Genome-wide assessment of runs of homozygosity to estimate inbreeding in a closed Nellore herd

Abstract

The objective of this study was to compare the inbreeding coefficients estimated from pedigree data (F_PED), traditionally used for internal monitoring by herds and breeding programs, with genomic estimates through the genomic relationship matrix (F_GRM) and runs of homozygosity (F_ROH). Besides, we used the genotype data to obtain the linkage disequilibrium (LD), population effective size (Ne), runs of homozygosity (ROH) islands and functional analysis of the genes presented in ROH islands. Male calves and sires from a closed Nellore herd (Lemgruber line) were genotyped with the Z-chip v2 (Neogen, Lincoln, Nebraska, USA) that contains approximately 30 thousand SNP markers. After quality control, 1088 animals and 21,351 SNPs remained for analysis. Runs of homozygosity (ROH) segments were identified in all analyzed animals, with an average number of 57.93 and average length of 2.95 Mb. We observed a higher occurrence of ROH up to 9 Mb, suggesting a proper mating scheme, which corroborate with LD and Ne analysis results. Estimates of F_PED, F_GRM and F_ROH ranged from 0 to 0.2856, from 0.0705 to 0.3686 and from 0.0229 to 0.2762, respectively. Low to moderate correlations were observed between F_PED and F_GRM (0.17, P < 0.001); F_PED and F_ROH (0.20, P < 0.001) and F_GRM and F_ROH (0.92, P < 0.001). Nevertheless, considering our results we were successful in use runs of homozygosity for estimating autozygosity in a closed Nellore herd. Besides, from ROH islands, we were able to identify a candidate gene (HTR1A) for docility in this Nellore herd.