Evidence for pleiotropism and recent selection in the 'PLAG1' region in Australian Beef cattle

Abstract

A putative functional mutation (rs109231213) near 'PLAG1' (BTA14) associated with stature was studied in beef cattle. Data from 8199 'Bos taurus', 'Bos indicus' and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA 14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF-I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10¯⁴). Frequency of the mutant 'C' allele of rs109231213 differed among 'B. indicus' (0.52), 'B. taurus' (0.96) and Tropical Composite (0.68). Most chromosomes carrying the 'C' allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from 'B. taurus' cattle. A region of reduced heterozygosity surrounds the 'C' allele; this is small in B. taurus but 20Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the 'B. taurus' breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.