Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data

Karimi, Karim; Koshkoiyeh, Ali Esmailizadeh; Gondro, Cedric

doi:10.1186/s40781-015-0080-2

Cited by 23 publications

(13 citation statements)

References 34 publications

(46 reference statements)

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“…However, Gautier et al (2007) and Khatkar et al (2008) suggested that 75,000 to 300,000 SNPs would be required for association mapping studies within worldwide cattle breeds, which is in agreement with the density suggested in the present study for American mink. For instance, similar to our results, r 2 > 0.3 extended up to distances of 10-20 kb in Nguni and Drakensberger cattle breeds of South Africa (Makina et al, 2015) and several cattle breeds of Iran (Karimi et al, 2015). In addition, short extensions of LD (average r 2 > 0.3 at distances of >20 kb) were reported at some breeds of sheep (Kijas et al, 2014;Chitneedi et al, 2017;Liu et al, 2017), pig (Amaral et al, 2008;Ai et al, 2013), and domestic cats (Alhaddad et al, 2013), which are comparable to the ranges obtained in our study.…”

Section: Discussionsupporting

confidence: 91%

Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data

et al. 2020

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Knowledge of linkage disequilibrium (LD) patterns is necessary to determine the minimum density of markers required for genomic studies and to infer historical changes as well as inbreeding events in the populations. In this study, we used genotyping-bysequencing (GBS) approach to detect single nucleotide polymorphisms (SNPs) across American mink genome and further to estimate LD, effective population size (Ne), and inbreeding rates based on excess of homozygosity (F HOM ) and runs of homozygosity (ROH). A GBS assay was constructed based on the sequencing of ApeKI-digested libraries from 285 American mink using Illumina HiSeq Sequencer. Data of 13,321 SNPs located on 46 scaffolds was used to perform LD analysis. The average LD (r 2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r 2 < 0.2 was observed at inter-marker distances of >40 kb, suggesting that at least 60,000 informative SNPs would be required for genomic selection in American mink. The Ne was estimated to be 116 at five generations ago. In addition, the most rapid decline of population size was observed between 100 and 200 generations ago. Our results showed that short extensions of homozygous genotypes (500 kb to 1 Mb) were abundant across the genome and accounted for 33% of all ROH identified. The average inbreeding coefficient based on ROH longer than 1 Mb was 0.132 ± 0.042. The estimations of F HOM ranged from −0.44 to 0.34 among different samples with an average of 0.15 over all individuals. This study provided useful insights to determine the density of SNP panel providing enough statistical power and accuracy in genomic studies of American mink. Moreover, these results confirmed that GBS approach can be considered as a useful tool for genomic studies in American mink.

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Section: Discussionsupporting

confidence: 91%

Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data

et al. 2020

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“…Minor allele frequency varied between breeds, ranging from 0.23 (Kangayam) to 0.26 (Vechur), with an average observed heterozygosity of 0.35 in all samples examined (Table 1). The similar estimates of MAF were also reported in Nellore, Holstein, Iranian, Ethiopian and South African cattle [22][23][24][25][26] , which varied from 0.21 to 0.25 in Bos indicus and Bos Taurus cattle breeds. However, higher/lower estimates were also reported in other cattle breeds [27][28][29] .…”

Section: Resultssupporting

confidence: 80%

Genome Analyses Revealed Genetic Admixture and Selection Signatures in Bos indicus

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Bhatia

Ganguly

et al. 2021

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The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (Fst ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of animals (> 76%) of the different populations under study except Vechur clustered into their own group of animals called breed. Vechur population contained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. There were also significant differences in number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height etc.) of short stature, Vechur, compared to large sized cattle. The HMGA2 gene was present in the selection signature on chromosome 5, which may explain the differences in stature of these cattle.

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“…The LD between markers provides insight in exploring the level of diversity between different breeds, inferring the frequency of recombination events, investigating the change in effective population size across generations, and identifying genomic regions to improve economically important traits [ 1 – 3 ]. The pattern of LD is mainly determined by the physical distance between markers, although several other demographic and evolutionary factors including population stratification, inbreeding, effective population size, genetic bottleneck, genetic drift, migration, mutation, selection, and recombination rate may also influence the extent and pattern of LD [ 4 – 6 ].…”

Section: Introductionmentioning

confidence: 99%

Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data

et al. 2021

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The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was having minor allele frequency of less than 0.20. The extent of LD between autosomal SNPs up to 10 Mb apart across the genome was measured using r2 statistic. The mean r2 value was 0.43, if pairwise distance of marker was less than10 kb and it decreased further to 0.21 for 25–50 kb markers distance. Further, the effect of minor allele frequency and sample size on LD estimate was investigated. The LD value decreased with the increase in inter-marker distance, and increased with the increase of minor allelic frequency. The estimated inbreeding coefficient and effective population size were 0.04, and 46 for present generation, which indicated small and unstable population of Vrindavani cattle. These findings suggested that a denser or breed specific SNP panel would be required to cover all genome of Vrindavani cattle for genome wide association studies (GWAS).

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Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data

Cited by 23 publications

References 34 publications

Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data

Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data

Genome Analyses Revealed Genetic Admixture and Selection Signatures in Bos indicus

Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data

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