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Advances in Cattle Genetics, Genomics and Breeding: From Molecular Insights to Sustainable Production

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Dr. Hinayah Rojas De Oliveira

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Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
Interests: animal breeding; genetic analysis; livestock; longitudinal traits; genotyping; computational biology

Special Issue Information

Dear Colleagues,

This Special Issue focuses on recent advances and emerging technologies in cattle genomics and breeding across all bovine species, including Bos taurus taurus, Bos taurus indicus, and their crosses. We welcome contributions that explore the fundamental molecular mechanisms underlying economically important traits and applied research demonstrating innovative breeding strategies. Topics of interest include but are not limited to genomic selection methodologies, genome-wide association studies, genome-editing applications, multi-omics approaches (genomics, transcriptomics, proteomics, and metabolomics), reproductive technologies, genetic diversity assessments, adaptation genetics, disease resistance, and epigenetic regulation in cattle. We particularly encourage submissions that address integrating novel technologies with traditional breeding practices, climate resilience and adaptation strategies, and sustainable production systems. This Special Issue aims to provide a comprehensive overview of current future directions in cattle genomics research, serving as a valuable resource for researchers, breeders, and industry stakeholders working to advance bovine genetics and genomics for improved productivity, welfare, and sustainability.

Dr. Hinayah Rojas De Oliveira
Guest Editor

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Research

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10 pages, 1354 KB

Open AccessArticle

Study on the Developmental Differences Between Female and Male Early Embryos in Cattle In Vivo

by Jie Wang, Fei Huang, Di Fang, Peng Niu, Jie-Ru Wang and Qing-Hua Gao

Genes 2025, 16(12), 1485; https://doi.org/10.3390/genes16121485 - 11 Dec 2025

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Abstract

Background: The developmental differences between female and male early embryos regarding sex development remain a topic of controversy. Objectives: This study aims to investigate whether there are significant developmental differences between female and male bovine embryos during in vivo development. Methods: The CIDR + FSH + PGF2α + GnRH method was employed to induce superovulation in 20 donor cows. Subsequently, artificial insemination was performed on the donor cows using high-purity X and Y frozen semen, with 10 cows receiving each type of semen. Seven days later, the embryos were flushed from the donor cows. The flushed embryos underwent embryonic sex determination, followed by immunofluorescence analysis to observe proliferation and apoptosis, and finally, RT-PCR was conducted to detect genes associated with proliferation and apoptosis. Results: The results indicated that the sex ratio of embryos obtained through artificial insemination using X/Y semen did not significantly differ based on semen purity (p ≥ 0.05). However, the fluorescence intensity of apoptotic cells in the X-BL group was significantly higher than that in the Y-BL group (p < 0.05). Conversely, the fluorescence intensity of proliferating cells in the X-BL group was significantly lower than that in the Y-BL group (p < 0.05). Furthermore, the expression levels of apoptosis-related genes in the X-BL group were significantly higher compared to the Y-BL group (p < 0.05), while the expression levels of proliferation-related genes in the X-BL group were significantly lower than those in the Y-BL group (p < 0.01). Conclusions: The above results indicate that during in vivo development of bovine early embryos, male embryos develop at a faster rate than female embryos. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics, Genomics and Breeding: From Molecular Insights to Sustainable Production)

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37 pages, 617 KB

Open AccessReview

Genetic and Environmental Architecture of Ram Fertility Traits: A Review

by Kaiyue Zheng, Krishani Sinhalage, Guilherme Henrique Gebim Polizel and Ángela Cánovas

Genes 2026, 17(2), 210; https://doi.org/10.3390/genes17020210 - 9 Feb 2026

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Abstract

Background/Objectives: Ram fertility is essential for sheep production, influenced by genetic, physiological, behavioral, and environmental factors. This narrative review synthesizes findings from over 190 peer-reviewed publications to evaluate the phenotypic indicators, genetic architecture, molecular candidates, and management conditions influencing testicular development, semen quality, and reproductive performance in rams. Methods: A narrative synthesis of peer-reviewed studies was conducted, integrating findings from quantitative genetics, genome-wide association studies, transcriptomics, and controlled environmental and management experiments. Emphasis was placed on studies evaluating fertility-related traits across breeds, ages, and production systems. Results: Recent genomic and transcriptomic studies have identified potential biomarkers (e.g., IGF1, IGFALS, FOXO1) and gene networks linked to ram fertility, including semen quality, scrotal circumference, and endocrine regulation. For instance, genome-wide association studies (GWASs) have identified candidate genes such as SLC2A8 and MAPK3, which are associated with spermatogenesis and semen quality. Additionally, Y-linked SNPs such as ZFY16: g.146 C > T have been linked to testicular development. Genetic potential is heavily modulated by environmental constraints. Heat stress emerges as a disruptor of testicular thermoregulation, with recent evidence highlighting the vulnerability of spermatogenesis even in adapted breeds. Management interventions, specifically nutritional supplementation and hormonal modulation via melatonin, are discussed as effective strategies to mitigate environmental impacts. Conclusion: Improving ram fertility will require an approach that prioritizes phenotypic traits supported by candidate genes identified through transcriptomic analyses and GWASs. Integrating these genetic tools together with cost-effective nutritional and hormonal management strategies can further improve semen quality, libido, and testicular traits, thereby enhancing fertility gains while maintaining sheep breed adaptability across production systems. Full article

(This article belongs to the Special Issue Advances in Cattle Genetics, Genomics and Breeding: From Molecular Insights to Sustainable Production)

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