Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle

Silva-Vignato, Bárbara; Coutinho, Luiz Lehmann; Poleti, Mirele Daiana; César, A. S. M.; Moncau, Cristina Tschorny; Regitano, Luciana Correia de Almeida; Balieiro, J. C. C.

doi:10.1186/s12864-018-5345-y

Cited by 44 publications

(34 citation statements)

References 68 publications

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“…FBXW7 was reported to be associated with lipid metabolism [ 41 ]. In previous research, ACAT1 was consider as one of the candidate genes affect ribeye area and backfat thickness [ 42 ]. And in the research of Gu et al [ 43 ], stabilization of FASN by ACAT1 -mediated GNPAT acetylation could promote lipid metabolism.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

Wang

Hou

et al. 2020

Animals

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Intramuscular fat (IMF) is essential for improving the palatability and flavor of meat, and it is strongly associated with human insulin resistance. RNA editing is a widespread regulating event in different tissues. Here, we investigated the global RNA editing difference of two groups of pig with different IMF contents to find the potential editing sites affecting IMF. In this research, RES-Scanner and REDItools were used to identify RNA editing sites based on the whole genome and transcriptome sequencing data of the high and low groups composed of three full-sib pairs with opposite IMF phenotypes. A total of 295 RNA editing sites were investigated in the longissimus dorsi muscle, and 90.17% of these sites caused A to G conversion. After annotation, most editing sites were located in noncoding regions (including five sites located on the 3′ UTR regions). Five editing sites (including two sites that could lead to nonsynonymous amino acid changes) were located in the exons of genes. A total of 36 intergroup (high and low IMF) differential RNA editing sites were found in 33 genes. Some candidate editing sites, such as sites in acyl-coenzymeA: cholesterol acyltransferase 1 (ACAT1), coatomer protein, subunit alpha (COPA), and nuclear receptor coactivator 3 (NCOA3), were selected as candidate RNA editing sites associated with IMF. One site located on the 3′ UTR region of growth hormone secretagogue receptor (GHSR) may regulate GHSR expression by affecting the interaction of miRNA and mRNA. In conclusion, we identified a total of 36 nonredundant RNA editing sites in the longissimus dorsi muscle, which may reveal the potential importance of RNA editing in IMF. Four were selected as candidate sites associated with IMF. Our findings provide some new insights of RNA editing function in pig longissimus dorsi muscle which useful for pig IMF breeding or human insulin resistances research.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

Wang

Hou

et al. 2020

Animals

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“…involved in growth regulation is confirmed by identification of additional notable candidate genes with known effect on body size and/or carcass traits, including Grb10 on BTA 4 [84][85][86], PDGFRA, MAD2L and UBE2K on BTA 6 [87][88][89][90], SIRT6 on BTA 7 [91][92][93], and ACAT1, KDELC2 on BTA 15 [94][95][96] in Yaroslavl breed, and EGR1, HSPA9 on BTA 7 [97,98], and CDH15, DPEP1, GAS8, GALNS, and MC1R on BTA 18 [30,[99][100][101][102] in Kholmogor breed. The second overlapping genomic region under positive selection in Yaroslavl, Kholmogor and Holstein breeds containing TNFRSF1B, MFN2, PLOD1, KIAA2013, NPPB, NPPA, CLCN6, MTHFR, AGTRAP, FBXO2, MTOR, ANGPTL7, EXOSC10, and MASP2 genes was found on BTA16 (Table 3, S6 Table).…”

Section: Plos Onementioning

confidence: 98%

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

et al. 2020

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Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

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“…This consequently impacts lean deposition and subcutaneous fat deposition, as well as growth rate in cattle (SILVA-VIGNATO et al, 2019).…”

Section: Gwas and Functional Analysesmentioning

confidence: 99%

Genomic studies in Montana Tropical Composite cattle

Grigoletto¹

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Beef cattle production is a major component of the Brazilian economy and places the country amongst the top worldwide beef producers and exporters. The development and use of composite populations represent a promising alternative to increase production efficiency and quality in beef cattle. The strategic combination of different breeds poses a great opportunity to maximize genetic variability and exploit heterosis and breed complementarity. In order to successfully implement genomic evaluations for beef cattle, various genomic approaches and methodologies need to be investigated. In addition, the majority of genomic models and methods currently used for genomic evaluations were developed based on purebred animals and the knowledge on the use of genomic information in synthetic or composite cattle breeds is still very limited. Therefore, studies investigating more sophisticated methodologies and genomic approaches will enable a more efficient use of the genomic information available for composite breeds and consequently, more accurate breeding values. The overall objectives of this thesis are to: 1) identify genomic regions and potential candidate genes associated with various economically important traits in composite beef cattle populations; 2) investigate genomic selection methodologies and imputation strategies to improve the accuracy of genomic prediction of breeding values in the genetically diverse population of Montana Tropical Composite ® cattle. Approximately 4,000 genotyped animals from multiple breeds (Montana, Nellore, Aberdeen Angus, Red Angus, Senepol, and Simmental) and SNP chip panels were available for this research. In summary, this project contributed to the application of genomic approaches to fastener genetic progress for a variety of economically important traits in composite beef cattle and increase the profitability of beef producers.

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Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle

Cited by 44 publications

References 68 publications

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Genomic studies in Montana Tropical Composite cattle

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