Research Article Genomic association study for adaptability traits in four Colombian cattle breeds

León, Carlos De; Manrique, Carlos; Martínez, R.; Rocha, Juan Felipe

doi:10.4238/gmr18373

Cited by 20 publications

(16 citation statements)

References 22 publications

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“…In a genome-wide association study, GIPC2 is located close to the most significant SNP, which is found to be associated with the adaptation in Columbian cattle (De León et al, 2019). In a similar manner, this gene was identified in our study, signifying its role in the adaptation of Sahiwal cattle for which they are better known.…”

Section: Growth Survival and Adaptationsupporting

confidence: 80%

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

et al. 2021

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BackgroundIn the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip.ResultDe-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent.ConclusionThe key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.

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Section: Growth Survival and Adaptationsupporting

confidence: 80%

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

et al. 2021

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“…In VBP, two higher peaks were identified on BTA6 and BTA23, where the maximum number of samples ( n = 59, 38.5%) and ( n = 45, 29.4%), respectively, shared intergenic and intragenic ( KHDRBS2 gene) homozygous regions. The KHDRBS2 gene has been associated with fertility traits in goats [ 44 ] and in Brahman cows [ 45 ], and more recently with adaptability traits in Colombian cattle breeds [ 46 ]. This finding may relate to the VBP as well as other Aosta breeds, which are well adapted to harsh environmental conditions, such as the alpine pastures farming.…”

Section: Discussionmentioning

confidence: 99%

The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System

Strillacci

Vevey²,

Blanchet³

et al. 2020

Animals

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The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were −0.003, −0.01 and −0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.

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“…This pseudogene, an annotated exon of ALKBH8 (alkylated DNA repair protein alkB homolog 8-like), has no previously reported function or associations in cattle. The nearest annotated gene is KHDRBS2 (KH RNA Binding Domain Containing, Signal Transduction Associated 2), which has been identified by other adaptation studies in cattle, sheep, and pigs [107][108][109] . Interestingly, this variant was not significantly associated with a single environmental variable in any analysis, suggesting that its adaptive benefits are unique to a particular combination of ecoregions or environmental variables.…”

Section: Ranmentioning

confidence: 99%

Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

Rowan

Durbin

Seabury

et al. 2020

Preprint

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Selection is a basic principle of evolution. Many approaches and studies have identified DNA mutations rapidly selected to high frequencies, which leave pronounced signatures on the surrounding sequence (selective sweeps). However, for many important complex, quantitative traits, selection does not leave these intense signatures. Instead, hundreds or thousands of loci experience small changes in allele frequencies, a process called polygenic selection. We know that directional selection and local adaptation are actively changing genomes; however we have been unable to identify the genomic loci responding to this polygenic, complex selection. Here we show that the use of novel dependent variables in linear mixed models (which allow us to account for population structure, relatedness, inbreeding) identify complex, polygenic selection and local adaptation. Thousands of loci are responding to artificial directional selection and hundreds of loci have evidence of local adaptation. While advanced reproduction and genomic technologies are increasing the rate of directional selection, local adaptation is being lost. In a changing climate, the loss of local adaptation may be especially problematic. These selection mapping approaches can be used in evolutionary, model, and agriculture contexts.

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Research Article Genomic association study for adaptability traits in four Colombian cattle breeds

Cited by 20 publications

References 22 publications

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle

The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System

Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

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