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Agriculture
Special Issues
Genetic Diversity, Adaptation and Evolution of Livestock
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Genetic Diversity, Adaptation and Evolution of Livestock

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Farm Animal Production".

Deadline for manuscript submissions: closed (20 September 2025) | Viewed by 2636

Special Issue Editors

Dr. Maria Chiara Fabbri

E-Mail Website
Guest Editor
Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, 50144 Firenze, Italy
Interests: genetic diversity; homozygosity; cattle; genomic selection; population genetics; animal genetics
Dr. Marcos Paulo Gonçalves De Rezende

E-Mail Website
Guest Editor
National Holstein, Brown Swiss and Jersey Association, 26100 Cremona, Italy
Interests: genetics; multivariate data analysis; genotyping; bovine

Special Issue Information

Dear Colleagues,

The assessment of genetic diversity and population structure is important for understanding the evolutionary history of breeds and providing important information on biodiversity conservation and/or management, both for local breeds and breeds under selective breeding programs. Maintaining genetic diversity should be a priority for countries where local breeds guarantee the economic survival of rural areas. Selection programs are not easy to apply to local populations given the reduced sample sizes, implying a higher level of inbreeding than in selected breeds. Furthermore, it is equally important to evaluate and manage the continuous increases in homozygosity in specialized breeds.

We invite original research, reviews, short communications, and case studies on a broad range of topics, including but not limited to genetic diversity, genomic selection, genome-wide association studies, genotype–environment interactions, genetic resources, and new phenotypes. This Special Issue aims to provide insights into the current state of cattle, sheep, pigs, and goats, offering valuable information for researchers and breeders involved in livestock production, genetic improvement programs, and conservation schemes.

Dr. Maria Chiara Fabbri
Dr. Marcos Paulo Gonçalves De Rezende
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 250 words) can be sent to the Editorial Office for assessment.

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. Agriculture 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 2600 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

  • local breeds
  • genomics
  • genetic diversity
  • livestock management
  • adaptation
  • evolution
  • selection
  • multi-omics
  • breeding strategies
  • biodiversity
  • inbreeding

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Published Papers (3 papers)

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Research

12 pages, 1250 KB  
Article
Longevity and Culling Dynamics of Holstein–Friesian Cows in Hungary
by Edit Mikó, Szilvia Kusza, Myrtill Kocsis-Gráff, Violetta Tóth and Gergő Sudár
Agriculture 2025, 15(24), 2529; https://doi.org/10.3390/agriculture15242529 - 5 Dec 2025
Viewed by 272
Abstract
Dairy cow longevity is a key driver of farm profitability, animal welfare, and environmental sustainability. Despite genetic progress in milk production, the average herd life has declined in many high-yielding dairy systems, raising concerns about early culling. This study analyzed data from 2057 [...] Read more.
Dairy cow longevity is a key driver of farm profitability, animal welfare, and environmental sustainability. Despite genetic progress in milk production, the average herd life has declined in many high-yielding dairy systems, raising concerns about early culling. This study analyzed data from 2057 Holstein–Friesian cows in Hungary to characterize the distribution and timing of culling events and to identify major risk factors affecting productive lifespan. We studied age, parity, milk yield, and culling reason using descriptive statistics, Kruskal–Wallis tests, multinomial logistic regression, and Kaplan–Meier survival analysis. Udder health problems were found to be the most frequent cause of culling (22.8%), followed by metabolic disorders (18.2%), locomotive problems (17.3%), and reproductive disorders (17.1%). Economic reasons such as low milk production contributed to a smaller proportion of culling. Most cows were culled after the second or third lactation, with survival probability dropping sharply within the first 1500–2000 days of life. Cows reaching four or more lactations represented a small but economically and genetically valuable subset of the herd. Our results indicated that in Hungary culling decisions are largely determined by health problems, which represent a greater limitation to the productive potential of dairy cows than economic factors. This research recommends that breeding programs prioritize genetic selection for robustness and that herd management adopts preventive health and reproductive strategies to prolong cow longevity, ultimately enhancing the efficiency and sustainability of dairy production systems. Additionally, prevention of animal wastage to foster animal welfare could be suggested as an additional advantage. Full article
(This article belongs to the Special Issue Genetic Diversity, Adaptation and Evolution of Livestock)
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16 pages, 1111 KB  
Article
Two-Stage Machine Learning-Based GWAS for Wool Traits in Central Anatolian Merino Sheep
by Yunus Arzık, Mehmet Kizilaslan, Sedat Behrem, Simge Tütenk and Mehmet Ulaş Çınar
Agriculture 2025, 15(21), 2287; https://doi.org/10.3390/agriculture15212287 - 3 Nov 2025
Viewed by 579
Abstract
Wool traits such as fiber diameter, fiber length, and greasy fleece yield are economically significant characteristics in sheep breeding programs. Traditional genome-wide association studies (GWAS) have identified relevant genomic regions but often fail to capture the non-linear and polygenic architecture underlying these traits. [...] Read more.
Wool traits such as fiber diameter, fiber length, and greasy fleece yield are economically significant characteristics in sheep breeding programs. Traditional genome-wide association studies (GWAS) have identified relevant genomic regions but often fail to capture the non-linear and polygenic architecture underlying these traits. In this study, we implemented a two-stage machine learning (ML)-based GWAS framework to dissect the genetic basis of wool traits in Central Anatolian Merino sheep. Phenotypic records were collected from 228 animals, genotyped with the Illumina OvineSNP50 BeadChip. In the first stage, feature selection was conducted using LASSO, Ridge Regression, and Elastic Net, generating a consensus SNP panel per trait. In the second stage, association modeling with Random Forest and Support Vector Regression (SVR) identified the most predictive models (R2 up to 0.86). Candidate gene annotation highlighted biologically relevant loci: MTHFD2L and EPGN (folate metabolism and keratinocyte proliferation) for fiber diameter; COL5A2, COL3A1, ITFG1, and ELMO1 (extracellular matrix integrity and actin remodeling) for staple length; and FAP, DPP4, PLCH1, and NPTX1 (extracellular matrix remodeling, proteolysis, and sebaceous gland function) for greasy fleece yield. These findings demonstrate the utility of ML-enhanced GWAS pipelines in identifying biologically meaningful markers and propose novel targets for genomic selection strategies to improve wool quality and yield in indigenous sheep populations. Full article
(This article belongs to the Special Issue Genetic Diversity, Adaptation and Evolution of Livestock)
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14 pages, 2450 KB  
Article
Assessment of Heterozygosity in European Local and Cosmopolitan Pig Populations
by Maria Chiara Fabbri, Katherine D. Arias, Marcos P. G. Rezende, Francesco Tiezzi, Stefano Biffani, Felix Goyache, Giuseppina Schiavo, Samuele Bovo, Luca Fontanesi, Marjeta Čandek-Potokar, Maria Muñoz, Cristina Ovilo, Klavdija Poklukar, Martin Škrlep and Riccardo Bozzi
Agriculture 2025, 15(7), 761; https://doi.org/10.3390/agriculture15070761 - 1 Apr 2025
Viewed by 1122
Abstract
Researchers focused on assessing differences in gene diversity within and between populations, whether cosmopolitan or local. However, the identification of patterns of variation in non-random heterozygous genomic stretches, known as Heterozygosity-Rich regions (HRRs), has not yet been determined in European local pig breeds. [...] Read more.
Researchers focused on assessing differences in gene diversity within and between populations, whether cosmopolitan or local. However, the identification of patterns of variation in non-random heterozygous genomic stretches, known as Heterozygosity-Rich regions (HRRs), has not yet been determined in European local pig breeds. A total of 23 pig breeds (20 local and 3 cosmopolitan) were assessed and compared in terms of heterozygosity-rich regions. The breeds with the highest number of HRRs were Large White, Lithuanian Old type, and Landrace, followed by Lithuanian Native, Mora Romagnola, and Duroc. The breeds with the lowest number were Alentejana, Iberian, and Majorcan Black. No shared HRR islands were found in all breeds, but gene enrichment analysis performed in the most common HRRs revealed several biologically important genes that cluster together and play significant roles, primarily related to the immune system. Permutation analysis indicated that some local breeds serve as true reservoirs of genetic diversity, displaying distinct and unique characteristics in terms of heterozygosity. This study suggests the importance of investigating heterozygosity to develop a comprehensive picture of pig breeds, regardless of the production system, country of origin, or population size. Full article
(This article belongs to the Special Issue Genetic Diversity, Adaptation and Evolution of Livestock)
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