Muscle transcriptomic analyses in Angus cattle with divergent tenderness

Beef tenderness contributes significantly to variation of beef palatability, and is largely influenced by various genetic and environmental factors. To identify candidate genes and pathways related to beef tenderness, we analyzed the longissimus dorsi (LD) muscle of Angus cattle that had different degrees of tenderness, measured by Warner-Bratzler shear force (WBSF). Microarray and RT-PCR analyses identified 53 genes that were differentially expressed in LD samples categorized as either tough or tender, including myosin, heavy chain 3 skeletal muscle embryonic (MYH3), myosin heavy chain 8 skeletal muscle perinatal (MYH8), guanylate binding protein 5 (GBP5), fatty acid binding protein 4 (FABP4), Stearoyl-coenzyme A desaturase (SCD), Fatty acid synthase (FASN), ubiquitin-like with PHD and ring finger domains 1 (UHRF1). Most of these genes are involved in lipid metabolism and skeletal muscle contraction. Employing Gene ontology (GO) and Ingenuity Pathway Analysis (IPA), several GO terms and pathways were found to be related to hydrolase, peptidase and GTPase activity, lipid metabolism, small molecule biochemistry, molecular transport, and tissue development. Overall, this analysis provides insight into the metabolic relationships between muscle biology and beef quality.     

Genetic variants in a lipid regulatory pathway as potential tools for improving the nutritional quality of grass‐fed beef

The aim of this study was to evaluate the effect of genetic variants on candidate genes corresponding to the sterol recognition element–binding protein‐1 (SREBP‐1) signaling pathway and stearoyl‐CoA desaturases (SCD1 and SCD5) on muscle fatty acid (FA) composition of Brangus steers fattened on grass. FA profiles were measured on Longissimus lumborum muscle samples using a gas chromatography–flame ionization detection technique. A total of 43 tag single‐nucleotide polymorphisms on the SCD1, SCD5, SREBP‐1, SCAP, INSIG1, INSIG2, MBTPS1, MBTPS2, and SRPR genes were genotyped on 246 steers to perform a marker–trait association study. To evaluate the influence of the Indicine breed in the composite breed, additional groups of 48 Angus, 18 Hereford, 75 Hereford x Angus, and 36 Limousin x Hereford–Angus steers were also genotyped. To perform the association analysis, FA data were grouped according to the number of carbon atoms and/or number of double bonds (i.e. SFA, MUFA, PUFA, etc.). In addition, different indexes that reflect the activity of FA desaturase and elongase enzymes were calculated. SCD1 markers significantly affected C14:1/(C14:0 + C14:1) and C18:1/(C18:0 + C18:1) indexes, whereas one SNP in SCD5 was correlated with the C16:1/(C16:0 + C16:1) index. Polymorphisms in the signal recognition particle receptor (SRPR) gene were associated with all the estimated desaturase indexes. Because the evaluated markers showed no effect on total lipid content of beef, this work supports the potential utilization of these markers for the improvement of grass‐fed beef without undesirable side effects.     

Dominance effects of ion transport and ion transport regulator genes on the final weight and backfat thickness of Landrace pigs by dominance deviation analysis

Although there have been plenty of dominance deviation analysis, few studies have dealt with multiple phenotypes. Because researchers focused on multiple phenotypes (final weight and backfat thickness) of Landrace pigs, the classification of the genes was possible. With genome-wide association studies (GWASs), we analyzed the additive and dominance effects of the single nucleotide polymorphisms (SNPs). The classification of the pig genes into four categories (overdominance in final weight, overdominance in backfat thickness and overdominance in final weight, underdominance in backfat thickness, etc.) can enable us not only to analyze each phenotype’s dominant effects, but also to illustrate the gene ontology (GO) analysis with different aspects. We aimed to determine the additive and dominant effect in backfat thickness and final weight and performed GO analysis. Using additive model and dominance deviation analysis in GWASs, Landrace pigs’ overdominant and underdominant SNP effects in final weight and backfat thickness were surveyed. Then through GO analysis, we investigated the genes that were classified in the GWASs. The major GO terms of the underdominant effects in final weight and overdominant effects in backfat thickness were ion transport with the SLC8A3, KCNJ16, P2RX7 and TRPC3 genes. Interestingly, the major GO terms in the underdominant effects in the final weight and the underdominant effects in the backfat thickness were the regulation of ion transport with the STAC, GCK, TRPC6, UBASH3B, CAMK2D, CACNG4 and SCN4B genes. These results demonstrate that ion transport and ion transport regulation genes have distinct dominant effects. Through GWASs using the mode of linear additive model and dominance deviation, overdominant effects and underdominant effects in backfat thickness was contrary to each other in GO terms (ion transport and ion transport regulation, respectively). Additionally, because ion transport and ion transport regulation genes are associative with adipose tissue accumulation, we could infer that these two groups of genes had to do with unique fat accumulation mechanisms in Landrace pigs.     

Tick susceptibility and its effects on growth performance and carcass characteristics of Nguni, Bonsmara and Angus steers raised on natural pasture

The objective of the current study was to compare tick loads, growth and carcass characteristics of dipped and non-dipped Nguni, Bonsmara and Angus steers raised on natural pasture. One hundred 7-month-old castrated weaners were kept at the University of Fort Hare Farm for 12 months. There were 30 weaners each of Angus and Bonsmara, and 40 weaners of the Nguni breed. Half the Bonsmara, Angus and 14 Nguni weaners were dipped every fortnight. The rest were not dipped. Monthly weights and tick counts under the tail, on scrotum, belly, sternum and ears of the steers were recorded. The dipped Nguni steers had lowest (P < 0.05) tick counts, and the non-dipped Angus steers had the highest (P < 0.05) tick counts. There were more ticks (P < 0.05) during the warm wet season than during the cool dry season. Ears had the highest (P < 0.05) tick infestation. Average daily gain (ADG) was similar (P > 0.05) among the three breeds. The non-dipped Bonsmara steers had the heaviest (P < 0.05) carcasses (142 ± 5.4) while the non-dipped Nguni steers had the lightest (P < 0.05) carcasses (111 ± 4.5 kg). The non-dipped Bonsmara had the highest (P < 0.05) eye muscle area (3996 ± 120.8 mm2) while the non-dipped Angus had the smallest (P < 0.05) eye muscle area (3291 ± 210.6 mm2). The non-dipped Bonsmara also had the highest (P < 0.05) dressing percentage (53.8 ± 1.01) while the non-dipped Nguni had the lowest (P < 0.05) dressing percentage (50.3 ± 0.84). The current study has shown that while the non-dipped steers had higher (P < 0.05) tick loads than the dipped steers, their growth and carcass characteristics were similar (P > 0.05). The study has also shown that, despite being a small-framed breed, the Nguni steers had similar (P > 0.05) ADG to the large-framed Bonsmara and Angus steers. Therefore, the Nguni cattle have the potential to produce organic beef. However, a reasonable assessment of organic beef production potential of the Nguni requires an evaluation of its meat quality traits under natural pasture.     

Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle

Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle.     

RNA-Seq Analysis of Abdominal Fat Reveals Differences between Modern Commercial Broiler Chickens with High and Low Feed Efficiencies

For economic and environmental reasons, chickens with superior feed efficiency (FE) are preferred in the broiler chicken industry. High FE (HFE) chickens typically have reduced abdominal fat, the major adipose tissue in chickens. In addition to its function of energy storage, adipose tissue is a metabolically active organ that also possesses endocrine and immune regulatory functions. It plays a central role in maintaining energy homeostasis. Comprehensive understanding of the gene expression in the adipose tissue and the biological basis of FE are of significance to optimize selection and breeding strategies. Through gene expression profiling of abdominal fat from high and low FE (LFE) commercial broiler chickens, the present study aimed to characterize the differences of gene expression between HFE and LFE chickens. mRNA-seq analysis was carried out on the total RNA of abdominal fat from 10 HFE and 12 LFE commercial broiler chickens, and 1.48 billion of 75-base sequence reads were generated in total. On average, 11,565 genes were expressed (>5 reads/gene/sample) in the abdominal fat tissue, of which 286 genes were differentially expressed (DE) at q (False Discover Rate) < 0.05 and fold change > 1.3 between HFE and LFE chickens. Expression levels from RNA-seq were confirmed with the NanoString nCounter analysis system. Functional analysis showed that the DE genes were significantly (p < 0.01) enriched in lipid metabolism, coagulation, and immune regulation pathways. Specifically, the LFE chickens had higher expression of lipid synthesis genes and lower expression of triglyceride hydrolysis and cholesterol transport genes. In conclusion, our study reveals the overall differences of gene expression in the abdominal fat from HFE and LFE chickens, and the results suggest that the divergent expression of lipid metabolism genes represents the major differences.     

Comparative effects of feeding citrus pulp and grape pomace on nutrient digestibility and utilization in steers

Feedlot beef production in tropics and subtropics is being limited by shortage of feed ingredients due to prolonged droughts resulting in high prices of cereal grains and reduced profitability. To alleviate feed shortages and increase profitability for the feedlot industry, it is important to explore underutilized non-conventional resources such as fruit by-products. The current study compared the nutrient intake, digestibility and utilization effects of feeding either 150 g/kg of dried citrus pulp (DCP) or grape pomace (DGP) as alternative dietary fibre sources to 7 months-old Angus steers (281 ± 15.7 kg) under feedlot conditions. Twenty-four steers were assigned to three dietary treatments (8 steers/treatment) in a completely randomised design. Each steer was treated as an experimental unit. Steers were adapted to diets for 21 d followed by 7 d of sample collection during which nutrient intake, digestibility, rumen fermentation parameters, nitrogen retention and microbial N supply were determined. All the data were analysed using the GLIMMIX procedures. Overall, steers fed DGP had the greatest dry matter intake (DM), organic matter (OM) crude protein (CP), ash free neutral detergent fibre (aNDFom), ether extract (EE) and starch intake followed by DCP and control (CON) diets (P ≤ .05). Apparent digestibilities of DM, OM and aNDFom were higher (P ≤ .05) for DCP diet compared to DGP and CON diets. Feeding DCP and DGP diets increased ruminal concentrations of total volatile fatty acids, acetate and isovalerate, and acetate to propionate ratio, and reduced propionate concentrations compared to the CON diet (P ≤ .05). The steers fed the CON diet had the greatest urinary excretions of allantoin, uric acid and total purine derivatives followed by those fed the DCP and DGP diets (P ≤ .05). Nitrogen intake, faecal nitrogen (N), N retention and N efficiency utilization were in the order of DGP > DCP > CON diets (P ≤ .05). Overall, feeding DGP as alternative fibre source to wheat bran improved nutrient intake, retention and efficiency of N utilization but reduced apparent nutrient digestibility compared to DCP. Current finding suggests that DGP may be a better fibre substitute for wheat bran in beef diets than DCP.     

玫烟色棒束孢诱导的小菜蛾免疫响应表达谱分析

【目的】本研究旨在筛选小菜蛾Plutella xylostella应对玫烟色棒束孢Isaria fumosorosea侵染的免疫应答及其网络调控基因,以进一步探讨小菜蛾对玫烟色棒束孢的防御机制。【方法】采用第二代高通量测序技术RNA-seq,对处理后12 h的感染玫烟色棒束孢和健康(平行对照)的小菜蛾4龄幼虫转录组进行了测序,通过生物信息学分析对得到的差异基因进行了功能注释和分类,对差异基因参与的信号通路进行了分析。【结果】在感菌和健康小菜蛾幼虫转录组两个表达谱里,分别获得了12 346 987和12 315 210个clean reads,有60.93%和61.26%的reads分别能比对到参考基因库里,其中完美匹配(perfect match)的比例分别为32.15%和32.73%。共得到351个显著差异表达基因(differentially expressed unigenes,DEUs),上调表达基因有275个,下调表达基因有76个,与免疫防御反应潜在相关的基因有156个。GO(Gene Ontology)富集分析有102个DEUs分布到46个GO term里,KEGG(Kyoto Encyclopedia of Genes and Genomes)pathway富集分析结果显示,有132个DEUs显著富集在13个代谢通路(pathway)里。【结论】这些差异表达基因中,大部分编码潜在的与免疫识别及调控相关的基因,集中在能量代谢、疾病反应和防御反应等相关通路。研究结果为挖掘与玫烟色棒束孢侵染相关的小菜蛾免疫应答候选基因提供了重要数据库,也为阐明小菜蛾对玫烟色棒束孢的免疫机制奠定理论基础。     

The effect of trans-10, cis-12 conjugated linoleic acid on gene expression profiles related to lipid metabolism in human intestinal-like Caco-2 cells

We conducted an in-depth investigation of the effects of conjugated linoleic acid (CLA) on the expression of key metabolic genes and genes of known importance in intestinal lipid metabolism using the Caco-2 cell model. Cells were treated with 80 μmol/L of linoleic acid (control), trans-10, cis-12 CLA or cis-9, trans-11 CLA. RNA was isolated from the cells, labelled and hybridized to the Affymetrix U133 2.0 Plus arrays (n = 3). Data and functional analysis were preformed using Bioconductor. Gene ontology analysis (GO) revealed a significant enrichment (P < 0.0001) for the GO term lipid metabolism with genes up-regulated by trans-10, cis-12 CLA. Trans-10, cis-12 CLA, but not cis-9, trans-11 CLA, altered the expression of a number of genes involved in lipid transport, fatty acid metabolism, lipolysis, β-oxidation, steroid metabolism, cholesterol biosynthesis, membrane lipid metabolism, gluconeogenesis and the citrate cycle. These observations warrant further investigation to understand their potential role in the metabolic syndrome.     

意大利蜜蜂幼虫肠道内球囊菌及其纯培养的高表达基因差异分析

【背景】球囊菌是一种典型的蜜蜂真菌性病原,特异性地侵染蜜蜂幼虫。目前,有关球囊菌在侵染过程中的基因表达规律的信息极为有限。【目的】通过深入分析胁迫意大利蜜蜂(意蜂)幼虫肠道的球囊菌及其纯培养的高表达基因(HEGs)差异,探索球囊菌在胁迫意蜂幼虫肠道后期与胁迫前的基因表达规律。【方法】利用RNA-Seq技术对球囊菌胁迫的意蜂6日龄幼虫肠道(Aam T)及球囊菌纯培养(AaCK)进行深度测序,根据FPKM值筛选得到球囊菌的HEGs,进而通过GO(Gene ontology)及KEGG(Kyoto Encyclopedia of Genes and Genomes)富集分析、Venn分析对上述HEGs进行功能预测和生物学意义挖掘。【结果】AaCK与Aam T的转录组测序共得到105 447 578条原始读段(Raw reads),经过滤得到88 466 344条有效读段(Clean reads),两端平均Q20为97.50%,平均Q30为93.81%。GO富集分析结果显示,AaCK的HEGs富集于26个GO terms,基因富集数最多的是细胞(22 Unigenes),其次是细胞组件(22 Unigenes)和代谢过程(21 Unigenes);Aam T的HEGs富集于22个GO terms,基因富集数最多的是催化活性(23 Unigenes),其次是细胞进程(18 Unigenes)和代谢过程(18 Unigenes)。KEGG代谢通路(Pathway)富集分析显示,AaCK的HEGs富集在109个Pathways上,基因富集数最多的是核糖体(179 Unigenes),其次是氨基酸生物合成(70Unigenes)和碳代谢(62 Unigenes);Aam T的HEGs富集在114个Pathways上,基因富集数量最多的是核糖体(178 Unigenes),其次是碳代谢(116 Unigenes)和氧化磷酸化(112 Unigenes)。Venn分析结果显示,AaCK与Aam T共有的HEGs有260个,二者特有的HEGs分别为2 161个和4 445个。【结论】提供了胁迫意蜂6日龄幼虫肠道的球囊菌及其纯培养的HEGs表达谱,揭示了球囊菌在胁迫前和胁迫后期的基因表达规律,也为阐明球囊菌致病的分子机理提供了有益的信息和线索。     

The effect of dietary addition of nitrate or increase in lipid concentrations,alone or in combination,on performance and methane emissions of beef cattle

Adding nitrate to or increasing the concentration of lipid in the diet are established strategies for reducing enteric methane (CH₄) emissions, but their effectiveness when used in combination has been largely unexplored. This study investigated the effect of dietary nitrate and increased lipid included alone or together on CH₄ emissions and performance traits of finishing beef cattle. The experiment was a 2×4 factorial design comprising two breeds (cross-bred Aberdeen Angus (AAx) and cross-bred Limousin (LIMx) steers) and four dietary treatments (each based on 550 g forage : 450 g concentrate/kg dry matter (DM)). The four dietary treatments were assigned according to a 2×2 factorial design where the control treatment contained rapeseed meal as the main protein source, which was replaced either with nitrate (21.5 g nitrate/kg DM); maize distillers dark grains (MDDG, which increased diet ether extract from 24 to 37 g/kg DM) or both nitrate and MDDG. Steers (n=20/dietary treatment) were allocated to each of the four treatments in equal numbers of each breed with feed offered ad libitum. After 28 days adaptation to dietary treatments, individual animal intake, performance and feed efficiency were recorded for 56 days. Thereafter, CH₄ emissions were measured over 13 weeks (six steers/week). Increasing dietary lipid did not adversely affect animal performance and showed no interactions with dietary nitrate. In contrast, addition of nitrate to diets resulted in poorer live-weight gain (P<0.01) and increased feed conversion ratio (P<0.05) compared with diets not containing nitrate. Daily CH₄ output was lower (P<0.001) on nitrate-containing diets but increasing dietary lipid resulted in only a non-significant reduction in CH₄. There were no interactions associated with CH₄ emissions between dietary nitrate and lipid. Cross-bred Aberdeen Angus steers achieved greater live-weight gains (P<0.01), but had greater DM intakes (P<0.001), greater fat depth (P<0.01) and poorer residual feed intakes (P<0.01) than LIMx steers. Cross-bred Aberdeen Angus steers had higher daily CH₄ outputs (P<0.001) but emitted less CH₄ per kilogram DM intake than LIMx steers (P<0.05). In conclusion, inclusion of nitrate reduced CH₄ emissions in growing beef cattle although the efficacy of nitrate was less than in previous work. When increased dietary lipid and nitrate inclusion were combined there was no evidence of an interaction between treatments and therefore combining different nutritional treatments to mitigate CH₄ emissions could be a useful means of achieving reductions in CH₄ while minimising any adverse effects.     

2型糖尿病模型大鼠肝脏脂代谢相关基因的筛选及生物信息学分析

肝的脂肪代谢异常和胰岛素抵抗（insulin resistance,IR）对促进2型糖尿病（type 2 diabetes mellitus,T2DM）的发生与发展具有显著影响。但此过程复杂,参与调控基因目前尚未完全清楚。有研究表明,脂肪酸分解、氨基酸代谢、肝糖原合成等生物过程对糖尿病的形成具有促进作用。为了阐明这一调控机制,本文通过基因芯片技术研究GK（Goto-Kakizaki）大鼠和WKY（Wistar-Kyoto）大鼠肝差异基因对肝的脂肪代谢和胰岛素抵抗的影响,探讨可引起2型糖尿病发病的分子机制。从基因表达数据库（GEO）获取GSE13271基因表达谱,并对原始数据进行标准化处理。通过GO（Gene Ontology）、KEGG（Kyoto Encyclopedia of Genes and Genomes enrichment）、String和Cytoscape软件对差异表达基因进行功能分析。结果从GK和WKY大鼠中分别获得179和278个差异基因,同时从排名前10的路径中筛选出21个差异基因(Aldh1a1, Cyp2c22, bp2,Fabp7,Cyp4a3, Acot1, Acot2,Hsd17b2, Ech1, Hmgcl,Bdh1, Crot, Pex11a, Cpt1a, Hadhb, Gda, Elovl2, Prodh, Agpat3, Sardh, Pigu),将这些基因与前10个的GO term取交集。最终得到10个显著差异基因(Aldh1a1, Fabp2, Acot1, Acot2, Ech1, Hmgcl, Bdh1, Crot, Cpt1a, Hadhb),功能分析结果显示,肝组织相关基因通过一系列生物过程对肝的脂肪代谢和胰岛素抵抗产生调节作用,从而也为临床糖尿病的治疗以及新作用靶点的发现提供更多参考依据。