Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats, 2nd Edition

Abstract submission deadline

31 October 2026

Manuscript submission deadline

31 December 2026

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Topic Information

Dear Colleagues,

Ruminant livestock, including cattle, sheep, and goats, are cornerstone species for global food security and rural livelihoods. To meet the rising demand for animal-sourced products while navigating the challenges of climate change, the integration of advanced molecular genetics into breeding programs is more critical than ever. This Topic aims to highlight the latest breakthroughs in the genetic and genomic landscape of these species.

We invite original research and comprehensive reviews that explore the molecular mechanisms underlying economically important traits in ruminant livestock. We are particularly interested in well-designed studies that apply molecular genetic approaches, ranging from targeted genetic analyses to high-throughput sequencing, genomic selection, and functional "omics" analyses, to elucidate the biological basis of traits such as growth, reproductive efficiency, milk/meat quality, wool and fiber traits, and resilience to environmental stressors or diseases. Furthermore, we encourage submissions focusing on innovative biotechnological approaches, such as gene editing, as well as studies addressing the conservation and sustainable use of genetic diversity in indigenous breeds. By bridging basic molecular research with practical breeding applications, this Topic seeks to foster sustainable and efficient livestock production for the future.

Dr. Xiukai Cao
Dr. Hui Li
Dr. Huitong Zhou
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Animals animals	3.2	5.5	2011	17.1 Days	CHF 2400	Submit
Biology biology	4.3	7.3	2012	16.8 Days	CHF 2700	Submit
Current Issues in Molecular Biology cimb	4.1	5.0	1999	16.3 Days	CHF 2200	Submit
DNA dna	-	-	2021	36 Days	CHF 1000	Submit
Genes genes	3.1	5.9	2010	14.6 Days	CHF 2600	Submit
International Journal of Molecular Sciences ijms	5.6	10.0	2000	17.8 Days	CHF 2900	Submit

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Related Topic

Published Papers (6 papers)

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All Animals CIMB DNA Genes IJMS Biology

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Open AccessArticle

Genetic Basis of Divergent Growth and Muscle Development in Purebred and Crossbred Leizhou Black Goats Revealed by Whole-Genome Resequencing

by Xiaotao Han, Jing Huang, Wenxi Qian, Yuelang Zhang, Ke Wang and Jiancheng Han

Biology 2026, 15(13), 1038; https://doi.org/10.3390/biology15131038 (registering DOI) - 29 Jun 2026

Abstract

The Leizhou black goat is a prized indigenous breed in southern China, renowned for its superior meat quality. However, its productivity is constrained by a relatively small body size. Understanding the genetic basis of growth differences between purebred and crossbred populations is essential [...] Read more.

The Leizhou black goat is a prized indigenous breed in southern China, renowned for its superior meat quality. However, its productivity is constrained by a relatively small body size. Understanding the genetic basis of growth differences between purebred and crossbred populations is essential for designing effective conservation and breeding strategies. To this end, we conducted comparative whole-genome resequencing on 22 purebred (WL) and 50 crossbred (JN: Nubian × Leizhou) goats. Population structure was assessed via principal component analysis, and genomic regions exhibiting elevated genetic differentiation were identified using the population differentiation index (F_ST). Functional enrichment analyses were subsequently applied to genes within these regions. Our results revealed clear genetic differentiation between the two populations. Among the highly differentiated genomic regions, we identified several genes, such as MYOM2, TMTC4, DPP6, and MIDN, whose known functions in neural signaling and muscle development make them plausible candidates for contributing to the growth differences between populations. A particularly notable discovery was a non-coding intronic mutation in the RNGTT gene (rs646826802), which is fixed in the paternal Nubian line and prevalent across 25 other global goat breeds but is completely absent in the purebred Leizhou black goat. This study identifies key genetic components associated with trait variation in crossbred goats and reports a breed-specific genomic marker that can serve as a practical tool for verifying breed purity, thereby supporting the conservation of this valuable indigenous genetic resource. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats, 2nd Edition)

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16 pages, 1968 KB  

Open AccessArticle

Generation-Specific Heterosis in Lactation, Reproduction, and Blood Transcriptomic Profiles of Chinese Simmental × Holstein Crossbred Cows

by Hongkun Zhao, Jingjing Wen, Jiajie Huang, Xiaoyun Liang, Qiuming Chen and Lei Xu

Animals 2026, 16(12), 1892; https://doi.org/10.3390/ani16121892 - 18 Jun 2026

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Abstract

This study investigated generation-specific heterosis in Chinese Simmental × Chinese Holstein crossbred cows by comparing lactation performance, reproductive performance, hematological traits, and blood transcriptomic profiles among Chinese Simmental (SIM), Chinese Holstein (HOL), F1 crossbreds, and first-generation backcrosses (BC1). Lactation analysis was based on [...] Read more.

This study investigated generation-specific heterosis in Chinese Simmental × Chinese Holstein crossbred cows by comparing lactation performance, reproductive performance, hematological traits, and blood transcriptomic profiles among Chinese Simmental (SIM), Chinese Holstein (HOL), F1 crossbreds, and first-generation backcrosses (BC1). Lactation analysis was based on 17,005 valid records, reproductive analysis was based on 5481 valid records, and transcriptomic analysis was conducted using blood samples from 31 cows. F1 showed the most favorable reproductive profile, whereas BC1 showed relatively strong milk-yield performance. Hematological analysis revealed group-level differences in leukocyte-related indicators. Main-text transcriptomic interpretation focused on SIM, F1, and BC1 comparisons because the HOL RNA-seq group included only three samples. These comparisons suggested that F1-related DEGs were mainly associated with immune and inflammatory processes, whereas BC1-related DEGs showed broader immune- and metabolism-related enrichment patterns. Candidate-gene expression heterosis and d/a-ratio analyses are presented as exploratory supplementary results with bootstrap uncertainty estimates because qPCR validation was not available. Overall, these results indicate that heterosis in this crossbreeding system is generation-specific rather than uniform. The integration of phenotypic and blood transcriptomic analyses provides candidate pathways and associated systemic expression patterns for future validation rather than definitive mechanistic evidence. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats, 2nd Edition)

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31 pages, 753 KB  

Open AccessReview

Heat Stress Effects on Milk Production and the Genomic Architecture of Thermotolerance in Dairy Cattle

by Qingshan Ma, Mohamed Tharwat, Fahad A. Alshanbari and Muhammad Zahoor Khan

Biology 2026, 15(10), 813; https://doi.org/10.3390/biology15100813 - 21 May 2026

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Abstract

Heat stress (HS) is among the most economically consequential environmental challenges to global dairy production, causing progressive declines in milk yield, compositional quality, and mammary cellular integrity. The temperature–humidity index (THI) is the primary thermal load metric, with performance-impairment thresholds typically beginning at [...] Read more.

Heat stress (HS) is among the most economically consequential environmental challenges to global dairy production, causing progressive declines in milk yield, compositional quality, and mammary cellular integrity. The temperature–humidity index (THI) is the primary thermal load metric, with performance-impairment thresholds typically beginning at THI 68 in Holstein cattle, with severe impacts manifesting beyond THI 72; breed-specific thresholds for Jersey, Brown Swiss, and Simmental cows differ owing to their lower metabolic heat load and greater inherent thermotolerance. At the molecular level, HS activates heat shock protein networks—notably HSPA1A, HSP90B1, and HSPH1—through HSF1/HSF4 transcriptional activation, while simultaneously suppressing casein genes (CSN1S1, CSN2, CSN3), lipogenic genes (FASN, SCD, CD36), amino acid transporters (SLC7A5, SLC38A2), and mTOR-AKT-STAT5 translational machinery, collectively impairing milk biosynthetic capacity. Pro-apoptotic signaling (BAX, CASP3 upregulation; BCL2 downregulation) and mitochondrial dysfunction further compromise mammary epithelial viability. Post-transcriptional regulation through miRNA, circRNA, and lncRNA competing endogenous RNA networks, alongside epitranscriptomic m6A modifications, adds further regulatory complexity. Genome-wide association studies have identified SNPs in HSP70A1A, HSPA4, TLR4, and PRLR as thermotolerance candidates compatible with sustained milk production. Nutritional supplementation with methionine, arginine, and taurine partially restores cellular synthetic capacity. Integrating multi-trait genomic selection with Bos indicus introgression, precision cooling, and targeted nutrition offers the most viable path toward climate-resilient, high-producing dairy cattle. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats, 2nd Edition)

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18 pages, 2958 KB  

Open AccessArticle

Dynamic Shifts in Gut Microbiota and Metabolic Pathways of Xinggao Mutton Sheep During Weaning: A Multi-Omics Analysis

by Xiaolong He, Jingda Yuan, Biao Wang, Qing Qin, Rigele Te, Lai Da, Xuewen Liu and Shaoyin Fu

Animals 2026, 16(10), 1532; https://doi.org/10.3390/ani16101532 - 16 May 2026

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Abstract

The composition and function of the intestinal microbiota of Xinggao mutton sheep were explored before and post-weaning using non-target metabolomics. Both 16S rDNA amplicon sequencing technology and serum non-target metabolomics were used to determine changes in sheep metabolites and intestinal flora. A random [...] Read more.

The composition and function of the intestinal microbiota of Xinggao mutton sheep were explored before and post-weaning using non-target metabolomics. Both 16S rDNA amplicon sequencing technology and serum non-target metabolomics were used to determine changes in sheep metabolites and intestinal flora. A random sampling method was used to collect fecal samples from 20 pre-weaning lambs and 20 lambs post-weaning. Analysis of the intestinal flora identified Firmicutes as the predominant phylum pre-weaning and Bacteroidota as the dominant phylum post-weaning. Joint multi-omics analysis revealed that Oscillospiraceae UCG-005 and Prevotella_9 were significantly correlated with serum L-tyrosine, Indole-3-acrylic acid, and taurine-related metabolites, suggesting their potential roles in modulating digestive health in Xinggao mutton sheep. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats, 2nd Edition)

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28 pages, 2742 KB  

Open AccessArticle

Biophysical Modeling Reveals How Gene Expression Drives Tissue-Scale Fat Deposition in Beef Breeds

by Heherson S. Cabrera, Alvin R. Caparanga and Lemmuel L. Tayo

Biology 2026, 15(8), 649; https://doi.org/10.3390/biology15080649 - 20 Apr 2026

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Abstract

Intramuscular fat (IMF) marbling is a key determinant of beef quality, yet predicting how breed-specific gene expression translates into tissue-scale fat patterning remains a major challenge. Using a small public transcriptomic dataset (n = 3 per breed), this study presents a proof-of-concept [...] Read more.

Intramuscular fat (IMF) marbling is a key determinant of beef quality, yet predicting how breed-specific gene expression translates into tissue-scale fat patterning remains a major challenge. Using a small public transcriptomic dataset (n = 3 per breed), this study presents a proof-of-concept omics-to-tissue modeling framework that converts RNA-seq data into biophysically interpretable parameters governing intramuscular adipogenesis. Using transcriptomic profiles from GSE161967 (Japanese Black Wagyu versus Chinese Red Steppes), we derived composite indices capturing the adipogenic commitment (φ) and lipid droplet capacity (ψ) from curated gene modules. These indices were mapped via calibrated linear functions to a Cellular Potts Model (CPM), parameterizing the fibro-adipogenic progenitor (FAP) differentiation probability, lipogenesis rate, adipocyte cohesion, and progenitor abundance. The gene-derived parameters placed Wagyu in a high-adipogenic regime ($p_{F\to A}^{\mathrm{base}}$ = 0.65; $k_{lipogenesis}$ = 0.12), while Chinese Red Steppes resided in a low-adipogenic regime (0.25; 0.04). The CPM simulations revealed a sharp, predictive threshold at $p_{F\to A}^{\mathrm{base}}$ ≈ 0.55, below which IMF remained negligible and above which stable adipocyte clusters and 8–9% IMF emerged. Without post hoc tuning, the gene-derived parameters correctly predicted robust marbling in Wagyu and a lean phenotype in Chinese Red Steppes. A sensitivity analysis identified the adipogenic commitment as the primary control parameter, with lipogenesis acting as an amplifier. Together, these results demonstrate that transcriptomic measurements can quantitatively predict emergent marbling phenotypes through a small set of interpretable biophysical parameters, establishing a generalizable framework for forecasting complex tissue traits from omics data. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats, 2nd Edition)

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26 pages, 3195 KB  

Open AccessReview

Decoding Complex Traits in Goats Through Genome-Wide Association Studies: Progress, Challenges, and Perspectives

by Da Feng, Chen Wei, Si-Yi Hu and Shang-Quan Gan

Int. J. Mol. Sci. 2026, 27(7), 2945; https://doi.org/10.3390/ijms27072945 - 24 Mar 2026

Cited by 1 | Viewed by 838

Abstract

Goats play a significant role in the global livestock industry, with breeders aiming to investigate genetic variations linked to crucial economic traits for enhancing production performance. Genome-wide association studies (GWASs) are a highly effective method for identifying the associations between complex traits or [...] Read more.

Goats play a significant role in the global livestock industry, with breeders aiming to investigate genetic variations linked to crucial economic traits for enhancing production performance. Genome-wide association studies (GWASs) are a highly effective method for identifying the associations between complex traits or diseases and genetic variations in goat at the whole-genome level. By analyzing large datasets of goat genomes, GWASs can offer valuable insights into the identification of genetic variations related to key economic traits in goats and aid in the discovery of new genetic variants. These discoveries hold the promise of improving the efficiency of goat production by molecular breeding strategies. This study reviews the fundamental theories and developmental processes of GWAS, focusing on its role in identifying potential genetic loci or genes associated with major economic traits in goats. Additionally, it delves into the challenges involved in unraveling the genetic architecture of complex traits in goats through GWAS and investigates future opportunities for progress to advance the goat molecular breeding. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats, 2nd Edition)

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