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18 pages, 3161 KB

Open AccessArticle

Genome-Wide Association Study and Whole-Genome Resequencing Reveal Key lincRNA and Candidate Gene for Polled Phenotype in Yak

by Chuang Zhong, Ziying Wang, Shujie Liu, Zhian Zhang and Zhanhong Cui

Animals 2026, 16(4), 599; https://doi.org/10.3390/ani16040599 - 14 Feb 2026

Viewed by 360

Abstract

Yaks are important livestock in high-altitude regions, and their polled trait can effectively improve breeding and management efficiency. In this study, whole-genome resequencing combined with a GWAS was employed to identify a significantly associated region of approximately 273.6 kb on chromosome 1 (36,313,286–36,586,879 [...] Read more.

Yaks are important livestock in high-altitude regions, and their polled trait can effectively improve breeding and management efficiency. In this study, whole-genome resequencing combined with a GWAS was employed to identify a significantly associated region of approximately 273.6 kb on chromosome 1 (36,313,286–36,586,879 bp) in Xueduo yaks. This region contains 1001 significant single-nucleotide polymorphism (SNP) loci and is located within a long intergenic non-coding RNA (lincRNA) region. Candidate genes EPCIP, OLIG1 and PAXBP1 adjacent to this region were identified. Among these, the PAXBP1 gene plays a crucial role in neural crest development, suggesting that it may be a core gene regulating horn development in yaks. Further analysis of Ashdan yaks (a polled breed developed from Datong yaks) indicated that the two breeds share the same candidate genes and a subset of associated genetic variants for the polled trait, suggesting a degree of genetic conservation underlying this trait across yak breeds. This study provides a theoretical basis for polled yak breeding. Full article

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

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18 pages, 1940 KB

Open AccessArticle

Association of Variants in CDC10 (Septin 7) Gene with Growth-Related Traits in Qinchuan Cattle

by Zixuan Cheng, Yongli Yue, Yilin Wang, Peinuo Zhou, Xinyue An, Jianyu Xu, Takahisa Yamada, Gong Cheng, Hugejiletu Bao, Linsen Zan and Bin Tong

Animals 2026, 16(3), 447; https://doi.org/10.3390/ani16030447 - 1 Feb 2026

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Abstract

As one of the five major indigenous yellow cattle breeds in China, Qinchuan cattle are characterized by stable genetic performance and desirable meat quality. However, compared with imported commercial breeds, Qinchuan cattle have a relatively slow growth rate. Therefore, improving the growth rate [...] Read more.

As one of the five major indigenous yellow cattle breeds in China, Qinchuan cattle are characterized by stable genetic performance and desirable meat quality. However, compared with imported commercial breeds, Qinchuan cattle have a relatively slow growth rate. Therefore, improving the growth rate of Qinchuan cattle has become a top priority in Qinchuan cattle breeding. The CDC10 (Septin 7) gene, an important member of the Septin family, participates in various cellular physiological processes including intracellular substance transport, cell division, cell cycle regulation, and apoptosis. Studies have repeatedly mapped the CDC10 gene to quantitative trait loci influencing growth-related traits, such as body weight and carcass weight in many beef cattle breeds. Previous study has also demonstrated the high expression of CDC10 in JB cattle with high performance for carcass weight, however, the association between CDC10 and growth-related traits in Qinchuan cattle remain unclear. Therefore, in this study, we selected five individuals each from Chinese Simmental, Mongolian cattle, Luxi cattle, and Qinchuan cattle for direct sequencing, aiming to identify mutations within the CDC10 gene of native Chinese yellow cattle. Subsequently, we performed genotyping of 367 Qinchuan cattle using the MassARRAY technology, followed by genetic diversity analysis of the identified mutations and association analysis between these sites and growth-related traits of Qinchuan cattle. This study demonstrated high expression of the CDC10 gene in Qinchuan cattle with high performance for carcass weight. Furthermore, we identified the g.61303052G>C and c.225A>G SNPs in the promoter and exon regions, respectively, as being significantly associated with multiple growth-related traits in Qinchuan cattle. The c.225A>G SNP was also found to alter the secondary structure of the CDC10 protein. These findings provide reliable molecular markers for enhancing the growth rate of Qinchuan cattle and establish a solid theoretical foundation for the development of the beef cattle industry. Full article

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

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20 pages, 2214 KB

Open AccessFeature PaperArticle

Evaluation of the Beef Cattle Systems Model to Replicate a Beef Cow Genotype × Nutritional Environment Interaction

by Ivy Elkins, Phillip A. Lancaster, Robert L. Larson and Logan Thompson

Animals 2026, 16(3), 372; https://doi.org/10.3390/ani16030372 - 24 Jan 2026

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Abstract

Cow efficiency is vitally important to beef sustainability, and computer simulation models may be useful tools to identify characteristics of the most efficient cow genotypes for a given production environment. The objective of this analysis was to determine whether the Beef Cattle Systems [...] Read more.

Cow efficiency is vitally important to beef sustainability, and computer simulation models may be useful tools to identify characteristics of the most efficient cow genotypes for a given production environment. The objective of this analysis was to determine whether the Beef Cattle Systems Model could replicate empirical research demonstrating a genotype–nutritional environment interaction for efficiency of feed conversion to calves weaned. Combinations of cow genotypes for lactation potential (8, 10, and 12 kg/d at peak milk) and growth potential (450, 505, and 650 kg mature weight) were simulated across four dry matter intake levels (58, 76, 93, and 111 g/kg BW^0.75). At lower dry matter intakes, cows had lesser body condition scores and weight and longer postpartum intervals, but dry matter intake had minimal influence on pregnancy percentage or calf-weaning weight. These trends match empirical research except for pregnancy percentage, where decreasing dry matter intake had a dramatic effect on pregnancy percentage in high-milking, high-growth-potential genotypes. Efficiency of feed conversion was greatest at low dry matter intake for the model simulation with no evidence of a genotype–dry matter intake interaction, which is in contrast to empirical research demonstrating a genotype–dry matter intake interaction. In conclusion, standard nutrition equations do not replicate the genotype–nutritional environment interaction observed in empirical research studies. Full article

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

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17 pages, 328 KB

Open AccessArticle

Optimized Animal Models for the Genetic Evaluation of Conformation Traits, Milking Ease, and Milking Temperament in Dairy Gir Cattle

by Samla M. F. Cunha, Flavio S. Schenkel, Tatiane C. S. Chud, Anderson A. C. Alves, Marcos Vinícius G. B. da Silva, Rui da S. Verneque, João Cláudio do C. Panetto and Danísio P. Munari

Animals 2026, 16(3), 363; https://doi.org/10.3390/ani16030363 - 23 Jan 2026

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Abstract

This study aimed to evaluate four different models for the genetic evaluation of sixteen conformation traits, milking ease, and milking temperament in Dairy Gir cattle. The models vary based on whether they include only statistically significant fixed effects or all recorded effects, along [...] Read more.

This study aimed to evaluate four different models for the genetic evaluation of sixteen conformation traits, milking ease, and milking temperament in Dairy Gir cattle. The models vary based on whether they include only statistically significant fixed effects or all recorded effects, along with contemporary groups (CGs) treated as fixed or random effects. Categorical traits were also analyzed using a threshold model. The adjusted R-squared (

R_{a d j}^{2}

) was used to compare the goodness-of-fit of the linear models. Spearman’s rank correlation and the average accuracy of bull estimated breeding values (EBVs) with at least 20 phenotyped daughters were compared. Models fitting CG as a random effect performed better based on their

R_{a d j}^{2}

values and had a greater average accuracy of EBVs for most traits. Spearman’s rank correlation coefficients indicated low to medium bull EBV re-ranking between most of the models. The linear models performed better than threshold models for almost all traits. When possible, more parsimonious linear models fitting only significant fixed effects should be used to reduce the standard error of estimation. Additionally, fitting CGs as a random effect seems more beneficial for the genetic evaluation of conformation and milking traits in Dairy Gir cattle in Brazil. Full article

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

16 pages, 1334 KB

Open AccessArticle

Weighted Single-Step Genome-Wide Association Study Identifies Candidate Genes for Carcass Traits and Primal Cut Yields in Hanwoo Cattle

by Jun Park, Ji Suk Yu, Sun Kyu Byun, Ho Sung Choe and Do Hyun Kim

Animals 2026, 16(1), 136; https://doi.org/10.3390/ani16010136 - 3 Jan 2026

Viewed by 669

Abstract

This study identified genomic regions associated with carcass traits and primal cut yields in Hanwoo cattle using weighted single-step genome-wide association study (WssGWAS). A total of 50,227 carcass records and genomic data from 23,573 animals with 45,057 single-nucleotide polymorphisms were analyzed. Heritability estimates [...] Read more.

This study identified genomic regions associated with carcass traits and primal cut yields in Hanwoo cattle using weighted single-step genome-wide association study (WssGWAS). A total of 50,227 carcass records and genomic data from 23,573 animals with 45,057 single-nucleotide polymorphisms were analyzed. Heritability estimates were 0.24 for carcass weight, 0.22 for eye muscle area, 0.31 for backfat thickness, and 0.36 for marbling score, while those for primal cut yields ranged from 0.02 to 0.26. For carcass traits, candidate genes were identified for carcass weight (XKR4 2.35%, COBL 1.26%), eye muscle area (LCORL 1.56%, TGFBR2 1.49%), backfat thickness (ATG7 1.27%, MYPN 1.33%), and marbling score (TWIST2 1.16%, BMP4 1.14%). For primal cut yields, the chromosome 6 region containing WDR1 was commonly identified across six traits and the chromosome 4 region containing CACNA2D1 across five traits; the chromosome 28 region containing SIRT1 explained the highest genetic variance (6.46%) for striploin. These pleiotropic regions are potential targets for genomic selection to improve production efficiency and carcass value in Hanwoo. Full article

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

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17 pages, 2690 KB

Open AccessArticle

Genome-Wide Association Study on the Estimated Breeding Values for Udder and Longevity and the Candidate Genes in Holstein-Friesian Cows in Hungary

by Attila Zsolnai, László Bognár, Szabolcs Albin Bene, Laszló Rózsa, Péter Póti, Ferenc Szabó and István Anton

Animals 2026, 16(1), 73; https://doi.org/10.3390/ani16010073 - 26 Dec 2025

Viewed by 605

Abstract

Our genome-wide association study identified single-nucleotide polymorphisms (SNPs) associated with estimated breeding values (EBVs) for udder traits and longevity in Holstein-Friesian cows. While no SNP was individually associated with multiple EBVs, the functional profiles of the associated genes revealed overlapping biological processes across [...] Read more.

Our genome-wide association study identified single-nucleotide polymorphisms (SNPs) associated with estimated breeding values (EBVs) for udder traits and longevity in Holstein-Friesian cows. While no SNP was individually associated with multiple EBVs, the functional profiles of the associated genes revealed overlapping biological processes across traits, including cell signaling, transcription regulation, immune response, metabolism, and cellular maintenance. Notably, nearby SNPs BTB-01738708 and ARS-BFGL-NGS-111478 were associated with EBV_longevity and EBV_udder and located near numerous genes, including GPR85, BMT2, IFRD1, and DOCK4, suggesting a potential for shared genetic influence on these traits. Our findings provide insights into the complex genetic architecture of these economically important traits and highlight the need for further research, including fine-mapping and functional genomics, to elucidate the specific variants and their effects. Full article

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

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15 pages, 1073 KB

Open AccessArticle

Assessing the Reliability of Automatic Milking Systems Data to Support Genetic Improvement in Dairy Cattle

by Enrico Ponzo, Riccardo Moretti, Fernando Masia, Elisa Vrieze, Paola Sacchi and Stefania Chessa

Animals 2026, 16(1), 1; https://doi.org/10.3390/ani16010001 - 19 Dec 2025

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Abstract

This study investigates the reliability and potential genetic utility of data recorded by automatic milking systems by comparing them with official milk recording data. Analyses focused on phenotypic distributions, correlations, systematic differences, and heritability estimates for milk production and quality traits including milk [...] Read more.

This study investigates the reliability and potential genetic utility of data recorded by automatic milking systems by comparing them with official milk recording data. Analyses focused on phenotypic distributions, correlations, systematic differences, and heritability estimates for milk production and quality traits including milk yield, fat and protein percentage, somatic cell count, and electrical conductivity. Automatic milking system data and official milk recording data shared similar distributions. Correlations between the two systems were high for milk yield (r = 0.93), but moderate for fat (r = 0.52) and protein percentage (r = 0.48), and somatic cell count (r = 0.62), suggesting that while the former provides consistent data for quantity traits, quality-related ones may be less reliable. Systematic deviations between automatic milking systems and official milk recordings emerged across different lactation stages. Heritability estimates based on automatic milking system data were generally higher than the official control for production traits, supporting their use in genetic evaluations. Electrical conductivity displayed a similar heritability to somatic cell count, but its measure is insufficiently detailed and its use as an indirect indicator of udder health is not recommended. Automatic milking system data demonstrates potential for integration into genetic selection programs, although further refinement of sensor accuracy is recommended. Full article

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

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16 pages, 599 KB

Open AccessArticle

Relationship Between Age at First Calving and 305-Day Milk Yield in Hungarian Holstein-Friesian Cows: Trends and Genetic Parameters

by Szabolcs Albin Bene, Zsolt Jenő Kőrösi, László Bognár, József Péter Polgár and Ferenc Szabó

Animals 2025, 15(24), 3648; https://doi.org/10.3390/ani15243648 - 18 Dec 2025

Cited by 2 | Viewed by 696

Abstract

Age at first calving (AFC) and 305-day milk yield in the first lactation (MY) data of 18,545 Holstein-Friesian cows born between 2008 and 2018 in six herds were evaluated. The effects of some genetic and environmental factors, population genetic parameters, breeding value (BV), [...] Read more.

Age at first calving (AFC) and 305-day milk yield in the first lactation (MY) data of 18,545 Holstein-Friesian cows born between 2008 and 2018 in six herds were evaluated. The effects of some genetic and environmental factors, population genetic parameters, breeding value (BV), and phenotypic and genetic trends of AFC and MY traits were estimated. The GLM method (ANOVA Type III) and BLUP animal model were used for the estimations. One-way linear regression analysis was used for trend calculations. The adjusted overall mean value (±SE) of the AFC and MY traits was 25.19 ± 0.02 months and 10,287.14 ± 24.79 kg, respectively. The percentage proportion contribution of the different factors in the phenotype in the case of AFC was as follows: herd 94.41%, birth year of cow 3.26%, birth season of cow 1.39%, and sire 0.71%. For MY, the contribution was as follows: herd 89.17%, birth season of cow 5.38%, birth year of cow 4.09%, and sire 1.05%. The heritability of AFC and MY traits by two different models proved to be moderate (0.26 ± 0.02, 0.19 ± 0.01 and 0.30 ± 0.02, 0.34 ± 0.01, respectively). There were relatively small differences between the sires in the estimated BV for the traits AFC and MY. The phenotypic and genetic correlations between AFC and MY traits were weak (between −0.05 and −0.16). Based on the phenotypic trend calculation, AFC showed a decreasing direction (−0.12 months per year) and MY an increasing direction (+42.30 kg per year). However, the genetic trend was very slightly decreasing for AFC (−0.00 and −0.05 months per year) and slightly increasing for MY (+5.52 and +16.49 kg per year) over the period studied. Full article

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

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16 pages, 2397 KB

Open AccessArticle

CircRNA_01754 Regulates Milk Fat Production Through the Hippo Signaling Pathway

by Xiaofen Li, Jiahao Chen, Rui Gao, Ye Feng, Zhifeng Zhang and Zhi Chen

Animals 2025, 15(24), 3606; https://doi.org/10.3390/ani15243606 - 15 Dec 2025

Viewed by 571

Abstract

Background: Milk fat metabolism is a complex process regulated by non-coding RNAs. circRNAs (circRNAs) can act as miRNA sponges to regulate target gene expression. Purpose: This study aimed to investigate the role and mechanism of the circRNA_01754/miR-302c/LATS2 axis in regulating milk fat metabolism [...] Read more.

Background: Milk fat metabolism is a complex process regulated by non-coding RNAs. circRNAs (circRNAs) can act as miRNA sponges to regulate target gene expression. Purpose: This study aimed to investigate the role and mechanism of the circRNA_01754/miR-302c/LATS2 axis in regulating milk fat metabolism in bovine mammary epithelial cells (BMECs). Methods: mRNA sequencing was performed on bovine mammary gland tissues from different lactation stages to analyze the expression profiles. The interactions between circRNA_01754, miR-302c, and LATS2 were verified using dual-luciferase reporter assays, qRT-PCR, and Western blot. The functional effects on triglyceride (TAG) and cholesterol synthesis were assessed. Results: CircRNA_01754 was identified as a direct sponge for miR-302c. Overexpression of circRNA_01754 increased LATS2 expression by sequestering miR-302c. Functional experiments showed that circRNA_01754 and LATS2 promoted TAG synthesis, whereas miR-302c inhibited it. Furthermore, miR-302c was found to regulate the expression of YAP1, a key effector of the Hippo pathway, through LATS2. Conclusions: Our findings reveal that circRNA_01754 promotes milk fat synthesis by acting as a ceRNA for miR-302c to upregulate LATS2. This study lays the groundwork for producing high-quality milk and opens up new avenues for enhancing public dietary health. Full article

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

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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 - 10 Dec 2025

Viewed by 572

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 < [...] Read more.

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 3 | Viewed by 1504

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 [...] Read more.

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

Cited by 1 | Viewed by 1161

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) [...] Read more.

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

Cited by 2 | Viewed by 1588

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 [...] Read more.

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 2180

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 [...] Read more.

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 1702

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 [...] Read more.

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 3 | Viewed by 2793

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 [...] Read more.

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 2405

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 [...] Read more.

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

Jump to: Research

17 pages, 418 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

Cited by 1 | Viewed by 1170

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 [...] Read more.

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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