Acta Veterinaria et Zootechnica Sinica ›› 2023, Vol. 54 ›› Issue (3): 989-1002.doi: 10.11843/j.issn.0366-6964.2023.03.013

• ANIMAL GENETICS AND BREEDING • Previous Articles     Next Articles

Identification and Analysis of mRNA and lncRNA Affecting Goat Fetal Muscle Development

YE Junning1, DENG Ming1, XUE Huiwen1, LIU Guangbin1, ZOU Xian2, SUN Baoli1, GUO Yongqing1, LIU Dewu1, LI Yaokun1*   

  1. 1. College of Animal Science, South China Agricultural University, Guangzhou 510642, China;
    2. Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
  • Received:2022-08-04 Online:2023-03-23 Published:2023-03-21

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Abstract: The study aimed to examine the differentially expressed mRNAs and lncRNAs as well as their target genes in the transcriptome sequencing of Leizhou goat fetuses at 70, 90 and 120 days, and to investigate important candidate genes controlling the development of skeletal muscle in Leizhou goat fetuses, functional enrichment analysis of differentially expressed genes was carried out. Leizhou female goats were separated into 3 groups of 70, 90, and 120 days of gestation, with 3 animals in each group, for a total of 9 animals. The goats were about 2.5-3.5 years old, in the same feeding condition, healthy, and disease-free. The transcriptome was sequenced using Illumina HiSeqTM2500 after the RNA of fetal longissimus dorsi was extracted in order to establish a library. The differential mRNAs and lncRNAs were screened at a threshold of Q<0.05, enriched for biological functions, and constructed into a target relationship network. In order to confirm the accuracy of the sequencing results, the expression levels of differential genes were lastly detected using fluorescence quantitative PCR. It was found that in the M70 vs. M90 group, a total of 185 differentially expressed mRNAs were identified, of which 170 were upregulated, 15 were downregulated, and 62 differentially expressed lncRNAs, 40 were upregulated, and 22 were downregulated. In the M120 vs. M90 group, we identified 1 048 differentially expressed mRNAs, 666 were upregulated, 382 were downregulated, 352 differentially expressed lncRNAs, 175 were upregulated, and 177 were downregulated. Among them, TNNT3, TNNI1, TNNT1, TNNI2, ITGA4, ITGA11, and ITGB4 genes were involved in regulatory pathways related to muscle development such as troponin complex, myofilament, adhesion plaque, ECM-receptor interaction, PI3K-Akt signaling pathways, etc. A total of 37 464 target genes were screened according to the positional relationship between lncRNA and mRNA for cis target gene prediction. Ten differentially expressed mRNAs were targeted by differentially expressed lncRNAs, among which NDUFB2, BRAF, METTL7B, and ITGA7 regulated adherent spots and the actin cytoskeleton, and METTL7B and ITGA7 were also engaged in PI3K-Akt signaling pathway. lncRNA TCONS_00214300 targeted METTL7B and ITGA7. Meanwhile, RT-PCR results of 8 differentially expressed mRNAs and lncRNAs showed that the expression levels of the 8 genes were similar to the expression trends of transcriptome sequencing, indicating that the sequencing results were reliable. The findings identify the lncRNAs and mRNAs that regulate fetal muscle development in Leizhou goats, as well as the potential regulatory linkages between some lncRNAs and mRNAs with differential expression. In addition, the studys also offer a theoretical foundation for molecular selection and breeding of Leizhou goats, and a novel source for studying the molecular regulatory mechanism of fetal muscle development in Leizhou goats.

Key words: Leizhou goat, mRNA, lncRNA, longissimus dorsi

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