METHODS AND MATERIALS
Genomes (>10×depth) of 46 Australian Boer goats (case group) were obtained from our unpublished parallel projects (PRJNA671542). For the control group dataset, 81 published deeply sequenced genomes of indigenous goats (non-specialized meat) from Europe, Asia, and Africa were applied. Information on all samples is shown in S Table1.
High-quality reads (HQRs) were initially filtered by removing the adapter, low-quality raw paired reads, and reads with an N ratio greater than 10%. The number of bases with a mass value of Q≤20 was ensured to be more than 50% of the entire read to achieve HQRs. HQRs were aligned to the goat reference genome (ASR1) using BWA (0.7.17-r1188 version). The resulting sequence alignment/map format (SAM) files were converted to Binary Alignment/Map (BAM) files by using samtools (Etheringtonet al., 2015) and picard (2.23.6 version). InDel variant was detected with GATK (version 4.1.9.0) Unified Genotyper. The InDels were filtered for quality purposes by considering the following standards: (filter- QD < 2.0 || FS > 60.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 3.0 || MQ < 40.0). The following secondary filtered standard was applied to select high-quality InDEls: –max-missing 1 –max-alleles 2 –min-alleles 2 –maf 0.05. InDels exhibiting segregation distortion or sequencing errors were discarded.
The selective sweep of each variant was quantified according to FST (Hudson et al., 1992), which was calculated for each InDel signal using VCFtools (version 0.1.16) and sweep regions with top 1% threshold used for next analysis. The annotation of each InDel physical position and attribution gene was determined by ANNOVAR (Wang et al., 2010).
KOBAS 3.0 online tool ( Zeng et al., 2019) was utilized to annotate the candidate genes for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Hypergeometric test was conducted on significantly enriched GO and KEGG terms based on the number of enriched genes. The calculated P value underwent corrected P-value, with corrected P-value≤0.05 set as a threshold.