From Genome to Phenome: Genotype × Environment Interactions in Organic and Conventional Dairy Systems and the Emergence of Genomically Optimized Organic Dairy (GOOD)
Aug 2026· Genes· Vol 17, pp. 990· 0 citations· 93 references
TL;DR
The evidence supports a shift from selection focused primarily on milk yield toward genomic improvement of robustness, disease resistance, reproductive resilience, grazing adaptation, and lifetime productivity.
Abstract
Organic dairy farming has expanded rapidly over the past three decades, driven by regulatory reforms, consumer demand, and growing recognition of its environmental, animal welfare, and potential human health benefits. Despite this growth, evidence comparing organic and conventional dairy systems remains fragmented across genetics, phenomics, animal health, and human health outcomes. This review synthesizes current knowledge through the lens of genotype × environment interactions, integrating evidence from four complementary domains: (1) genomic architecture and breeding strategies; (2) phenotypic performance, including milk production and composition, meat quality, nutrition, and reproductive traits; (3) animal health, disease resistance, antimicrobial use, and welfare; and (4) implications for human health. Holstein–Friesian cattle remain the predominant breed in both systems; however, organic production favors animals with greater robustness, longevity, grazing efficiency, and disease resilience. Genetic studies further demonstrate that highly heritable production traits share similar genetic architecture across production systems, whereas health, fertility, longevity, and other low-heritability functional traits exhibit stronger genotype × environment interactions and more system-specific genomic signatures. These findings suggest that breeding strategies developed for high-input conventional systems are unlikely to maximize performance under organic management. Collectively, the evidence supports a shift from selection focused primarily on milk yield toward genomic improvement of robustness, disease resistance, reproductive resilience, grazing adaptation, and lifetime productivity. We propose Genomically Optimized Organic Dairy (GOOD) as an emerging framework that integrates genomic selection, precision phenotyping, health monitoring, and environmental adaptation to develop dairy cattle better suited to organic production.
Background: Livestock production is indispensable for global food security, yet it faces constant pressure to maintain a sustainable balance between environmental, economic, and ethical demands. Objective: This study explores the past, present, and future of the livestock industry through genomic technologies. Methods/Approach: Tools such as Next-Generation Sequencing (NGS), Whole-Genome Sequencing (WGS), Genome-Wide Association Studies (GWAS), and Genomic Selection (GS) have accelerated precise genetic improvement of traits like feed efficiency, productivity, and disease resistance. Key Tools: CRISPR-Cas9 gene-editing further fosters livestock with improved genetic potential. Impact: Genomic-based breeding strategies reduce environmental impacts through lower methane-emitting ruminants and rumen microbiome utilization, while enhancing animal welfare via selection for stress resilience and innate disease resistance, reducing veterinary intervention. Conclusion: Overall, genomic approaches provide a powerful pathway for healthier, more productive, and sustainable livestock, supporting global food security amid climate and resource challenges.
Muhammad Younus· Zeugma Biological Science· 0 citations
Throughout human history, meat consumption has served as a critical driver of evolutionary encephalization, providing dense, highly bioavailable essential amino acids and micronutrients vital for human physiology. However, modern global livestock production faces mounting environmental and ethical challenges, accelerating academic and industrial interest in lab-grown (cultured) meat as a cellular agriculture alternative. This paper investigates the viability of cultured meat across nutritional, historical, technical, and consumer dimensions, complemented by a quantitative cross-sectional survey (N = 132) examining consumer attitudes, perceptions, and behavioral intent within Romania. Comprehensive desk research reveals major technical and economic bottlenecks; despite promises of land reduction, industrial growth media purification currently generates significant global warming potential while maintaining non-competitive production costs (17–38/kg). Furthermore, nutritional profiling of in-vitro tissue demonstrates key compositional disparities, including reduced indispensable amino acid density alongside elevated sodium and saturated fatty acids. Empirical survey results gathered in 2026 indicate a strong initial openness among a predominantly younger demographic, with 67.4% expressing a willingness to purchase cultured meat. Nonetheless, substantial psychological and perceptual barriers persist: 81.1% of respondents view cultured meat as inherently unnatural, 69.7% harbor severe concerns regarding long-term health risks, and 70.5% remain skeptical that cellular agriculture can replace conventional livestock farming within the next 50 years. Evaluated via five-point Likert scales, environmental sustainability (4.06/5.00) and animal welfare (3.97/5.00) emerged as the primary drivers of adoption, whereas health uncertainties (3.73/5.00) and retail pricing (3.57/5.00) remain significant deterrents. Ultimately, while conditional consumer openness exists, successful commercial transition requires key biotechnological enhancements, transition to renewable energy inputs, transparent ingredient disclosures, and proactive regulatory frameworks to address deep-seated consumer anxieties regarding food naturalness and long-term safety.
Unknown authors· EPRA International Journal o...· 0 citations
This review proposes an Africa-specific approach that develops locally grounded, scalable, and resource-sensitive precision nutrition strategies, strengthening antimicrobial stewardship, animal health, food safety, climate resilience, sustainable livestock production, and broader One Health objectives.
K. T. Ncube, F. Tugizimana· Agriculture· 0 citations
Simple Summary Growth and body conformation traits are important determinants of meat production and economic performance in sheep. Understanding their genetic basis can enhance breeding efficiency and support sustainable genetic improvement. In this study, we conducted a genome-wide association study (GWAS) to identify genomic regions associated with seven growth and body conformation traits in 401 sheep from four populations: Qira Black, Kyrgyz, Dorset × Hu crossbred, and Suffolk × Karakul crossbred sheep. After genotype quality control, 47,674 SNP markers were analyzed using a mixed linear model accounting for population structure and genetic relatedness. A total of 44 independent genomic regions were detected at a nominal significance threshold, containing 112 candidate genes potentially involved in skeletal development, cartilage formation, muscle growth, and metabolic regulation.
Erkinbay Azbergenov, Tao Jiang, Rui-zhi Yang et al.· Animals· 0 citations
Genomic selection (GS) has transformed modern animal breeding by enabling the prediction of genetic merit using dense genome-wide molecular markers rather than relying solely on pedigree and phenotypic information. Since its conceptual introduction in 2001, GS has become a cornerstone of genetic improvement programs in livestock species, particularly dairy cattle, and has subsequently expanded to beef cattle, sheep, goats, swine, poultry, and aquaculture. The integration of high-density single nucleotide polymorphism (SNP) genotyping with advanced statistical prediction models has substantially increased the accuracy of breeding value estimation, shortened generation intervals, and accelerated rates of genetic gain. Compared with conventional best linear unbiased prediction (BLUP) and marker-assisted selection (MAS), genomic selection captures the combined effects of thousands of loci distributed throughout the genome, making it highly effective for complex quantitative traits governed by many genes of small effect. Recent advances, including single-step genomic BLUP, Bayesian prediction methods, whole-genome sequence analysis, functional genomics, multi-omics integration, artificial intelligence, and precision livestock farming technologies, have further enhanced the scope and efficiency of genomic prediction. These innovations are facilitating simultaneous improvement in productivity, fertility, feed efficiency, disease resistance, animal welfare, and environmental sustainability. Moreover, genomic information is increasingly being integrated with genome editing technologies such as CRISPR to support precision breeding strategies. This review summarizes the historical evolution, fundamental principles, methodological developments, and practical applications of genomic selection in livestock breeding while highlighting emerging innovations and future research directions that are expected to shape next-generation animal improvement programs.
S. Pathak, Amit Kumar, Vaishali Sah· International Journal of Env...· 0 citations
Dairy cow performance in tropical production systems results from complex interactions among nutritional efficiency, postpartum health, reproductive management, and housing environment. Advancing sustainable dairy production therefore requires an integrated understanding of how these biological and management components influence productivity, resilience, and environmental outcomes. This thesis investigated key determinants of dairy system performance through four complementary studies combining controlled experimentation, large- scale retrospective analyses, and on-farm environmental assessment. The first study evaluated supplementation with the live yeast Saccharomyces cerevisiae CNCM I- 1077 and demonstrated improvements in rumen degradability of fibrous feeds, enhanced nutrient utilization, and greater feed efficiency. These findings indicate that optimizing rumen kinetics can improve metabolic efficiency and help mitigate environmental stress without necessarily altering microbial diversity. The second study analyzed retained placenta in commercial dairy herds under tropical conditions using a large retrospective dataset. Retained placenta was associated with cows’ breed, parity, and calving characteristics, and consistently resulted in reduced pregnancy per insemination, increased pregnancy loss, and greater risk of culling. These results confirm that postpartum disorders exert persistent effects on reproductive outcomes and herd longevity, highlighting the importance of preventive health strategies. The third study examined herd-level reproductive performance and showed that management intensity and housing system are major determinants of reproductive efficiency. More frequent reproductive monitoring was primarily associated with improved service rate and shorter intervals between inseminations, whereas compost barn and free stall systems had superior reproductive outcomes compared with dry lot systems. These findings emphasize that reproductive success in commercial herds is strongly related to management rather than fertility itself. The fourth study evaluated manure excretion dynamics in compost barn systems and demonstrated that the concentration of feces and urine within the bedding promotes composting and substantially reduces nitrogen requiring external treatment. This redistribution of nutrient flows enhances recycling efficiency and illustrates how housing design can simultaneously support environmental sustainability and animal welfare. Together, these studies demonstrate that improving dairy production in tropical environments requires a system-level approach integrating digestive efficiency, postpartum health, reproductive management, and production system design. Collectively, these findings highlight how nutrition, reproduction, management, and production system design shape productivity and sustainability in modern dairy systems. Keywords: dairy systems; herd management; reproductive efficiency; rumen function; sustainability; tropical production.
K. R. Oliveira· 0 citations
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