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Animals
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Phenotypic and Genotypic Characterization of Farm Animals
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Phenotypic and Genotypic Characterization of Farm Animals

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

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 15231

Special Issue Editor

Dr. E. Ann Staiger

E-Mail Website
Guest Editor
Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA
Interests: genomics; animal genetics; epigenetics; animal Breeding; precision phenotyping

Special Issue Information

Dear Colleagues,

Until recently, much of animal genetics/genomics research has focused on sequencing animal genomes and applying genome-wide association studies to identify genetic variation associated with economically important traits, and then using the genomic variation to select for predicted phenotypic variation. Phenotyping technologies have not developed as quickly as genotyping technologies in animals, therefore the ability to generate accurate and reproducible phenotypes is a major limitation in the ability to characterize and predict an animal’s phenotype based on its genotype and environment.

This special issue invites original research papers that address methods for phenotyping farm animal species for genetic/genomic mapping, along with the application of modern molecular genetic methods to define genetic variation among farm animals. Papers in the areas of population genetics, genomics/proteomics, epigenetics, and the application of novel phenotyping methods such as biomarkers, computer learning algorithms, etc. for health, nutrition, production, and reproduction are welcome.

Dr. E. Ann Staiger
Guest Editor

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

  • Genomics
  • Population Analysis
  • Livestock
  • aquaculture
  • technology

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Published Papers (4 papers)

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Research

13 pages, 2207 KiB  
Communication
Genome-Wide Association Analysis and Genetic Parameters for Feed Efficiency and Related Traits in Yorkshire and Duroc Pigs
by Weining Li, Zhaojun Wang, Shenghao Luo, Jianliang Wu, Lei Zhou and Jianfeng Liu
Animals 2022, 12(15), 1902; https://doi.org/10.3390/ani12151902 - 26 Jul 2022
Cited by 1 | Viewed by 2156
Abstract
Feed efficiency (FE) traits are key factors that can influence the economic benefits of pig production. However, little is known about the genetic architecture of FE and FE-related traits. This study aimed to identify SNPs and candidate genes associated with FE and FE-related [...] Read more.
Feed efficiency (FE) traits are key factors that can influence the economic benefits of pig production. However, little is known about the genetic architecture of FE and FE-related traits. This study aimed to identify SNPs and candidate genes associated with FE and FE-related traits, namely, average daily feed intake (ADFI), average daily gain (ADG), the feed conversion ratio (FCR), and residual feed intake (RFI). The phenotypes of 5823 boars with genotyped data (50 K BeadChip) from 1365 boars from a nucleus farm were used to perform a genome-wide association study (GWAS) of two breeds, Duroc and Yorkshire. Moreover, we performed a genetic parameter estimation for four FE and FE-related traits. The heritabilities of the FE and FE-related traits ranged from 0.13 to 0.36, and there were significant genetic correlations (−0.69 to 0.52) of the FE and FE-related traits with two growth traits (age at 100 kg and backfat thickness at 100 kg). A total of 61 significant SNPs located on eight different chromosomes associated with the four FE and FE-related traits were identified. We further identified four regions associated with FE and FE-related traits that have not been previously reported, and they may be potential novel QTLs for FE. Considering their biological functions, we finally identified 35 candidate genes relevant for FE and FE-related traits, such as the widely reported MC4R and INSR genes. A gene enrichment analysis showed that FE and FE-related traits were highly enriched in the biosynthesis, digestion, and metabolism of biomolecules. This study deepens our understanding of the genetic mechanisms of FE in pigs and provides valuable information for using marker-assisted selection in pigs to improve FE. Full article
(This article belongs to the Special Issue Phenotypic and Genotypic Characterization of Farm Animals)
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11 pages, 2927 KiB  
Article
Genetic Diversity of Creole Sheep Managed by Indigenous Communities of the Central Region of Veracruz, Mexico
by Ruth Guadalupe Castillo-Rodríguez, Obdulia Lourdes Segura-León, Martha Hernández-Rodríguez, Ricardo Serna-Lagunes, Josafhat Salinas-Ruiz and Juan Salazar-Ortiz
Animals 2022, 12(4), 456; https://doi.org/10.3390/ani12040456 - 13 Feb 2022
Cited by 2 | Viewed by 2611
Abstract
In the indigenous communities of central Veracruz, herds of creole sheep have been established and managed through traditional practices of crossing, but their genetic characteristics have never been examined in order to evaluate their state of endogamy, and to help the management programs [...] Read more.
In the indigenous communities of central Veracruz, herds of creole sheep have been established and managed through traditional practices of crossing, but their genetic characteristics have never been examined in order to evaluate their state of endogamy, and to help the management programs to protect this genetic resource. The objective of the present study was to characterize the genetic diversity of three populations of creole sheep managed by indigenous communities in the central region of Veracruz, Mexico. Indigenous family producers of creole sheep were located and blood samples taken from 90 individual sheep from the municipalities of Tehuipango, Astacinga and Tlaquilpa, Veracruz. In the laboratory, the genomic DNA was extracted and genetic diversity characterized using four microsatellites (ILSTS11, ILSTS5, SRCRSP9 and OarFCB128) amplified by PCR and visualized on polyacrylamide gels. The four microsatellites were highly informative (PIC = 85%) and presented values of 0.6 to 0.81 of heterozygosity, with an average number of 16 alleles. According to the Hardy–Weinberg equilibrium model, three of the loci were not significant (p < 0.05), presumably this means that they do not deviate significantly from H–W predictions and there was slight genetic differentiation (FST = 0.025), along with a slight decrease in homozygotes (FIS = −0.021). According to the analysis of variance, 99% of the total variation was hosted at the individual level. It is concluded that the three creole sheep populations still present genetic diversity at the four loci and non-random pairings have occurred. Full article
(This article belongs to the Special Issue Phenotypic and Genotypic Characterization of Farm Animals)
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25 pages, 4650 KiB  
Article
Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations
by Alana Selli, Ricardo V. Ventura, Pablo A. S. Fonseca, Marcos E. Buzanskas, Lucas T. Andrietta, Júlio C. C. Balieiro and Luiz F. Brito
Animals 2021, 11(9), 2696; https://doi.org/10.3390/ani11092696 - 15 Sep 2021
Cited by 19 | Viewed by 3944
Abstract
In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich [...] Read more.
In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions. Full article
(This article belongs to the Special Issue Phenotypic and Genotypic Characterization of Farm Animals)
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9 pages, 930 KiB  
Article
Genetic Aspects of Somatic Cell Count in Holstein Dairy Cows in Iran
by Hadi Atashi and Miel Hostens
Animals 2021, 11(6), 1637; https://doi.org/10.3390/ani11061637 - 1 Jun 2021
Cited by 5 | Viewed by 4628
Abstract
The aim of this study was to estimate the genetic parameters of somatic cell count (SCC) and its relationship with production traits in the first three parities in Iranian Holstein dairy cows. Data were 1,891,559 test-day records of SCC, milk yield, and milk [...] Read more.
The aim of this study was to estimate the genetic parameters of somatic cell count (SCC) and its relationship with production traits in the first three parities in Iranian Holstein dairy cows. Data were 1,891,559 test-day records of SCC, milk yield, and milk compositions on 276,217 lactations on 147,278 cows distributed in 134 herds. The number of test-day records in the first, second and third parities were 995,788 (on 147,278 cows), 593,848 (on 85,153 cows), and 301,923 (on 43,786 cows), respectively. Test-day SCCs were transformed to somatic cell scores (SCS). A random regression test-day animal model through four-trait three-lactation was used to estimate variance components for test-day records of SCS and lactation traits were included. Gibbs sampling was used to obtain marginal posterior distributions for the various parameters using a single chain of 200,000 iterates in which the first 50,000 iterates of each chain were regarded as a burn-in period. The mean heritability estimates for SCS (0.15 to 0.18) were lower than those for milk yield (0.36 to 0.38), fat yield (0.30 to 0.31), protein yield (0.31 to 0.32), fat percentage (0.21 to 0.25), and protein percentage (0.21 to 0.22). Low negative genetic correlations ranging from −0.05 to −0.30 were found between SCS and yield traits (milk, fat, and protein yields). The genetic correlation found between SCS and fat percentage was close to zero, however, a low positive genetic correlation ranging from 0.12 to 0.17 was found between SCS and protein percentage. Based on the results, it can be concluded that genetic selection for decreasing SCS would also increase lactation yield. The estimates found in this study can be used to perform breeding value estimations for national genetic evaluations in Iranian Holsteins using a multiple-trait, multiple-lactation random regression model. Full article
(This article belongs to the Special Issue Phenotypic and Genotypic Characterization of Farm Animals)
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