Dataset Information

Genome-Wide Association Study of Feed Efficiency Related Traits in Ducks.

ABSTRACT: Feed efficiency (FE) is the most important economic trait in the poultry and livestock industry. Thus, genetic improvement of FE may result in a considerable reduction of the cost and energy burdens. As genome-wide association studies (GWASs) can help identify candidate variants influencing FE, the present study aimed to analyze the phenotypic correlation and identify candidate variants of the seven FE traits in ducks. All traits were found to have significant positive correlations with varying degrees. In particular, residual feed intake presented correlation coefficients of 0.61, 0.54, and 0.13 with feed conversion ratio, and feed intake, respectively. Furthermore, data from seven FE-related GWAS revealed 4 (FCR), 3 (FI), 36 (RFI), 6 (BWG), 8 (BW21), and 10 (BW42) SNPs were significantly associated with body weight gain, feed intake, residual feed intake, feed conversion ratio, and weight at 21 and 42 days, respectively. Candidate SNPs of seven FE trait-related genes were involved in galactose metabolism, starch, propanoate metabolism, sucrose metabolism and etc. Taken together, these findings provide insight into the genetic mechanisms and genes involved in FE-related traits in ducks. However, further investigations are warranted to further validate these findings.

SUBMITTER: Guo Q

PROVIDER: S-EPMC9219419 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study of Feed Efficiency Related Traits in Ducks.

Guo Qixin Q Huang Lan L Jiang Yong Y Wang Zhixiu Z Bi Yulin Y Chen Guohong G Bai Hao H Chang Guobin G

Animals : an open access journal from MDPI 20220613 12

Feed efficiency (FE) is the most important economic trait in the poultry and livestock industry. Thus, genetic improvement of FE may result in a considerable reduction of the cost and energy burdens. As genome-wide association studies (GWASs) can help identify candidate variants influencing FE, the present study aimed to analyze the phenotypic correlation and identify candidate variants of the seven FE traits in ducks. All traits were found to have significant positive correlations with varying ...[more]

PMID: 35739869

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Project description:BackgroundSingle nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations.ResultsModerate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained).ConclusionsFourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

Project description:BackgroundFeeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated.ResultsA total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF.ConclusionsA total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

Dataset Information

Genome-Wide Association Study of Feed Efficiency Related Traits in Ducks.

Publications

Genome-Wide Association Study of Feed Efficiency Related Traits in Ducks.

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