Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages

Wu, Pengfei; Zhang, Xinchao; Zhang, Genxi; Chen, Fuxiang; He, Ming‐Liang; Zhang, Tao; Wang, Jinyu; Xie, Kaizhou; Dai, Guojun

doi:10.7717/peerj.8950

Cited by 19 publications

(16 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Transcriptome sequencing of 16-week-old Bian chickens with varying growth rates revealed 108 differential genes; 17 were up-regulated, whereas 91 were down-regulated [19]. Moreover, 364, 219, and 111 differentially expressed genes (F8FvsF4F, F8SvsF4S, and M8SvsM4S) were detected for the three comparison groups, respectively, which used the 4-week old and 8-week old males and female of Jinghai yellow chicken with different growth rates [13]. In the later stage of embryonic development, the number of differentially expressed genes decreased sharply.…”

Section: Discussionmentioning

confidence: 98%

“…RNA-seq technology proved helpful in revealing the essential genes and pathways associated with muscle development. In previous experiments, different growth rate chicken (Jinghai Yellow Chicken) muscle was used to analyze the expression difference of genes about muscle development, which revealed the regulation mechanism of the growth chickens [12,13].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Ren

Liu

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21. Results: Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P<0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,251 (E12vsE16), 4,324 (E12vsE19), and 5,224 (E12vsE21), 1,274 (E16vsE19), 2,735 (E16vsE21) and 857 (E19vsE21) differentially expressed mRNAs were identified. It is worth noting that 6,726 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The downward trend was the most important and was enriched in 3,963 DEGs. GO enrichment analysis provided three significantly enriched categories of the down-trending genes, including 91 cellular components, 53 molecular functions, and 248 biological processes. Through KEGG analysis, we explored the pathway of downtrend genes. A total of 183 KEGG pathways were enriched, including 17 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P<0.05), MAPK signalingpathway, TGF-beta signaling pathway, and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3. Conclusion: Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.

show abstract

Section: Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Ren

Liu

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Zhang ZR et al also found that the ECM-receptor interaction, MAPK signaling pathway, and focal adhesion, were the most enriched DEGs in breast muscle of chickens [ 15 ]. Zhao YQ et al found that focal adhesion, protein digestion and absorption, GABAergic synapse, axon guidance, ECM-receptor interaction, MAPK signaling pathway, arginine, and proline metabolism were closely related to skeletal muscle of Tongcheng pigs, while oxidative phosphorylation, Huntington’s disease, ribosome biogenesis in eukaryotes, metabolic pathways, Alzheimer’s disease, glycolysis/gluconeogenesis, and proteasome were found to be more associated with the DEGs in skeletal muscle of Yorkshire pigs at developmental stages [ 73 ]. The biological processes categories in this study, including “negative regulation of skeletal muscle tissue development”, “embryonic skeletal system morphogenesis”, and “regulation of skeletal muscle contraction”, were significantly regulated by the DEGs, indicating that these DEGs played a key role in regulating duck skeletal muscle development at different stages.…”

Section: Discussionmentioning

confidence: 99%

Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq

Cao

Zhang

et al. 2021

Biomolecules

View full text Add to dashboard Cite

As one of the most important poultry worldwide, ducks (Anas platyrhynchos) are raised mainly for meat and egg products, and muscle development in ducks is important for meat production. Therefore, an investigation of gene expression in duck skeletal muscle would significantly contribute to our understanding of muscle development. In this study, twenty-four cDNA libraries were constructed from breast and leg muscles of Hanzhong Ma ducks at day 17, 21, 27 of the embryo and postnatal at 6-month-old. High-throughput sequencing and bioinformatics were used to determine the abundances and characteristics of transcripts. A total of 632,172,628 (average 52,681,052) and 637,213,938 (average 53,101,162) reads were obtained from the sequencing data of breast and leg muscles, respectively. Over 71.63% and 77.36% of the reads could be mapped to the Anas platyrhynchos genome. In the skeletal muscle of Hanzhong duck, intron variant (INTRON), synonymous variant (SYNONYMOUS_CODING), and prime 3′ UTR variant (UTR_3_PRIME) were the main single nucleotide polymorphisms (SNP) annotation information, and “INTRON”, “UTR_3_PRIME”, and downstream-gene variant (DOWNSTREAM) were the main insertion-deletion (InDel) annotation information. The predicted number of alternative splicing (AS) in all samples were mainly alternative 5′ first exon (transcription start site)-the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)-the last exon splicing (TTS). Besides, there were 292 to 2801 annotated differentially expressed genes (DEGs) in breast muscle and 304 to 1950 annotated DEGs in leg muscle from different databases. It is worth noting that 75 DEGs in breast muscle and 49 DEGs in leg muscle were co-expressed at all developmental points of comparison, respectively. The RNA-Seq data were confirmed to be reliable by qPCR. The identified DEGs, such as CREBL2, RHEB, GDF6, SHISA2, MYLK2, ACTN3, RYR3, and STMN1, were specially highlighted, indicating their strong associations with muscle development in the Hanzhong Ma duck. KEGG pathway analysis suggested that regulation of actin cytoskeleton, oxidative phosphorylation, and focal adhesion were involved in the development of skeletal muscle. The findings from this study can contribute to future investigations of the growth and development mechanism in duck skeletal muscle.

show abstract

“…RNA-seq technology proved helpful in revealing the essential genes and pathways associated with muscle development. In previous studys, different growth rate chicken (Jinghai Yellow Chicken) muscle was used to analyze the expression difference of genes about muscle development, which revealed the regulation mechanism of the differently growth chickens [ 11 , 12 ]. Transcriptome sequencing was performed on the breast muscle and leg muscle of Hanzhong Mabu ducks at several time points during embryo and postnatal period to find the key genes that play regulatory roles at different time points, and to provide a basis for further research on the growth and development mechanism of duck skeletal muscle[ 13 ].Zhao et al[ 14 ] used longissimus dorsi muscle of Lantang and Landrace pig at different gestation times as the research object to explore the muscle development rules of pig embryos of different breeds.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of embryonic muscle development in Chengkou Mountain Chicken

et al. 2021

View full text Add to dashboard Cite

Background Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21. Results Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P < 0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,262 in E12vsE16, 5,058 in E12vsE19, 6139 in E12vsE21, 1,282 in E16vsE19, 2,920 in E16vsE21, and 646 in E19vsE21differentially expressed mRNAs were identified. It is worth noting that 7,572 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The significant enrichment trends included 3,150 DEGs. GO enrichment analysis provided three significantly enriched categories of significantly enriched differential genes, including 65 cellular components, 88 molecular functions, and 453 biological processes. Through KEGG analysis, we explored the biological metabolic pathways involved in differentially expressed genes. A total of 177 KEGG pathways were enriched, including 19 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P < 0.05), MAPK signalingpathway, TGF-beta signaling pathway, PI3K-Akt signaling pathway and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3. Conclusions Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.

show abstract

Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages

Cited by 19 publications

References 61 publications

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq

Transcriptome analysis of embryonic muscle development in Chengkou Mountain Chicken

Contact Info

Product

Resources

About