Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes

Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BACKGROUND

The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities.

MAIN TEXT

Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability.

CONCLUSION

This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

Decoding epigenetic markers: implications of traits and genes through DNA methylation in resilience and susceptibility to mastitis in dairy cows

Cattle farming faces challenges linked to intensive exploitation and climate change, requiring the reinforcement of animal resilience in response to these dynamic environments. Currently, genetic selection is used to enhance resilience by identifying animals resistant to specific diseases; however, certain diseases, such as mastitis, pose difficulties in genetic prediction. This study introduced the utilization of enzymatic methyl sequencing (EM-seq) of the blood genomic DNA from twelve dairy cows to identify DNA methylation biomarkers, with the aim of predicting resilience and susceptibility to mastitis. The analysis uncovered significant differences between cows resilient and susceptible to mastitis, with 196,275 differentially methylated cytosines (DMCs) and 1,227 Differentially Methylated Regions (DMRs). Key genes associated with the immune response and morphological traits, including ENOPH1, MYL10 and KIR2DL5A, were identified by our analysis. Quantitative trait loci (QTL) were also highlighted and the body weight trait was the most targeted by DMCs and DMRs. Based on our results, the risk of developing mastitis can potentially be estimated with as few as fifty methylation biomarkers, paving the way for early animal selection. This research sets the stage for improved animal health management and economic yields within the framework of agricultural sustainability through early selection based on the epigenetic status of animals.

Embryonic temperature has long-term effects on muscle circRNA expression and somatic growth in Nile tilapia

Embryonic temperature has a lasting impact on muscle phenotype in vertebrates, involving complex molecular mechanisms that encompass both protein-coding and non-coding genes. Circular RNAs (circRNAs) are a class of regulatory RNAs that play important roles in various biological processes, but the effect of variable thermal conditions on the circRNA transcriptome and its long-term impact on muscle growth plasticity remains largely unexplored. To fill this knowledge gap, we performed a transcriptomic analysis of circRNAs in fast muscle of Nile tilapia (Oreochromis niloticus) subjected to different embryonic temperatures (24°C, 28°C and 32°C) and then reared at a common temperature (28°C) for 4 months. Nile tilapia embryos exhibited faster development and subsequently higher long-term growth at 32°C compared to those reared at 28°C and 24°C. Next-generation sequencing data revealed a total of 5,141 unique circRNAs across all temperature groups, of which 1,604, 1,531, and 1,169 circRNAs were exclusively found in the 24°C, 28°C and 32°C groups, respectively. Among them, circNexn exhibited a 1.7-fold (log2) upregulation in the 24°C group and a 1.3-fold (log2) upregulation in the 32°C group when compared to the 28°C group. Conversely, circTTN and circTTN_b were downregulated in the 24°C groups compared to their 28°C and 32°C counterparts. Furthermore, these differentially expressed circRNAs were found to have multiple interactions with myomiRs, highlighting their potential as promising candidates for further investigation in the context of muscle growth plasticity. Taken together, our findings provide new insights into the molecular mechanisms that may underlie muscle growth plasticity in response to thermal variation in fish, with important implications in the context of climate change, fisheries and aquaculture.

Intergenerational impact of dietary protein restriction in dairy ewes on epigenetic marks in the perirenal fat of their suckling lambs

In sheep, nutrition during the prepubertal stage is essential for growth performance and mammary gland development. However, the potential effects of nutrient restriction in a prepuberal stage over the progeny still need to be better understood. Here, the intergenerational effect of maternal protein restriction at prepubertal age (2 months of age) on methylation patterns was evaluated in the perirenal fat of Assaf suckling lambs. In total, 17 lambs from ewes subjected to dietary protein restriction (NPR group, 44% less protein) and 17 lambs from control ewes (C group) were analyzed. These lambs were ranked based on their carcass proportion of perirenal and cavitary fat and classified into HighPCF and LowPCF groups. The perirenal tissue from 4 NPR-LowPCF, 4 NPR-HighPCF, 4 C-LowPCF, and 4 C-HighPCF lambs was subjected to whole-genome bisulfite sequencing and differentially methylated regions (DMRs) were identified. Among other relevant processes, these DMRs were mapped in genes responsible for regulating the transition of brown to white adipose tissue and nonshivering thermoregulation, which might be associated with better adaptation/survival of lambs in the perinatal stage. The current study provides important biological insights about the intergenerational effect on the methylation pattern of an NPR in replacement ewes.

Environmental Pollutants and Oxidative Stress in Terrestrial and Aquatic Organisms: Examination of the Total Picture and Implications for Human Health

There is current great international concern about the contribution of environmental pollution to the global burden of disease particularly in the developing, low- and medium-income countries. Industrial activities, urbanization, developmental projects as well as various increased anthropogenic activities involving the improper generation, management and disposal of pollutants have rendered today's environment highly polluted with various pollutants. These pollutants include toxic metals (lead, cadmium, mercury, arsenic), polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pesticides and diesel exhaust particles most of which appear to be ubiquitous as well as have long-term environmental persistence with a wide range of toxicities such as oxidative stress among others. Oxidative stress, which may arise from increased production of damaging free radicals emanating from increased pollutant burden and depressed bioavailability of antioxidant defenses causes altered biochemical and physiological mechanisms and has been implicated in all known human pathologies most of which are chronic. Oxidative stress also affects both flora and fauna and plants are very important components of the terrestrial environment and significant contributors of nutrients for both man and animals. It is also remarkable that the aquatic environment in which sea animals and creatures are resident is also highly polluted, leading to aquatic stress that may affect the survival of the aquatic animals, sharing in the oxidative stress. These altered terrestrial and aquatic environments have an overarching effect on human health. Antioxidants neutralize the damaging free radicals thus, they play important protective roles in the onset, progression and severity of the unmitigated generation of pollutants that ultimately manifest as oxidative stress. Consequently, human health as well as that of aquatic and terrestrial organisms may be protected from environmental pollution by mitigating oxidative stress and employing the principles of nutritional medicine, essentially based on antioxidants derived mainly from plants, which serve as the panacea of the vicious state of environmental pollutants consequently, the health of the population. Understanding the total picture of oxidative stress and integrating the terrestrial and aquatic effects of environmental pollutants are central to sustainable health of the population and appear to require multi-sectoral collaborations from diverse disciplinary perspectives; basically the environmental, agricultural and health sectors.