ArticlePloS one2014
Investigation of de novo unique differentially expressed genes related to evolution in exercise response during domestication in Thoroughbred race horses.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 21 citations in OpenAlex.
- Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach.Genetics, selection, evolution : GSE · 2023Article
- Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon.Scientific reports · 2021Article
- Transcriptomic comparison of communally reared wild, domesticated and hybrid Atlantic salmon fry under stress and control conditions.BMC genetics · 2020Article
- Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.Animal genetics · 2019Review
- Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations.Scientific reports · 2019Article
- Analysis of cross-population differentiation between Thoroughbred and Jeju horses.Asian-Australasian journal of animal sciences · 2018Article
- Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Evolutionary bioinformatics online · 2018Article
- Exercise induced upregulation of glutamate-cysteine ligase catalytic subunit and glutamate-cysteine ligase modifier subunit gene expression in Thoroughbred horses.Asian-Australasian journal of animal sciences · 2017Article
- Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression.Genetics, selection, evolution : GSE · 2016Article
- Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds.Genomics & informatics · 2015Article
- Genetic Susceptibility to Rhodococcus equi.Journal of veterinary internal medicineReview
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Previous studies of horse RNA-seq were performed by mapping sequence reads to the reference genome during transcriptome analysis. However in this study, we focused on two main ideas. First, differentially expressed genes (DEGs) were identified by de novo-based analysis (DBA) in RNA-seq data from six Thoroughbreds before and after exercise, here-after referred to as "de novo unique differentially expressed genes" (DUDEG). Second, by integrating both conventional DEGs and genes identified as being selected for during domestication of Thoroughbred and Jeju pony from whole genome re-sequencing (WGS) data, we give a new concept to the definition of DEG. We identified 1,034 and 567 DUDEGs in skeletal muscle and blood, respectively. DUDEGs in skeletal muscle were significantly related to exercise-induced stress biological process gene ontology (BP-GO) terms: 'immune system process'; 'response to stimulus'; and, 'death' and a KEGG pathways: 'JAK-STAT signaling pathway'; 'MAPK signaling pathway'; 'regulation of actin cytoskeleton'; and, 'p53 signaling pathway'. In addition, we found TIMELESS, EIF4A3 and ZNF592 in blood and CHMP4C and FOXO3 in skeletal muscle, to be in common between DUDEGs and selected genes identified by evolutionary statistics such as FST and Cross Population Extended Haplotype Homozygosity (XP-EHH). Moreover, in Thoroughbreds, three out of five genes (CHMP4C, EIF4A3 and FOXO3) related to exercise response showed relatively low nucleotide diversity compared to the Jeju pony. DUDEGs are not only conceptually new DEGs that cannot be attained from reference-based analysis (RBA) but also supports previous RBA results related to exercise in Thoroughbred. In summary, three exercise related genes which were selected for during domestication in the evolutionary history of Thoroughbred were identified as conceptually new DEGs in this study.
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