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Table 4 Selection of the eight genes potentially related to domestication and/or selection from the 1220 genes found in ROH islands in at least one of the 11 caprine populations investigated

From: Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection

Coordinates of the selected genes Average fraction per breed
Chr Gene Start End APZ BEZ BST CAG GFG NER PFA SAN STG TOG VAG
2 RUNX3 7,884,247 7,949,392 0.66 0.28 1.00a 0.75a 0.66 0.42 0.79a 1.00a 0.51 0.43 0.83a
3 LEPR 41,024,000 41,180,997 0.61 0.22b 0.68 0.68 0.19b 0.88a 0.35 0.41 0.50 0.29 0.28
6 LCORL 37,904,351 38,069,012 0.60 0.56 0.61 0.81a 0.58 0.52 0.80a 0.93a 0.68 0.37 0.53
8 STC1 70,791,218 70,806,076 0.96a 0.22b 0.92a 1.00a 0.84a 0.88a 0.96a 0.84a 0.92a 0.79a 0.83a
10 TSHR 10,656,656 10,833,540 0.58 0.59 0.71a 0.92a 0.53 0.50 0.54 0.74 0.96a 0.61 0.70
13 ASIP 63,228,709 63,249,542 0.21b* 0.11b 0.83a 0.17b 0.39* 0.25 0.34* 0.16b* 0.41* 0.84a 0.51
20 SLC9A3 71,521,733 71,560,687 1.00a 0.44 0.98a 1.00a 1.00a 1.00a 1.00a 0.84a 1.00a 0.97a 1.00a
29 MUC6 46,244,530 46,267,909 0.46 1.00a 0.83a 0.83a 0.63 0.92a 0.71 0.68 0.42 0.71 0.96a
  1. Average fraction per breed: fraction of individuals for which all intragenic SNVs are within a ROH, and for each population. aGene fractions, higher than 0.75. bGene fractions lower than 0.25
  2. *Goats from these five breeds are nearly fixed for specific ASIP alleles that control breed-specific coat color patterns ([9] and Table 1). However, the vcf-files from Illumina whole-genome sequence data contain a large number of erroneous heterozygous genotype calls because these goats carry amplified CNV alleles with some nucleotide differences between the individual copies. Therefore, due to the technical limitations of short read sequencing, the ROH islands at ASIP are not detected in all of these five breeds