44 Inbreeding levels of the Line 1 and Line 4 Hereford cattle populations

Abstract

Abstract The Line 1 and Line 4 Hereford populations have been linebred for decades. Since these populations share origins but have been managed differently, they offer a unique opportunity to understand molecular mechanisms contributing to inbreeding depression. The study attempted to identify areas of the genome impacting inbreeding depression. Inbreeding was estimated using a complete pedigree (FPED), genomic inbreeding (FG), and genomic pedigree inbreeding (FGPED). Average rate of change in inbreeding per year was evaluated. Runs of homozygosity (ROH) analyses were performed in Golden Helix SVS software, and ROH were defined as a minimum length of 2,500 kb, 250 single nucleotide polymorphism (SNP) appearing in 20 samples. Expected phenotypes for five traits were calculated by adjusting each animal’s individual phenotype with published negative impacts of inbreeding depression. Regression association analyses were performed (Golden Helix) on phenotype and genotype data. Markers above 5 x 10–4 genome-wide significance were considered strongly significant. Line 1 FPED, FG, and FGPED average inbreeding was 42.1% (range 0–71%), 14.4% (range 0–46%), and 31.0% (range 0–63%), respectively. Line 4 FPED, FG, and FGPED average inbreeding was 12.6% (range 0–36%), 12.3% (range 0–49%), and 17.7% (range 0–29%), respectively. Average rate of change in inbreeding per year for Line 1 was -0.03% over 83 yr and 0.03% over 55 yr for Line 4. Fifty ROH regions, 93 strongly significant SNP, three strongly significant SNP within ROH, and some significant SNP within 11 previously identified genes were identified for Line 1. Forty-five ROH regions, 35 strongly significant SNP, three strongly significant SNP within ROH, and some significant SNP within 12 previously identified genes were identified for Line 4. Variation in identified regions of the genome of both lines indicate management is impacting results of inbreeding and the expressed inbreeding depression.