Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels

Espigolan, Rafael; Baldi, Fernando; Boligon, Arione Augusti; Souza, Fernanda Fernandes; Júnior, Gerardo Alves Fernandes; Gordo, Daniel Gustavo Mansan; Venturini, G. C.; Camargo, Gregório Miguel Ferreira de; Feitosa, Fabieli Loise Braga; Garcia, Diogo Anastácio; Tonhati, Humberto; Chardulo, Luis Artur Loyola; Oliveira, Henrique Nunes de; Albuquerque, Lúcia Galvão de

doi:10.4238/2015.september.22.7

Cited by 14 publications

(7 citation statements)

References 20 publications

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“…Further, BTA5 within the composite breeds contains the lowest heterozygosity, while BTA27 and BTA28 contain the highest heterozygosity. BTA13, BTA14 and BTA28 have been reported to harbour QTL for carcass traits [ 55 ] while QTL on BTA5 are known to have a pronounced effect on reproductive efficiency in cattle [ 56 – 58 ]. The heterozygosity analysis brings to light some of the important regions in the cattle genome for breed discrimination.…”

Section: Resultsmentioning

confidence: 99%

The Bos taurus–Bos indicus balance in fertility and milk related genes

et al. 2017

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Numerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene’s contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility.

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Section: Resultsmentioning

confidence: 99%

The Bos taurus–Bos indicus balance in fertility and milk related genes

et al. 2017

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“…While GPSM is able to detect Mendelian selection, the overwhelming majority of signatures PLOS GENETICS identified represent selection on complex, quantitative traits. Of the regions identified in multiple populations, many possessed positional candidate genes with production-related functions in cattle (DACH1-Growth [37,38], LRP12-Growth [39], MYBPH-Muscle Growth [40], RHOU-Carcass Weight [41], BIRC5-Feed Intake [42]). However, GPSM did not identify any of the well-established large-effect growth loci (e.g., chromosome 14 locus containing PLAG1, chromosome 6 locus containing LCORL).…”

Section: Detecting Ongoing Polygenic Selection With Generation Proxy Selection Mapping (Gpsm)mentioning

confidence: 99%

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

et al. 2021

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Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animal’s birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for historical local adaptation. These candidate loci highlight the nervous system’s possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, understanding the genomic loci implicated in adaptation may help us breed more adapted and efficient cattle, and begin to understand the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts.

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“…(histone deacetylase 7), a gene which plays an important role in macrophage differentiation (Das Gupta, Shakespear, Iyer, Fairlie, & Sweet, 2016), while 7033_88 was within an intron of VSTM2L (Vset and transmembrane domain containing 2 like), a poorly characterized gene with conserved immunoglobulin-like domains, related to neuronal modulation and associated with growth traits in cattle (Espigolan et al, 2015). Both outlier loci were within the confidence interval of a growth-related QTL (Sánchez-Molano et al, 2011) and…”

Section: Identification Of Neutral and Outlier Locimentioning

confidence: 99%

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Prado

Vera

Hermida

et al. 2018

Evolutionary Applications

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Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double‐digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

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Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels

Cited by 14 publications

References 20 publications

The Bos taurus–Bos indicus balance in fertility and milk related genes

The Bos taurus–Bos indicus balance in fertility and milk related genes

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

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

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