Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant ...genomes that are interspersed by hypomethylated gene‐rich regions. Gene‐enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene‐enrichment strategy, we have compared assemblies using methyl‐filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA‐seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single‐nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.
MicroRNAs (miRNAs) are key regulators of gene expression, potentially affecting several biological processes, whose function can be altered by sequence variation. Hence, the integration of single ...nucleotide polymorphisms (SNP) and miRNAs can explain individual differences in economic traits. To provide new insights into the effects of SNPs on miRNAs and their related target genes, we carried out a multi-omic analysis to identify SNPs in miRNA mature sequences (miR-SNPs) associated with fatty acid (FA) composition in the Nelore cattle. As a result, we identified 3 miR-SNPs in different miRNAs (bta-miR-2419-3p, bta-miR-193a-2, and bta-miR-1291) significantly associated with FA traits (
-value < 0.02, Bonferroni corrected). Among these, the rs110817643C>T, located in the seed sequence of the bta-miR-1291, was associated with different ω6 FAs, polyunsaturated FA, and polyunsaturated:saturated FA ratios. Concerning the other two miR-SNPs, the rs43400521T>C (located in the bta-miR-2419-3p) was associated with C12:0 and C18:1 cis-11 FA, whereas the rs516857374A>G (located in the bta-miR-193a-2) was associated with C18:3 ω6 and ratio of ω6/ω3 traits. Additionally, to identify potential biomarkers for FA composition, we described target genes affected by these miR-SNPs at the mRNA or protein level. Our multi-omics analysis outlines the effects of genetic polymorphism on miRNA, and it highlights miR-SNPs and target candidate genes that control beef fatty acid composition.
Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying ...co-expression analysis in
RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (
-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs)
,
,
,
, and
, were identified with binding sites in at least one hub gene. Gene expression of
,
,
, and
was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the
and
hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.
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.
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.
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.
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.
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.
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.
Summary
Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (
WGS
). Large tracts of methylated repeats ...occur in plant genomes that are interspersed by hypomethylated gene‐rich regions. Gene‐enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with Mcr
BC
endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene‐enrichment strategy, we have compared assemblies using methyl‐filtered (
MF
) and unfiltered (
UF
) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (
CDS
) by
MF
scaffolds was at least 36% higher than by the use of
UF
scaffolds. Using
MF
technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The
MF
reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (
BAC
s), 97.2% of sugarcane expressed sequence tags (
EST
s), 92.7% of sugarcane
RNA
‐seq reads and 98.4% of sorghum protein sequences. Analysis of
MF
scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single‐nucleotide polymorphisms (
SNP
s) in the wild sugarcane species,
S
. spontaneum
and
S
. officinarum
. A large number of micro
RNA
genes was also identified in the
MF
scaffolds. The information achieved by the
MF
dataset provides a valuable tool for genomic research in the genus
S
accharum
and for improvement of sugarcane as a biofuel crop.
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