Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

Onteru, Suneel Kumar; Gorbach, Danielle M.; Young, J. M.; Garrick, Dorian J.; Dekkers, Jack C. M.; Rothschild, Max F.

doi:10.1371/journal.pone.0061756

Cited by 112 publications

(124 citation statements)

References 62 publications

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“…In this same region, Onteru et al (2013) reported significant QTL for ADG when considering Yorkshire derived lines. Similarly, Pierzchala et al (2003) detected significant QTLs for ADG in this region when using purebred pigs of the three genetically diverse founder groups: Meishan, Pietrain, and European Wild Boar.…”

Section: Snp Derived Candidate Gene Annotationmentioning

confidence: 76%

Genome association study through nonlinear mixed models revealed new candidate genes for pig growth curves

Silva

Zambrano

Varona

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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Genome association analyses have been successful in identifying quantitative trait loci (QTLs) for pig body weights measured at a single age. However, when considering the whole weight trajectories over time in the context of genome association analyses, it is important to look at the markers that affect growth curve parameters. The easiest way to consider them is via the two-step method, in which the growth curve parameters and marker effects are estimated separately, thereby resulting in a reduction of the statistical power and the precision of estimates. One efficient solution is to adopt nonlinear mixed models (NMM), which enables a joint modeling of the individual growth curves and marker effects. Our aim was to propose a genome association analysis for growth curves in pigs based on NMM as well as to compare it with the traditional two-step method. In addition, we also aimed to identify the nearest candidate genes related to significant SNP (single nucleotide polymorphism) markers. The NMM presented a higher number of significant SNPs for adult weight (A) and maturity rate (K), and provided a direct way to test SNP significance simultaneously for both the A and K parameters. Furthermore, all significant SNPs from the two-step method were also reported in the NMM analysis. The ontology of the three candidate genes (SH3BGRL2, MAPK14, and MYL9) derived from significant SNPs (simultaneously affecting A and K) allows us to make inferences with regards to their contribution to the pig growth process in the population studied.

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Section: Snp Derived Candidate Gene Annotationmentioning

confidence: 76%

Genome association study through nonlinear mixed models revealed new candidate genes for pig growth curves

Silva

Zambrano

Varona

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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“…PGM1 catalyzes conversion of glucose 1-phosphate to glucose 6-phosphate, which is a useful metabolic intermediate [15]- [24]. Although the glucose 1-phosphate molecule is not a useful metabolic intermediate, PGM1 catalyzes conversion of glucose 1-phosphate to glucose 6-phosphate [23].…”

Section: Discussionmentioning

confidence: 99%

“…If the cell is in a low-energy state, glucose 6-phosphate will be metabolized along the glycolytic pathway, eventually yielding two molecules of adenosine triphosphate [22] [23]. On the other hand, the cell is in need of biosynthetic intermediates, glucose 6-phosphate enters the pentose phosphate pathway, where it undergoes a series of reactions to yield ribose and/or NADPH, depending on cellular conditions [24].…”

Section: Introductionmentioning

confidence: 99%

“…In this case, PGM1 catalyzes the conversion of glucose 6-phosphate, a product generated from glucose by hexokinase, to glucose 1-phosphate. Glucose-1-phosphate then reacts with UTP to yield UDP-glucose in a reaction catalyzed by UDP-glucose-pyrophosphorylase [23] [24]. If activated by insulin, glycogen synthase will attach the glucose molecule from the UDP-glucose complex onto a glycogen polymer [23].…”

Section: Introductionmentioning

confidence: 99%

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Phosphorylation on TRPV4 Serine Residue 824 Enhances Its Association with PGM1

Sein

Lee

Hyun

et al. 2016

AJMB

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The TRPV4 cation channel is expressed in a broad range of tissues and participates in the generation of a Ca 2+ signal and/or depolarization of membrane potential. Here, human phosphoglucomutase-1 (PGM1), an enzyme that converts glucose-6 phosphate to glucose-1 phosphate in the glycolysis pathway, as the first auxiliary protein of TRPV4 Ca 2+ channels, is identified with yeast two hybrid system, coimmunoprecipitation, confocal microscopy, and GST pull-down assays. TRPV4 forms a complex with PGM1 through its C-terminal cytoplasmic domain. Because it is demonstrated that TRPV4 serine residue 824 (S824) is phosphorylated by serum/glucocorticoid regulated kinase 1, we elucidate the effect of TRPV4 S824 phosphorylation on TRPV association with PGM1. Even an inactivated mutant version of TRPV4, S824A, exhibited a decreased ability to bind PGM1, an activated phosphomimetic mutant version of TRPV4, S824D, exhibited enhanced binding to PGM1. Thus, formation of the TRPV4/PGM1 complex and localization of this complex to the plasma membrane appear to be regulated by the phosphorylation status of residue S824 in TRPV4. The newly identified interactor of TRPV4 may help the molecular pathways modulating transport activity or glucose metabolism, respectively.

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“…(BARENDSE et al, 2007;SHERMAN et al, 2008;MUJIBI;ROLF et al, 2011;SNELLING et al, 2011;MUJIBI et al, 2011;PRYCE et al, 2012;ONTERU et al, 2013), porém, as metodologias utilizadas para esse fim são diversas, além de populações avaliadas extremamente distintas, o que pode acarretar que as associações realizadas em uma determinada raça e população podem não ser aplicáveis em outras …”

Section: Conclusãounclassified

Estudo genético e genômico da ingestão e eficiência alimentar em bovinos da raça Nelore (Bos indicus)

Santana¹

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O objetivo dessa pesquisa foi avaliar os parâmetros genéticos e correlações das medidas de ingestão e eficiência alimentar com desempenho e características de carcaça, além de realizar o estudo de associação de amplo genoma (GWAS) para ingestão de matéria seca (IMS), consumo alimentar residual (CAR) e ganho de peso (GMD) em bovinos da raça Nelore (Bos indicus). Foram utilizados dados de 1.058 animais com fenótipo para IMS, taxa de conversão alimentar (CA), CAR, ganho de peso residual (GPR), consumo e ganho residuais (CGR), ganho de peso diário (GMD) e características de carcaça. Os parâmetros genéticos da IMS, CA, CAR, GPR e CGR e suas as correlações com GMD e características de carcaça foram estimados utilizando abordagem bayesiana. Quatro marcadores do tipo SNP (Single Nucleotide Polymorphism), localizados em genes relacionados ao controle de apetite (NPY e PDE3B) e transporte iônico (TRPM3 e ITPR1), foram associados com o desempenho, ingestão e medidas de eficiência alimentar. Adicionalmente, os animais foram genotipados em dois chips distintos (Illumina Bovine HD e Illumina BovineSNP50) e as informações genotípicas foram combinadas por meio de estudo de imputação. As centenas de milhares de SNPs foram utilizadas para o GWAS da IMS, CAR e GMD pelo teste de associação GRAMMAR-Gamma. A herdabilidade da IMS, CAR e CGR foi de 0,40, 0,38 e 0,54, respectivamente. Não foram encontradas associações nos SNPs localizados nos genes TRPM3, NPY e ITPR1, no entanto, o SNP no gene PDE3B foi associados significativamente (P≤0,05) com IMS, CAR e CGR. Os SNPs mais associados com a IMS e CAR, no GWAS, estão localizados nos cromossomos 4, 8, 14 e 21 em regiões genômicas relacionadas com transporte iônico e regulação da ingestão. O GWAS para o GMD apontou os cromossomos 3, 6 e 10 como os que continham os marcadores com maior associação. A ingestão e eficiência alimentar são passíveis de seleção genética, principalmente o CGR. O gene PDE3B deve ser melhor estudado pois, aparenta ter relação com esses fenótipos. Por fim, esse trabalho apontou regiões genômicas, por meio de associação de amplo genoma, relacionadas com a IMS, CAR e GMD, acredita-se ser o primeiro estudo desse tipo para esses fenótipos em animais da raça Nelore. The aim of this study was to evaluate the genetic parameters and correlations of intake and feed efficiency with performance and carcass traits, and perform the genome-wide association study (GWAS) for dry matter intake (DMI), residual feed intake (RFI) and average daily gain (ADG) in Nelore cattle (Bos indicus). Data from 1,058 animals phenotyped for DMI, feed conversion ratio (FCR), RFI, residual body weight gain (RG), residual intake and body weight gain (RIG), average daily gain (ADG) and carcass traits were used. Genetic parameters of DMI, FCR, RFI, RG and RIG and their correlations with ADG and carcass traits were estimated using Bayesian approach. Four SNPs (Single Nucleotide Polymorphism), located in genes related to appetite control (NPY and PDE3B) and ion transport (TRPM3 and ITPR1), were associat...

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Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

Cited by 112 publications

References 62 publications

Genome association study through nonlinear mixed models revealed new candidate genes for pig growth curves

Genome association study through nonlinear mixed models revealed new candidate genes for pig growth curves

Phosphorylation on TRPV4 Serine Residue 824 Enhances Its Association with PGM1

Estudo genético e genômico da ingestão e eficiência alimentar em bovinos da raça Nelore (Bos indicus)

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