BackgroundTo better understand which genes play a role in cattle feed intake and gain, we evaluated differential expression of genes related to gain and intake in the liver of crossbred beef steers. Based on past transcriptomics studies on cattle liver, we hypothesized that genes related to metabolism regulation and the inflammatory response would be differentially expressed. This study used 16 animals with diverse gain and intake phenotypes to compare transcript abundance after a 78 day ad libitum feed study.ResultsA total of 729 genes were differentially expressed. These genes were analyzed for over-representation among biological and cellular functions, and pathways. Cell transport processes and metabolic processes, as well as functions related to transport, were identified. Pathways related to immune function, such as the proteasome ubiquitination pathway and the chemokine signaling pathway, were also identified.ConclusionsOur results were consistent with past transcriptomics studies that have found immune and transport processes play a role in feed efficiency. Gain and intake are impacted by complex processes in the liver, which include cellular transport, metabolism regulation, and immune function.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2345-3) contains supplementary material, which is available to authorized users.

BackgroundIn a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P ≤ 0.003) with average daily gain (ADG) and 3 of these were also associated (P ≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. The SNP were clustered in a 570 kb region around 38 Mb on the draft sequence of bovine chromosome 6 (BTA6), an interval containing several positional and functional candidate genes including the bovine LAP3, NCAPG, and LCORL genes. The goal of the present study was to develop and examine additional markers in this region to optimize the ability to distinguish favorable alleles, with potential to identify functional variation.ResultsAnimals from the original study were genotyped for 47 SNP within or near the gene boundaries of the three candidate genes. Sixteen markers in the NCAPG-LCORL locus displayed significant association with both ADFI and ADG even after stringent correction for multiple testing (P ≤ 005). These markers were evaluated for their effects on meat and carcass traits. The alleles associated with higher ADFI and ADG were also associated with higher hot carcass weight (HCW) and ribeye area (REA), and lower adjusted fat thickness (AFT). A reduced set of markers was genotyped on a separate, crossbred population including genetic contributions from 14 beef cattle breeds. Two of the markers located within the LCORL gene locus remained significant for ADG (P ≤ 0.04).ConclusionsSeveral markers within the NCAPG-LCORL locus were significantly associated with feed intake and body weight gain phenotypes. These markers were also associated with HCW, REA and AFT suggesting that they are involved with lean growth and reduced fat deposition. Additionally, the two markers significant for ADG in the validation population of animals may be more robust for the prediction of ADG and possibly the correlated trait ADFI, across multiple breeds and populations of cattle.

Feed cost for beef cattle is the largest expense incurred by cattle producers. The development of genetic markers to enhance selection of more efficient animals that require less feed while still achieving acceptable levels of production has the potential to substantially reduce production costs. A genome-wide marker association approach based on the Illumina BovineSNP50 BeadChip™ was used to identify genomic regions affecting average daily feed intake (ADFI), average daily gain (ADG) and residual feed intake traits in a population of 1159 crossbred steers. This approach identified a region on BTA14 from 22.02 to 23.92 Mb containing several single-nucleotide polymorphisms (SNPs) that have significant association with at least one of the traits. Two genes in this region, lysophospholipase 1 (LYPLA1) and transmembrane protein 68 (TMEM68), appeared to be logical positional and functional candidate genes. LYPLA1 deacylates ghrelin, a hormone involved in the regulation of appetite in the rat stomach, while TMEM68 is expressed in bovine rumen, abomasum, intestine and adipose tissue in cattle, and likely affects lipid biosynthetic processes. SNPs lying in or near these two genes were identified by sequencing a subset of animals with extreme phenotypes. A total of 55 SNPs were genotyped and tested for association with the same population of steers. After correction for multiple testing, five markers within 22.79-22.84 Mb, located downstream of TMEM68, and between TMEM68 and the neighbouring gene XKR4, were significant for both ADFI and ADG. Genetic markers predictive of feed intake and weight gain phenotypes in this population of cattle may be useful for the identification and selection of animals that consume less feed, although further evaluation of these markers for effects on other production traits and validation in additional populations will be required.

Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV. We identified and characterized CNV regions by utilizing exome sequence from 175 influential sires used in the Germplasm Evaluation project, representing 10 breeds. We examined various evolutionary and functional aspects of these CNVs, including selective constraint on CNV-overlapped genes, centrality of CNV genes in protein-protein interaction networks, and tissue-specific expression of CNV genes. Patterns of CNV in the Bos taurus genome reveal that reduced functional constraint and mutational bias may play a prominent role in shaping this type of structural variation.

A region on bovine chromosome 6 has been implicated in cattle birth weight, growth, and length. Non-SMC conodensin I complex subunit G (NCAPG) and ligand dependent nuclear receptor corepressor-like protein (LCORL) are positional candidate genes within this region. Previously identified genetic markers in both genes were associated with average daily gain (ADG) and average daily feed intake (ADFI) in a crossbred population of beef steers. These markers were also associated with hot carcass weight, ribeye area and adjusted fat thickness suggesting that they may have a role in lean muscle growth and/or fat deposition. The purpose of this study was to determine whether the transcript abundance of either of these genes in cattle adipose and muscle tissue was associated with variation in feed intake and average daily gain phenotypes. Transcript abundance for NCAPG and LCORL in adipose and muscle tissue was measured in heifers (adipose only), cows and steers using real-time polymerase chain reaction. In the adipose tissue from cows and heifers, a negative correlation between LCORL transcript abundance and ADFI were detected (P = 0.05). In the muscle tissue from cows, transcript abundance of NCAPG was associated with ADG (r = 0.26; P = 0.009). A positive correlation between LCORL transcript abundance from muscle tissue of steers and ADFI was detected (P = 0.04). LCORL protein levels in the muscle of steers were investigated and were associated with ADFI (P = 0.01). These data support our earlier genetic associations with ADFI and ADG within this region and represent the potential for biological activity of these genes in the muscle and adipose tissues of beef cattle; however, they also suggest that sex, age and/or nutrition-specific interactions may affect the expression of NCAPG and LCORL in these tissues.

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Small intestine mass and cellularity were previously associated with cattle feed efficiency. The small intestine is responsible for the digestion of nutrients and absorption of fatty acids, amino acids and carbohydrates, and it contributes to the overall feed efficiency of cattle. The objective of this study was to evaluate transcriptome differences among the small intestine from cattle with divergent gain and feed intake. Animals most divergent from the bivariate mean in each of the four phenotypic Cartesian quadrants for gain × intake were selected, and the transcriptomes of duodenum, jejunum and ileum were evaluated. Gene expression analyses were performed comparing high gain vs. low gain animals, high intake vs. low intake animals and each of the phenotypic quadrants to all other groups. Genes differentially expressed within the high gain-low intake and low gain-high intake groups of animals included those involved in immune function and inflammation in all small intestine sections. The high gain-high intake group differed from the high gain-low intake group by immune response genes in all sections of the small intestine. In all sections of small intestine, animals with low gain-low intake displayed greater abundance of heat-shock genes compared to other groups. Several over-represented pathways were identified. These include the antigen-processing/presentation pathway in high gain animals and PPAR signaling, starch/sucrose metabolism, retinol metabolism and melatonin degradation pathways in the high intake animals. Genes with functions in immune response, inflammation, stress response, influenza pathogenesis and melatonin degradation pathways may have a relationship with gain and intake in beef steers.

This study aimed to identify transcriptome differences between distinct or transitional stage spherical, ovoid, and tubular porcine blastocysts throughout the initiation of elongation. We performed a global transcriptome analysis of differential gene expression using RNA‐Seq with high temporal resolution between spherical, ovoid, and tubular stage blastocysts at specific sequential stages of development from litters containing conceptus populations of distinct or transitional blastocysts. After RNA‐Seq analysis, significant differentially expressed genes (DEGs) and pathways were identified between distinct morphologies or sequential development stages. Overall, 1898 significant DEGs were identified between distinct spherical and ovoid morphologies, with 311 total DEGs between developmental stages throughout this first morphological transition, while 15 were identified between distinct ovoid and tubular, with eight total throughout these second morphological transition developmental stages. The high quantity of DEGs and pathways between conceptus stages throughout the spherical to ovoid transition suggests the importance of gene regulation during this first morphological transition for initiating elongation. Further, extensive DEG coverage of known elongation signaling pathways was illustrated from spherical to ovoid, and regulation of lipid signaling and membrane/ECM remodeling across these early conceptus stages were implicated as essential to this process, providing novel insights into potential mechanisms governing this rapid morphological change.