Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses

Abstract

The athletic abilities of the horse serve as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. We analyzed differentially expressed genes in triceps brachii muscle tissues collected from Eonjena Taeyang and Jigusang Seryeok Thoroughbred horses and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. High-quality horse transcriptome data were generated, with over 22 million 90-bp pair-end reads. By comparing the annotations, we found that MYH3, MPZ, and PDE8B genes in Eonjena Taeyang and PDE8B and KIF18A genes in Jigusang Seryeok were upregulated before exercise. Notably further, we observed that PPP1R27, NDUFA3, TNC, and ANK1 in Eonjena Taeyang and HIF1A, BDNF, ADRB2, OBSCN, and PER3 in Jigusang Seryeok have shown upregulation at the postexercise period. This investigation suggested that genes responsible for metabolism and oxidative phosphorylations associated with endurance and resistance exercise were highly expressed, whereas genes encoding structural proteins were generally suppressed. The expression profile of racehorses at pre- and postexercise will provide credible reference for further studies on biological effects such as responses to stress and adaption of other Thoroughbred horse, which might be useful for selective breeding for improvement of traits in commercial production.

Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability

“…In our analysis, HIF1A is not in the top 10, but is also significantly upregulated (FC = 2.33). This is also in agreement with the results of a study in Thoroughbred horses [84]. Furthermore, HIF1A can stimulate promotor elements of PFKFB3 [85], a regulatory molecule that controls glycolysis, which is upregulated (FC = 9.14) in our study but also in other studies [16].…”

Comparison for immunophysiological responses of Jeju and Thoroughbred horses after exercise

“…Thoroughbred horse is the best breed for racing performance [4]. Thoroughbred horses have been intensively studied as model organisms in the study of exercise, especially at the molecular level, with the Thoroughbred horse genome being well-studied using RNA-seq and the associated epigenetics also receiving significant attention from academics [5,6]. Comparative studies have investigated the differences between Thoroughbred and Jeju horses in order to identify genetic differences using microsatellites [7] and single nucleotide polymorphism (SNP) chip arrays [8,9].…”

Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance

“…The regulator of calcineurin 1 (RCAN1) was reported significantly different in L muscles of Leizhou Black goats in postnatal muscle development [2]. The muscle RNA-seq data from the Eonjena Taeyang horses observed that PPP1R27 shown upregulation at the postexercise period [46]. The protein phosphatase 1 regulatory subunit 27 (PPP1R27) also reported as candidate genes of wool-related traits in Sheep [47].…”