A genome-wide scan for signatures of differential artificial selection in ten cattle breeds

Rothammer, Sophie; Seichter, Doris; Förster, M.; Međugorac, Ivica

doi:10.1186/1471-2164-14-908

Cited by 97 publications

(112 citation statements)

References 81 publications

(117 reference statements)

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“…Additionally, we provide evidence that the p.F279Y variant similarly affects milk production traits in FV, corroborating its presumed causal role. The p.F279Y variant has likely been a target of recent selection for protein content because the frequency of the PP-enhancing (i.e., phenylalanine-encoding) allele increased in both FV and HF, which agrees with selection signature analyses in several cattle breeds (Hayes et al, 2009;Rothammer et al, 2013).…”

Section: Short Communicationsupporting

confidence: 62%

Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation

Pausch

Wurmser

Reinhardt³

et al. 2015

Journal of Dairy Science

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Most association studies for pinpointing trait-associated variants are performed within breed. The availability of sequence data from key ancestors of several cattle breeds now enables immediate assessment of the frequency of trait-associated variants in populations different from the mapping population and their imputation into large validation populations. The objective of this study was to validate the effects of 4 putatively causative variants on milk production traits, male fertility, and stature in German Fleckvieh and Holstein-Friesian animals using targeted sequence imputation. We used whole-genome sequence data of 456 animals to impute 4 missense mutations in DGAT1, GHR, PRLR, and PROP1 into 10,363 Fleckvieh and 8,812 Holstein animals. The accuracy of the imputed genotypes exceeded 95% for all variants. Association testing with imputed variants revealed consistent antagonistic effects of the DGAT1 p.A232K and GHR p.F279Y variants on milk yield and protein and fat contents, respectively, in both breeds. The allele frequency of both polymorphisms has changed considerably in the past 20 yr, indicating that they were targets of recent selection for milk production traits. The PRLR p.S18N variant was associated with yield traits in Fleckvieh but not in Holstein, suggesting that it may be in linkage disequilibrium with a mutation affecting yield traits rather than being causal. The reported effects of the PROP1 p.H173R variant on milk production, male fertility, and stature could not be confirmed. Our results demonstrate that population-wide imputation of candidate causal variants from sequence data is feasible, enabling their rapid validation in large independent populations.

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Section: Short Communicationsupporting

confidence: 62%

Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation

Pausch

Wurmser

Reinhardt³

et al. 2015

Journal of Dairy Science

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“…Finally, there is a very strong signature of selection on BTA11 for the BP population, where the closest gene to the maximum signal is BMP10 ( bone morphogenetic protein 10 ). Within this genomic region on BTA11, some authors [46, 47] identified signatures of selection and several genes that could be associated with fertility: PROKR1 ( prokineticin receptor 1 ), GFPT1 ( glutamine - fructose - 6 - phosphate transaminase 1 ), GMCL1 ( germ cell - less spermatogenesis associated 1 ), PCBP1 ( poly ( rC ) binding protein 1 ) and EHD3 ( EH - domain containing 3 ).…”

Section: Resultsmentioning

confidence: 99%

On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations

et al. 2016

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Background Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations.ResultsAnalysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic–pituitary–thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors.ConclusionsWe show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0258-1) contains supplementary material, which is available to authorized users.

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“…Previous investigations also elucidated that MAP2K6 was associated with various economic traits in livestock, some of which are related to bone development. A genomewide scan for selection signatures in ten cattle breeds revealed that MAP2K6 is associated with carcass weight, back fat and marbling in Korean beef cattle (Rothammer, Seichter, Förster, & Medugorac, ). Furthermore, MAP2K6 participates in the gonadotropin signalling pathway, which has been identified to be associated with divergent growth traits according to a multiomics analysis in an F 2 Charolais × Holstein population (Widmann et al., ).…”

Section: Discussionmentioning

confidence: 99%

Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

Miao

Wang

Bao³

et al. 2018

J Animal Breeding Genetics

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Bone weight, defined as the total weight of the bones in all the forequarter and hindquarter joints, can reflect somebody conformation traits and skeletal diseases. To gain a better understanding of the genetic determinants of bone weight, we used a composite strategy including multimarker and rare-marker association to perform genomewide association studies (GWAS) for that character in Simmental cattle. Our strategy consisted of three models: (i) A traditional linear mixed model (LMM) was applied (Q+K-LMM); (ii) single nucleotide polymorphisms (SNPs) with p-values less than .05 from the LMM were selected to undergo the least absolute shrinkage and selector operator (Lasso) in the second stage (LMM-Lasso); (iii) genes containing two or more rare SNPs were examined by performing the sequence kernel association test (gene-based SKAT). A total of 1,225 cattle were genotyped with an Illumina BovineHD BeadChip containing 770,000 SNPs. After the quality-control procedures, 1,217 individuals with 608,696 common SNPs and 105,787 rare SNPs (with 0.001 < minor allele frequency [MAF] <0.05) remained in the sample for analysis. A traditional LMM successfully mapped three genes associated with bone weight, while LMM-Lasso identified nine genes, which included all genes found by traditional LMM. Only a single gene, EPHB3, surpassed the significance threshold after Bonferroni correction in gene-based SKAT. In conclusion, based on functional annotation and results from previous endeavours, we believe that LCORL, RIMS2, LAP3, PRKAR2B, CHSY1, MAP2K6 and EPHB3 are candidate genes for bone weight. In general, such a comprehensive strategy for GWAS may be useful for researchers seeking to probe the full genetic architecture underlying economic traits in livestock.

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A genome-wide scan for signatures of differential artificial selection in ten cattle breeds

Cited by 97 publications

References 81 publications

Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation

Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation

On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations

Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

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