Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Abstract

Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.

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

“…In the current study, minimizing relationships based on matrix A had an unfavorable effect on the diversity at the genomic level compared to both genomic metrics SNPRM or ROHRM . This is in agreement with previous simulation studies that spanned multiple generations in the context of conservation [65, 66] and livestock breeding programs [19, 25, 27, 30, 67]. Based on simulations, Sonesson et al [25] found that the genomic rate of inbreeding was around 3 times higher when using optimal contributions constrained by pedigree versus genomic information.…”

“…4). Previous simulations, based on multiple generations showed that SNPRM maintains heterozygosity to a greater degree than ROHRM [66, 67], which is not surprising since the SNPRM is more closely related to the heterozygosity than the ROHRM . Within one generation, the level of heterozygosity was numerically the highest when the SNPRM was used for the majority of the quantiles across breeds compared to the ROHRM , which is in line with previous work, although the across-replicate standard deviation covered both means.…”

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

“…The best know strategy to achieve these goals is optimizing the contributions of the parents to minimize global coancestry in their offspring (Fernández et al, 2003). Recently, measures of coancestry based on IBD segments and on shared segments of the genome (Bosse et al, 2015) have been proposed as good balance between maintaining diversity and fitness, with a higher fitness than managing with molecular coancestry and higher diversity than managing with genealogical coancestry. Therefore, determining the occurrence of IBD segments in potential parents, thereby measuring their relatedness and coancestry, can be used to minimize the occurrence of long ROH in the offspring.…”

Genomic dissection of inbreeding depression: a gate to new opportunities

“…Thus, according to Szpiech et al (2013), a significantly greater fraction of all genome-wide predicted damaging homozygotes falls in ROH, especially in long ROH, than would be expected from the corresponding fraction of non-damaging homozygotes in ROH. In livestock breeding and conservation, the power and potential benefit of this concept were recognised very soon by Bosse et al (2015), Zhang et al (2015b), and Nuijten et al (2016). We believe that this approach, when combined with estimation of inbreeding depression and some other innovative technologies such as gene editing (gene editing or genome editing is the insertion, deletion, or replacement of DNA at a specific site in the genome; Kim and Kim, 2014), might open the door to the management of detrimental load in genetically small populations.…”