RNA-seq analysis identifies differentially expressed gene in different types of donkey skeletal muscles

Chai, Wenqiong; Qu, Honglei; Ma, Qiugang; Zhu, Mingxia; Li, Mengmeng; Zhan, Yandong; Liu, Ziwen; Xu, Jing; Yao, Huanfen; Li, Zeyu; Wang, Changfa

doi:10.1080/10495398.2022.2050920

Cited by 12 publications

(19 citation statements)

References 30 publications

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“…Skeletal muscle fiber is not only closely related to human muscle health but also affects meat quality in livestock production [ 1 , 4 , 15 ]. In our previous studies, we observed differences in meat quality among various muscles of donkeys (e.g., donkey gluteus vs. longissimus dorsi) [ 20 ] as well as genes related to donkey meat tenderness, as reported by Chai et al [ 9 ]. However, the molecular mechanisms determining the muscle fiber profiles of donkeys remain unclear, especially with respect to miRNA regulation.…”

Section: Discussionmentioning

confidence: 88%

“…It has also been shown that the expression of CALM1 , a subunit of CaM, is negatively correlated with intramuscular fat in pigs [ 38 ] and influences meat quality. Furthermore, genes such as MYH1 , MYH7 , MYH4 and MYL2 have been identified as candidate genes affecting meat tenderness in our previous work [ 9 ]. These results indicated that there is a difference between PM and BF at the transcription level, which is consistent with the data from the histochemical analysis of the study subjects.…”

Section: Discussionmentioning

confidence: 99%

“…To validate the transcriptome results, six mRNAs and two miRNAs were randomly selected for qRT-PCR. The relative expression analysis of genes was assessed by qRT-PCR as described in our previous study [ 9 ]. Trizol reagent was used to extract the total RNA of muscle samples, and reverse transcription was carried out using the PrimeScript RT Reagent Kit (TaKaRa, Dalian, China).…”

Section: Methodsmentioning

confidence: 99%

“…Thus, understanding the differential expression patterns of muscle fiber at the transcript level in domestic animals is of critical importance. Donkey meat is drawing research interest, mainly due to characteristics including its high protein content and low fat content [ 9 ]. Although some studies have reported the differences among the various muscle fiber types in terms of physiology and functionality, the molecular mechanisms and signaling pathways involved in determining muscle fiber types in donkeys remain largely unknown.…”

Section: Introductionmentioning

confidence: 99%

“…The Dezhou donkey, an important breed in China, with a large size, is famous for its excellent characteristics (including its large size, muscular body and excellent skin quality) [ 19 ]. Past studies in our lab have found differences in meat quality among various muscles of Dezhou donkeys (such as the donkey gluteus vs. longissimus dorsi) [ 20 ], and Chai et al identified some differentially expressed genes (DEGs) related to tenderness in donkey meat (including MYH1 , MYH7 , MYH4 and MYL2 ) [ 9 ]. However, the regulation mechanisms underlying muscle fiber type specification in Dezhou donkeys at the transcript level still need to be further elucidated.…”

Section: Introductionmentioning

confidence: 99%

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Comparative Transcriptome Analysis of Slow-Twitch and Fast-Twitch Muscles in Dezhou Donkeys

Shi

et al. 2022

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The skeletal muscle fiber profile is closely related to livestock meat quality. However, the molecular mechanisms determining muscle fiber types in donkeys are not completely understood. In this study, we selected the psoas major muscle (PM; mainly composed of oxidative-type muscle fibers) and biceps femoris muscle (BF; mainly composed of glycolytic-type muscle fibers) and systematically compared their mRNA and microRNA transcriptomes via RNA-seq. We identified a total of 2881 differentially expressed genes (DEGs) and 21 known differentially expressed miRNAs (DEmiRs). Furthermore, functional enrichment analysis showed that the DEGs were mainly involved in energy metabolism and actin cytoskeleton regulation. The glycolysis/gluconeogenesis pathway (including up-regulated genes such as PKM, LDHA, PGK1 and ALDOA) was more highly enriched in BF, whereas the oxidative phosphorylation pathway and cardiac muscle contraction (including down-regulated genes such as LDHB, ATP2A2, myosin-7 (MYH7), TNNC1, TPM3 and TNNI1) was more enriched in PM. Additionally, we identified several candidate miRNA–mRNA pairs that might regulate muscle fiber types using the integrated miRNA–mRNA analysis. Combined with the results of protein–protein interaction (PPI) analysis, some interesting DEGs (including ACTN3, TNNT3, TPM2, TNNC2, PKM, TNNC1 and TNNI1) might be potential candidate target genes involved in the miRNA-mediated regulation of the myofibril composition. This study is the first to indicate that DEmiRs, especially eca-miR-193a-5p and eca-miR-370, and potential candidate target genes that are mainly involved in actin binding (e.g., ACTN3, TNNT3 and TNNC1) and the glycolysis/gluconeogenesis pathways (e.g., PKM) might coregulate the myofibril composition in donkeys. This study may provide useful information for improving meat quality traits in Dezhou donkeys.

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