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

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

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	1.00^a	0.75^a	0.66	0.42	0.79^a	1.00^a	0.51	0.43	0.83^a
3	LEPR	41,024,000	41,180,997	0.61	0.22^b	0.68	0.68	0.19^b	0.88^a	0.35	0.41	0.50	0.29	0.28
6	LCORL	37,904,351	38,069,012	0.60	0.56	0.61	0.81^a	0.58	0.52	0.80^a	0.93^a	0.68	0.37	0.53
8	STC1	70,791,218	70,806,076	0.96^a	0.22^b	0.92^a	1.00^a	0.84^a	0.88^a	0.96^a	0.84^a	0.92^a	0.79^a	0.83^a
10	TSHR	10,656,656	10,833,540	0.58	0.59	0.71^a	0.92^a	0.53	0.50	0.54	0.74	0.96^a	0.61	0.70
13	ASIP	63,228,709	63,249,542	0.21^b*	0.11^b	0.83^a	0.17^b	0.39*	0.25	0.34*	0.16^b*	0.41*	0.84^a	0.51
20	SLC9A3	71,521,733	71,560,687	1.00^a	0.44	0.98^a	1.00^a	1.00^a	1.00^a	1.00^a	0.84^a	1.00^a	0.97^a	1.00^a
29	MUC6	46,244,530	46,267,909	0.46	1.00^a	0.83^a	0.83^a	0.63	0.92^a	0.71	0.68	0.42	0.71	0.96^a

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
^*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

ISSN: 1297-9686