Investigation of De Novo Unique Differentially Expressed Genes Related to Evolution in Exercise Response during Domestication in Thoroughbred Race Horses

Woncheoul Park,Heebal Kim,Seoae Cho,Chang-Kyu Lee,Jaemin Kim,Seong-Keun Cho,Jun-Kyu Park,Jeong-Woong Park,Jaeyoung Choi,Jae Yeon Hwang,Byeong-Woo Kim,Hyeon Jeong Kim,Hak-Kyo Lee,Teak-Soon Shin,Hyun-Woo Cho,Byung-Wook Cho,Myung Hum Park,Marc Robinson-Rechavi

doi:10.1371/journal.pone.0091418

Woncheoul Park, Heebal Kim + Show 16 more

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https://doi.org/10.1371/journal.pone.0091418

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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.

Highlights

Since domestication, at around 3500 B.C.E, horses have mainly been used for riding and racing [1]
We found 12 genes (ZNF592, CD58, C1orf162, USP37, FOXM1, TIMELESS, TRMT1, CALR, ASNA1, EIF4A3, SYNRG and FADS1) in blood and 14 genes (HERC2, CHD9, DDX28, CAPZA1, TSEN15, CHMP4C, FOXO3, PLD2, ANKRD13D, UNKL, CBFA2T2, NECAB3, SLC25A29 and FBLN1) in skeletal muscle that were both identified as de novo unique differentially expressed genes’’ (DUDEG) and implicated in FST analysis as a selected gene (Table S4 in File S1)
de novo-based analysis (DBA) used in align--assemble method assembles the unmapped sequence reads after reference-based analysis (RBA), which supplements the inherent weakness of RBA

Summary

Introduction

At around 3500 B.C.E, horses have mainly been used for riding and racing [1]. The Thoroughbred is an excellent breed for competitive horse racing and by extension a valuable model for studying exercise response. Due to the combined effect of natural selection and human-controlled selective breeding, phenotypic changes, which are related to genetic mutation, accompany the domestication process. Selective sweep regions in the genome can potentially be identified by a genome scan, and the low variation interval surrounding the selected gene can be found by fine-scale mapping. Using such genome scans, selective sweeps have been identified in domestic and natural (wild progenitor) populations [8,9]

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