An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

Gutiérrez-Gil, Beatriz; Arranz, Juan José; Wiener, Pamela

doi:10.3389/fgene.2015.00167

Cited by 91 publications

(116 citation statements)

References 152 publications

(213 reference statements)

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“…These regions included well-known genes that were previously reported as potential candidates of selection signatures in cattle [38], such as MTSN ( myostatin ) on BTA2, suggested in several beef cattle populations [39–41], KIT - LG ( kit - ligand ) on BTA5 with a very large peak in the BP population, MC1R ( melanocortin 1 receptor ) on BTA18, which controls the production of eumelanin (black) or pheomelanin (red) pigments [42] and appears to be relevant in populations with black (AV and Mo) or red (Re) coat color. Moreover, it should be also highlighted that the region on BTA6 that includes LAP3 ( leucine aminopeptidase3 ), LCORL ( ligand dependent nuclear receptor corepressor - like ) and NCAPG ( non - SMC condensing I complex, subunit G ) and was identified in two meta-analyses [38, 43] as one the genomic regions that is most frequently identified with signatures of selection in the bovine genome. The genomic region identified on BTA7 includes the CAMLG ( calcium modulating ligand ) and TCF ( transcription factor 7 ) genes, which are close to a strong signature of selection that was reported by Gautier [44] and is associated with the VDAC1 ( voltage - dependent anion - selective channel protein 1 ) gene.…”

Section: Resultsmentioning

confidence: 99%

“…3) confirmed some of the signals of selection that were detected in the first axis, but also revealed several new ones that are shared by several populations and located on five chromosomes: BTA2 (between 61,684,232 and 62,199,344 and between 72,158,144 and 73,356,296 bp), BTA7 (between 20,612,988 and 21,163,812 bp), BTA13 (between 11,860,881 and 12,062,522 bp), BTA16 (between 44,612,592 and 45,846,144 bp) and BTA21 (between 32,207,264 and 32,414,316 bp). Previously, two meta-analyses [38, 43] showed that these regions were also associated with signatures of selection in other populations. Among the genes included in these regions, some of them may be good candidates for being affected by selection i.e.…”

Section: Resultsmentioning

confidence: 99%

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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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Section: Resultsmentioning

confidence: 99%

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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“…These signatures must be related to favorable alleles that either started to increase in frequency before the divergence of the breeds or were selected in parallel in different breeds. However, selection signatures that are specific to one breed are interesting because they illustrate the importance of this breed for cattle functional diversity (Gutierrez-Gil et al 2015). We therefore derived a way of finding clear breedspecific sweeps as follows.…”

Section: Analysis Of Neutral Samplesmentioning

confidence: 99%

Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds

et al. 2016

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Detecting the molecular basis of adaptation is one of the major questions in population genetics. With the advance in sequencing technologies, nearly complete interrogation of genome-wide polymorphisms in multiple populations is becoming feasible in some species, with the expectation that it will extend quickly to new ones. Here, we investigate the advantages of sequencing for the detection of adaptive loci in multiple populations, exploiting a recently published data set in cattle (Bos taurus). We used two different approaches to detect statistically significant signals of positive selection: a within-population approach aimed at identifying hard selective sweeps and a population-differentiation approach that can capture other selection events such as soft or incomplete sweeps. We show that the two methods are complementary in that they indeed capture different kinds of selection signatures. Our study confirmed some of the well-known adaptive loci in cattle (e.g., MC1R, KIT, GHR, PLAG1, NCAPG/LCORL) and detected some new ones (e.g., ARL15, PRLR, CYP19A1, PPM1L). Compared to genome scans based on medium-or high-density SNP data, we found that sequencing offered an increased detection power and a higher resolution in the localization of selection signatures. In several cases, we could even pinpoint the underlying causal adaptive mutation or at least a very small number of possible candidates (e.g., MC1R, PLAG1). Our results on these candidates suggest that a vast majority of adaptive mutations are likely to be regulatory rather than protein-coding variants.KEYWORDS F ST ; domestication; linkage disequilibrium; next-generation sequencing; selective sweeps D ETECTING the molecular basis of adaptation in natural species is one of the major questions in population genetics. With the spectacular progress of genotyping and sequencing technologies, genome-wide scans for positive selection have been performed in multiple species and populations within the last decade. Livestock species provide a considerable resource for these selection scans, because they have been subjected to strong artificial selection since their initial domestication, leading to a large variety of breeds with distinct morphology, coat color, or specialized production. In addition, the economic value of these species and the need to improve them has motivated the development of standardized single-nucleotide polymorphism (SNP) chips and the genotyping of millions of animals using these chips, providing considerable data for population genetics analyses. For instance, in taurine cattle, at least 21 genomic scans for selection have already been published and were reviewed in GutierrezGil et al. (2015). Numerous genomic scans for selection have also been published in other livestock species; see de Simoni Gouveia et al. (2014) for a review.The regions detected by these studies are generally convincing, because they contain interesting positional and functional candidate genes (e.g., Fariello et al. 2014) and/or are statistically enriched with ...

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“…The SERPIND1 gene in mammals plays a crucial role in the control of the endopeptidases that mediate important pathways, such as blood coagulation, fibrinolysis, inflammation and complement activation (Rau et al 2007;Silverman et al 2001), some of which are considered the host's first line of defence to hematophagous and blood-dwelling parasites. The POU1F1 gene encodes a protein reportedly involved in productive life (Huang et al 2008), whereas PTK2 , FOXF2 (Capomaccio et al 2015) and LAMB3 (Gutiérrez-Gil et al 2015) reportedly encode proteins associated with milk production traits. ZBTB20 is a gene that overlaps the bovine QTL regions associated with milk traits and encodes a transcription factor that has been implicated in hematopoiesis, oncogenesis and the immune response in mammals (dos Santos et al 2017).…”

Section: Cnvr Gene Contents and Functional Annotationsmentioning

confidence: 99%

Genome-wide detection of copy-number variations in local cattle breeds

et al. 2019

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Abstract. The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina's BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRs identified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total, 178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathway analyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases. Our results have provided significant information for the construction of more-complete CNV maps of the bovine genome and offer an important resource for the investigation of genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for future studies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.

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An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

Cited by 91 publications

References 152 publications

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

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

Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds

Genome-wide detection of copy-number variations in local cattle breeds

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