Identification of Candidate Genes Regulating Spermatogenesis in Breeder Cocks by miRNA Sequencing

doi:10.7668/hbnxb.20193391

Abstract

Abstract:

Spermatogenesis is a complex process.At present,the mechanism of spermatogenesis in poultry has not been fully clarified.Therefore,Identification of candidate genes regulating spermatogenesis in breeder cocks is of great significance to explore the mechanism of spermatogenesis in poultry.miRNA sequencing was performed on testis and epididymis samples of 8 Hailan brown cocks,the differentially expressed miRNAs were screened and their target genes were predicted and analyzed.A total of 718 miRNAs were detected in testis and epididymis samples,of which 109 miRNAs were differentially expressed,among these differentially expressed miRNAs,40 were significantly up-regulated in testicular tissue and 69 in epididymis.The target genes of differentially expressed miRNAs were predicted and intersected.A total of 11 077 target genes were obtained,among them,4 784 target genes up-regulated differentially expressed miRNA in testis and 6 293 target genes up-regulated differentially expressed miRNA in epididymis.Functional analysis of target genes differentially expressing miRNA,Go enrichment analysis showed that the target genes in testis and epididymis were mainly concentrated in biological processes such as negative regulation of cell process,regulation of cell biosynthesis process,regulation of biosynthesis process and so on.KEGG analysis showed that the target genes related to spermatogenesis were significantly enriched in MAPK signaling pathway.It found that miR-31,miR-499,mir-375 and miR-34c might be candidate genes to regulate chicken spermatogenesis.

Key words: Chicken, Testis, Epididymis, miRNA, Spermatogenesis

CONG Bailin, XUE Lüfan, GAI Kai, ZHAO Yanhui, CHEN Peng, CHEN Yu, WANG Liang, LÜ Xueze, GUO Yong, SHENG Xihui. Identification of Candidate Genes Regulating Spermatogenesis in Breeder Cocks by miRNA Sequencing[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(S1): 333-338. doi: 10.7668/hbnxb.20193391.

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http://www.hbnxb.net/EN/Y2022/V37/IS1/333

Figures/Tables 8

Fig.1 Correlation analysis of expression levels among samples G.Testis;F.Epididymis.

Tab.1 Ten miRNAs with the highest expression in testis and epididymis

miRNA	睾丸中表达量 (平均值) Expression in testis (average value)	miRNA	附睾中表达量 (平均值) Expression in epididymis (average value)
gga-mir-21	99 010.250	gga-mir-21	1 107 495.250
gga-mir-19b	88 695.375	gga-mir-26a	945 307.625
gga-mir-29a	87 730.000	gga-mir-34b	623 894.500
gga-mir-29c	87 001.625	gga-mir-101	524 502.125
gga-mir-101	85 919.250	gga-mir-125b	466 637.375
gga-mir-26a	82 653.000	gga-mir-34c	330 340.625
gga-mir-19a	69 895.625	gga-mir-29a	302 676.000
gga-mir-125b	4 8597.875	gga-mir-29c	300 093.250
gga-let-7a	33 634.000	gga-mir-142	191 980.125
gga-let-7j	32 795.875	gga-mir-199	179 682.750

Fig.2 Differentially expressed miRNAs in chicken testis and epididymis Red.Up regulation;Green.Down;Blue.No significant difference;FC.Expression difference;FDR.Error discovery rate.

Tab.2 The 10 miRNAs with the highest multiple differences between testis and epididymis

miRNA	Log₂(FC)	P-value	差异类型 Different type
gga-mir-146c	6.902 743 454	9.08E-37	上调
gga-mir-203a	6.309 846 537	7.50E-34	上调
gga-mir-216c	6.565 912 100	1.91E-31	上调
gga-mir-31	5.788 709 614	3.41E-29	上调
gga-mir-499	5.535 957 062	4.64E-28	上调
gga-mir-375	-8.685 414 283	1.94E-50	下调
gga-mir-34c	-6.647 415 315	1.78E-41	下调
gga-mir-34b	-6.060 662 629	1.42E-37	下调
gga-mir-429	-7.167 204 066	3.12E-35	下调
gga-mir-200b	-6.557 815 014	8.41E-35	下调

Fig.3 Enrichment analysis of up-regulated differentially expressed miRNA target gene go in testicular tissue 1.Negative regulation of cellular process;2.Nervous system development;3.Cell development;4.Cell differentiation;5.Regulation of cellular macromolecule biosynthetic;6.Cellular developmental process;7.Regulation of macromolecule biosynthetic;8.Regulation of biosynthetic process;9.Neuron projection;10.Axon;11.Plasma membrane bounded cell projection;12.Cell projection;13.Somatodendritic compartment;14.Transcription repressor complex;15.Synapse;16.Cell junction;17.Transcription corepressor activity;18.Protein kinase activity;19.Transcription regulator activity;20.Transmembrane receptor protein kinase activity;21.DNA binding;22.Sequence-specific DNA binding;23.Transcription regulatory region sequence-specific DNA binding;24.Regulatory region nucleic acid binding.

Fig.4 Up regulation of differentially expressed miRNA target gene KEGG pathway in testis 1.MAPK signaling pathway;2.Regulation of actin cytoskeleton;3.Focal adhesion;4.Cellular senescence;5.Autophagy-animal;6.Adrenergic signaling in cardiomyocytes;7.Fox signaling pathway;8.TGF-beta signaling pathway;9.ErbB signaling pathway;10.Adheres junction.

Fig.5 Down regulation and enrichment of differentially expressed miRNA target gene GO in testicular tissue 1.Regulation of RNA metabolic process;2.Regulation of nucleobase-containing compound metabolic process;3.Nervous system development;4.Regulation of macromolecule biosynthetic process;5.Regulation of cellular biosynthetic process;6.Regulation of biosynthetic process;7.Regulation of nuclei acid-templated transcription;8.Regulation of RNA biosynthetic process;9.Axon;10.Transcription regulator activity;11.Sequence-specific DNA binding;12.DNA binding;13.Nucleic acid binding;14.DNA-binding transcription factor activity;15.Transcription regulatory region sequence-specific DNA binding;16.Regulatory region nucleic acid binding;17.Sequence-specific double-stranded DNA binding.

Fig.6 Down regulation of differentially expressed miRNA target gene KEGG pathway in testis 1.MAPK signaling pathway;2.Endocytosis;3.Focal adhesion;4.Regulation of actin cytoskeleton;5.Wnt signaling pathway;6.Tight junction;7.Cellular senescence;8.TGF-beta signaling pathway;9.Adheres junction;10.Notch signaling pathway.

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