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（CM）是一种原产于当地的山羊品种，具有适应本地环境和人工选择的独特性状。通过对全基因组重测序，我们从10个家养山羊品种中生成14-20倍的覆盖度序列，以探索崇明品种的基因组特性和选择标记。在读取映射和变异调用后，我们总共鉴定出2,350,855,001个单核苷酸多态性（SNPs）和2,830,800个插入-缺失突变（indels）。与另外九个山羊品种相比，我们进一步特别鉴定出崇明品种特有的1.2% SNPs（2,717,133）和0.9% indels（24,843）。在崇明品种的183个蛋白质编码基因中，鉴定出错义（SIFT < 0.05）、移码、剪接位点、起始丢失、终止丢失和终止增益变异。其中，包括AP4E1、FSHR、COL11A2和DYSF在内的36个基因与神经系统、矮身材和骨骼肌形态相关的表型本体术语有关。此外，基于全基因组FST和混合杂合性（Hp）的计算，我们还进一步鉴定了崇明品种与其他九个山羊品种之间的选择标记基因。这些基因与神经系统（C2CD3、DNAJB13、UCP2、ZMYND11、CEP126、SCAPER和TSHR）、生长（UCP2、UCP3、TSHR、FGFR1、ERLIN2和ZNF703）和毛色（KITLG、ASIP、AHCY、RALY和MC1R）显著相关。我们的结果表明，崇明品种可能在神经系统方面与其他山羊品种有所区别，这可能是由于自然或人工选择所致。全基因组分析为理解这一原产山羊品种的遗传多样性和性状探索提供了更深入的见解。