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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: 31 December 2025 | Viewed by 10615

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Prof. Dr. Ferenc Szabó

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Albert Kázmér Faculty of Mosonmagyaróvár, Széchenyi István University, Vár Sguare 2, H-9200 Mosonmagyaróvár, Hungary
Interests: beef and dairy cattle breeding
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Dr. Gabriella Holló

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Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Str. 40, H-7400 Kaposvar, Hungary
Interests: beef quality; carcass value; feed intake; genome-wide association study; smart farming
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The scope of this Special Issue is to publish the latest population genetic and molecular genetic research results related to regenerative milk and beef production. Notably, the genetic background of cattle product quality, reproduction, disease resistance, environment and technology tolerance, and robustness of cattle are the focus of interest. Similarly, manuscripts concerning new aspects of breeding value estimation, selection response, association, and genetic trends of various production, reproduction, longevity, and conformation traits are of interest for this Special Issue. Furthermore, recent crossbreeding results regarding the time-based efficiency and sustainability of cattle breeding will be considered for publication.

Prof. Dr. Ferenc Szabó
Dr. Gabriella Holló
Guest Editors

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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.

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Keywords

cattle
population genetics
molecular genetics
breeding value
reproduction
production
longevity
conformation

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Published Papers (9 papers)

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Research

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21 pages, 4445 KB

Open AccessArticle

The SCD5 Gene Modulates Adipogenic Differentiation via the WNT5B Signaling Pathway in Xinjiang Brown Cattle

by Yiran Wang, Wanping Ren, Wei Shao, Yuxin Zhou, Yili Liu, Junwei Cao, Fengju Wang, Jingdong Bi and Liang Yang

Animals 2025, 15(24), 3547; https://doi.org/10.3390/ani15243547 (registering DOI) - 10 Dec 2025

Abstract

This study investigated the role of SCD5 in bovine preadipocyte proliferation and adipogenic differentiation. SCD5 overexpression suppressed proliferation, reducing the percentage of EdU-positive cells and overall cell viability (p < 0.05). It also downregulated proliferative factors CDK1 and CDK2 (p < 0.05), and reduced lipid accumulation (p < 0.001) along with key adipogenic markers PPARγ, C/EBPα, and FABP4 (p < 0.01). Conversely, SCD5 knockdown promoted these processes. Mechanistically, SCD5 overexpression downregulated WNT5B (p < 0.05), while knockdown had the opposite effect. Silencing WNT5B significantly decreased β-catenin transcription (p < 0.05), total protein (p < 0.05), and phosphorylation (p < 0.001). In conclusion, our findings identify SCD5 as a novel negative regulator of bovine preadipocyte proliferation and differentiation, which exerts its function through the WNT5B/β-catenin signaling axis. This discovery elucidates previously uncharacterized regulatory mechanisms underlying adipogenesis in livestock species. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

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18 pages, 1033 KB

Open AccessFeature PaperArticle

Weighted Single-Step GWAS Reveals Genomic Regions Associated with Female Fertility in the Spanish Retinta Beef Cattle

by Rosa María Morales, Gabriel Anaya Calvo-Rubio, Chiraz Ziadi, María Ángeles Vargas-Pérez, Sebastián Demyda-Peyrás and Antonio Molina

Animals 2025, 15(18), 2665; https://doi.org/10.3390/ani15182665 - 11 Sep 2025

Cited by 1 | Viewed by 876

Abstract

Improving reproductive efficiency in beef cattle remains a key objective for sustainable genetic progress, particularly in extensively managed autochthonous breeds such as the Spanish Retinta. In this study, we applied a weighted single-step genome-wide association approach (wssGWAS) to identify genomic regions associated with four fertility-related traits: age at first calving (AFC), interval between first and second calving (IC12), average calving interval (ACI), and reproductive efficiency (RE). A total of 215,125 calving records from 44,032 cows and the genomic information of 1030 animals (Axiom™ Bovine Genotyping v3 Array 65k) were analyzed. Heritability was estimated using a single-step genomic best linear unbiased prediction (ssGBLUP) that incorporated both pedigree and genomic data, and estimates ranged from 0.15 (0.008) for AFC to 0.27 (0.012) for ACI. The wssGWAS identified 96 1 Mb-windows explaining over 1% of additive genetic variance (40 of them are common for more than one trait and 46 windows are unique), notably on chromosomes 2 and 5. Candidate genes related to folliculogenesis, steroidogenesis, immune modulation, and cell cycle control were identified, including ACVR1B, AMHR2, CYP27B1, CDK2, and IFNG. Additionally, a significant proportion of lncRNAs were detected, suggesting regulatory roles in reproductive processes through the modulation of gene expression at different levels. These findings enhance our understanding of the genetic architecture underlying female fertility in beef cattle and provide valuable markers for incorporation into genomic selection programs aimed at improving reproductive performance and long-term sustainability in the Retinta breed. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

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11 pages, 1086 KB

Open AccessArticle

The High Frequency of a G-Allele Variant of the FOXP3 Gene in Old Asian Cattle Breeds, Water Buffaloes, and Holstein Friesian Cows: A Potential Link to Infertility

by Abdullah Al Faruq, Oky Setyo Widodo, Mitsuhiro Takagi, Tita Damayanti Lestari, Muhammad Fadhlullah Mursalim, Nanang Tedjo Laksono, Hiroaki Okawa, Md Shafiqul Islam, Shinichiro Maki, Tofazzal Md Rakib, Akira Yabuki and Osamu Yamato

Animals 2025, 15(16), 2407; https://doi.org/10.3390/ani15162407 - 16 Aug 2025

Viewed by 809

Abstract

Reproductive failure in cattle production is a global concern and is influenced by various factors, including genetic alterations. This study explored the relationship between an X-linked single-nucleotide variant (NC_037357.1: g.87298881A>G, rs135720414) in the upstream of the bovine forkhead box P3 (FOXP3) gene and infertility. To this end, we examined the genotypes of the variant in old Asian cattle breeds, including 48 Bali and 5 Jaliteng cattle, and 20 water buffaloes, which have recently shown subclinical signs of infertility and repeated breeding problems among populations in Indonesia. We also examined the genotypes in 69 parous and 39 non-parous Holstein Friesian (HF) cows and investigated the relationship between the genotypes and serum concentration of anti-Müllerian hormone (AMH). The G allele frequency was markedly high in Bali (0.944) and Jaliteng cattle (0.714), and water buffaloes (1), suggesting that the G allele may be originally a wild-type variant in old Asian cattle and buffaloes. In HF cows, the G allele frequency was moderately high, and the AMH concentration was significantly lower (p < 0.05) in parous cows carrying the G allele (A/G and G/G genotypes) than in parous cows with the A/A genotype. In contrast, there were no significant differences in AMH concentrations among the three genotypes of non-parous HF cows. This suggests that both G allele and aging are associated with infertility in HF cows. In conclusion, the G allele of the FOXP3 gene variant may potentially be associated with infertility in different bovine breeds and species. Therefore, special attention should be paid to this variant, and infertility in bovine herds may be improved by selection and/or introduction of the A allele. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

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20 pages, 1429 KB

Open AccessArticle

Beef Breeding Systems and Preferences for Breeding Objective Traits

by Zuzana Krupová, Emil Krupa, Michaela Brzáková, Zdeňka Veselá and Kamil Malát

Animals 2025, 15(15), 2175; https://doi.org/10.3390/ani15152175 - 23 Jul 2025

Viewed by 831

Abstract

Our study aimed to identify the overall and cluster-specific characteristics of Czech beef cattle breeding systems. We used data from an online survey to ascertain farmers’ preferences in breeding objectives. Considering various evaluation criteria and clustering approaches in 41 farms, three beef systems were defined according to herd size, management, marketing, breeding strategies and structures, and farmer age. Breeding values and performance were jointly used as the primary information in all three systems. Cow temperament and calf viability, maternal fertility and longevity, and animal health were found to be the most important traits. Cluster 1 represents pure-breeding farms that specialize in producing breeding animals. Farms in clusters 2 and 3 combined pure- and crossbreeding strategies with production, which was partially (cluster 2) and fully (cluster 3) diversified for all beef categories. Farms also prioritized calving performance and calf growth (clusters 1 and 2) and exterior traits (cluster 3). Production type scores significantly (p < 0.05) differed in clusters 3 (4.12) and 2 (3.25). The proportion of production, functional, and exterior trait categories was 12:37:51, with low variability among clusters (±1 to 2 percentage points). The inter-cluster comparison showed that specific characteristics were compatible with certain breeding goal trait preferences. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

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14 pages, 474 KB

Open AccessArticle

Calcium Metabolism, Immunity and Reproduction in Early Postpartum Dairy Cows

by Szilvia Kusza, Zoltán Bagi, Putri Kusuma Astuti, George Wanjala, Ottó Szenci and Árpád Csaba Bajcsy

Animals 2025, 15(14), 2103; https://doi.org/10.3390/ani15142103 - 16 Jul 2025

Cited by 1 | Viewed by 1585

Abstract

Vitamin D is essential for calcium homeostasis, bone mineralization, immunity, and disease prevention. In a field study with Holstein-Friesian dairy cows, the impact of prepartum vitamin D₃ treatment on early postpartum placental gene expression, focusing on calcium metabolism, feto-placental growth, and immune response, had been investigated. Eight multiparous cows were treated with 10 mL vitamin D₃ (1 million IU cholecalciferol/mL) intramuscularly on day 273 of pregnancy, while eight others remained untreated and served as controls. Placental tissues were collected post-calving, and gene expression was analyzed using quantitative real-time PCR. Among 23 genes, 5 showed significant downregulation in the treated group: CaBP-9k (reduced by 88.1% from 32.80 ± 91.50 to 3.90 ± 8.54), ESR1 (reduced by 95.7% from 7.89 ± 17.87 to 0.34 ± 0.34), LHR (reduced by 96.5% from 3.75 ± 5.45 to 0.13 ± 0.17), NOD1 (reduced by 94.1% from 4.21 ± 7.00 to 0.25 ± 0.30), and TLR1 (reduced by 99.7% from 24.80 ± 61.45 to 0.07 ± 0.08). These results suggest that vitamin D₃ supplementation affects key pathways related to calcium transport, reproductive function, and immune response in the bovine placenta. These molecular changes may help to explain improved calcium homeostasis and reduced postpartum complications, offering insights into how targeted nutritional interventions can enhance reproductive efficiency in high-producing dairy cows. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

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19 pages, 9677 KB

Open AccessArticle

Development and Application of a 40 K Liquid Capture Chip for Beef Cattle

by Qing Liu, Liangyu Shi, Pu Zhang, Bo Yu, Chenhui Liu, Min Xiang, Shuilian Li, Lei Liu, Lei Cheng and Hongbo Chen

Animals 2025, 15(9), 1346; https://doi.org/10.3390/ani15091346 - 7 May 2025

Viewed by 1193

Abstract

The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics of species by exploring genetic diversity to aid genetic selection. The SNP chip is a cost-effective genotyping platform essential for molecular breeding of livestock. In this study, we developed a liquid SNP capture chip suitable for five Hubei (China) indigenous beef cattle breeds based on whole-genome sequencing datasets. The panel consisted of 42,686 SNPs (~40 K). These SNPs were evenly distributed on each bovine chromosome, with the majority of SNPs having minor allele frequencies >0.05 and located within intergenic regions. The performance evaluation of this SNP chip panel was proceeded by genotyping 200 individuals, revealing that this panel has a high SNP call rate of 99.48%. The SNP chip panel was further used to examine the population structure of a beef cattle population with 205 individuals and demonstrated the ability to differentiate between foreign and indigenous cattle breeds. The SNP chip was also used to determine the runs of homozygosity (ROH) within a local Hubei beef cattle population of 195 individuals. We identified 2547 ROH and several genes associated with economically important traits in the study population. Our findings demonstrate that this chip not only contributes to the understanding of the genetic characteristics of local beef cattle breeds but also provides valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

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12 pages, 267 KB

Open AccessFeature PaperArticle

Distribution of Recessive Genetic Defect Carriers in Holstein Friesian Cattle: A Polish Perspective

by Marta Gozdek, Sebastian Mucha, Adam Prostek, Dariusz Kamola and Tomasz Sadkowski

Animals 2024, 14(22), 3170; https://doi.org/10.3390/ani14223170 - 6 Nov 2024

Cited by 1 | Viewed by 2105

Abstract

Genetic disorders are caused by a hereditary change in the structure of DNA that may hurt the health and life of animals. Several recessive haplotypes and a few causative mutations are known in Holstein Friesian cattle: CDH (Holstein cholesterol deficiency), haplotypes with a homozygous deficiency in Holstein (HH1, HH3, HH4, HH5, HH6, HH7), BLAD (bovine leukocyte adhesion deficiency), DUMPS (deficiency of uridine monophosphate synthase), FXI (factor XI deficiency), HHM (mule foot, syndactyly), and BC (citrullinaemia). From a breeding point of view, these genetic diseases have highly negative effects and are a significant problem for breeders, exposing them to economic losses and hurting animal welfare. This study aimed to characterize the Polish population of Holstein Friesian dairy cattle, considering the carrier status of twelve selected genetic defects. This study was based on genotype data collected from 78,884 cows and 691 bulls of the Holstein Friesian variety. The studies were performed using Illumina Infinium microarrays. Among both bulls and cows, the highest numbers of carriers were detected for HH5 (appropriately 6.7% and 5.4%). The lowest numbers of carriers were detected for DUMPS, factor XI, and HHM. The study revealed one calf suffering from cholesterol deficiency. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

12 pages, 277 KB

Open AccessArticle

Association of Production and Selected Dimensional Conformation Traits in Holstein Friesian Cows

by Zsolt Jenő Kőrösi, Gabriella Holló, Szabolcs Bene, László Bognár and Ferenc Szabó

Animals 2024, 14(18), 2753; https://doi.org/10.3390/ani14182753 - 23 Sep 2024

Cited by 1 | Viewed by 2084

Abstract

The objective of this study was to estimate the heritability of dairy production traits and that for dimensional traits and to calculate the correlation between the two heritability values in a Holstein Friesian cow herd bred in Hungary. Data of 15,032 Holstein Friesian cows born in the period 2008–2018 from 666 sires were collected for the study in 6 large dairy herds. Among the conformation traits, stature (ST), chest width (CW), body depth (BD), and rump width (RW), and for production traits, in the first lactation of cows, the 305-day milk yield (MY), milk butterfat yield (FY), and milk protein yield (MY) were evaluated. Heritability estimates of ST, CW, BD, and RW were 0.49, 0.25, 0.31, and 0.30, and those of MY, FY, and PY were 0.40, 0.35, and 0.30, respectively. BD and RW had no phenotypic (b = −0.01) or genetic (b = 0.00–0.01) change. The production traits (MY, FY, PY) increased to a greater extent (b = 2.2–43.3) than the examined conformation traits over time. Consequently, it is indicated that the selection for dairy production did not result in an increase in the studied dimensional traits. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

Review

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18 pages, 417 KB

Open AccessReview

Low-Coverage Whole-Genome Sequencing (lcWGS) in Cattle: Analysis of Potential and Prospects for Application

by Olga Kostyunina, Nikita Koldichev, Gleb Nemkovskiy, Alexey Traspov, Anton Ermilov, Faridun Bakoev, Dmitriy Chesnokov, Anna Panova, Kseniia Antonovskaia, Alexander Kusnetzov and Vladimir Belyakov

Animals 2025, 15(24), 3538; https://doi.org/10.3390/ani15243538 - 8 Dec 2025

Abstract

Whole-genome studies in cattle play a key role in exploring both individual and population-level genetic variability. Recently, low-coverage whole-genome sequencing (0.5–2×) has been considered as an alternative to traditional approaches. Low-coverage whole-genome sequencing (lcWGS), which provides uniform coverage of the entire genome at relatively low cost, combined with subsequent imputation, enables the reconstruction of genotypes with high accuracy and density. lcWGS enables detection of rare and functionally important variants and provides exploratory potential for structural variation analysis; however, accurate SV imputation still presents significant challenges. The aim of this review is to analyze the potential and prospects of lcWGS as a tool for genomic selection and genetic studies in cattle. The review systematizes current advances in the application of lcWGS in cattle, focusing on imputation accuracy, factors affecting it, and the comparative efficiency of different software solutions. A literature survey was conducted using PubMed and Google Scholar databases, with preference given to original studies, systematic reviews, and large-scale projects addressing imputation accuracy, reference panel composition and size, cost-effectiveness, and practical applications of lcWGS in cattle genomics. Key factors influencing efficiency include sequencing depth, reference panel size and composition, as well as the choice of imputation algorithm. lcWGS represents a cost-effective and powerful alternative to traditional genome-wide approaches, capable of capturing rare and breed-specific variants; however, its application to structural variation still requires methodological improvement and integration with high-resolution reference pangenomes or long-read sequencing. Despite significant progress and the high potential of lcWGS in cattle genomics, several challenges and limitations remain, requiring further investigation and resolution to fully realize the advantages of this technology. Addressing these challenges will enable more efficient use of lcWGS for genetic research and accelerate genetic progress in cattle breeding. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics and Breeding)

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