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Genomics and Phenomics for Improving the Sustainability of Livestock Production

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

Deadline for manuscript submissions: closed (15 June 2022) | Viewed by 17608

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Special Issue Editor

Dr. Sara Pegolo

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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 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
phenomics
novel phenotypes
genomic selection
sustainability
animal welfare
product quality
environmental impact

Published Papers (6 papers)

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Research

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14 pages, 5112 KiB

Open AccessArticle

MiR-22-3p Inhibits Proliferation and Promotes Differentiation of Skeletal Muscle Cells by Targeting IGFBP3 in Hu Sheep

by Shan Wang, Xiukai Cao, Ling Ge, Yifei Gu, Xiaoyang Lv, Tesfaye Getachew, Joram M. Mwacharo, Aynalem Haile and Wei Sun

Animals 2022, 12(1), 114; https://doi.org/10.3390/ani12010114 - 04 Jan 2022

Cited by 10 | Viewed by 2020

Abstract

The growth and development of skeletal muscle require a series of regulatory factors. MiRNA is a non-coding RNA with a length of about 22 nt, which can inhibit the expression of mRNA and plays an important role in the growth and development of muscle cells. The role of miR-22-3p in C2C12 cells and porcine skeletal muscle has been reported, but it has not been verified in Hu sheep skeletal muscle. Through qPCR, CCK-8, EdU and cell cycle studies, we found that overexpression of miR-22-3p inhibited proliferation of skeletal muscle cells (p < 0.01). The results of qPCR and immunofluorescence showed that overexpression of miR-22-3p promoted differentiation of skeletal muscle cells (p < 0.01), while the results of inhibiting the expression of miR-22-3p were the opposite. These results suggested that miR-22-3p functions in growth and development of sheep skeletal muscle cells. Bioinformatic analysis with mirDIP, miRTargets, and RNAhybrid software suggested IGFBP3 was the target of miR-22-3p, which was confirmed by dual-luciferase reporter system assay. IGFBP3 is highly expressed in sheep skeletal muscle cells. Overexpression of IGFBP3 was found to promote proliferation of skeletal muscle cells indicated by qPCR, CCK-8, EdU, and cell cycle studies (p < 0.01). The results of qPCR and immunofluorescence experiments proved that overexpression of IGFBP3 inhibited differentiation of skeletal muscle cells (p < 0.01), while the results of interfering IGFBP3 with siRNA were the opposite. These results indicate that miR-22-3p is involved in proliferation and differentiation of skeletal muscle cells by targeting IGFBP3. Full article

(This article belongs to the Special Issue Genomics and Phenomics for Improving the Sustainability of Livestock Production)

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20 pages, 1860 KiB

Open AccessArticle

Transcriptome Adaptation of the Ovine Mammary Gland to Dietary Supplementation of Extruded Linseed

by Giuseppe Conte, Tommaso Giordani, Alberto Vangelisti, Andrea Serra, Mariano Pauselli, Andrea Cavallini and Marcello Mele

Animals 2021, 11(9), 2707; https://doi.org/10.3390/ani11092707 - 16 Sep 2021

Cited by 3 | Viewed by 1838

Abstract

Several dietary strategies were adopted to reduce saturated fatty acids and increase beneficial fatty acids (FA) for human health. Few studies are available about the pathways/genes involved in these processes. Illumina RNA-sequencing was used to investigate changes in the ovine mammary gland transcriptome following supplemental feeding with 20% extruded linseed. Comisana ewes in mid-lactation were fed a control diet for 28 days (control period) followed by supplementation with 20% DM of linseed panel for 28 days (treatment period). Milk production was decreased by 30.46% with linseed supplementation. Moreover, a significant reduction in fat, protein and lactose secretion was also observed. Several unsaturated FAs were increased while short and medium chain saturated FAs were decreased by linseed treatment. Around four thousand (1795 up- and 2133 down-regulated) genes were significantly differentially regulated by linseed supplementation. The main pathways affected by linseed supplementation were those involved in the energy balance of the mammary gland. Principally, the mammary gland of fed linseed sheep showed a reduced abundance of transcripts related to the synthesis of lipids and carbohydrates and oxidative phosphorylation. Our study suggests that the observed decrease in milk saturated FA was correlated to down-regulation of genes in the lipid synthesis and lipid metabolism pathways. Full article

(This article belongs to the Special Issue Genomics and Phenomics for Improving the Sustainability of Livestock Production)

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19 pages, 3426 KiB

Open AccessArticle

Genomic Prediction in Local Breeds: The Rendena Cattle as a Case Study

by Enrico Mancin, Beniamino Tuliozi, Cristina Sartori, Nadia Guzzo and Roberto Mantovani

Animals 2021, 11(6), 1815; https://doi.org/10.3390/ani11061815 - 18 Jun 2021

Cited by 7 | Viewed by 1960

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 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

(This article belongs to the Special Issue Genomics and Phenomics for Improving the Sustainability of Livestock Production)

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22 pages, 1498 KiB

Open AccessArticle

Genome-Wide Association Studies Reveal Susceptibility Loci for Digital Dermatitis in Holstein Cattle

by Ellen Lai, Alexa L. Danner, Thomas R. Famula and Anita M. Oberbauer

Animals 2020, 10(11), 2009; https://doi.org/10.3390/ani10112009 - 31 Oct 2020

Cited by 6 | Viewed by 1979

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) 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

(This article belongs to the Special Issue Genomics and Phenomics for Improving the Sustainability of Livestock Production)

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Review

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11 pages, 288 KiB

Open AccessReview

Progress in Genomic Mating in Domestic Animals

by Pengfei Zhang, Xiaotian Qiu, Lixian Wang and Fuping Zhao

Animals 2022, 12(18), 2306; https://doi.org/10.3390/ani12182306 - 06 Sep 2022

Cited by 3 | Viewed by 1927

Abstract

Selection is a continuous process that can influence the distribution of target traits in a population. From the perspective of breeding, elite individuals are selected for breeding, which is called truncated selection. With the introduction and application of the best linear unbiased prediction (BLUP) method, breeders began to use pedigree-based estimated breeding values (EBV) to select candidates for the genetic improvement of complex traits. Although truncated selection based on EBV can significantly improve the genetic progress, the genetic relationships between individuals with a high breeding value are usually closed, and the probability of being co-selected is greater, which will lead to a rapid increase in the level of inbreeding in the population. Reduced genetic variation is not conducive to long-term sustainable breeding, so a trade-off between genetic progress and inbreeding is required. As livestock and poultry breeding enters the genomic era, using genomic information to obtain optimal mating plans has formally been proposed by Akdemir et al., a method called genomic mating (GM). GM is more accurate and reliable than using pedigree information. Moreover, it can effectively control the inbreeding level of the population and achieve long-term and sustainable genetic gain. Hence, GM is more suitable for modern animal breeding, especially for local livestock and poultry breed conservation and genetic improvement. This review mainly summarized the principle of genomic mating, the methodology and usage of genomic mating, and the progress of its application in livestock and poultry. Full article

(This article belongs to the Special Issue Genomics and Phenomics for Improving the Sustainability of Livestock Production)

28 pages, 938 KiB

Open AccessReview

Selection for Favorable Health Traits: A Potential Approach to Cope with Diseases in Farm Animals

by Guoyu Hu, Duy Ngoc Do, Janine Gray and Younes Miar

Animals 2020, 10(9), 1717; https://doi.org/10.3390/ani10091717 - 22 Sep 2020

Cited by 17 | Viewed by 6430

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 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

(This article belongs to the Special Issue Genomics and Phenomics for Improving the Sustainability of Livestock Production)

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