Identifying the future needs for long-term USDA efforts in agricultural animal genomics

Emerging trends and applications of metabolomics in food science and nutrition

The study of all chemical processes involving metabolites is known as metabolomics. It has been developed into an essential tool in several disciplines, such as the study of plant physiology, drug development, human diseases, and nutrition. The field of food science, diagnostic biomarker research, etiological analysis in the field of medical therapy, and raw material quality, processing, and safety have all benefited from the use of metabolomics recently. Food metabolomics includes the use of metabolomics in food production, processing, and human diets. As a result of changing consumer habits and the rising of food industries all over the world, there is a remarkable increase in interest in food quality and safety. It requires the employment of various technologies for the food supply chain, processing of food, and even plant breeding. This can be achieved by understanding the metabolome of food, including its biochemistry and composition. Additionally, Food metabolomics can be used to determine the similarities and differences across crop kinds, as an indicator for tracking the process of ripening to increase crops' shelf life and attractiveness, and identifying metabolites linked to pathways responsible for postharvest disorders. Moreover, nutritional metabolomics is used to investigate the connection between diet and human health through detection of certain biomarkers. This review assessed and compiled literature on food metabolomics research with an emphasis on metabolite extraction, detection, and data processing as well as its applications to the study of food nutrition, food-based illness, and phytochemical analysis. Several studies have been published on the applications of metabolomics in food but further research concerning the use of standard reproducible procedures must be done. The results published showed promising uses in the food industry in many areas such as food production, processing, and human diets. Finally, metabolome-wide association studies (MWASs) could also be a useful predictor to detect the connection between certain diseases and low molecular weight biomarkers.

Effects of age on subcutaneous adipose tissue proteins in Chinese indigenous Ningxiang pig by TMT-labeled quantitative proteomics

Adipose tissue not only affects meat quality and animal productivity, but also participates in inflammation and immunity. Ningxiang pig is famous for their excellent meat quality, disease resistance and tolerance of roughage. It is not yet well known how proteins in adipose tissue is dynamically regulated during the growth of Ningxiang pig. This report studies the proteomic changes in subcutaneous adipose tissue in Ningxiang pigs to gain a better understanding of the molecular mechanism of fat development during the growth period. By TMT-labeled quantitative proteomic analysis of subcutaneous adipose tissue of 9 purebred Ningxiang pigs of different ages, we identified 2533 unique proteins and 716 differentially abundant proteins (DAPs), of which more than half of the DAPs were concentrated in the 90d-210d period. Retrograde endocannabinoid signaling was only significantly enriched in DAPs of N90d vs N30d, Alcoholism and Graft-versus-host disease were only significantly enriched in DAPs of N210d vs N90d. Proteins related to dilated cardiomyopathy was found to be an important pathway in fat development and lipid metabolism. A variety of novel DAPs involved in maintaining mitochondrial function and cell viability, such as NDUFS6, SDHB, COX5A, ATP5D and TNNT1, which play a role in controlling the prediction networks, may indirectly regulate the development and functional maintenance of adipocytes. SIGNIFICANCE: These age-dependent DAPs discovered in this study may help expand the understanding of the molecular mechanisms of the development, function maintenance and transformation of adipose tissue in Ningxiang pig for developing new strategies for improving meat quality and pig breeding in the future.

Sequencing technologies and genome sequencing

The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.

MicroRNAome of porcine pre- and postnatal development

The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies.

Precision genetics for complex objectives in animal agriculture

Indirect modification of animal genomes by interspecific hybridization, cross-breeding, and selection has produced an enormous spectrum of phenotypic diversity over more than 10,000 yr of animal domestication. Using these established technologies, the farming community has successfully increased the yield and efficiency of production in most agricultural species while utilizing land resources that are often unsuitable for other agricultural purposes. Moving forward, animal well-being and agricultural sustainability are moral and economic priorities of consumers and producers alike. Therefore, these considerations will be included in any strategy designed to meet the challenges produced by global climate change and an expanding world population. Improvements in the efficiency and precision of genetic technologies will enable a timely response to meet the multifaceted food requirements of a rapidly increasing world population.

Flexi vector cloning

A protocol for ligation-dependent cloning using the Flexi Vector method in a 96-well format is described. The complete protocol includes PCR amplification of the desired gene to append Flexi Vector cloning sequences, restriction digestion of the PCR products, ligation of the digested PCR products into a similarly digested acceptor vector, transformation and growth of host cells, analysis of the transformed clones, and storage of a sequence-verified clone. The protocol also includes transfer of the sequence-verified clones into another Flexi Vector plasmid backbone. Smaller numbers of cloning reactions can be undertaken by appropriate scaling of the indicated reaction volumes.

Challenges of functional genomics applied to farm animal gametes and pre-hatching embryos

The genomes of many commercially important farm animals have already been or are in the process of being decrypted. The genomic era is generating an important wave of downstream developments and derived disciplines are also progressing at a very fast pace. The post-genomic era is already ongoing as exemplified by the introduction of new concepts such as phenomics and functional genomics. These new fields are complementary but do not necessarily target similar applications even though they are often used to refer to one another. In an attempt to categorize the fields according to their respective potential applications, a brief comparative description of phenomics and functional genomics has been put together. However, the focus of this paper is mainly directed toward the introduction of functional genomics specifically applied to the study of the molecular mechanisms underlying gamete and early mammalian developments. Many aspects of the peculiar nature of these cells are introducing numerous methodological challenges to the applicability of functional genomics to unravel their molecular physiology. This is particularly true for transcriptomic studies and it is currently of high relevance for the field of reproductive biology to take into consideration these technical hurdles before tackling the implementation of this technology on a large scale. Nonetheless, functional genomics should prove to be up to the expectations in providing sound information to better understand the fascinating window spanning gamete development that leads to the first weeks of life.

Impact of genomics on animal agriculture and opportunities for animal health

Livestock production is an important source of animal protein worldwide. In the developed world meat consumption will remain steady but demand is forecast to grow enormously in developing countries. The use of genomics will speed genetic improvement and increase levels of production quickly in the developed world but might face problems in the developing world, including scientific, economic and political challenges. Considerable increases in public and private research funding will be required to develop and utilize novel tools and collections of detailed trait information on appropriate animals. The development of policies protecting the environment and managing all genetic resources will also be needed. Advances in livestock genomics have major implications for increasing food output as well as improving human health.

Swine genome science comes of age

Pigs were among the first animals to be domesticated and pork is one of the most widely eaten meats in the world today. The pig has also been an excellent biomedical model for understanding a variety of human health issues such as obesity, diabetes, cancer, female reproductive health, cardiovascular disease, and infectious diseases. Genome sequencing, mapping, expression and functional analyses have significantly advanced our ability to unravel the secrets of the pig. Therefore, this edition, with six reviews from leading scientists, offers the opportunity for all interested researchers and readers to see the big picture of porcine genomics.