J. E. Sawyer

Cellular regulation of bovine intramuscular adipose tissue development and composition.

It is well documented that grain feeding stimulates adipogenesis in beef cattle, whereas pasture feeding depresses the development of adipose tissues, including intramuscular (i.m.) adipose tissue. Additionally, production practices that depress adipocyte differentiation also limit the synthesis of MUFA. Marbling scores and MUFA increase in parallel suggesting that stearoyl-coenzyme A desaturase (SCD) gene expression is closely associated with and necessary for marbling adipocyte differentiation. Similarly, marbling scores and fatty acid indices of SCD activity are depressed in response to dietary vitamin A restriction. In bovine preadipocytes, vitamins A and D both decrease glycerol-3-phosphate dehydrogenase (GPDH) activity, an index of adipocyte differentiation, whereas incubation of bovine preadipocytes with l-ascorbic acid-2-phosphate increases GPDH activity. Exposing bovine preadipocytes to zinc also stimulates adipogenesis, putatively by inhibiting nitric oxide (NO) production. However, incubation of bovine preadipocytes with arginine, a biological precursor of NO, strongly promotes differentiation in concert with increased SCD expression. This suggests that the effect of either arginine or zinc on adipogenesis is independent of NO synthesis in bovine preadipocytes. Enhanced expression of SCD is associated with a greater accumulation of MUFA both in bovine preadipocyte cultures and during development in growing steers. In bovine preadipocytes, trans-10, cis-12 CLA strongly depresses adipocyte differentiation and SCD gene expression, thereby reducing MUFA concentrations. The bovine preadipocyte culture studies suggest that any production practice that elevates vitamins A or D or trans-10, cis-12 CLA in bovine adipose tissue will reduce i.m. adipose tissue development. Conversely, supplementation with vitamin C or zinc may promote the development of i.m. adipose tissue.

Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

We present a new transcriptome assembly of the Pacific whiteleg shrimp (Litopenaeus vannamei), the species most farmed for human consumption. Its functional annotation, a substantial improvement over previous ones, is provided freely. RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality of this assembly and the affiliated targeted homology searches greatly enrich the curated transcripts currently available in public databases for this species. Comparison with the model arthropod Daphnia allows some insights into defining characteristics of decapod crustaceans. This large-scale gene discovery gives the broadest depth yet to the annotated transcriptome of this important species and should be of value to ongoing genomics and immunogenetic resistance studies in this shrimp of paramount global economic importance.

Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare

BackgroundThe catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing.ResultsUsing massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horses genome was enriched in sensory perception, signal transduction, and immunity and defense pathways.ConclusionsThis is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

Effects of Fertility on Gene Expression and Function of the Bovine Endometrium

Infertility and subfertility are important and pervasive reproductive problems in both domestic animals and humans. The majority of embryonic loss occurs during the first three weeks of pregnancy in cattle and women due, in part, to inadequate endometrial receptivity for support of embryo implantation. To identify heifers of contrasting fertility, serial rounds of artificial insemination (AI) were conducted in 201 synchronized crossbred beef heifers. The heifers were then fertility classified based on number of pregnancies detected on day 35 in four AI opportunities. Heifers, classified as having high fertility, subfertility or infertility, were selected for further study. The fertility-classified heifers were superovulated and flushed, and the recovered embryos were graded and then transferred to synchronized recipients. Quantity of embryos recovered per flush, embryo quality, and subsequent recipient pregnancy rates did not differ by fertility classification. Two in vivo-produced bovine embryos (stage 4 or 5, grade 1 or 2) were then transferred into each heifer on day 7 post-estrus. Pregnancy rates were greater in high fertility than lower fertility heifers when heifers were used as embryo recipients. The reproductive tracts of the classified heifers were obtained on day 14 of the estrous cycle. No obvious morphological differences in reproductive tract structures and histology of the uterus were observed in the heifers. Microarray analysis revealed differences in the endometrial transcriptome based on fertility classification. A genome-wide association study, based on SNP genotyping, detected 7 moderate associations with fertility across 6 different chromosomes. Collectively, these studies support the idea that innate differences in uterine function underlie fertility and early pregnancy loss in ruminants. Cattle with defined early pregnancy success or loss is useful to elucidate the complex biological and genetic mechanisms governing endometrial receptivity and uterine competency for pregnancy.

Impact of the Ethanol Boom on Livestock and Dairy Industries: What Are They Going to Eat?

Increased demand for corn for ethanol production has helped push grain prices to record levels. This has increased livestock production costs, and producers have responded with changes to production systems. This paper explores the degree to which costs can be mitigated with alternative feeds, the effect this might have on physical performance, and the impact of alternative feeds on the competitive position of different species.

Adipogenic gene expression and fatty acid composition in subcutaneous adipose tissue depots of Angus steers between 9 and 16 months of age

We have demonstrated that among carcass adipose tissue depots, brisket subcutaneous adipose tissue contains the greatest concentration of MUFA and lowest concentration of SFA. Therefore, we hypothesized that brisket subcutaneous adipose tissue depots would exhibit greater adipogenic gene expression over time than other major subcutaneous adipose tissue depots. Four Angus steers, each at 9, 12, 14, and 16 mo of age, were harvested and fresh subcutaneous adipose tissue samples were collected from over the brisket, chuck, rib, loin, sirloin, round, flank, and plate. Relative gene expression for C/EBPβ, PPARγ, carnitine palmitoyltransferase-1 beta (CPT-1β), stearoyl-coenzyme A desaturase (SCD), AMP-activated protein kinase alpha (AMPKα), and G-coupled protein receptor 43 (GPR43) was analyzed by quantitative real-time PCR. Expression of C/EBPβ, PPARγ, and CPT-1β was greatest at 12 to 14 mo of age (all P < 0.0001) and declined to very low abundance by 16 mo of age in all depots. Expression of PPARγ and CPT-1β was greater (P < 0.03) in flank, rib, and sirloin subcutaneous adipose tissues than in brisket and round adipose tissues. The expression of the SCD gene did not differ among the 4 age groups (P = 0.95). The palmitoleic:stearic acid ratio (an estimate of SCD activity) was greater (P < 0.001) in the subcutaneous adipose tissues from brisket, plate, and round than in the loin, rib, and sirloin. Conversely, subcutaneous adipose tissue from the loin, rib, and sirloin had greater (P < 0.001) SCD gene expression than the brisket, plate, and round. In general, subcutaneous adipose tissues with the highest concentration of MUFA and least SFA consistently exhibited the least SCD gene expression and adipogenic gene expression. We conclude that MUFA in the brisket and other depots with large SCD indices were deposited before 9 mo of age, during a time when the subcutaneous adipocytes were highly differentiated.

Effect of increasing amounts of postextraction algal residue on straw utilization in steers

Algal biomass has been identified as a third-generation biofuel. Significant quantities of the coproduct postextraction algal residue (PEAR) remain after lipid extraction. After extraction, PEAR is concentrated in protein (17.9% CP on a DM basis and 32.5% CP on an ash-free basis), suggesting it may be an alternative to cottonseed meal (CSM) as a protein supplement. Our objectives were to determine the optimal level of PEAR supplementation to steers consuming straw and to compare the effects of PEAR supplementation on straw utilization and N metabolism with an isonitrogenous level of CSM. Five steers (198.2 ± 6.1 kg of BW), in a 5 × 5 Latin square, had ad libitum access to oat straw (80% NDF and 4.5% CP on a DM basis). Treatments were infused ruminally once daily and included no supplemental protein (CON); PEAR at 50, 100, and 150 mg N/kg BW; and CSM at 100 mg N/kg BW. Provision of PEAR increased total digestible OM intake (TDOMI) quadratically (P = 0.01) from 0.9 (CON) to 1.6 kg/d (100 mg N/kg BW of PEAR). Organic matter digestibility (OMD) increased quadratically (P < 0.01) with supplementation and was maximized (55% OMD) at 50 mg N/kg BW of PEAR. At isonitrogenous levels of PEAR and CSM, TDOMI was similar (P = 0.13) as was OMD (P = 0.50). Negative N balance was observed for all treatments except PEAR provided at 100 or 150 mg of N/kg BW. Nitrogen balance was quadratic (P < 0.01) with the greatest retention (1.84 g N/d) occurring at 100 mg N/kg BW of PEAR. There were no differences (P ≥ 0.22) between isonitrogenous PEAR and CSM supplementation in measurements of ruminal ammonia or VFA concentrations. Straw utilization was maximized when PEAR was provided at 100 mg N/kg BW. Our observations suggest cattle provided PEAR utilize straw in a manner similar to those supplemented CSM, indicating PEAR has potential to substitute for CSM as a protein supplement in forage-based operations.

Effect of postextraction algal residue supplementation on the ruminal microbiome of steers consuming low-quality forage

Cattle consuming low-quality forages (LQF) require protein supplementation to increase forage utilization via ruminal fermentation. Biofuel production from algal biomass results in large quantities of postextraction algal residue (PEAR), which has the potential to elicit LQF utilization responses similar to cottonseed meal (CSM); however, its effect on ruminal bacterial communities is unknown. Five ruminally and duodenally cannulated Angus steers in a 5 × 5 Latin square had ad libitum access to oat straw diets. Treatments were infused ruminally and consisted of an unsupplemented control; PEAR at 50, 100, and 150 mg N/kg BW; and CSM at 100 mg N/kg BW. Ruminal samples were collected 4 h after supplementation on d 14 of each period and separated into solid and liquid fractions. Each sample was extracted for genomic DNA, PCR amplified for the V4 to V6 region of the 16S rRNA, sequenced on the 454 Roche pyrosequencing platform, and analyzed using the QIIME pipeline. Weighted UniFrac analysis and Morisita-Horn index demonstrated different community composition between liquid and solid fractions. Measures of richness including observed operational taxonomic units (OTU) and abundance coverage estimator metric decreased with greater PEAR provision (P ≤ 0.09). There were 42 core microbiome OTU observed in all solid fraction samples while the liquid fraction samples contained 30 core OTU. Bacteroidetes was the predominant phylum followed by Firmicutes in both fractions, which together characterized more than 90% of sequences. Relative abundance of Firmicutes increased with PEAR supplementation in the liquid fraction (linear, P = 0.02). Among Firmicutes, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae families increased in the liquid fraction with greater PEAR supplementation (linear, P ≤ 0.03). Prevotella represented over 25% of sequences in all treatments, and relative abundance decreased in the solid fraction with increasing PEAR provision (linear, P = 0.01). Fibrobacter and Treponema decreased in the liquid fraction with increasing PEAR (linear, P < 0.10). Results suggest PEAR supplementation increased forage utilization by increasing members of Firmicutes within the liquid fraction of the rumen microbiome.

Effects of different growing diets on performance, carcass characteristics, insulin sensitivity, and accretion of intramuscular and subcutaneous adipose tissue of feedlot cattle

Forty-eight individually fed crossbred steers (British and British x Continental; BW=296+/-16.7 kg) were used to evaluate effects of different growing diets on changes in accretion of intramuscular (IMF) and subcutaneous (SCF) adipose tissues, insulin sensitivity, and carcass traits. Dietary treatments were AL-LC (a low-corn diet fed to allow cattle ad libitum access to feed), AL-HC (a high-corn diet fed to allow cattle ad libitum access to feed), LF-HC (a limit fed high-corn diet with the energy intake equal to that provided by AL-LC), and AL-IC (a diet with approximately the midpoint daily energy intake between AL-LC and AL-HC). Steers received treatments until d 56, after which all groups were fed AL-HC until d 140. Real-time ultrasound and BW measurements were taken every 28 d, and 3 glucose tolerance tests (GTT) were conducted on d 0, 28, and 56 of the growing period to assess insulin sensitivity. Based on ultrasound IMF and SCF readings during the growing phase, AL-HC and AL-IC increased accretion of IMF (P=0.01), and AL-LC and LF-HC diets resulted in less accretion of SCF (P<0.01) compared with other treatments. During the finishing period, accretion of IMF (P=0.13) and SCF (P=0.81) did not differ among treatments, which diluted differences in overall (d 0 to 140) accretion of IMF (P=0.28) and SCF (P=0.52), such that final real-time ultrasound measures of IMF and SCF did not differ (P >or= 0.36) among treatments. Actual carcass marbling scores, however, were greater for the AL-HC and AL-IC treatments (P=0.02), and 12th-rib fat thickness tended (P=0.08) to be greater for AL-HC and AL-IC groups. Based on incremental area under the curve and area over the curve as indicators of insulin release and glucose uptake, respectively, no differences (P >or= 0.10) in insulin sensitivity were observed among treatments. Our results suggest that high-corn diets increase growing phase accretion of IMF and SCF; however, these differences were not related to differences in glucose and insulin kinetics.

Fatty acid biosynthesis and lipogenic enzyme activities in subcutaneous adipose tissue of feedlot steers fed supplementary palm oil or soybean oil

We hypothesized that supplementing finishing diets with palm oil would promote adipocyte differentiation in subcutaneous adipose tissue of feedlot steers, and that soybean oil supplementation would depress adipocyte differentiation. Twenty-eight Angus steers were assigned randomly to 3 groups of 9 or 10 steers and fed a basal diet without additional fat (control), with 3% palm oil (rich in palmitic acid), or with 3% soybean oil (rich in polyunsaturated fatty acids), for 10 wk, top-dressed daily. Palm oil had no effect (P > 0.05) on ADG, food intake, or G:F, whereas soybean oil depressed ADG (P = 0.02), food intake (P = 0.04), and G:F (P = 0.05). Marbling scores tended (P = 0.09) to be greater in palm oil-fed steers (Modest(09)) than in soybean oil-fed steers (Small(55)). Subcutaneous adipocyte mean volume was greater in palm oil-fed steers (515.9 pL) than in soybean-supplemented cattle (395.6 pL; P = 0.01). Similarly, glucose and acetate incorporation into total lipids in vitro was greater in subcutaneous adipose tissue of palm oil-fed steers (119.9 and 242.8 nmol·3h(-1)·10(5) cells, respectively) than adipose tissue of soybean oil-fed steers in (48.9 and 95.8 nmol·3h(-1)·10(5) cells, respectively). Glucose-6-phosphate dehydrogenase and NADP-malate dehydrogenase activities were greater (P ≤ 0.05) in subcutaneous adipose tissue of palm oil-fed steers than in adipose tissue of control steers. Palm oil did not increase palmitic acid or decrease oleic acid in subcutaneous adipose tissue or LM, but decreased (P ≤ 0.05) myristoleic, palmitoleic, and cis-vaccenic acid in adipose tissue, indicating a depression in stearoyl-coenzyme A desaturase activity. Soybean oil increased the proportion of α-linolenic acid in adipose tissue and muscle and increased linoleic acid and 18:1trans-10 in muscle. We conclude that palm oil supplementation promoted lipid synthesis in adipose tissue without depressing feed efficiency or increasing the palmitic acid content of beef.