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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0269-y) contains supplementary material, which is available to authorized users.

Estimates of autozygosity through runs of homozygosity in farmed coho salmon

“…According to our results, this strategy was 349 effective in reducing the inbreeding levels and changing the patterns of ROH, clearly 350 differentiating from POP A and B. These results are in accordance with some studies 351 [15,48,60,61] Each vertical line represent an animal and the black vertical lines were used to separate different populations. Each row represents one individual and each bar a ROH segment.…”

“…For both POP A and B 284 it was possible to identify short and long segments in most of the animals analyzed, whereas 285 in the POP C a small number of animals (n = 7) presented ROH8-16 Mb and none ROH>16 Mb. 286 In recent years, some studies have investigated different genomic methods to estimate 287 inbreeding coefficients in cattle [12,25,26,45,47,48], pigs [27,28,49,50], goats [51][52][53] and 288 rainbow trout [32]. However, this is the first study aimed at characterizing the ROH patterns 289 and comparing different genomic-and pedigree-based methods to estimate inbreeding 290 coefficients in farmed coho salmon populations.…”

Geno‐Diver: A combined coalescence and forward‐in‐time simulator for populations undergoing selection for complex traits

“…These metrics disregard the fact that genetic diversity and inbreeding depression are heterogeneous across the genome. The heterogeneity of genetic diversity across the genome has been recently discussed by Jim enez-Mena, Hospital, and Bataillon (2016) and Howard et al (2016). Jim enez- Mena et al (2016) found the effective population size (Ne) to vary considerably across the genome (Ne: 40-250) in a Danish Holstein population, implying the accumulation of inbreeding is heterogeneous across the genome.…”

“…Variation in the autozygosity frequency across the genome due to multiple factors including genetic drift and selection is an important aspect of genomes in real livestock populations. To determine the autozygosity levels and the change across generations, the frequency of a SNP occurring in a contiguous run of homozygosity (ROH) with a length of at least 5 Mb was calculated as outlined by Howard et al (2016) for one of the replicates. As illustrated in Panel 2 of Figure 3, the frequency of a SNP being in an ROH is heterogeneous across the genome and increased from the unselected founder generation.…”

“…Conversely the ability to use this information to efficiently manage agricultural populations at the genomic level, both for preserving genetic diversity and lessening inbreeding depression, has received comparatively less attention (Henryon et al, 2014). Previous research has highlighted that genomic information maintains greater diversity compared to traditionally utilized pedigree information in the context of minimizing parental relationships (Howard, Tiezzi, Huang, Gray, & Maltecca, 2016;Rodr ıguez-Ramilo, Garc ıa-Cort es, & de Cara, 2016). Furthermore, in the context of optimal contribution selection, genomic information allows for specific regions to be constrained and in some cases (i.e., large full-sib families) results in increased genetic gain compared to pedigree information (Clark, Kinghorn, Hickey, & van der Werf, 2013;G omez-Romano, Villanueva, Fern andez, Woolliams, & Pong-Wong, 2016).…”