Runs of homozygosity and analysis of inbreeding depression

Sumreddee, Pattarapol; Toghiani, Sajjad; Hay, El Hamidi; Roberts, A. J.; Aggrey, Samuel E.; Rekaya, Romdhane

doi:10.1093/jas/skaa361

Cited by 14 publications

(16 citation statements)

References 47 publications

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“…Conversely, a gain of 1.33 kg in the same trait was associated with an increase of 1% in ancient inbreeding (ROH < 4 Mb). A recent research study conducted in beef cattle by Sumreddee et al [38] demonstrated that although the recessive load is expected to be larger in longer ROH segments, short ROH segments (<5 Mb) can still harbor some deleterious mutations with substantial joint effects on some traits.…”

Section: Inbreeding Coefficientsmentioning

confidence: 99%

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Hidalgo

Cesarani

Garcia

et al. 2021

Animals

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The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.

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Section: Inbreeding Coefficientsmentioning

confidence: 99%

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Hidalgo

Cesarani

Garcia

et al. 2021

Animals

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“…Additionally, the efficiency of purging of deleterious alleles from short ROH segments depends on several factors. In fact, Sumreddee et al [ 53 ] showed using the same data set and minimum length threshold (1 Mb) that the efficiency of purging depended on selection pressure and rate of inbreeding within the population. Thus, short ROH segments may still harbor harmful alleles in spite of their distant origin.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, short ROH segments may still harbor harmful alleles in spite of their distant origin. Furthermore, the large number of short ROH segments, each potentially with small effect, could collectively have a non-negligible contribution to inbreeding depression [ 53 ]. All these factors combined, complicate the discrimination between ROH segment classes using the proposed approach (Fig.…”

Section: Discussionmentioning

confidence: 99%

Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

et al. 2021

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Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration.

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“…Given the lack of pedigree information for the individuals included in this research, inbreeding coefficient (F) was estimated from runs of homozygosity (Froh) [ 28 ]. This was deemed as the most appropriate method to estimate the levels of inbreeding of both Muskellunge populations included in the study.…”

Section: Methodsmentioning

confidence: 99%

Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America

Chinchilla-Vargas

Meerbeek

Rothschild

et al. 2021

Genes

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Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.

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Runs of homozygosity and analysis of inbreeding depression

Cited by 14 publications

References 47 publications

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America

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