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Animals
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Genome-Wide Associations for Growth Traits in Livestock Species
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Genome-Wide Associations for Growth Traits in Livestock Species

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 February 2023) | Viewed by 7198

Special Issue Editors

Prof. Dr. Gregório Miguel Ferreira De Camargo

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Guest Editor
Departamento de Zootecnia, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA) - 500, Av. Milton Santos, Ondina, Salvador 40170110, BA, Brazil
Interests: animal genetics; breeding research; molecular genetics; animal breeding
Prof. Dr. Raphael Bermal Costa

E-Mail Website
Guest Editor
Departamento de Medicina Veterinária Preventiva e Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA) - 500, Av. Milton Santos, Ondina, Salvador 40170110, BA, Brazil
Interests: genomic selection; genome-wide association studies; genetic improvement; quantitative genetics; molecular genetics

Special Issue Information

Dear Colleagues, 

This Special Issue focuses on gathering a compendium of genome-wide association studies (GWAS) related to growth traits in livestock. Growth traits are very important for production and are the first to be selected in many species. They show moderate-to-high heritability and potential for genetic gain. GWAS results show that growth traits follow the infinitesimal model, with a few genes making small contributions to expression. However, the main associated regions vary according to the species, trait, breed, population and methodologies applied. Thus, this Special Issue aims to shed light on these not fully understood questions in order to further our understanding of the biological expression of growth traits and to evaluate them.

Prof. Dr. Gregório Miguel Ferreira De Camargo
Prof. Dr. Raphael Bermal Costa
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SNP
  • weight
  • morphometry
  • height
  • genes
  • domestic animals

Published Papers (4 papers)

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Research

18 pages, 2239 KiB  
Article
Utilizing Variants Identified with Multiple Genome-Wide Association Study Methods Optimizes Genomic Selection for Growth Traits in Pigs
by Ruifeng Zhang, Yi Zhang, Tongni Liu, Bo Jiang, Zhenyang Li, Youping Qu, Yaosheng Chen and Zhengcao Li
Animals 2023, 13(4), 722; https://doi.org/10.3390/ani13040722 - 17 Feb 2023
Cited by 2 | Viewed by 1795
Abstract
Improving the prediction accuracies of economically important traits in genomic selection (GS) is a main objective for researchers and breeders in the livestock industry. This study aims at utilizing potentially functional SNPs and QTLs identified with various genome-wide association study (GWAS) models in [...] Read more.
Improving the prediction accuracies of economically important traits in genomic selection (GS) is a main objective for researchers and breeders in the livestock industry. This study aims at utilizing potentially functional SNPs and QTLs identified with various genome-wide association study (GWAS) models in GS of pig growth traits. We used three well-established GWAS methods, including the mixed linear model, Bayesian model and meta-analysis, as well as 60K SNP-chip and whole genome sequence (WGS) data from 1734 Yorkshire and 1123 Landrace pigs to detect SNPs related to four growth traits: average daily gain, backfat thickness, body weight and birth weight. A total of 1485 significant loci and 24 candidate genes which are involved in skeletal muscle development, fatty deposition, lipid metabolism and insulin resistance were identified. Compared with using all SNP-chip data, GS with the pre-selected functional SNPs in the standard genomic best linear unbiased prediction (GBLUP), and a two-kernel based GBLUP model yielded average gains in accuracy by 4 to 46% (from 0.19 ± 0.07 to 0.56 ± 0.07) and 5 to 27% (from 0.16 ± 0.06 to 0.57 ± 0.05) for the four traits, respectively, suggesting that the prioritization of preselected functional markers in GS models had the potential to improve prediction accuracies for certain traits in livestock breeding. Full article
(This article belongs to the Special Issue Genome-Wide Associations for Growth Traits in Livestock Species)
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22 pages, 2275 KiB  
Article
Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture–Based Systems
by Pamela C. Machado, Luiz F. Brito, Rafaela Martins, Luis Fernando B. Pinto, Marcio R. Silva and Victor B. Pedrosa
Animals 2022, 12(24), 3526; https://doi.org/10.3390/ani12243526 - 13 Dec 2022
Cited by 3 | Viewed by 1618
Abstract
Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. [...] Read more.
Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle. Full article
(This article belongs to the Special Issue Genome-Wide Associations for Growth Traits in Livestock Species)
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14 pages, 1060 KiB  
Article
Genetic Parameter Estimation and Genome-Wide Association Analysis of Social Genetic Effects on Average Daily Gain in Purebreds and Crossbreds
by Ha-Seung Seong, Young-Sin Kim, Soo-Jin Sa, Yongdae Jeong, Joon-Ki Hong and Eun-Seok Cho
Animals 2022, 12(17), 2300; https://doi.org/10.3390/ani12172300 - 5 Sep 2022
Viewed by 1450
Abstract
Average daily gain (ADG) is an important growth trait in the pig industry. The direct genetic effect (DGE) has been studied mainly to assess the association between genetic information and economic traits. The social genetic effect (SGE) has been shown to affect ADG [...] Read more.
Average daily gain (ADG) is an important growth trait in the pig industry. The direct genetic effect (DGE) has been studied mainly to assess the association between genetic information and economic traits. The social genetic effect (SGE) has been shown to affect ADG simultaneously with the DGE because of group housing systems. We conducted this study to elucidate the genetic characteristics and relationships of the DGE and SGE of purebred Korean Duroc and crossbred pigs by single-step genomic best linear unbiased prediction and a genome-wide association study. We used the genotype, phenotype, and pedigree data of 1779, 6022, and 7904 animals, respectively. Total heritabilities on ADG were 0.19 ± 0.04 and 0.39 ± 0.08 for purebred and crossbred pigs, respectively. The genetic correlation was the greatest (0.77 ± 0.12) between the SGE of purebred and DGE of crossbred pigs. We found candidate genes located in the quantitative trait loci (QTLs) for the SGE that were associated with behavior and neurodegenerative diseases, and candidate genes in the QTLs for DGE that were related to body mass, size of muscle fiber, and muscle hypertrophy. These results suggest that the genomic selection of purebred animals could be applied for crossbred performance. Full article
(This article belongs to the Special Issue Genome-Wide Associations for Growth Traits in Livestock Species)
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9 pages, 1679 KiB  
Article
Genome-Wide Association Study of Body Weight Trait in Yaks
by Jiabo Wang, Xiaowei Li, Wei Peng, Jincheng Zhong and Mingfeng Jiang
Animals 2022, 12(14), 1855; https://doi.org/10.3390/ani12141855 - 21 Jul 2022
Cited by 4 | Viewed by 1760
Abstract
The yak is the largest meat-producing mammal around the Tibetan Plateau, and it plays an important role in the economic development and maintenance of the ecological environment throughout much of the Asian highlands. Understanding the genetic components of body weight is key for [...] Read more.
The yak is the largest meat-producing mammal around the Tibetan Plateau, and it plays an important role in the economic development and maintenance of the ecological environment throughout much of the Asian highlands. Understanding the genetic components of body weight is key for future improvement in yak breeding; therefore, genome-wide association studies (GWAS) were performed, and the results were used to mine plant and animal genetic resources. We conducted whole genome sequencing on 406 Maiwa yaks at 10 × coverage. Using a multiple loci mixed linear model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK), we found that a total of 25,000 single-nucleotide polymorphisms (SNPs) were distributed across chromosomes, and seven markers were identified as significantly (p-values < 3.91 × 10−7) associated with the body weight trait,. Several candidate genes, including MFSD4, LRRC37B, and NCAM2, were identified. This research will help us achieve a better understanding of the genotype–phenotype relationship for body weight. Full article
(This article belongs to the Special Issue Genome-Wide Associations for Growth Traits in Livestock Species)
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