Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs

Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.

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Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Animals ◽

10.3390/ani9060350 ◽

2019 ◽

Vol 9 (6) ◽

pp. 350 ◽

Cited By ~ 4

Author(s):

Haile Berihulay ◽

Rabiul Islam ◽

Lin Jiang ◽

Yuehui Ma

Keyword(s):

Linkage Disequilibrium ◽

Genetic Parameter ◽

Genetic Selection ◽

Chromosome 1 ◽

Effective Population ◽

Genome Wide ◽

Population Sizes ◽

Trait Locus ◽

D Values ◽

Genome Wide Linkage Disequilibrium

Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r2 and D’ values, respectively. The average r2 between all the populations varied little and ranged from 0.055 r2 for the Jining Grey to 0.128 r2 for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.

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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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The formation of avian montane diversity across barriers and along elevational gradients

Nature Communications ◽

10.1038/s41467-021-27858-5 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

José Martín Pujolar ◽

Mozes P. K. Blom ◽

Andrew Hart Reeve ◽

Jonathan D. Kennedy ◽

Petter Zahl Marki ◽

...

Keyword(s):

Gene Flow ◽

Population Differentiation ◽

Bird Species ◽

Geographic Area ◽

Effective Population ◽

Tropical Mountains ◽

Mountainous Regions ◽

Pleistocene Climate ◽

Genome Wide ◽

Population Sizes

AbstractTropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species’ altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.

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Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

Archives Animal Breeding ◽

10.5194/aab-62-143-2019 ◽

2019 ◽

Vol 62 (1) ◽

pp. 143-151 ◽

Cited By ~ 6

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Nahid Parna ◽

Pourya Davoudi ◽

Majid Khansefid

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Association Studies ◽

Genome Wide Association Studies ◽

Effective Population ◽

High Genetic Diversity ◽

Single Nucleotide ◽

Genome Wide ◽

Snp Panel ◽

Zandi Sheep

Abstract. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD (r2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between SNP pairs (40–60 kb). The Ne of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long (> 10 Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.

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Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster.

Genetics ◽

10.1093/genetics/120.4.1043 ◽

1988 ◽

Vol 120 (4) ◽

pp. 1043-1051

Author(s):

Z Smit-McBride ◽

A Moya ◽

F J Ayala

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Assay Method ◽

Effective Population ◽

Population Mixing ◽

Locus Pair ◽

Two Samples ◽

In The Wild ◽

Population Sizes ◽

Experimental Populations

Abstract We have studied linkage disequilibrium in Drosophila melanogaster in two samples from a wild population and in four large laboratory populations derived from the wild samples. We have assayed four polymorphic enzyme loci, fairly closely linked in the third chromosome: Sod Est-6, Pgm, and Odh. The assay method used allows us to identify the allele associations separately in each of the two homologous chromosomes from each male sampled. We have detected significant linkage disequilibrium between two loci in 16.7% of the cases in the wild samples and in 27.8% of the cases in the experimental populations, considerably more than would be expected by chance alone. We have also found three-locus disequilibria in more instances than would be expected by chance. Some disequilibria present in the wild samples disappear in the experimental populations derived from them, but new ones appear over the generations. The effective population sizes required to generate the observed disequilibria by randomness range from 40 to more than 60,000 individuals in the natural population, depending on which locus pair is considered, and from 100 to more than 60,000 in the experimental populations. These population sizes are unrealistic; the fact that different locus-pairs yield disparate estimates within the same population argues against the likelihood that the disequilibria may have arisen as a consequence of population bottlenecks. Migration, or population mixing, cannot be excluded as the process generating the disequilibria in the wild samples, but can in the experimental populations. We conclude that linkage disequilibrium in these populations is most likely due to natural selection acting on the allozymes, or on loci very tightly linked to them.

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

Genes ◽

10.3390/genes11050577 ◽

2020 ◽

Vol 11 (5) ◽

pp. 577

Author(s):

Huiwen Zhan ◽

Saixian Zhang ◽

Kaili Zhang ◽

Xia Peng ◽

Shengsong Xie ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Effective Population Size ◽

Average Length ◽

The Other ◽

Runs Of Homozygosity ◽

Effective Population ◽

Inbreeding Coefficients ◽

Genome Wide ◽

Genomic Regions

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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Estimations of genomic linkage disequilibrium and effective population sizes in three sheep populations

Livestock Science ◽

10.1016/j.livsci.2014.10.015 ◽

2014 ◽

Vol 170 ◽

pp. 22-29 ◽

Cited By ~ 10

Author(s):

Fuping Zhao ◽

Guangkai Wang ◽

Tao Zeng ◽

Caihong Wei ◽

Li Zhang ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Effective Population ◽

Genomic Linkage ◽

Population Sizes

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Adaptation in outbred sexual yeast is repeatable, polygenic, and favors rare haplotypes

10.1101/2021.08.27.457900 ◽

2021 ◽

Cited By ~ 1

Author(s):

Robert A. Linder ◽

Behzad Zabanavar ◽

Arundhati Majumder ◽

Hannah Chiao-Shyan Hoang ◽

Vanessa Genesaret Delgado ◽

...

Keyword(s):

Rare Variants ◽

Intermediate Frequency ◽

Effective Population ◽

Entire Genome ◽

Frequency Shifts ◽

Haplotype Blocks ◽

Genome Wide ◽

Population Sizes ◽

Drug Treatments ◽

Per Gene

AbstractWe describe the results of a 200 generation Evolve and Resequence (E&R) study initiated from an outbred dipliod recombined synthetic base population derived from 18 genetically diverse founders. Replicate populations were maintained at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing implies a per gene per cell-division recombination rate higher than that achieved in Drosophila E&R studies. In 55 sexual populations we observe large fitness gains and highly repeatable patterns of genome-wide haplotype change within each chemical challenge. There was little evidence for pervasive pleiotropy, as evidenced by patterns of haplotype change between drug treatments. Within treatment adaptation appears highly polygenic with almost the entire genome showing significant consistent haplotype change. Finally, adaptation was almost always associated with only one of the 18 founder alleles, suggesting selection primarily acts on rare variants private to a founder or haplotype blocks harboring multiple mutations. This observation contradicts the notion that adaptation is often due to subtle frequency shifts at intermediate frequency variants.

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