Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition

Topic Information

Dear Colleagues,

The worldwide demand for animal-derived products will increase dramatically in the next 30 years due to global population growth. Therefore, a comprehensive understanding of animal breeding through reproduction performance and genomic selection will be of the utmost importance to satisfy the growing food demand. In view of this, combining assisted reproductive techniques (ARTs) and genetic/genomic molecular tools (GMTs) for animal selection will play a key role in improving and maximizing animal production systems' efficiency. This Topic aims to present original research and/or reviews related to ARTs and GMTs. We welcome all studies on factors affecting livestock performance with a particular focus on reproduction management, health control, longevity improvement, and welfare practices based on ART- and GMT-derived results. Furthermore, we encourage studies that contribute significantly to further advancing these fields and those based on ARTs, such as in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), in vitro/in vivo embryo production (IVP), embryo transfer (ET), controlled ovarian hyperstimulation (superovulation), gamete sex determination, artificial insemination (AI), gamete cryopreservation, nuclear transfer/cloning, stem cell technologies (SCTs), etc. Moreover, we invite contributions focused on complementary techniques for ARTs, including DNA isolation and analysis (DIA), polymerase chain reaction (PCR/rtPCR), DNA sequencing, recombinant plasmids, gene cloning, transgenesis, Southern blotting, single-nucleotide polymorphisms (SNPs), genome-wide association studies (GWASs), etc., are welcome as well.

Potential subtopics of interest include, but are not limited to, the following:

• The reproductive basis of important fertility traits;
• The application of ARTs to genetic resources for increasing reproductive/productive performance traits;
• Reproduction–nutrition interactions and efficient reproductive and production traits;
• Genes implicated in reproductive and production traits;
• Sequencing research surrounding breeding and genetics;
• Reproduction–health control interactions and efficient production traits;
• Biodiversity protection programs, germplasm banking, and ex situ preservation;
• Reproduction–welfare practices and efficient production traits;
• Reproduction–environment (climate) interactions and their impact on reproductive and production traits;
• Reproduction–longevity interactions for increasing fertility and productivity traits. We look forward to receiving your contributions.

Dr. Manuel García-Herreros
Prof. Dr. Pedro Manuel Aponte
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	4.5	7.8	2011	17.4 Days	CHF 2600	Submit
Animals animals	3.2	5.5	2011	15.7 Days	CHF 2400	Submit
Dairy dairy	3.0	5.4	2020	31.2 Days	CHF 1400	Submit
Genes genes	3.1	5.9	2010	13.3 Days	CHF 2600	Submit
Poultry poultry	2.5	3.7	2022	21.2 Days	CHF 1200	Submit
Ruminants ruminants	2.0	2.9	2021	18.8 Days	CHF 1200	Submit
Veterinary Sciences vetsci	2.7	3.9	2014	16.3 Days	CHF 2100	Submit

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Published Papers (11 papers)

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Open AccessSystematic Review

Global Evidence for the Effects of BMPR1B, BMP15, and GDF9 Polymorphisms on Litter Size in Sheep: A Systematic Review and Meta-Analysis

by María T. Espinoza-León, Itzel López-Rosas, Arlette Camacho-Lizárraga, Higinio Cepeda-Quintero, Jesús J. Portillo-Loera, Soila M. Gaxiola-Camacho, José Luis Villalpando-Aguilar and Arnulfo Montero-Pardo

Ruminants 2026, 6(3), 58; https://doi.org/10.3390/ruminants6030058 - 17 Jul 2026

Viewed by 367

Abstract

Major fecundity (Fec) genes play a central role in regulating the ovulation rate and litter size in sheep and have become important targets for genetic improvement programs. This study aimed to systematically evaluate the global evidence regarding the association of the [...] Read more.

Major fecundity (Fec) genes play a central role in regulating the ovulation rate and litter size in sheep and have become important targets for genetic improvement programs. This study aimed to systematically evaluate the global evidence regarding the association of the major fecundity genes BMPR1B, BMP15, and GDF9 with litter size through a systematic review and meta-analysis. A total of 104 studies met the eligibility criteria for the systematic review, 31 of which provided sufficient quantitative data for meta-analysis. Random-effects models were used to compare litter size among genotypes, and subgroup analyses together with meta-regression were performed to investigate the contribution of gene identity, mutation type, climatic region, and production system to the observed between-study heterogeneity. Overall, heterozygous carriers of fecundity-associated polymorphisms produced significantly larger litters than wild-type animals. Gene-specific analyses showed that BMPR1B exhibited the strongest positive association with litter size, followed by BMP15, whereas GDF9 showed no significant overall pooled effect. Meta-regression identified gene identity (Pseudo-R² = 38.57%) and mutation type (Pseudo-R² = 31.12%) as the principal sources of between-study heterogeneity, while climatic region and production system had no significant moderating effects. These findings provide robust quantitative evidence supporting the use of validated fecundity-associated markers, particularly BMPR1B, in marker-assisted and genomic selection programs aimed at improving reproductive performance in sheep. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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Open AccessArticle

Intravaginal Probiotics in Transition Dairy Cows: A Randomized Multi-Farm Field Trial on Health and Milk Production

by Eduardo Rosales Barahona, Andre Luiz Garcia Dias, Ashley Egyedy and Burim N. Ametaj

Vet. Sci. 2026, 13(6), 595; https://doi.org/10.3390/vetsci13060595 - 18 Jun 2026

Viewed by 610

Abstract

Uterine infections (metritis and endometritis) are a leading cause of culling and reproductive failure in transition dairy cows, and antibiotic-resistant Gram-negative pathogens limit conventional therapy. This randomized, controlled, multi-farm field trial evaluated whether four intravaginal infusions of a host-adapted lactic acid bacteria (LAB) [...] Read more.

Uterine infections (metritis and endometritis) are a leading cause of culling and reproductive failure in transition dairy cows, and antibiotic-resistant Gram-negative pathogens limit conventional therapy. This randomized, controlled, multi-farm field trial evaluated whether four intravaginal infusions of a host-adapted lactic acid bacteria (LAB) cocktail (Lactobacillus sakei FUA3089, Pediococcus acidilactici FUA3138, P. acidilactici FUA3140; 10⁸–10⁹ cfu/dose) at −3, −2, +3, and +4 weeks relative to calving reduce periparturient disease and improve milk production. A total of 526 pregnant cows (426 Holstein, 100 Jersey) from four commercial Alberta farms (automatic-milking, parlor, and certified-organic systems) were block-randomized within farm and parity to TRT1 (saline; n = 175), TRT2 (saline + skim milk; n = 176), or TRT3 (LAB cocktail in saline + skim milk; n = 175). Uterine infection incidence was assessed by Metricheck™ mucus scoring and transrectal ultrasonography at +3 and +4 weeks postpartum. Across the principal peripartum infectious outcomes, TRT3 showed a consistent protective effect: uterine infection incidence was lowest in TRT3 (18.8% vs. 25.1% in pooled controls; OR = 0.69; 95% CI, 0.44–1.09; an approximately 25% relative reduction; exact p = 0.12), and this metritis signal was additionally supported by a repeated-measures mixed model accounting for farm, parity, and week (p = 0.0175), although the Bonferroni-adjusted pairwise contrasts were tendencies (adjusted p ≈ 0.12), and the effect did not differ by parity (treatment × lactation interaction, p = 0.97). Subclinical mastitis was numerically lower in TRT3 than in pooled controls (5.3% vs. 8.9%; OR = 0.57; 95% CI, 0.27–1.24; exact p = 0.16), whereas retained placenta, milk fever, displaced abomasum, and lameness showed no clear cow-level treatment effect in the cow-level exact analyses. Milk yield increased significantly in multiparous cows, which produced 4.6 L/day more milk than TRT1 and 3.22 L/day more than TRT2 over the first 50 days in milk (p < 0.01 for both contrasts; treatment × parity interaction, p = 0.01). No effect was seen on milk composition, uterine involution, or reproductive performance. The trial supports intravaginal LAB as a candidate antibiotic-free prophylactic whose response depends on farm- and cow-level contexts and whose mechanisms require confirmation through microbiological and metabolic measurements. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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21 pages, 8152 KB  

Open AccessReview

Genomics and Reproductive Biotechnologies in Goat Production Systems in Peru

by Yolanda Romero, Emmanuel Alexander Sessarego, René Pinazo-Herencia and Juancarlos Cruz-Luis

Ruminants 2026, 6(2), 37; https://doi.org/10.3390/ruminants6020037 - 1 Jun 2026

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Abstract

Goat production in Peru is primarily carried out under extensive systems shaped by climatic variability, forage seasonality, infrastructure limitations, and persistent sanitary pressure. In this context, Creole goats represent a strategic animal genetic resource due to their capacity to adapt to arid and [...] Read more.

Goat production in Peru is primarily carried out under extensive systems shaped by climatic variability, forage seasonality, infrastructure limitations, and persistent sanitary pressure. In this context, Creole goats represent a strategic animal genetic resource due to their capacity to adapt to arid and high-Andean environments. This review integrates the available evidence on production typologies in the main goat-producing regions of the country, the major sanitary and structural bottlenecks, and the state of the art of genomic, multi-omics, and reproductive biotechnology tools applicable to goats. It discusses how the transition from traditional markers to SNP genotyping, together with functional approaches such as microbiome analysis, transcriptomics, and proteomics, can contribute to understanding the biological basis of complex traits related to resilience, feed efficiency, and reproductive performance. Likewise, the potential of precision livestock farming to generate longitudinal phenotypes and strengthen genetic improvement programs in low-input systems is highlighted. Finally, priorities and considerations are outlined to advance the integration of phenotyping, genomics, and reproductive biotechnologies in extensive contexts, with emphasis on the generation of systematic data, interinstitutional coordination, and technology transfer aimed at the sustainability and conservation of goat resources. These insights may also inform genetic improvement strategies in other developing countries facing similar environmental and structural constraints in low-input goat production systems, particularly in arid and semi-arid regions. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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16 pages, 9435 KB  

Open AccessArticle

Development and Validation of a 40K Liquid SNP Array for Meat-Type Duck Breeding and Germplasm Identification

by Jie Wang, Yufeng Li, Dan Hao, Jie Liu, Yan Zhou, Haixia Han, Wei Liu, Yan Sun, Fuwei Li, Dingguo Cao and Qiuxia Lei

Agriculture 2026, 16(11), 1188; https://doi.org/10.3390/agriculture16111188 - 28 May 2026

Cited by 1 | Viewed by 359

Abstract

High-density SNP chips have been demonstrated to be effective instruments for simultaneously genotyping large numbers of loci, thereby facilitating genome-scale analyses and advancing genomic selection (GS) in poultry and livestock. The meat-type duck, an economically valuable poultry species in China, has so far [...] Read more.

High-density SNP chips have been demonstrated to be effective instruments for simultaneously genotyping large numbers of loci, thereby facilitating genome-scale analyses and advancing genomic selection (GS) in poultry and livestock. The meat-type duck, an economically valuable poultry species in China, has so far lacked precise and high-throughput genotyping systems, which has constrained the broader implementation of GS and genome-wide association analyses (GWASs) and consequently slowed genetic progress. In this study, we developed and validated a novel SNP array based on Genotyping-by-Targeted-Sequencing (GBTS) technology. The array comprises 40,875 SNP markers evenly distributed across 32 duck chromosomes. Using data generated from this array, genomic heritability estimates were obtained for six economic traits in a cultured duck population (n = 400), with values of 0.61 ± 0.09, 0.69 ± 0.08, 0.80 ± 0.08, 0.11 ± 0.09, 0.14 ± 0.08, 0.31 ± 0.09 for age at first egg (AFE), egg production number at 38 weeks (EN38w), egg weight at 38 weeks (EW38w), body weight at 35 days (BW35d), shank length at 35 days (SL35d) and thickness of breast muscle at 40 days (TB40d). A total of 163 significant SNPs associated with economic traits were identified through GWAS, and annotation revealed 28 candidate genes related to five of these traits. Moreover, the prediction accuracy of ssGBLUP for AFE, EN38w, EW38w, BW35d, SL35d, and TB40d reached 0.55 ± 0.16, 0.56 ± 0.12, 0.57 ± 0.08, 0.25 ± 0.19, 0.31 ± 0.19, and 0.47 ± 0.17, respectively—values that exceeded those obtained using BLUP. Population genomic analyses of 400 ducks demonstrated that this SNP array provides improved genomic prediction accuracy over pedigree-based BLUP for most analyzed traits. Overall, the developed SNP array provides a robust, high-efficiency, and cost-effective genotyping platform that will accelerate genetic progress and promote the sustainable development of the meat-type duck industry. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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16 pages, 716 KB  

Open AccessSystematic Review

Genome-Wide Association Studies on Litter Size in Sheep: A Systematic Review and Gene Prioritization Analysis

by Rui Zhao, Siqi Chen, Qingjie Jiao, Xinyan Zhu, Haiyan Jia, Lei Hou, Dan Wang, Jiaqing Hu, Jianmin Wang and Tianle Chao

Ruminants 2026, 6(2), 36; https://doi.org/10.3390/ruminants6020036 - 27 May 2026

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Abstract

Sheep litter size is of major economic importance, yet its polygenic nature and low heritability limit the effectiveness of traditional selection methods. Following PRISMA guidelines, this systematic review integrated genome-wide association study (GWAS) evidence for sheep litter size and prioritized candidate genes. Four [...] Read more.

Sheep litter size is of major economic importance, yet its polygenic nature and low heritability limit the effectiveness of traditional selection methods. Following PRISMA guidelines, this systematic review integrated genome-wide association study (GWAS) evidence for sheep litter size and prioritized candidate genes. Four databases were searched, yielding 24 eligible studies comprising a total effective analytical sample of 7618 animals from 98 breeds/populations across nine countries. Following standardized re-annotation of genomic coordinates, 245 significant variations and 316 candidate genes were extracted. Gene prioritization using ToppGene identified 96 high-priority genes, including 10 core genes: GRIN2A, DLG2, FLT4, ESR2, AMH, ALK, INHBB, NF1, CAMK2D, and ERCC2. These genes collectively operate through four functional axes: the gonadal axis regulation, follicular development, hormonal signal transduction, and DNA damage repair. Functional enrichment analysis revealed significant involvement in protein binding and metal ion binding. Marked breed-specificity was observed, with only the BMPR1B (FecB) locus replicated across three studies. Key limitations include restriction to English-language publications, small median sample sizes in the included studies, and the inherent bias of ToppGene training genes toward previously reported loci. These findings clarify the molecular genetic architecture of sheep litter size and provide a validated candidate gene framework to support precision genomic breeding strategies. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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17 pages, 14936 KB  

Open AccessArticle

Efficient and Safe Knockout of AR and DMRT1 Mediated by Cytosine Base Editors in Chicken DF-1 and PGCs

by Xiaori Gao, Na Tang, Zhifeng Zhao, Yanhua He, Yitong Shen, Xian Zou and Chenglong Luo

Vet. Sci. 2026, 13(5), 455; https://doi.org/10.3390/vetsci13050455 - 6 May 2026

Viewed by 690

Abstract

This study aimed to establish an efficient and precise cytosine base editor (CBE)-mediated knockout system in chicken somatic cells and primordial germ cells (PGCs). PGCs are pivotal for generating genome-edited chickens, but low transfection efficiency limit their application. Unlike CRISPR/Cas9, CBEs achieve precise [...] Read more.

This study aimed to establish an efficient and precise cytosine base editor (CBE)-mediated knockout system in chicken somatic cells and primordial germ cells (PGCs). PGCs are pivotal for generating genome-edited chickens, but low transfection efficiency limit their application. Unlike CRISPR/Cas9, CBEs achieve precise C-to-T conversion without DNA double-strand breaks or donor templates, making them safer for avian genome engineering. We used CBEs to introduce premature stop codons in exon 1 of the sex-determining AR and DMRT1 genes for targeted knockout. Among 12 screened sgRNAs, sgRNA6 (AR, 94.67 ± 6.66%) and sgRNA9 (DMRT1, 6.67 ± 6.51%) performed best in DF-1 cells; in PGCs, their editing efficiencies reached 51.0% and 91.0%, respectively. No off-target mutations were detected in edited DF-1 cells. These findings confirm that CBE-mediated knockout is highly efficient and safe in chicken somatic and germ cells, providing a robust tool for avian genome editing. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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17 pages, 1303 KB  

Open AccessArticle

Kinship and Network Analysis of Two South African Beef Cattle Breeds Using Pedigree and High-Density SNP Markers

by Khulekani S. Khanyile, Azwihangwisi Maiwashe, Nozipho A. Magagula, Este van Marle-Köster and Avhashoni A. Zwane

Agriculture 2026, 16(6), 696; https://doi.org/10.3390/agriculture16060696 - 19 Mar 2026

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Abstract

Accurate genealogical records are essential in livestock breeding for maintaining genetic diversity, preventing inbreeding, and mapping of economically important traits in beef production. This study aimed to assess parent–offspring relationships within South African Bonsmara and Nguni cattle populations using both traditional pedigree records [...] Read more.

Accurate genealogical records are essential in livestock breeding for maintaining genetic diversity, preventing inbreeding, and mapping of economically important traits in beef production. This study aimed to assess parent–offspring relationships within South African Bonsmara and Nguni cattle populations using both traditional pedigree records and genomic data. Hair samples from 119 Nguni and 311 Bonsmara cattle were genotyped using the BovineSNP50 array, and these were imputed to Illumina BovineHD BeadChip using updated SNP coordinates from the assembly genome (ARC—UCSD 1.2). Quality control and data filtering were performed using PLINK v1.9, while relationship inference was conducted using KING v2.2.8 and PLINK v1.9 software for principal component analysis, IBD metrics and Mendelian error-based exclusion. Categories of relatedness through network relationship analysis revealed a predominance of half-sibling relationships in both breeds, with 2317 such relationships identified in Nguni and 1221 in Bonsmara. Inference of parent–offspring pairs showed discrepancies with the recorded pedigrees, with 49 inferred pairs compared to 47 recorded pairs in Nguni, and 62 inferred pairs compared to 75 pairs recorded in Bonsmara. Relationships based on IBD using PLINK with a ‘PI-HAT’ threshold greater than 0.45 revealed unique parent–offspring inferences that differed from those obtained using KING v2.2.8. Phylogenetic network analysis assigned each individual’s genomic origin independent of the pedigree records, supporting the efficiency of SNP data for genetic assignment. These results demonstrated that SNP-based pedigree verification can accurately identify parent–offspring and half-sibling relationships, providing a reliable foundation for recombination analysis and supporting precise trait mapping and informed selection in breeding programs. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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21 pages, 1262 KB  

Open AccessArticle

Application of the “Yuyang Muxin” Breeding Chip in Huang-Huai Sheep: A Six-Year Comprehensive Evaluation of Production and Meat Quality Traits

by Kai Quan, Haoyuan Han, Kun Liu, Caihong Wei, Huihua Wang, Meilin Jin, Wei Sun, Huibin Shi and Jun Li

Animals 2026, 16(6), 884; https://doi.org/10.3390/ani16060884 - 12 Mar 2026

Viewed by 630

Abstract

The Huang-huai sheep (Dorper × Small-tailed Han), certified in China in 2019, initially exhibited issues with genetic uniformity and meat quality. A six-year (2020–2025) breeding program was conducted at two core farms (collectively housing ~2400 breeding ewes representing 12 bloodlines) using the custom [...] Read more.

The Huang-huai sheep (Dorper × Small-tailed Han), certified in China in 2019, initially exhibited issues with genetic uniformity and meat quality. A six-year (2020–2025) breeding program was conducted at two core farms (collectively housing ~2400 breeding ewes representing 12 bloodlines) using the custom “Yuyang Muxin” 10 K SNP chip containing functional markers for reproduction (FecB), growth (CLPG, ACTC1), and meat quality (FABP3, CIDEa). Genotyping and marker-assisted selection were integrated with BLUP breeding values. After six years, favorable FecB genotype frequency increased from 68.97% to 82.58% (p < 0.05), while genetic diversity remained stable (F_IS < 0.05). Mixed model analysis accounting for farm and year random effects revealed significant genetic gains: 6-month ram body weight increased by 9.1% (58.50 to 63.80 kg, p < 0.05), dressing percentage improved from 56.02% to 57.8% (p < 0.05), and loin muscle area expanded by 9.4% (24.50 to 26.8 cm², p < 0.05). Meat quality was enhanced, with shear force decreasing by 14.1% (38.65 to 33.20 N, p < 0.05) and intramuscular fat increasing by 40.0% (2.0% to 2.8%, p < 0.05). Lambs weaned per ewe per year increased from 2.38 to 2.56 (p < 0.05). EBV trend analysis confirmed that improvements were primarily genetic. After Bonferroni correction, CIDEa expression was strongly correlated with intramuscular fat (r = 0.89, p < 0.001) and FABP3 expression with arachidonic acid (r = 0.70, p < 0.001). Nine months was identified as the optimal slaughter age. The “Yuyang Muxin” breeding chip effectively accelerated genetic improvement in Huang-huai sheep, enabling synergistic enhancement of multiple traits. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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Open AccessArticle

Exploring the Genetic Heritage of the Yucatán Black Hairless Pig: A Comparative Worldwide ROH Study

by Jorge Barzilai Lara-Castillo, Clemente Lemus-Flores, Raúl Sansor-Nah, Néstor Gerardo Michel-Regalado, Fernando Grageola-Núñez, William Orlando Burgos-Paz and Job Oswaldo Bugarín-Prado

Vet. Sci. 2026, 13(1), 54; https://doi.org/10.3390/vetsci13010054 - 7 Jan 2026

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The Yucatán Black Hairless Pig (YBHP) is an indigenous Mexican breed shaped by tropical environments and traditional management systems. This study aimed to characterize its runs of homozygosity (ROH) and compare its ROH patterns with those of indigenous and commercial pig breeds worldwide [...] Read more.

The Yucatán Black Hairless Pig (YBHP) is an indigenous Mexican breed shaped by tropical environments and traditional management systems. This study aimed to characterize its runs of homozygosity (ROH) and compare its ROH patterns with those of indigenous and commercial pig breeds worldwide using the GGP Porcine 50K SNP array. After applying standard quality-control filters, ROH were identified, classified by length, and evaluated for shared homozygous regions across populations. The YBHP showed intermediate levels of genomic homozygosity (FROH = 0.09), with most ROH segments falling within the 5–20 Mb range. Comparative analyses indicated that the YBHP shared a higher number of ROH segments with indigenous populations than with cosmopolitan breeds. Gene annotation within ROH regions revealed SNPs located in genes previously reported in indigenous populations, including FGF5, BMP2K, PAQR3, RASGEF1B and ANTXR2, which participate in developmental and regulatory biological pathways. Overall, these results provide a detailed description of ROH distribution in the YBHP and offer complementary information to previous studies on its genetic characterization, supporting future conservation and management strategies. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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Open AccessArticle

Single-Cell Transcriptomic Profiling of Longissimus Dorsi and Biceps Femoris Muscles in Kazakh Horses Reveals Cellular Heterogeneity and Myogenic Regulation

by Jianwen Wang, Zexu Li, Luling Li, Ran Wang, Shikun Ma, Yi Su, Dehaxi Shan and Qiuping Huang

Animals 2025, 15(19), 2778; https://doi.org/10.3390/ani15192778 - 23 Sep 2025

Cited by 1 | Viewed by 1401

Abstract

Kazakh horses are renowned for their endurance and adaptability, with distinct muscle groups such as the longissimus dorsi (LD) and biceps femoris (BF) muscles serving specialized functions. However, the molecular mechanisms underlying the functional specialization of these muscles in Kazakh horses remain poorly [...] Read more.

Kazakh horses are renowned for their endurance and adaptability, with distinct muscle groups such as the longissimus dorsi (LD) and biceps femoris (BF) muscles serving specialized functions. However, the molecular mechanisms underlying the functional specialization of these muscles in Kazakh horses remain poorly understood. This study aims to address this gap by utilizing single-cell RNA sequencing (scRNA-seq) to investigate the transcriptomic differences between these muscle groups, with a focus on understanding their molecular adaptations. Our analysis revealed that the BF muscle, specialized for explosive movements, exhibited upregulation of genes associated with anaerobic metabolism, muscle contraction, and oxidative stress response, reflecting its reliance on glycolysis for sustained energy production. In contrast, the LD muscle, primarily responsible for postural support and endurance, showed a metabolic shift toward lipid utilization and energy production. Differential gene expression analysis also revealed distinct enrichment in biological pathways, with LD cells being enriched in pathways related to muscle contraction and calcium signaling, while BF cells were enriched in energy metabolism pathways. These findings provide valuable insights into the molecular adaptations of Kazakh horses’ muscle tissues, highlighting the functional specialization of LD and BF muscles and offering a foundation for future research on improving muscle performance and breeding programs in equines. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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27 pages, 832 KB  

Open AccessEditor’s ChoiceReview

Enhancing Genomic Selection in Dairy Cattle Through Artificial Intelligence: Integrating Advanced Phenotyping and Predictive Models to Advance Health, Climate Resilience, and Sustainability

by Karina Džermeikaitė, Monika Šidlauskaitė, Ramūnas Antanaitis and Lina Anskienė

Dairy 2025, 6(5), 50; https://doi.org/10.3390/dairy6050050 - 1 Sep 2025

Cited by 12 | Viewed by 9910

Abstract

The convergence of genomic selection and artificial intelligence (AI) is redefining precision breeding in dairy cattle, enabling earlier, more accurate, and multi-trait selection for health, fertility, climate resilience, and economic efficiency. This review critically examines how advanced genomic tools—such as genome-wide association studies [...] Read more.

The convergence of genomic selection and artificial intelligence (AI) is redefining precision breeding in dairy cattle, enabling earlier, more accurate, and multi-trait selection for health, fertility, climate resilience, and economic efficiency. This review critically examines how advanced genomic tools—such as genome-wide association studies (GWAS), genomic breeding values (GEBVs), machine learning (ML), and deep learning (DL) models to accelerate genetic gain for complex, low heritability traits. Key applications include improved resistance to mastitis and metabolic diseases, enhanced thermotolerance, reduced enteric methane emissions, and increased milk yield. We discuss emerging computational frameworks that combine sensor-derived phenotypes, omics datasets, and environmental data to support data-driven selection decisions. Furthermore, we address implementation challenges related to data integration, model interpretability, ethical considerations, and access in low-resource settings. By synthesizing interdisciplinary advances, this review provides a roadmap for developing AI-augmented genomic selection pipelines that support sustainable, climate-smart, and economically viable dairy systems. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection: 2nd Edition)

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