Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

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Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations

Frontiers in Genetics ◽

10.3389/fgene.2018.00688 ◽

2019 ◽

Vol 9 ◽

Cited By ~ 5

Author(s):

Tingxian Deng ◽

Aixin Liang ◽

Jiajia Liu ◽

Guohua Hua ◽

Tingzhu Ye ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Effective Population Size ◽

Effective Population ◽

Snp Data ◽

Genome Wide

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Evaluating the use of ABBA-BABA statistics to locate introgressed loci

10.1101/001347 ◽

2013 ◽

Cited By ~ 17

Author(s):

Simon H. Martin ◽

John W. Davey ◽

Chris D. Jiggins

Keyword(s):

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Ancestral Population ◽

Whole Genome ◽

Effective Population ◽

Genome Data ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

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Natural selection does not affect the estimates of effective population size based on linkage disequilibrium

10.1101/2021.08.16.456457 ◽

2021 ◽

Author(s):

Irene Novo ◽

Armando Caballero ◽

Enrique Santiago

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Effective Population Size ◽

Recombination Rate ◽

Nucleotide Diversity ◽

Loss Of Function ◽

Effective Population ◽

Genomic Regions ◽

The Relationship ◽

Key Parameter

The effective population size ( N e ) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in N e across time using measures of genome diversity or linkage disequilibrium between markers. Selection is expected to reduce diversity and N e , and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and of recombination rate heterogeneity in the estimation of historical N e . We also investigate the relationship between diversity parameters and N e across the different regions of the genome using human marker data. We show that the estimates of historical N e obtained from linkage disequilibrium between markers ( N e LD ) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, what could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of N e LD obtained for particular genomic regions do not correlate with recombination rate, nucleotide diversity, polymorphism, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that N e LD measures are merely indicative of demographic changes in population size across generations.

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Runs of homozygosity in killer whale genomes provide a global record of demographic histories

10.22541/au.162496924.41380105/v1 ◽

2021 ◽

Author(s):

Andy Foote ◽

Rebecca Hooper ◽

Alana Alexander ◽

Robin Baird ◽

Charles Baker ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Killer Whale ◽

Demographic History ◽

Population History ◽

Runs Of Homozygosity ◽

Effective Population ◽

High Background ◽

Genome Wide ◽

Conservation Concern

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations and populations of known conservation concern, including a Scottish population, for which 37.8% of the autosomes comprised of ROH >1.5 Mb in length.

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The evaluation of genomic diversity and selection signals in the autochthonous Slovak Spotted cattle

Czech Journal of Animal Science ◽

10.17221/265/2020-cjas ◽

2021 ◽

Author(s):

Radovan Kasarda ◽

Nina Moravčíková ◽

Barbora Olšanská ◽

Gábor Mészáros ◽

Luboš Vostrý ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Coat Colour ◽

Genomic Diversity ◽

Runs Of Homozygosity ◽

Effective Population ◽

Dual Purpose ◽

High Selection ◽

Genomic Regions

The aim of this study was to evaluate the effective population size based on linkage disequilibrium and the trend of inbreeding derived from runs of homozygosity (ROH) in the Slovak Spotted cattle. The ROH segments longer than 4 Mb were then analysed to identify selection signals. Eighty-five individuals were genotyped using the ICBF International Dairy and Beef chip (dams of sires) and Illumina BovineSNP50 BeadChip (sires). The ROH segments > 1 Mb occurred most often in the autosomal genome with an average number of 16.75 ± 7.23. The ROH segments > 16 Mb covering 0.41% of the genome pointed to the long-term effort of breeders to reduce inbreeding in the population of Slovak Spotted cattle. However, the average observed heterozygosity indicated a decrease in overall diversity in the current population. The decrease of heterozygosity per generation also confirmed the estimates of historical and recent effective population size (a decrease of 6.88 animals per generation). The predicted current effective population size was 58 animals. Twenty-one regions across 12 different autosomes were fixed due to the high selection pressure. Within these genomic regions were identified various genes associated with reproduction (SLC9C1, PTPN12), milk production (IGF1, ABCG2), beef production (IFRD1, PTPN4), developmental processes (FMNL2, GLI2), immune system (CD96, CSK) and coat colour (KIT). These selection signals detected in the genome of Slovak Spotted cattle confirm the constant effort of breeders to preserve the dual-purpose nature of this breed.

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