Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Silva-Vignato, Bárbara; Coutinho, Luiz Lehmann; Poleti, Mirele Daiana; Regitano, Luciana Correia de Almeida; Balieiro, Júlio César de Carvalho

doi:10.1186/s12864-017-3897-x

Cited by 57 publications

(57 citation statements)

References 111 publications

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“…Non-overlapping islands within the lineages were explored for gene content and among the genes identified within the regions we can highpoint those described in Table 5 . Remarkably, six genes were also reported in Nellore-specific studies associated with carcass traits [ 64 ] ( PPM1 ), age at first calving [ 65 ] ( NPBWR1, OPRK1, and MRPL1 ), and birth weight [ 66 ] ( RPS20 and TGS1 ).…”

Section: Discussionmentioning

confidence: 97%

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

et al. 2018

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BackgroundThe aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED).ResultsThe average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands.ConclusionsLow FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 97%

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

et al. 2018

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“…An intricate balance between synthesis and degradation of protein, i.e., protein turnover, is crucial for animal growth (Silva-Vignato et al, 2017). Richardson and Herd (2004) estimated that protein turnover and tissue metabolism account for the largest proportion of variation in RFI among animals, i.e., 37% of the difference in RFI for beef cattle.…”

Section: Introductionmentioning

confidence: 99%

RAPID COMMUNICATION: Residual feed intake in beef cattle is associated with differences in protein turnover and nutrient transporters in ruminal epithelium

Elolimy

Abdel-Hamied

et al. 2019

Journal of Animal Science

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Residual feed intake (RFI) is a widely used measure of feed efficiency in cattle. Although the precise biologic mechanisms associated with improved feed efficiency are not well-known, most-efficient steers (i.e., with low RFI coefficient) downregulate abundance of proteins controlling protein degradation in skeletal muscle. Whether cellular mechanisms controlling protein turnover in ruminal tissue differ by RFI classification is unknown. The aim was to investigate associations between RFI and signaling through the mechanistic target of rapamycin (MTOR) and ubiquitin-proteasome pathways in ruminal epithelium. One hundred and forty-nine Red Angus cattle were allocated to 3 contemporary groups according to sex and herd origin. Animals were offered a finishing diet for 70 d to calculate the RFI coefficient for each. Within each group, the 2 most-efficient (n = 6) and least-efficient animals (n = 6) were selected. Compared with least-efficient animals, the most-efficient animals consumed less feed (P < 0.05; 18.36 vs. 23.39 kg/d DMI). At day 70, plasma samples were collected for insulin concentration analysis. Ruminal epithelium was collected immediately after slaughter to determine abundance and phosphorylation status of 29 proteins associated with MTOR, ubiquitin-proteasome, insulin signaling, and glucose and amino acid transport. Among the proteins involved in cellular protein synthesis, most-efficient animals had lower (P ≤ 0.05) abundance of MTOR, p-MTOR, RPS6KB1, EIF2A, EEF2K, AKT1, and RPS6KB1, whereas MAPK3 tended (P = 0.07) to be lower. In contrast, abundance of p-EEF2K, p-EEF2K:EEF2K, and p-EIF2A:EIF2A in most-efficient animals was greater (P ≤ 0.05). Among proteins catalyzing steps required for protein degradation, the abundance of UBA1, NEDD4, and STUB1 was lower (P ≤ 0.05) and MDM2 tended (P = 0.06) to be lower in most-efficient cattle. Plasma insulin and ruminal epithelium insulin signaling proteins did not differ (P > 0.05) between RFI groups. However, abundance of the insulin-responsive glucose transporter SLC2A4 and the amino acid transporters SLC1A3 and SLC1A5 also was lower (P ≤ 0.05) in most-efficient cattle. Overall, the data indicate that differences in signaling mechanisms controlling protein turnover and nutrient transport in ruminal epithelium are components of feed efficiency in beef cattle.

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“…High-throughput RNA sequencing (RNA-Seq) has been proven to be an efficient method for studying the regulation of gene expression (Wang et al, 2009). In recent years, RNA-Seq has been applied to domestic animals, with a major focus on productivity traits (Bai et al, 2016; Li et al, 2016; Pokharel et al, 2018; Silva-Vignato et al, 2017). A number of transcriptome studies have been conducted in different Holstein breeds (Bai et al, 2016; Li et al, 2016; Sandri et al, 2015), but to date, there are no reports on gene expression studies in either Yakutian cattle or Northern Finncattle.…”

Section: Introductionmentioning

confidence: 99%

Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions

Pokharel

Weldenegodguad

Popov

et al. 2018

Preprint

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SummaryIndigenous cattle breeds in northern Eurasia have adapted to harsh climate conditions. The local breeds are important genetic resources with cultural and historical heritages, and therefore, their preservation and genetic characterization are important. In this study, we aim to identify genes and biological processes that are important for their adaptation to the cold and harsh conditions. For this purpose, we profiled the whole-blood transcriptome of two native breeds and one commercial breed using high-throughput RNA sequencing. More than 15,000 genes were identified, of which 2, 89, and 162 genes were significantly upregulated exclusively in Northern Finncattle, Yakutian cattle and Holstein cattle, respectively. The functional classification of these significantly differentially expressed genes identified several biological processes and pathways related to signalling mechanisms, cell differentiation, and host-pathogen interactions that, in general, point towards immunity and disease resistance mechanisms. The gene expression pattern observed in Northern Finncattle was more similar to that of Yakutian cattle, despite sharing similar living conditions as the Holstein cattle included in our study. In conclusion, our study identified unique biological processes in these breeds that help them to adapt and survive in sub-arctic environments.

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Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Cited by 57 publications

References 111 publications

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

RAPID COMMUNICATION: Residual feed intake in beef cattle is associated with differences in protein turnover and nutrient transporters in ruminal epithelium

Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions

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