Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient–gene interactions in agricultural animals.

Methionine (Met), the second or third limiting amino acid (AA) in typical swine diets, plays important roles in promoting swine health and growth, especially, muscle growth. Whereas dl-Met products have been used in swine industry for many years, l-Met products have been developed recently. This research was conducted to study the effects of supplemental l-Met or dl-Met on nutrient metabolism, muscle gene expression, and growth performance of pigs. Twenty crossbred young barrows (initial body weight [BW] 21.2 ± 2.7 kg) were randomly assigned to 20 individual pens and two dietary treatments according to a completely randomized design with pigs serving as the experiment unit (n = 10). Two corn and soybean meal-based diets (diets 1 and 2) were formulated to meet or exceed the recommended requirements for energy, AA, and other nutrients (NRC. 2012. Nutrient requirements of swine, 11th ed. Washington, DC: The National Academies Press; AMINODat 5.0). Crystalline l-Met and dl-Met were supplemented to diets 1 and 2 (both at 0.13%, as-fed basis), respectively. After 4 wk of an ad libitum feeding trial, BW and feed intake were measured to calculate average daily gain (ADG), average daily feed intake (ADFI), and gain-to-feed ratio (G:F). Blood samples were collected from the jugular vein for analyses of plasma AA and metabolite concentrations. The longissimus dorsi muscle samples were collected for analysis of myogenesis gene expression. Data were analyzed using Student’s t-test. There were no differences (P = 0.56 to 0.94) in ADG, ADFI, or G:F between pigs fed the two experimental diets and no differences between diets were observed in plasma free AA concentrations. No differences were observed between pigs fed the two diets in expression of mRNA for eight myogenesis-related genes, which were myogenic differentiation 1, myogenin, myogenic factors 5, muscle regulatory factor 4 (a.k.a. myogenic factors 6), and myocyte enhancer factors 2A, 2B, 2C, and 2D. In conclusion, results of this experiment indicate that the bioefficacy of l-Met is not different from that of dl-Met, which is likely because of an efficient conversion of d-Met to l-Met by pigs.

Lysine is the first limiting amino acid (AA) in typical swine diets. Our previous research showed that dietary lysine restriction compromised the growth performance of late-stage finishing pigs, which was associated with the changes in plasma concentrations of nutrient metabolites and hormone insulin-like growth factor 1 (IGF-1). This study was conducted to investigate how dietary lysine restriction affects the plasma concentrations of selected metabolites and three anabolic hormones in growing pigs. Twelve individually penned young barrows (Yorkshire × Landrace; 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (n = 6). Two corn and soybean meal based diets were formulated to contain 0.65% and 0.98% standardized ileal digestible lysine as a lysine-deficient (LDD) and a lysine-adequate (LAD) diets, respectively. During the 8-week feeding trial, pigs had ad libitum access to water and their respective diets, and the growth performance parameters including average daily gain (ADG), average daily feed intake (ADFI), and gain-to-feed ratio (G:F) were determined. At the end of the trial, jugular vein blood was collected for plasma preparation. The plasma concentrations of free AA and six metabolites were analyzed with the established chemical methods, and the hormone concentrations were analyzed with the commercial ELISA kits. Data were analyzed with Student’s t-test. The ADG of LDD pigs was lower (P < 0.01) than that of LAD pigs, and so was the G:F (P < 0.05) since there was no difference in the ADFI between the two groups of pigs. In terms of free AA, the plasma concentrations of lysine, methionine, leucine, and tyrosine were lower (P < 0.05), while that of β-alanine was higher (P < 0.01), in the LDD pigs. The total plasma protein concentration was lower (P < 0.02) in the LDD pigs, whereas no differences were observed for the other metabolites between the two groups. No differences were observed in the plasma concentrations of growth hormone (GF), insulin, and IGF-1 between the two groups as well. These results indicate that the lack of lysine as a protein building block must be the primary reason for a reduced body protein synthesis and, consequently, the compromised G:F ratio and ADG. The changes in the plasma concentrations of total protein and four AA suggest that the compromised growth performance might be associated with some cell signaling and metabolic pathways that may not involve the GH/IGF-1 axis.

22This study was conducted to investigate how dietary lysine level affects the intramuscular 23 fat (IMF) content and fatty acid (FA) composition in late-stage finishing pigs. Nine crossbred 24 barrows (94.4 ± 6.7 kg BW) were randomly allotted to three treatment groups (n = 3). Three corn 25 and soybean-meal based diets were formulated to meet the NRC (2012) requirements for various 26 nutrients except for lysine, whose concentrations were 0.43%, 0.71%, and 0.98% (as-fed basis) 27for Diets 1 (lysine-deficient), 2 (lysine-adequate), and 3 (lysine-excess), respectively. After 5 28 weeks of ad libitum access to diets, pigs were harvested and longissimus dorsi samples were 29 collected. The IMF content and FA composition of the samples were analyzed by gas 30 chromatography. Results showed that the IMF content of the muscle was increased linearly (P < 31 0.05) with decreasing dietary lysine level from 0.98% to 0.43%. Dietary lysine level altered the 32 composition of FA, especially the unsaturated FA, in the muscle. Particularly, the percentages of 33 C18:1 n-9 and total mono-unsaturated FA were higher, while the percentages of C18:2 n-6 and 34 total poly-unsaturated FA were lower, in the muscle of the pigs fed Diet 1. Collectively, dietary 35 lysine deficiency increased the proportion of mono-unsaturated FA and decreased the proportion 36 of poly-unsaturated FA, which may benefit pork palatability. 37

This study was undertaken to investigate the effects of dietary lysine on the plasma concentrations of three growth-related hormones in pigs. Nine late-stage finishing barrows were assigned to three dietary treatments according to a completely randomized experimental design (3 pigs/treatment). Three corn and soybean meal-based diets were formulated to contain three levels of lysine, which were 0.43, 0.71, and 0.98% for Diets 1 (lysine deficient), 2 (lysine adequate), and 3 (lysine excess), respectively. The feeding trial lasted 4 weeks, during which the pigs were allowed ad libitum access to the diets and water. After the 4 weeks, blood was collected and plasma samples were obtained. Then, the plasma concentrations of insulin, growth hormone (GH), and insulin-like growth factor 1 (IGF-1) were measured. No difference in the plasma concentration of insulin or GH among the three treatments was found (P > 0.10). However, the plasma IGF-1 concentration was lower (P < 0.05) in the pigs fed Diet 1 or 3 than fed Diet 2, suggesting that either dietary lysine deficiency or excess can lead to a lower concentration of plasma IGF-1. It was concluded that IGF-1, instead of insulin or GH, in the blood may be a key controlling growth factor in response to dietary lysine supply for regulating muscle growth in late-stage finishing pigs.