Screening and functional analysis of differentially expressed genes in breast muscle transcriptome between Plateau raindrop pigeon and Janssen pigeon

doi:10.3969/j.issn.1004-1524.2022.03.11

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (3): 507-516.DOI: 10.3969/j.issn.1004-1524.2022.03.11

• Animal Science • Previous Articles Next Articles

Screening and functional analysis of differentially expressed genes in breast muscle transcriptome between Plateau raindrop pigeon and Janssen pigeon

LAN Guoxiang¹(), JIN Siqi¹, LI Xingrun², LIU Xiyu², LI Guomei¹, DONG Xinxing¹^,^*

1. College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
2. Department of Animal Science, Dali Vocational and Technical College of Agriculture and Forestry, Dali 671003, Yunnan, China

Received:2021-07-02 Online:2022-03-25 Published:2022-03-30
Contact: DONG Xinxing

Abstract

Abstract:

Screening key genes for the difference in pectoral flight ability between Plateau raindrop pigeon and Janssen pigeon can lay foundation for breeding pigeons. Each 3 Plateau raindrop pigeons (JG) and Janssen pigeons (JS) with the same sex, similar body condition and age were selected. After slaughter, breast muscle tissues were taken for transcriptome sequencing and then differentially expressed genes (DEGs) were screened, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and protein interaction network analysis were performed on the DEGs. The results showed that there were 75 significantly DEGs in the breast muscle transcriptome between JG and JS, including 49 up-regulated genes and 26 down-regulated genes. GO enrichment analysis results showed that DEGs were enriched in items such as skeletal muscle cell differentiation, regulation of cellular metabolic process. KEGG pathway analysis showed that DEGs were significant enriched in insulin signaling pathway, AMPK signaling pathway, etc. Compared with the JS,SMYD1, STAT1, VEGFA, PPM1K and PLCE1 genes in breast muscle of the JG were up-regulated, while MYOD1, SOCS3 and MGLL genes were down-regulated. The results showed that STAT1 and MYOD1 might cause breast muscle growth of JG to be slower than that of JS. SOCS3 might cause muscle fiber diameter of the breast muscle of the JG to become smaller and explosive power to decrease at the same time. PLCE1 might cause increase of muscle fibers in the breast muscle of JG. SMYD1 might cause muscle fiber differentiation to form more red muscle fibers. VEGFA might cause white adipose in JGs to be converted into brown adipose. PPM1K and MGLL might catalyze the decomposition of branched chain amino acids, providing enough energy for the long-distance load-bearing flight of the JG, which made they more suitable for long-distance flight.

Key words: Plateau raindrop pigeons, Janssen pigeons, transcriptome, differentially expressed genes, breast muscle

CLC Number:

S836

LAN Guoxiang, JIN Siqi, LI Xingrun, LIU Xiyu, LI Guomei, DONG Xinxing. Screening and functional analysis of differentially expressed genes in breast muscle transcriptome between Plateau raindrop pigeon and Janssen pigeon[J]. Acta Agriculturae Zhejiangensis, 2022, 34(3): 507-516.

Figures/Tables 8

References 51

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基因名 Gene name	上游引物序列(5'→3') Forward primer sequence(5'→3')	下游引物序列(5'→3') Reverse primer sequence(5'→3')	产物长度 Length of product/bp
MGLL	GAGCTGCCCGTTCTCATTCT	CGACAGGTTTGGGAGGACAA	189
SOCS3	GCCACCAGAGAACGGAAAGA	TTAGTCCCCCGGAAAATGGC	201
PPM1K	AGATGGCTGCTGATGCAACT	AGCCACCGCACTTCCTAATC	201
PLCE1	ATGCTTCCTTCACCTGGGC	TGGTAGGTGTGGTGGGGTTG	163
SMYD1	ATCTGTCATACCTGCTTCAAACG	CCAGCCTGATGTTTTCGGT	169
β-actin	TTACCCACACTGTGCCCATC	AGGGCAACATAGCACAGCTT	187

基因名 Gene name	上游引物序列(5'→3') Forward primer sequence(5'→3')	下游引物序列(5'→3') Reverse primer sequence(5'→3')	产物长度 Length of product/bp
MGLL	GAGCTGCCCGTTCTCATTCT	CGACAGGTTTGGGAGGACAA	189
SOCS3	GCCACCAGAGAACGGAAAGA	TTAGTCCCCCGGAAAATGGC	201
PPM1K	AGATGGCTGCTGATGCAACT	AGCCACCGCACTTCCTAATC	201
PLCE1	ATGCTTCCTTCACCTGGGC	TGGTAGGTGTGGTGGGGTTG	163
SMYD1	ATCTGTCATACCTGCTTCAAACG	CCAGCCTGATGTTTTCGGT	169
β-actin	TTACCCACACTGTGCCCATC	AGGGCAACATAGCACAGCTT	187

样品 Sample	原始读段 Raw reads	高质量序列所占比例 Clean reads rate/%	Q30/%	比对基因组所占比例 Mapping rate/%
JG1	50 784 230	94.47	93.57	83.09
JG2	49 764 078	95.51	93.26	84.60
JG3	48 035 956	93.37	94.08	83.03
JS1	51 604 076	91.46	93.81	85.33
JS2	49 022 332	91.97	93.85	85.90
JS3	47 948 950	94.94	93.56	84.03

样品 Sample	原始读段 Raw reads	高质量序列所占比例 Clean reads rate/%	Q30/%	比对基因组所占比例 Mapping rate/%
JG1	50 784 230	94.47	93.57	83.09
JG2	49 764 078	95.51	93.26	84.60
JG3	48 035 956	93.37	94.08	83.03
JS1	51 604 076	91.46	93.81	85.33
JS2	49 022 332	91.97	93.85	85.90
JS3	47 948 950	94.94	93.56	84.03

类别 Category	登记号 Accession	条目 Term	P值 P value	差异表达基因数量 Number of DEGs
肌肉生长	GO:0007259	JAK-STAT级联JAK-STAT cascade	0.003 5	2
Muscle growth	GO:0035914	骨骼肌细胞分化Skeletal muscle cell differentiation	0.005 7	2
	GO:0010830	肌管分化调控Regulation of myotube differentiation	0.008 4	2
	GO:0045661	成肌细胞分化调控Regulation of myoblast differentiation	0.011 0	2
	GO:0051153	横纹肌细胞分化调控Regulation of striated muscle cell differentiation	0.024 0	2
	GO:0006937	肌肉收缩调节Regulation of muscle contraction	0.044 0	1
能量利用	GO:0009083	支链氨基酸分解过程Branched-chain amino acid catabolic process	0.000 9	2
Energy utilization	GO:0016042	脂质分解过程Lipid catabolic process	0.001 0	5
	GO:0009081	支链氨基酸代谢过程Branched-chain amino acid metabolic process	0.001 3	2
	GO:0006651	甘油二酯生物合成过程Diacylglycerol biosynthetic process	0.007 1	1
	GO:0036155	酰基甘油链重构Acylglycerol acyl-chain remodeling	0.007 1	1
	GO:0006638	中性脂质代谢过程Neutral lipid metabolic process	0.017 0	2
	GO:0006639	酰基甘油代谢过程Acylglycerol metabolic process	0.017 0	2
	GO:0006633	脂肪酸生物合成过程Fatty acid biosynthetic process	0.030 0	2
	GO:0046339	二酰基甘油代谢过程Diacylglycerol metabolic process	0.031 0	2
	GO:0019433	甘油三酯分解过程Triglyceride catabolic process	0.038 0	2
	GO:0006629	脂质代谢过程Lipid metabolic process	0.041 0	7
	GO:0006631	脂肪酸代谢过程Fatty acid metabolic process	0.047 0	3
肌肉生长与能量利用	GO:0031323	细胞代谢过程调节Regulation of cellular metabolic process	8.5×10^-6	27
Muscle growth and	GO:0080090	初级代谢过程调节Regulation of primary metabolic process	1.8×10^-5	26
energy utilization	GO:0019222	代谢过程调节Regulation of metabolic process	3.5×10^-5	27
	GO:0060255	大分子代谢过程调控Regulation of macromolecule metabolic process	0.000 2	26
	GO:0051171	氮化合物代谢过程的调节	0.000 8	24
		Regulation of nitrogen compound metabolic process
	GO:0044238	初级代谢过程Primary metabolic process	0.003 5	29
	GO:0071704	有机物代谢过程Organic substance metabolic process	0.008 2	28
	GO:0008152	代谢过程Metabolic process	0.018 0	28

Screening and functional analysis of differentially expressed genes in breast muscle transcriptome between Plateau raindrop pigeon and Janssen pigeon

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功能ID Function ID	功能描述 Description of function	P值 P value	差异表达基因 DEGs
map04910	胰岛素信号通路Insulin signaling pathway	0.000 4	SOCS3、ACACB、PPP1R3C
map04931	胰岛素抵抗Insulin resistance	0.003 3	SOCS3、ACACB、PPP1R3C
map04919	甲状腺激素信号通路Thyroid hormone signaling pathway	0.003 8	STAT1、HIF1A、PLCE1
map04920	脂肪细胞因子信号通路Adipocytokine signaling pathway	0.014 0	SOCS3、ACACB
map00061	脂肪酸生物合成Fatty acid biosynthesis	0.039 0	ACACB
map04152	AMPK信号通路AMPK signal pathway	0.042 0	ACACB
map04630	Jak-STAT信号通路Jak-STAT signaling pathway	0.050 0	SOCS3、STAT1

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