Dataset Information

A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens.

ABSTRACT: Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with carcass traits in chickens. For that, we performed a genome-wide association analysis (GWAS) for breast, thigh and drumstick traits in meat-type chickens and detected 19 unique quantitative trait loci (QTL). We then used: (1) the identified windows; (2) QTL for abdominal fat detected in a previous study with the same population and (3) previously obtained whole genome sequence data, to identify 18 predicted deleterious single nucleotide polymorphisms (SNPs) in those QTL for further association with breast, thigh, drumstick and abdominal fat traits. Using the additive model, a predicted deleterious SNP c.482C > T (SIFT score of 0.4) was associated (p-value < 0.05) with abdominal fat weight and percentage. This SNP is in the second exon of the MYBPH gene, and its allele frequency deviates from Hardy-Weinberg equilibrium. In conclusion, our study provides evidence that the c.482C > T SNP in the MYBPH gene is a putative causal mutation for fat deposition in meat-type chickens.

SUBMITTER: Trevisoli PA

PROVIDER: S-EPMC8386115 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A Missense Mutation in the <i>MYBPH</i> Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens.

Trevisoli Priscila Anchieta PA Moreira Gabriel Costa Monteiro GCM Boschiero Clarissa C Cesar Aline Silva Mello ASM Petrini Juliana J Margarido Gabriel Rodrigues Alves GRA Ledur Mônica Corrêa MC Mourão Gerson Barreto GB Garrick Dorian D Coutinho Luiz Lehmann LL

Frontiers in genetics 20210811

Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with c ...[more]

PMID: 34456973

Similar Datasets

Project description:Feed represents the major cost of chicken production. Selection for improving feed utilization is a feasible way to reduce feed cost and greenhouse gas emissions. The objectives of this study were to investigate the efficiency of genomic prediction for feed conversion ratio (FCR), residual feed intake (RFI), average daily gain (ADG) and average daily feed intake (ADFI) and to assess the impact of selection for feed efficiency traits FCR and RFI on eviscerating percentage (EP), breast muscle percentage (BMP) and leg muscle percentage (LMP) in meat-type chickens. Genomic prediction was assessed using a 4-fold cross-validation for two validation scenarios. The first scenario was a random family sampling validation (CVF), and the second scenario was a random individual sampling validation (CVR). Variance components were estimated based on the genomic relationship built with single nucleotide polymorphism markers. Genomic estimated breeding values (GEBV) were predicted using a genomic best linear unbiased prediction model. The accuracies of GEBV were evaluated in two ways: the correlation between GEBV and corrected phenotypic value divided by the square root of heritability, i.e., the correlation-based accuracy, and model-based theoretical accuracy. Breeding values were also predicted using a conventional pedigree-based best linear unbiased prediction model in order to compare accuracies of genomic and conventional predictions. The heritability estimates of FCR and RFI were 0.29 and 0.50, respectively. The heritability estimates of ADG, ADFI, EP, BMP and LMP ranged from 0.34 to 0.53. In the CVF scenario, the correlation-based accuracy and the theoretical accuracy of genomic prediction for FCR were slightly higher than those for RFI. The correlation-based accuracies for FCR, RFI, ADG and ADFI were 0.360, 0.284, 0.574 and 0.520, respectively, and the model-based theoretical accuracies were 0.420, 0.414, 0.401 and 0.382, respectively. In the CVR scenario, the correlation-based accuracy and the theoretical accuracy of genomic prediction for FCR was lower than RFI, which was different from the CVF scenario. The correlation-based accuracies for FCR, RFI, ADG and ADFI were 0.449, 0.593, 0.581 and 0.627, respectively, and the model-based theoretical accuracies were 0.577, 0.629, 0.631 and 0.638, respectively. The accuracies of genomic predictions were 0.371 and 0.322 higher than the conventional pedigree-based predictions for the CVF and CVR scenarios, respectively. The genetic correlations of FCR with EP, BMP and LMP were -0.427, -0.156 and -0.338, respectively. The correlations between RFI and the three carcass traits were -0.320, -0.404 and -0.353, respectively. These results indicate that RFI and FCR have a moderate accuracy of genomic prediction. Improving RFI and FCR could be favourable for EP, BMP and LMP. Compared with FCR, which can be improved by selection for ADG in typical meat-type chicken breeding programs, selection for RFI could lead to extra improvement in feed efficiency.

Project description:Excessive deposition of abdominal fat is a public concern in the yellow chicken industry related to human nutrition. The common practice of nutritionists is to increase the fiber content in feed to control abdominal fat deposition of chickens. Corncob meal (CCM) is the cheapest ingredient widely used in animal diets. The possible effects of CCM on chicken abdominal fat deposition and the possible mechanism involving cecal microbiota remain unknown. The objectives of this study were to investigate the effects of CCM in modulating abdominal fat deposition and the role of the cecal microbiota and their metabolites. A total of 200 ninety-day-old Huxu female chickens were divided into 2 dietary treatments, each with 10 replicates of 10 birds, and were fed two finisher diets, from 90 to 135 d. The diets were a typical corn-soybean control diet (CON) and that diet with CCM partially replacing corn and corn gluten meal. Results showed that the CCM diet markedly decreased live weight and abdominal fat percentage (P < 0.05); chickens fed the CCM diet exhibited lower (P < 0.01) expression in abdominal fat of fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), fatty acid synthase (FAS), and peroxisome proliferator-activated receptor γ (PPARγ) but higher (P < 0.05) expression of estrogen receptor alpha (ESR1). The CCM increased the abundance of Akkermansia (P < 0.05) and markedly reduced the relative cecal abundance of Phascolarctobacterium (P < 0.01), Rikenellaceae (P < 0.05), and Faecalibacterium (P < 0.01). The metabolomic and biochemical analyses demonstrated that the CCM diet increased (P < 0.05) the concentrations of butyrate in cecal contents. The majority of the metabolites in cecal digesta with differences in abundance were organic acids. The CCM diet increased (P < 0.05) contents of (R)-5-diphosphomevalote, pantothenic acid, 2-epi-5-epi-valiolone 7-phosphate, D-ribose 5-diphosphate, arbutin 6-phosphate, D-ribitol 5-phosphate, undecanoic acid, nicotinic acid, 4-methyl-2-oxovaleric acid, while decreasing (P < 0.05) those of oleic acid, glutaric acid, adipic acid, suberic acid, and L-fuculose 1-phosphate. In conclusion, these findings demonstrated that the dietary CCM treatment significantly decreased abdominal fat and altered the cecal microbiota and metabolite profiles of the yellow chickens.

Dataset Information

A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens.

Publications

A Missense Mutation in the <i>MYBPH</i> Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets