Inbreeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 19809

Special Issue Editors


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Guest Editor
Animal Breeding & Genomics Centre, Wageningen UR Livestock Research, Wageningen, The Netherlands
Interests: genetic diversity; inbreeding; livestock; dogs; conservation genetics; animal health

E-Mail Website
Guest Editor
Animal Breeding & Genomics Centre, Wageningen UR Livestock Research, Wageningen, The Netherlands
Interests: conservation genomics; population genomics; ecology; wildlife; inbreeding; science communication

Special Issue Information

Dear Colleagues,

Genetics plays an important role in the extinction of populations. Small populations suffer from inbreeding, which is manifested in the genome as reduced genetic diversity and an increase in homozygous segments that are identical by descent. Inbreeding, the result of mating relatives, leads to a higher expression of genetic defects and inbreeding depression. These effects are widespread in both the animal and plant kingdoms, but not all species and populations suffer equally. Moreover, there are opportunities to genetically manage populations and reduce inbreeding rates. Ever since the start of conservation genetics in the early 1970s, inbreeding, its effects, and ways in which to avoid small effective population sizes and high inbreeding rates have been of great interest in this field. With the advent of genomics in the last 15 years or so, more detailed analyses of inbreeding have been made possible. This should lead to a deeper insight into the underlying mechanisms and processes involved.

 In this Special Issue, we aim to bring together insights from all areas impacted by inbreeding, that is, in captive breeding settings such as livestock, pets, zoo animals, as well as in situ conservation studies on wild populations. We welcome theoretical, quantitative genetic, and genomic analyses, as well as contributions evaluating the methods to mitigate the effects of small population sizes.

Dr. Jack J. Windig
Dr. Mirte Bosse
Guest Editors

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Keywords

  • inbreeding
  • conservation genetics
  • genomics
  • genetic management
  • genetic diversity

Published Papers (5 papers)

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Research

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16 pages, 1741 KiB  
Article
Changes in Allele Frequencies When Different Genomic Coancestry Matrices Are Used for Maintaining Genetic Diversity
by Elisabeth Morales-González, Jesús Fernández, Ricardo Pong-Wong, Miguel Ángel Toro and Beatriz Villanueva
Genes 2021, 12(5), 673; https://doi.org/10.3390/genes12050673 - 29 Apr 2021
Cited by 5 | Viewed by 2561
Abstract
A main objective in conservation programs is to maintain genetic variability. This can be achieved using the Optimal Contributions (OC) method that optimizes the contributions of candidates to the next generation by minimizing the global coancestry. However, it has been argued that maintaining [...] Read more.
A main objective in conservation programs is to maintain genetic variability. This can be achieved using the Optimal Contributions (OC) method that optimizes the contributions of candidates to the next generation by minimizing the global coancestry. However, it has been argued that maintaining allele frequencies is also important. Different genomic coancestry matrices can be used on OC and the choice of the matrix will have an impact not only on the genetic variability maintained, but also on the change in allele frequencies. The objective of this study was to evaluate, through stochastic simulations, the genetic variability maintained and the trajectory of allele frequencies when using two different genomic coancestry matrices in OC to minimize the loss of diversity: (i) the matrix based on deviations of the observed number of alleles shared between two individuals from the expected numbers under Hardy–Weinberg equilibrium (θLH); and (ii) the matrix based on VanRaden’s genomic relationship matrix (θVR). The results indicate that the use of θLH resulted in a higher genetic variability than the use of θVR. However, the use of θVR maintained allele frequencies closer to those in the base population than the use of θLH. Full article
(This article belongs to the Special Issue Inbreeding)
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12 pages, 3101 KiB  
Article
Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs
by Grażyna Polak, Artur Gurgul, Igor Jasielczuk, Tomasz Szmatoła, Jędrzej Krupiński and Monika Bugno-Poniewierska
Genes 2021, 12(3), 429; https://doi.org/10.3390/genes12030429 - 17 Mar 2021
Cited by 15 | Viewed by 2566
Abstract
Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the [...] Read more.
Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (FPED) and genomic inbreeding estimates was found for FROH (runs of homozygosity-based F coefficient) and FUNI (F coefficient based on the correlation between uniting gametes). FROH correlation with FPED tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations. Full article
(This article belongs to the Special Issue Inbreeding)
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16 pages, 2044 KiB  
Article
Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments
by Adam Abied, Lei Xu, Bahlibi W. Sahlu, Feng Xing, Abulgasim Ahbara, Yabin Pu, Jiang Lin, Haile Berihulay, Rabiul Islam, Xiaohong He, Joram M. Mwacharo, Qianjun Zhao and Yuehui Ma
Genes 2020, 11(12), 1480; https://doi.org/10.3390/genes11121480 - 9 Dec 2020
Cited by 15 | Viewed by 3731
Abstract
Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs [...] Read more.
Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (5S_rRNA), the innate and adaptive immune response (HERC2 and CYFIP1), digestion and metabolism (CENPJ), growth (SPP1), body size and developments (GJB2 and GJA3). This study highlighted new insights into the ROH patterns and provides a basis for future breeding and conservation strategies of Chinese sheep breeds. Full article
(This article belongs to the Special Issue Inbreeding)
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14 pages, 2082 KiB  
Article
Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data
by Rabiul Islam, Zhangfa Liu, Yefang Li, Lin Jiang and Yuehui Ma
Genes 2020, 11(6), 652; https://doi.org/10.3390/genes11060652 - 13 Jun 2020
Cited by 9 | Viewed by 3792
Abstract
Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to [...] Read more.
Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. We investigated the genomic relationship, inbreeding coefficient and effective population size in these three breeds from three state goat farms using the Illumina goat SNP50 BeadChip. Genomic relationships and phylogenetic analysis revealed that the breeds are clearly separated and formed separate clusters based on their genetic relationship. We obtained a high proportion of informative SNPs, ranging from 91.8% in the Arbas Cashmere male to 96.2% in the Jining Grey male goat breeds with an average mean of 96.8%. Inbreeding, as measured by FROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High FROH values, elevated genomic coverage of very long ROH (>30 Mb) and severe decline in effective population size were recorded in ACM goat farm. The existence of a high correlation between FHOM and FROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The Ne estimates 13 generations ago were 166, 69 and 79 for ZWM, ACM and JGM goat farm, respectively indicating that these goat breeds were strongly affected by selection pressure or genetic drift. This study provides insight into the genomic relationship, levels of inbreeding and effective population size in the studied goat populations conserved in the state goat farms which will be valuable in prioritizing populations for conservation and for developing suitable management practices for further genetic improvement of these Chinese male goats. Full article
(This article belongs to the Special Issue Inbreeding)
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Review

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21 pages, 1736 KiB  
Review
How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock
by Harmen P. Doekes, Piter Bijma and Jack J. Windig
Genes 2021, 12(6), 926; https://doi.org/10.3390/genes12060926 - 18 Jun 2021
Cited by 54 | Viewed by 6452
Abstract
Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as [...] Read more.
Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates. Full article
(This article belongs to the Special Issue Inbreeding)
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