A genomewide association mapping study using ultrasound‐scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

Santana, Miguel Henrique de Almeida; Ventura, Ricardo Vieira; Utsunomiya, Yuri Tani; Neves, Haroldo Henrique de Rezende; Oliveira, G.A.; Gomes, Rodrigo da Costa; Bonin, Michael; Coutinho, Luiz Lehmann; Garcia, José Fernando; Silva, S.L.; Fukumasu, Heidge; Leme, Paulo Roberto; Ferraz, José Bento Sterman

doi:10.1111/jbg.12167

Cited by 36 publications

(30 citation statements)

References 27 publications

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“…LNX2 functions as an E3-ubiqutin ligase and its silencing affects the Notch and Wnt signaling pathways66, which play a key role in cellular proliferation and differentiation. Intriguingly, the cattle LNX2 was also identified in the genomic region associated with residual body weight gain67, suggesting that LNX2 may be a conserved regulator for individual growth in both invertebrate and vertebrate. PAK2, a serine/threonine kinase, acts as an effector of GTPases Rac1 and Cdc42 and is required for actin cytoskeletal remodeling, cell cycle progression, apoptosis or proliferation6869.…”

Section: Resultsmentioning

confidence: 99%

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

Qiu

Xiong

Han

et al. 2017

Sci Rep

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The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs.

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Section: Resultsmentioning

confidence: 99%

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

Qiu

Xiong

Han

et al. 2017

Sci Rep

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“…Santana et al . () proposed DPYD as a candidate gene for the trait rib eye area in Nellore cattle. Rib eye area is related to muscle quantity and, consequently, to body size (Table ).…”

Section: Resultsmentioning

confidence: 99%

“…; Santana et al . ); GDF9 and PDGFD for reproduction traits (Amills ; Wei et al . ); IL2 for immune response (Pariset et al .…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

et al. 2016

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We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (F ) with pedigree-based inbreeding coefficients (F ). The linear relationship between F and F was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). F appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

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“…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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A genomewide association mapping study using ultrasound‐scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

Cited by 36 publications

References 27 publications

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

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

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