Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Bos grunniens)

Figures & data

Table 1. Annotation information of all SNPs in 8 yak populations.

Breeds		Changtai	Jiulong	Meiren	Muli	Pamier	Sibu	Tianzhu	Zhongdian
Samples		6	16	19	15	10	11	8	8
SNPs		10343725	13971741	10257729	10957636	10325426	13529944	10671202	10769073
Ts/Tv ratio		2.55	2.54	2.52	2.55	2.56	2.54	2.56	2.56
Hom/Het		0.52	0.55	0.6	0.57	0.62	0.53	0.54	0.54
SNP types
Exon	Synonymous variant	44888	61547	33982	47958	44738	59384	46066	46158
	Initiator codon variant	15	27	13	15	16	22	12	14
	Start lost	159	219	95	183	158	226	159	158
	Stop gained	745	1222	926	815	765	1252	776	795
	Stop lost	236	337	110	293	245	317	256	239
	Stop retained variant	62	80	50	65	64	75	61	63
Splice sites	Splice region variant	8305	11737	6241	9156	8288	11239	8501	8452
	Splice acceptor variant	276	486	170	338	299	497	301	286
	Splice donor variant	385	665	227	490	390	649	403	397
Intron	Intron variant	3298309	4399517	3149398	3483506	3275875	4206247	3406730	3415608
	Intragenic variant	68	103	37	90	74	94	79	78
UTR	5 prime UTR variant	8487	12597	4745	9923	8788	12362	8952	8772
	5 prime UTR premature start codon gain variant	1195	1722	961	1273	1180	1697	1262	1249
	3 prime UTR variant	20953	28415	16743	22526	20832	27821	21573	21594
Intergenic	Upstream gene variant	675057	936438	649511	716339	668501	910370	693423	695661
	Downstream gene variant	215081	297034	212150	228446	212998	291258	220750	222108
	Intergenic region	6017519	8141055	6141606	6375723	6028438	7929077	6207902	6294148

Figure 1. Cluster differentiation and affinities of yak populations. (A) Phylogenetic tree. (B) Principal component analysis of yak populations. (C) Ancestral component analysis. (D) Analysis of genetic relationships in yak populations.

Figure 2. Population genomics analysis. (A) analysis of heterozygosity in yak populations. (B) Linkage disequilibrium analysis. (C,D) ROH analysis of yak populations. (E) Population differentiation index analysis. (F) Genetic polymorphism analysis.

Figure 3. Enrichment analysis results. (A) Select signal analysis. Based on θπ ratio and Fst analysis to take the intersection for selection signal analysis. The horizontal coordinate is the ratio of θπ (MR/PM) and the vertical coordinate is the Fst value, which corresponds to the frequency distribution plots on the top and on the right, respectively, and the dot plots in the centre represent the corresponding Fst and θπ ratios within different windows. The top blue and green regions are the regions selected by θπ, the red regions are the regions selected by Fst, and the Middle blue and green regions are the intersection of Fst and θπ, i.e., the candidate regions. The blue dots are candidate areas for MR and the green dots are candidate areas for PM yaks. (B) KEGG enrichment analysis of genes in selected regions(the area of green dots in Figure 3(A)).

Data availability statement

The datasets generated during the current study are available in the [FigShare] repository, [10.6084/m9.figshare.23723817].