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group) were obtained from our unpublished parallel projects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.