Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content.

BACKGROUND: Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene expression regulation associated with FA content in cattle. RESULTS: Skeletal muscle transcriptome analysis of 164 Nellore steers revealed no differentially expressed genes (DEGs, FDR 10%) for samples with extreme values for linoleic acid (LA) or stearic acid (SA), and only a few DEGs for eicosapentaenoic acid (EPA, 5 DEGs), docosahexaenoic acid (DHA, 4 DEGs) and palmitic acid (PA, 123 DEGs), while large numbers of DEGs were associated with oleic acid (OA, 1134 DEGs) and conjugated linoleic acid cis9 trans11 (CLA-c9t11, 872 DEGs). Functional annotation and functional enrichment from OA DEGs identified important genes, canonical pathways and upstream regulators such as SCD, PLIN5, UCP3, CPT1, CPT1B, oxidative phosphorylation mitochondrial dysfunction, PPARGC1A, and FOXO1. Two important genes associated with lipid metabolism, gene expression and cancer were identified as DEGs between animals with high and low CLA-c9t11, specifically, epidermal growth factor receptor (EGFR) and RNPS. CONCLUSION: Only two out of seven classes of molecules of FA studied were associated with large changes in the expression profile of skeletal muscle. OA and CLA-c9t11 content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. These results contribute to our understanding of how some FAs modulate metabolism and may have protective health function.

Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle.

BACKGROUND: Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample. RESULTS: Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches. CONCLUSIONS: The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.

Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes.

BACKGROUND: Efficiency of feed utilization is important for animal production because it can reduce greenhouse gas emissions and improve industry profitability. However, the genetic basis of feed utilization in livestock remains poorly understood. Recent developments in molecular genetics, such as platforms for genome-wide genotyping and sequencing, provide an opportunity to identify genes and pathways that influence production traits. It is known that transcriptional networks influence feed efficiency-related traits such as growth and energy balance. This study sought to identify differentially expressed genes in animals genetically divergent for Residual Feed Intake (RFI), using RNA sequencing methodology (RNA-seq) to obtain information from genome-wide expression profiles in the liver tissues of Nelore cattle. RESULTS: Differential gene expression analysis between high Residual Feed Intake (HRFI, inefficient) and low Residual Feed Intake (LRFI, efficient) groups was performed to provide insights into the molecular mechanisms that underlie feed efficiency-related traits in beef cattle. A total of 112 annotated genes were identified as being differentially expressed between animals with divergent RFI phenotypes. These genes are involved in ion transport and metal ion binding; act as membrane or transmembrane proteins; and belong to gene clusters that are likely related to the transport and catalysis of molecules through the cell membrane and essential mechanisms of nutrient absorption. Genes with functions in cellular signaling, growth and proliferation, cell death and survival were also differentially expressed. Among the over-represented pathways were drug or xenobiotic metabolism, complement and coagulation cascades, NRF2-mediated oxidative stress, melatonin degradation and glutathione metabolism. CONCLUSIONS: Our data provide new insights and perspectives on the genetic basis of feed efficiency in cattle. Some previously identified mechanisms were supported and new pathways controlling feed efficiency in Nelore cattle were discovered. We potentially identified genes and pathways that play key roles in hepatic metabolic adaptations to oxidative stress such as those involved in antioxidant mechanisms. These results improve our understanding of the metabolic mechanisms underlying feed efficiency in beef cattle and will help develop strategies for selection towards the desired phenotype.

Identification of genomic regions associated with feed efficiency in Nelore cattle.

BACKGROUND: Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology. RESULTS: Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7. CONCLUSIONS: Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle.

Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle.

BACKGROUND: Meat from Bos taurus and Bos indicus breeds are an important source of nutrients for humans and intramuscular fat (IMF) influences its flavor, nutritional value and impacts human health. Human consumption of fat that contains high levels of monounsaturated fatty acids (MUFA) can reduce the concentration of undesirable cholesterol (LDL) in circulating blood. Different feeding practices and genetic variation within and between breeds influences the amount of IMF and fatty acid (FA) composition in meat. However, it is difficult and costly to determine fatty acid composition, which has precluded beef cattle breeding programs from selecting for a healthier fatty acid profile. In this study, we employed a high-density single nucleotide polymorphism (SNP) chip to genotype 386 Nellore steers, a Bos indicus breed and, a Bayesian approach to identify genomic regions and putative candidate genes that could be involved with deposition and composition of IMF. RESULTS: Twenty-three genomic regions (1-Mb SNP windows) associated with IMF deposition and FA composition that each explain ≥1% of the genetic variance were identified on chromosomes 2, 3, 6, 7, 8, 9, 10, 11, 12, 17, 26 and 27. Many of these regions were not previously detected in other breeds. The genes present in these regions were identified and some can help explain the genetic basis of deposition and composition of fat in cattle. CONCLUSIONS: The genomic regions and genes identified contribute to a better understanding of the genetic control of fatty acid deposition and can lead to DNA-based selection strategies to improve meat quality for human consumption.

Morfologia e histoquímica das glândulas sexuais acessórias de Metachirus nudicaudatus, Didelphidae-Marsupialia / Morphology and histochemistry of accessory sex glands of Metachirus nudicaudatus, Didelphidae-Marsupialia

São descritas a morfologia e a distribuição de glicogênio e mucossubstâncias na próstata e nas glândulas bulbouretrais de Metachirus nudicaudatus (Geoffroy, 1803), única espécie do gênero. A próstata é envolvida pelas túnicas adventícia e muscular, e o estroma é formado pelo conjuntivo da mucosa uretral. O parênquima é constituído pelos túbulos secretores, disseminados na mucosa uretral, e que diferem histológica e histoquimicamente nos segmentos cranial, médio e caudal. Essas diferenças morfo-histoquímicas também são observadas nas partes externa, média e interna de cada túbulo. De um modo geral, os três segmentos prostáticos secretam mucossubstâncias neutras, porém o segmento caudal produz também glicogênio. Os três pares de glândulas bulbouretrais (laterais, intermédias e mediais) do Metachirus são envolvidas por uma cápsula conjuntiva e músculo estriado esquelético. O maior par é a bulbouretral lateral que é constituída por longos túbulos secretores de mucossubstâncias neutras. As bulbouretrais intermédias são formadas por túbulos ramificados, que produzem mucossubstâncias neutras, ácidas carboxiladas e ácidas sulfatadas. Os túbulo-ácinos ramificados das bulbouretrais mediais secretam mucossubstâncias neutras. O Metachirus não possui glândulas ampulares, vesículas seminais nem glândulas de coagulação.(AU)

This paper describes the morphology and distribution of glycogen and mucous substances in the prostate and the bulbourethral glands of Metachirus nudicaudatus (Geoffroy, 1803), the only species of the genus. The prostate is surrounded by the tunica adventitia, and muscle and stroma is formed by connective urethral mucosa. The glandular parenchyma consists of secretory tubules, scattered throughout the connective tissue of the urethral mucosa which differs histologically and histochemically in cranial, middle, and caudal segments of the prostate. These morpho-histochemical differences are also observed in the outer, middle and inner parts of the tubular epithelium of each prostatic segment. In general, prostatic segments secrete neutral mucous substances, and the caudal segment also produces glycogen. The three pairs of bulbourethral glands (lateral, intermediate and medial) are surrounded by a capsule of dense connective tissue and skeletal striated muscle. The glandular parenchyma is formed by tubules or branched tubuloacinar, covered by simple epithelium which is characteristic for each pair of glands. The lateral bulbourethral glands and the medial bulbourethral glands produce neutral mucous substances and the secretion of the intermediate bulbourethral glands consists of neutral mucous substances, carboxylated acids, and sulfated acids. The M. nudicaudatus does not have ampullary glands, seminal vesicles or coagulating glands.(AU)

Morfologia do escroto, do testículo e das vias espermáticas de Metachirus nudicaudatus (Geoffroy, 1803), Didelphidae-Marsupialia / Morphology of scrotum and testicle, and spermatic pathways of Metachirus nudicaudatus (Geoffroy, 1803), Didelphidae-Marsupialia

Foram utilizadas as gônadas e vias espermáticas de cinco animais machos, adultos em fase reprodutiva, da espécie Metachirus nudicaudatus Geoffroy 1803, única espécie do gênero, para descrever a morfologia do escroto, do testículo e das vias espermáticas. O Metachirus possui escroto pré-peniano e que contém os testículos permanentemente. A pele escrotal é não pigmentada e com poucos pelos e glândulas. A lâmina parietal da túnica vaginal apresenta-se pouco pigmentada. Os testículos são ovais e ligados ao epidídimo através do pedículo testículo-epididimário. Eles são envolvidos, externamente, pela cápsula testicular e sustentados por um estroma de natureza conjuntiva. As células intersticiais são os elementos predominantes no abundante tecido intertubular. Os túbulos seminíferos são largos, enovelados e envolvidos por uma túnica própria fibroelástica, contendo células mióides. O epitélio seminífero é formado pelas células espermatogênicas e de Sertoli intercaladas. Os túbulos seminíferos convergem em direção à extremidade capitata do testículo, ficando revestidos por apenas células de sustentação, caracterizando uma região de transição entre túbulos seminíferos e túbulos retos, ocupada por uma estrutura tipo "válvula" que obstrui parcialmente o lume tubular. Os túbulos retos reúnem-se para formar um único dúctulo eferente, que percorre uma pequena extensão intratesticular, atravessa a albugínea e penetra no pedículo testículo-epididimário. A parte flexuosa do dúctulo eferente forma um lóbulo separado na parte medial do corpo do epidídimo. O epidídimo é envolvido pela cápsula epididimária e constituído pelo ducto epididimário, que se encontra bastante enovelado. O ducto epididimário é revestido por epitélio simples colunar pseudoestratificado apresentando células principais, basais, apicais e de "halo claro". As células principais são predominantes e apresentam características morfológicas e histoquímicas que diferem ao longo do ducto, possibilitando a caracterização de nove diferentes zonas epididimárias. É no lume da zona sete (início da cauda) que começa o pareamento de espermatozoides. Esse fenômeno coincide com alterações morfológicas bem evidentes e uma maior quantidade de mucossubstâncias neutras é secretada nessa zona.O ducto deferente apresenta-se dividido em três partes: justa-epididimária, funicular e abdominal, baseando nas variações histológicas e histoquímicas de seu epitélio e componentes envolventes. O ducto deferente não apresenta ampola e nem cruza o ureter antes de desembocar na uretra. O funículo espermático contém o ducto deferente, artéria e veias testiculares, vasos linfáticos, nervos e um desenvolvido músculo cremáster. Seus componentes apresentam modificações estruturais nas regiões proximal, média e distal, sendo notável a peculiar rede admirável.(AU)

Gonads and sperm pathways of five adult male Metachirus nudicaudatus in the reproductive phase were used to describe the morphology of scrotum, testicle, and spermatic tract. M. nudicaudatus has a scrotum pre-penis which contains the testicles permanently. The scrotal skin is not pigmented and has few hairs and glands. The parietal vaginal tunic is slightly pigmented. The testicles are oval and connected to the epididymis by testicular-epididymal pedicle; they are surrounded externally by the testicular capsule and supported by a stroma of connective nature. Interstitial cells are the predominant elements in abundant intertubular tissue. The seminiferous tubules are wide, meandering and surrounded by a fibro-elastic coat, containing myoid cells. The seminiferous epithelium is composed of spermatogenic cells and Sertoli cells interspersed. The seminiferous tubules converge toward the end of the testis capitata, getting coated only support cells, featuring a transition region between the seminiferous tubules and straight tubules, occupied by a type "valve" structure that partially blocks the tubular lumen. Straight tubules together to form a single efferent ductule, which runs a small intra-testicular extent, penetrates through the tunica and the pedicle testis-epididymis. The flexuosa part of the efferent ductule forms a separate lobe in the medial part of the body of the epididymis. The epididymis is enveloped by a capsule and epididymal comprising the epididymal duct, which is quite entangled. The epididymal duct is lined by pseudostratified columnar epithelium with simple principal, basal, apical and "clear halo" cells. The main cells are prevalent and have morphological and histochemical differing characteristics along the duct, enabling to characterize nine different epididymal areas. In the lumen of the seventh area (top of tail) that starts the pairing of sperm. This phenomenon coincides well with morphological change and a larger amount of neutral muco-substances is secreted in that area. Vas deferens has three parts: fair-epididymal, abdominal and funicular part, based on histological and histochemical changes of the epithelium and surrounding components. The vas deferens has no bulb and even crosses the ureter before flowing into the urethra. The spermatic cord contains the vas deferens, testicular artery and veins, lymphatic vessels, nerves and developed cremaster muscle. Its components have structural changes in the proximal, middle and distal region, with a peculiar admirable network.(AU)