Yijian Huang

In nucleus populations, regions of the genome that have a high frequency of runs of homozygosity (ROH) occur and are associated with a reduction in genetic diversity, as well as adverse effects on fitness. It is currently unclear whether, and to what extent, ROH stretches persist in the crossbred genome and how genomic management in the nucleus population might impact low diversity regions and its implications on the crossbred genome. We calculated a ROH statistic based on lengths of 5 (ROH5) or 10 (ROH10) Mb across the genome for genotyped Landrace (LA), Large White (LW) and Duroc (DU) dams. We simulated crossbred dam (LA × LW) and market [DU × (LA × LW)] animal genotypes based on observed parental genotypes and the ROH frequency was tabulated. We conducted a simulation using observed genotypes to determine the impact of minimizing parental relationships on multiple diversity metrics within nucleus herds, i.e. pedigree-(A), SNP-by-SNP relationship matrix or ROH relationship matrix. Genome-wide metrics included, pedigree inbreeding, heterozygosity and proportion of the genome in ROH of at least 5 Mb. Lastly, the genome was split into bins of increasing ROH5 frequency and, within each bin, heterozygosity, ROH5 and length (Mb) of ROH were evaluated. We detected regions showing high frequencies of either ROH5 and/or ROH10 across both LW and LA on SSC1, SSC4, and SSC14, and across all breeds on SSC9. Long haplotypes were shared across parental breeds and thus, regions of ROH persisted in crossbred animals. Averaged across replicates and breeds, progeny had higher levels of heterozygosity (0.0056 ± 0.002%) and lower proportion of the genome in a ROH of at least 5 Mb (−0.015 ± 0.003%) than their parental genomes when genomic relationships were constrained, while pedigree relationships resulted in negligible differences at the genomic level. Across all breeds, only genomic data was able to target low diversity regions. We show that long stretches of ROH present in the parents persist in crossbred animals. Furthermore, compared to using pedigree relationships, using genomic information to constrain parental relationships resulted in maintaining more genetic diversity and more effectively targeted low diversity regions.

Feed intake and growth are economically important traits in swine production. Previous genome wide association studies (GWAS) have utilized average daily gain or daily feed intake to identify regions that impact growth and feed intake across time. The use of longitudinal models in GWAS studies, such as random regression, allows for SNPs having a heterogeneous effect across the trajectory to be characterized. The objective of this study is therefore to conduct a single step GWAS (ssGWAS) on the animal polynomial coefficients for feed intake and growth. Corrected daily feed intake (DFI Adj ) and average daily weight measurements (DBW Avg ) on 8981 (n = 525,240 observations) and 5643 (n = 283,607 observations) animals were utilized in a random regression model using Legendre polynomials (order = 2) and a relationship matrix that included genotyped and un-genotyped animals. A ssGWAS was conducted on the animal polynomials coefficients (intercept, linear and quadratic) for animals with genotypes (DFIAdj: n = 855; DBWAvg: n = 590). Regions were characterized based on the variance of 10-SNP sliding windows GEBV (WGEBV). A bootstrap analysis (n =1000) was conducted to declare significance. Heritability estimates for the traits trajectory ranged from 0.34-0.52 to 0.07-0.23 for DBWAvg and DFIAdj, respectively. Genetic correlations across age classes were large and positive for both DBWAvg and DFIAdj, albeit age classes at the beginning had a small to moderate genetic correlation with age classes towards the end of the trajectory for both traits. The WGEBV variance explained by significant regions (P < 0.001) for each polynomial coefficient ranged from 0.2-0.9 to 0.3-1.01 % for DBWAvg and DFIAdj, respectively. The WGEBV variance explained by significant regions for the trajectory was 1.54 and 1.95 % for DBWAvg and DFIAdj. Both traits identified candidate genes with functions related to metabolite and energy homeostasis, glucose and insulin signaling and behavior. We have identified regions of the genome that have an impact on the intercept, linear and quadratic terms for DBWAvg and DFIAdj. These results provide preliminary evidence that individual growth and feed intake trajectories are impacted by different regions of the genome at different times.

The Yorkshire breed uses white coat color as a selection requirement to indicate breed purity. In this study, genomic information from chromosomal regions, as well as the whole genome, was applied to estimate breed composition of purebred Yorkshire animals. Genotypes for approximately 60,000 SNP from the Illumina PorcineSNP60 BeadChip (60K) were available for reference animals for which the genetic background was known, study animals that included Yorkshire sires (Tes_York, n = 889), and known crossbred animals that had Yorkshire heritage (Tes_U, n = 12). Haplotypes of SNP flanking the KIT (Dominant white locus) and MC1R (Melanocortin receptor 1) genes were developed for reference animals for the Duroc, Hampshire, Landrace, Yorkshire, and Pietrain breeds. For the KIT region, haplotypes observed in Yorkshire reference animals were also found in 84 and 7% of the haplotypes in Landrace and Pietrain reference animals, respectively. They were not found in Duroc or Hampshire reference animals. The sensitivity and specificity of haplotype analysis was 0.93 and 0.75, respectively. In addition, whole genome SNP information was used in regression analyses to further differentiate breed composition. Using 60K, 90% of regression coefficients for Yorkshire, indicating relative Yorkshire composition, ranged from 0.791 to 1.073 and 0.524 to 1.06 in Tes_York and Tes_U, respectively. Regression coefficients for 90% of Hampshire ranged from –0.029 to 0.052 and –0.005 to 0.379 in Tes_York and Tes_U, respectively. Animals in Tes_U were likely of Yorkshire and Hampshire breed origin. The sensitivity and specificity of regression analysis was 0.96 and 0.58, respectively. Combining haplotype and regression analyses, 810 Tes_York animals were accepted as purebred Yorkshire. Genomic information can be used as a tool to describe an animal’s breed composition and reduce the need for progeny testing for white coat color verification. Copyright © 2014. American Society of Animal Science .