Extended Data Fig. 9: Associations of cis-eQTLs and GWAS loci for important agronomic traits in cattle.
(a) cis-eQTLs discovered in monocytes, and mammary gland show enrichments for top SNPs (top 10%) associated with age at first calving (AFC) (P = 0.001, the two-sided permutation test with 1,000 times), and somatic cell score (SCS) (P = 0.001, the two-sided permutation test with 1,000 times) respectively, compared to the null expectation (shown in gray) defined by ‘Not eQTLs’. (b) Pearson correlation between z-scores from permutation tests (1000 times) and sample sizes of cis-eQTL tissues for milk yield trait (top, r = 0.70, the two-sided Student’s t-test: P = 0.0002) and ketosis trait (bottom, r = 0.49, the two-sided Student’s t-test: P = 0.02). (c) An example of a colocalization of cis-eQTLs of TIGAR gene in muscle and GWAS loci of strength in cattle on chromosome 5. Four independent GWAS signals (that is, rs210875465, rs381714832, rs1115089453 and rs135928140) are located within the region. The All-but-One conditional analysis across the individual GWAS signals shows that only rs135928140 in strength GWAS is colocalized with cis-eQTLs of TIGAR in muscle, when conditioning on the remaining three signals. The colocalized SNP (that is, rs132865837) of TIGAR in muscle is in LD (r2 = 0.49) with the GWAS loci rs135928140. (d) Colocalization between GWAS loci of sire calving ease (Sire_Calv_Ease) in cattle and cis-eQTLs across 23 distinct tissues.
