Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle

Santana, Miguel Henrique de Almeida; Oliveira, G.A.; Cesar, Aline Silva Mello; Freua, Mateus Castelani; Gomes, Rodrigo da Costa; Silva, Saulo da Luz e; Leme, Paulo Roberto; Fukumasu, Heidge; Carvalho, Minos Esperândio; Ventura, Ricardo Vieira; Coutinho, Luiz Lehmann; Kadarmideen, Haja N.; Ferraz, José Bento Sterman

doi:10.1007/s13353-016-0344-7

Cited by 55 publications

(27 citation statements)

References 71 publications

(89 reference statements)

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“…Similarly, candidate genes in pathways related to protein metabolism have been suggested in genomic regions accounting for feed conversion ratio in cattle [7]. Ribosome biogenesis and translation processes were notably enriched in over-expressed genes in tissues of pigs from the low RFI line.…”

Section: Discussionmentioning

confidence: 99%

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A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

et al. 2017

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BackgroundAnimal’s efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI).ResultsPigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines.ConclusionsNon-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3639-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

“…To date, some DNA variants playing a role in feed efficiency traits have been proposed from analyses of SNP locations by whole-genome association in pigs [4, 5] and beef cattle [6, 7]. Based on their genomic location in the vicinity of these SNPs, putative gene candidates for feed efficiency traits including RFI have been suggested.…”

Section: Introductionmentioning

confidence: 99%

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

et al. 2017

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“…Most of these pathways (Additional file 3) were related to nutrients (fatty acids, carbohydrates and proteins) and metabolism. de Almeida Santana et al (2016) [35] reported that the retinol metabolic pathway was involved in the feed conversion ratio in beef cattle in relation to rump fat thickness. The authors also discussed that lipid and protein metabolisms were well-known important factors in feed efficiency physiology.…”

Section: Discussionmentioning

confidence: 99%

“…The authors also discussed that lipid and protein metabolisms were well-known important factors in feed efficiency physiology. The relationship between retinol metabolism and the feed conversion ratio phenotype in Nellore beef cattle has been previously described [36] and [35]. …”

Section: Discussionmentioning

confidence: 99%

RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

et al. 2017

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BackgroundThe selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE.ResultsThe bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450.ConclusionWe used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular pathways. The DEGs that were identified were the CYP’s and GIMAP genes for the Holstein and Jersey cows, respectively, which are related to the primary immunodeficiency pathway and play a major role in feed utilization and the metabolism of lipids, sugars and proteins.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3622-9) contains supplementary material, which is available to authorized users.

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“…Another candidate region identified on OAR6:80.6-81.0 Mb (S7 Fig and Table 4), shown by the Ethiopian group (eleven breeds) and the Libyan Barbary and including the EPHA5 gene, was also detected in a GWAS for wool production traits in a Chinese Merino sheep population and reported to be significantly associated with fiber diameter [33]. Moreover, it has been identified through GWAS as a candidate gene for feed conversion ratio in Nellore cattle [34]. The signal on OAR7:33.5-33.9 Mb (S8 Fig and Table 4) was detected in the Barbaresca and Laticauda, as well as in a previous study [9].…”

Section: Discussionmentioning

confidence: 99%

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

Mastrangelo¹,

Bahbahani²,

Moioli³

et al. 2018

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34Genomic regions subjected to selection frequently show signatures such as within-35 population reduced nucleotide diversity and outlier values of differentiation among differentially 36 selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging 37 to 23 sheep breeds of different geographic origins using the Rsb and F ST statistical approaches, to 38 identify loci associated with the fat-tail phenotype. We also checked if these putative selection 39 signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel 40 signals and confirmed the presence of selection signature in genomic regions that harbor candidate 41 genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH 42 were also identified within each breed, but only two ROH islands overlapped with the putative 43 selection signatures. The results reported herein provide the most complete genome-wide study of 44 selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights 45 into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the 46 mechanisms that underlie quantitative traits, such as the fat-tail. 47 48 3 51been widely applied to livestock species to achieve more desirable/profitable phenotypes [1]. For 52 instance, sheep (Ovis aries) have been selected since domestication, approximately 9,000 years ago 53 [2]. This process of selection resulted in divergent sheep breeds, reared in different geographic 54 regions due to their different adaptability. Among these, fat-tail are an important class of sheep 55 breeds and represent about 25% of the world's sheep population [3] mainly distributed in the 56 Middle East, North and East Africa and Central Asia. According to Xu et al. [4] fat tails represent 57 the energy reserve necessary to survive critical conditions such as drought seasons and food 58 shortage. This statement being emphasized by Mwacharo et al. [5] who confirmed that the fat-tails 59 are the predominant sheep across the deserts of northern Africa, and in the highlands, semi-arid and 60 arid environments of eastern and southern Africa while the thin-tails occur in Sudan and in the sub-61 humid and humid regions of West Africa. 62The unique genetic patterns inscribed in the genome of individuals by natural and/or 63 artificial selection are defined as signatures of selection, which are usually regions of the genome 64 that harbor functionally important sequence variants [6]. Although human consumption of animal 65 fat has dramatically reduced in preference of leaner meat, the investigation of the potential 66 candidate genes involved in the fat-tail might contribute to exploring the genetics of fat deposition, 67 energy storage and adaptation to climate changes [7][8][9]. With the aim to identify candidate genes 68 with a potential role in these traits, several authors performed studies targeting the fat-tail 69 phenotype contrasted with the thi...

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Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle

Cited by 55 publications

References 71 publications

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

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