2,830,800个插入缺失突变（insertion–deletion mutations, indels）。进一步与其余9个山羊品种对比后，我们特异性鉴定出仅存在于崇明白山羊的1.2%单核苷酸多态性位点（共计271,713个）与0.9%插入缺失突变（共计24,843个）。在崇明白山羊的183个蛋白质编码基因中，我们鉴定到错义突变（SIFT评分<0.05）、移码突变、剪接位点变异、起始密码子丢失、终止密码子丢失与终止密码子获得等变异类型。在这183个基因中，包括AP4E1、FSHR、COL11A2与DYSF在内的36个基因，参与了与神经系统、矮小体型以及骨骼肌形态相关的表型本体注释。此外，基于全基因组固定指数（FST）与混合杂合度（pooled heterozygosity, Hp）计算，我们进一步鉴定出崇明白山羊与其余9个山羊品种间的选择印记基因。这些基因显著关联于神经系统（C2CD3、DNAJB13、UCP2、ZMYND11、CEP126、SCAPER与TSHR）、生长发育（UCP2、UCP3、TSHR、FGFR1、ERLIN2与ZNF703）以及毛色（KITLG、ASIP、AHCY、RALY与MC1R）相关性状。本研究结果表明，崇明白山羊可能因自然选择或人工选育，在神经系统相关性状上与其他山羊品种产生了分化。本次全基因组分析，有助于加深对这一本土山羊品种遗传多样性的认知，并为其性状挖掘提供理论支撑。