Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny

Genetics Selection Evolution

Research Article

Jeremy T. Howard¹  Francesco Tiezzi¹  Christian Maltecca²  Kent A. Gray³  Yijian Huang³ 

[1] Department of Animal Science, North Carolina State University, 27695-7627, Raleigh, NC, USA;Department of Animal Science, North Carolina State University, 27695-7627, Raleigh, NC, USA;Genetics Program, North Carolina State University, 27695-7627, Raleigh, NC, USA;Smithfield Premium Genetics, 28458, Rose Hill, NC, USA;

关键词: Parental Genome;    Relationship Matrice;    Large White;    Parental Breed;    Nucleus Population;   

DOI  :  10.1186/s12711-016-0269-y

 received in 2016-02-12, accepted in 2016-11-10,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundIn 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.MethodsWe 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.ResultsWe 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.ConclusionsWe 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.

【 授权许可】

CC BY   
© The Author(s) 2016