Inbreeding and inbreeding depression in linebred beef cattle

Abstract

This research applied genomics and phenotypic information in three different beef cattle populations. The methods applied were association analyses, runs of homozygosity, and genetic correlations. This incorporated both genomic and phenotypic approaches to identify the results of linebreeding in two closed Hereford populations. Further work evaluated carcass and maternal traits from the American Simmental Association Carcass Merit Program using genomic and phenotypic information to identify how carcass-based selection decisions impact maternal performance of Simmental-based cattle. Line 4 pedigree inbreeding, genomic inbreeding, and genomic pedigree inbreeding ranges were 0 - 36%, 0 - 49%, and 0 - 29%, respectively, and average inbreeding was 12.6%, 12.3%, and 17.7%, respectively. Line 1 pedigree inbreeding, genomic inbreeding, and genomic pedigree inbreeding ranges were 0 - 71%, 0 - 46%, and 0 - 63%, respectively, and average inbreeding was 42.1%, 14.4%, and 31.0%, respectively. Average rate of change in inbreeding per year was 0.03% over 55 years for Line 4 and -0.03% over 83 years for Line 1. Identified for Line 4 were 45 ROH regions, 35 strongly significant single nucleotide polymorphisms, three strongly significant SNP within ROH, and some significant SNP within 12 previously identified genes. Identified for Line 1 were 50 ROH regions, 93 strongly significant SNP, three strongly significant SNP within ROH, and some significant SNP within 11 previously identified genes. Within the Simmental dataset, nine chromosomes had genome-wide significance, explaining 0.2142 percent of total phenotypic information. The single-locus model identified 365 novel regions and 251 novel positional candidate genes. The multi-locus model identified 393 novel regions and 283 novel positional candidate genes. Also, detrimental genetic correlations between carcass characteristics and maternal traits were less than previously reported. Analyses utilized in this study indicate ROH and significant SNP can be used to identify regions of the genome affected by inbreeding. Also, simultaneous selection for carcass and maternal traits reduced the negative impact seen with single-trait selection for carcass traits.