Special Issue "Genomics and Phenomics for Improving the Sustainability of Livestock Production"

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

Deadline for manuscript submissions: 31 December 2021.

Special Issue Editor

Dr. Sara Pegolo
E-Mail Website
Guest Editor
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Padua, Italy
Interests: genetics; genomics; biological pathways; Fourier-transformed infrared spectroscopy; cattle; mastitis; metabolic diseases; product quality

Special Issue Information

Dear Colleagues,

The idea of sustainability of livestock production relies on the development of technologies and breeding practices that i) do not have negative impacts on the environment, ii) are accessible and effective for farmers, iii) improve food production and quality with positive feedback on environmental good and services, and iv) ensure animal health and welfare. In a worldwide context of climate change, demographic increase and rarefaction of natural resources, improving the sustainability of livestock production is of paramount importance. In the last decades, advances in DNA sequencing technologies has dramatically increased the efficiency and the affordability of gaining genome information. This has pushed for the need to reduce the genome-to-phenome gap by developing simple, fast, accurate and high throughput phenotyping technologies (e.g. sensors, infrared spectroscopy).

Implementing genomic and phenomic tools into animal production can help to face the ongoing challenges with the final goals of increasing the efficiency and the sustainability of animal production.

We invite original research papers that address the application of genomic and phenomic technologies focused on the reduction of the environmental impact of livestock production, on the improvement of animal welfare as well as on the improvement of the quality of animal products.

Dr. Sara Pegolo
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 papers will be 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 monthly 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 1800 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
  • phenomics
  • novel phenotypes
  • genomic selection
  • sustainability
  • animal welfare
  • product quality
  • environmental impact

Published Papers (3 papers)

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Research

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Article
Genomic Prediction in Local Breeds: The Rendena Cattle as a Case Study
Animals 2021, 11(6), 1815; https://doi.org/10.3390/ani11061815 - 18 Jun 2021
Viewed by 355
Abstract
The maintenance of local cattle breeds is key to selecting for efficient food production, landscape protection, and conservation of biodiversity and local cultural heritage. Rendena is an indigenous cattle breed from the alpine North-East of Italy, selected for dual purpose, but with lesser [...] Read more.
The maintenance of local cattle breeds is key to selecting for efficient food production, landscape protection, and conservation of biodiversity and local cultural heritage. Rendena is an indigenous cattle breed from the alpine North-East of Italy, selected for dual purpose, but with lesser emphasis given to beef traits. In this situation, increasing accuracy for beef traits could prevent detrimental effects due to the antagonism with milk production. Our study assessed the impact of genomic information on estimated breeding values (EBVs) in Rendena performance-tested bulls. Traits considered were average daily gain, in vivo EUROP score, and in vivo estimate of dressing percentage. The final dataset contained 1691 individuals with phenotypes and 8372 animals in pedigree, 1743 of which were genotyped. Using the cross-validation method, three models were compared: (i) Pedigree-BLUP (PBLUP); (ii) single-step GBLUP (ssGBLUP), and (iii) weighted single-step GBLUP (WssGBLUP). Models including genomic information presented higher accuracy, especially WssGBLUP. However, the model with the best overall properties was the ssGBLUP, showing higher accuracy than PBLUP and optimal values of bias and dispersion parameters. Our study demonstrated that integrating phenotypes for beef traits with genomic data can be helpful to estimate EBVs, even in a small local breed. Full article
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Article
Genome-Wide Association Studies Reveal Susceptibility Loci for Digital Dermatitis in Holstein Cattle
Animals 2020, 10(11), 2009; https://doi.org/10.3390/ani10112009 - 31 Oct 2020
Cited by 1 | Viewed by 761
Abstract
Digital dermatitis (DD) causes lameness in dairy cattle. To detect the quantitative trait loci (QTL) associated with DD, genome-wide association studies (GWAS) were performed using high-density single nucleotide polymorphism (SNP) genotypes and binary case/control, quantitative (average number of FW per hoof trimming record) [...] Read more.
Digital dermatitis (DD) causes lameness in dairy cattle. To detect the quantitative trait loci (QTL) associated with DD, genome-wide association studies (GWAS) were performed using high-density single nucleotide polymorphism (SNP) genotypes and binary case/control, quantitative (average number of FW per hoof trimming record) and recurrent (cases with ≥2 DD episodes vs. controls) phenotypes from cows across four dairies (controls n = 129 vs. FW n = 85). Linear mixed model (LMM) and random forest (RF) approaches identified the top SNPs, which were used as predictors in Bayesian regression models to assess the SNP predictive value. The LMM and RF analyses identified QTL regions containing candidate genes on Bos taurus autosome (BTA) 2 for the binary and recurrent phenotypes and BTA7 and 20 for the quantitative phenotype that related to epidermal integrity, immune function, and wound healing. Although larger sample sizes are necessary to reaffirm these small effect loci amidst a strong environmental effect, the sample cohort used in this study was sufficient for estimating SNP effects with a high predictive value. Full article
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Review

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Review
Selection for Favorable Health Traits: A Potential Approach to Cope with Diseases in Farm Animals
Animals 2020, 10(9), 1717; https://doi.org/10.3390/ani10091717 - 22 Sep 2020
Cited by 3 | Viewed by 1228
Abstract
Disease is a global problem for animal farming industries causing tremendous economic losses (>USD 220 billion over the last decade) and serious animal welfare issues. The limitations and deficiencies of current non-selection disease control methods (e.g., vaccination, treatment, eradication strategy, genome editing, and [...] Read more.
Disease is a global problem for animal farming industries causing tremendous economic losses (>USD 220 billion over the last decade) and serious animal welfare issues. The limitations and deficiencies of current non-selection disease control methods (e.g., vaccination, treatment, eradication strategy, genome editing, and probiotics) make it difficult to effectively, economically, and permanently eliminate the adverse influences of disease in the farm animals. These limitations and deficiencies drive animal breeders to be more concerned and committed to dealing with health problems in farm animals by selecting animals with favorable health traits. Both genetic selection and genomic selection contribute to improving the health of farm animals by selecting certain health traits (e.g., disease tolerance, disease resistance, and immune response), although both of them face some challenges. The objective of this review was to comprehensively review the potential of selecting health traits in coping with issues caused by diseases in farm animals. Within this review, we highlighted that selecting health traits can be applied as a method of disease control to help animal agriculture industries to cope with the adverse influences caused by diseases in farm animals. Certainly, the genetic/genomic selection solution cannot solve all the disease problems in farm animals. Therefore, management, vaccination, culling, medical treatment, and other measures must accompany selection solution to reduce the adverse impact of farm animal diseases on profitability and animal welfare. Full article
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