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36 results for “genomic inbreeding”
Data from: Inbreeding and selection shape genomic diversity in captive populations: implications for the conservation of endangered species
Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.
Data from: Inbreeding depression in self-incompatible North American Arabidopsis lyrata: disentangling genomic and S-locus specific genetic load
Newly formed selfing lineages may express recessive genetic load and suffer inbreeding depression. This can have a genome-wide genetic basis, or be due to loci linked to genes under balancing selection. Understanding the genetic architecture of inbreeding depression is important in the context of the maintenance of self-incompatibility and understanding the evolutionary dynamics of S-alleles. We addressed this using North-American subspecies of Arabidopsis lyrata. This species is normally self-incompatible and outcrossing, but some populations have undergone a transition to selfing. The goals of this study were to: (1) quantify the strength of inbreeding depression in North-American populations of A. lyrata; and (2) disentangle the relative contribution of S-linked genetic load compared with overall inbreeding depression. We enforced selfing in self-incompatible plants with known S-locus genotype by treatment with CO2, and compared the performance of selfed vs outcrossed progeny. We found significant inbreeding depression for germination rate (δ=0.33), survival rate to 4 weeks (δ=0.45) and early growth (δ=0.07), but not for flowering rate. For two out of four S-alleles in our design, we detected significant S-linked load reflected by an under-representation of S-locus homozygotes in selfed progeny. The presence or absence of S-linked load could not be explained by the dominance level of S-alleles. Instead, the random nature of the mutation process may explain differences in the recessive deleterious load among lineages.
Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats
<p>Genotypic data from 1,040 Murciano-Granadina female goats genotyped with the Goat SNP50 BeadChip, as well as milk production records of 817 Murciano-Granadina goats for the traits milk yield measured in kilograms at 210 days (MY210), 240 days (MY240) and 305 days (MY305), the natural logarithm of the somatic cell count divided by 1,000 (lnSCC, to convert this value into a somatic cell count please use the formula: e<sup>lnSCC</sup> × 10<sup>3</sup> cells/mL), fat percentage (FP), protein percentage (PP) and lactose percentage (LP).</p>
Data from: Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations
Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long-term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101'822 genome-wide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive-breeding and secondary reintroductions from established populations. This step-wise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genome-wide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.
Genomic signatures of inbreeding and mutation load in a threatened rattlesnake
<p>Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their genetic load, but recent work suggests that the impact of load may be minimized by purging resulting from long-term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use individual genome resequencing data to compare levels of inbreeding, levels of genetic load (estimated as mutation load), and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus), which exist in small isolated populations, and closely-related yet outbred Western massasauga rattlesnakes (S. tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of ROHs of varying sizes, indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of mutation load in the form of greater numbers of derived deleterious mutations compared to S. catenatus, presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped species-level drift effects within S. catenatus populations were in general more frequent and more often found in homozygous genotypes than in S. tergeminus, suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations for most mutations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present, which impacts implementation of conservation actions such as genetic rescue.</p>
Data from: Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens
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Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats
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Data from: Inbreeding and selection shape genomic diversity in captive populations: implications for the conservation of endangered species
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Data from: Application of genomic estimation methods of inbreeding and population structure in an Arabian horse herd
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Genomic inbreeding and population structure of northern pike (Esox lucius) in Xinjiang, China
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Data from: Inbreeding depression in self-incompatible North American Arabidopsis lyrata: disentangling genomic and S-locus specific genetic load
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Genomic signatures of inbreeding and mutation load in a threatened rattlesnake
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Data from: Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations
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Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line
GEO Series GSE157935. Sus scrofa. 49 samples. Type: Genome variation profiling by high throughput sequencing; Genome variation profiling by SNP array; SNP genotyping by SNP array.
Data from: Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees
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Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line [Seq]
GEO Series GSE157688. Sus scrofa. 1 samples. Type: Genome variation profiling by high throughput sequencing.
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