转录组和蛋白组筛选就巢鸡卵巢发育候选基因及其调控网络构建

doi:10.11843/j.issn.0366-6964.2024.11.015

摘要/Abstract

摘要：

为了研究蛋鸡就巢性的潜在调控机制，本研究选用300日龄体况良好、体重一致的城口山地鸡12只，其中3只个体处于正常产蛋期，其余9只个体分别处于就巢期10、20和30天。采集各组蛋鸡卵巢组织进行组织解剖学形态观察，然后利用转录组(RNA-seq)和蛋白组(iTRAQ)测序技术分别对产蛋组正常卵巢(normal ovary，NO)和就巢组萎缩卵巢(atrophic ovary，AO)进行测序分析。筛选差异表达基因(DEGs)和差异表达蛋白(DEPs)并进行功能富集分析，鉴定与家禽就巢性相关的候选基因。结果表明：就巢导致蛋鸡卵巢发生萎缩，卵泡大量闭锁。在卵巢组织中鉴定出930个DEGs，其中430个基因上调，500个基因下调；同时鉴定出546个DEPs，其中178个蛋白上调，368个蛋白下调。通过功能注释和富集分析发现，这些DEGs和DEPs显著富集在细胞外基质(extracellular matrix，ECM)受体相互作用、黏着和PI3K-Akt等信号通路。最后通过转录组和蛋白组联合分析，筛选出7个蛋鸡就巢性的候选基因：COMP、FN1、ITGA8、THBS1、COL4A2、COL4A1和COL1A1。综上所述，本研究通过分析转录组测序和蛋白组测序结果筛选了蛋鸡就巢性关键候选基因，并构建了家禽就巢状态下卵巢发育的调控网络。本研究为深入解析就巢期卵巢萎缩的分子调控机制提供了理论参考，丰富了调控家禽就巢性状的候选基因，为蛋鸡的遗传改良和分子育种研究提供理论依据。

关键词: 就巢, 卵巢, 转录组学, 蛋白组学, 城口山地鸡

Abstract:

The study aimed to investigate the potential regulatory mechanism of nesting ability of laying hens. The 12 300-day-old Chengkou mountain chickens with good body condition and the same body weight were used in this study. Among them, 3 individuals were in normal laying period, and the remaining 9 individuals were in nesting period for 10, 20 and 30 days, respectively. The ovarian tissues of laying hens in each group were collected for anatomical observation. Normal ovary (NO) and atrophic ovary (AO) of laying hens were analyzed by RNA-seq and iTRAQ sequencing technology. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were screened and functional enrichment analysis was performed to identify candidate genes related to nesting in poultry. The results showed that ovary atrophy and follicle atresia occurred in nesting hens. A total of 930 DEGs were identified in ovarian tissues, of which 430 genes were up-regulated and 500 genes were down-regulated. Meanwhile, 546 DEPs were identified, of which 178 proteins were up-regulated and 368 proteins were down-regulated. Through functional annotation and enrichment analysis, it was found that these DEGs and DEPs were significantly enriched in ECM receptor interaction, adhesion and PI3K-Akt signaling pathways. Finally, 7 candidate genes for nesting ability COMP, FN1, ITGA8, THBS1, COL4A2, COL4A1 and COL1A1 were selected by combined transcriptome and proteome analysis. In summary, key candidate genes for nesting ability were identified by transcriptome and proteome analysis, and a regulatory network for ovarian development in nesting poultry was constructed. This study provides a theoretical reference for further understanding the molecular regulation mechanism of ovarian atrophy at nesting stage, enriches the candidate genes regulating poultry nesting traits, and provides theoretical basis for genetic improvement and molecular breeding research of laying hens.

Key words: nesting, ovary, transcriptome, proteome, Chengkou mountain chicken

中图分类号:

S831.2

蒋婷, 李文东, 李兴起, 黄雨, 王启贵, 王海威, 杨朝武, 刘凌斌. 转录组和蛋白组筛选就巢鸡卵巢发育候选基因及其调控网络构建[J]. 畜牧兽医学报, 2024, 55(11): 4950-4967.

Ting JIANG, Wendong LI, Xingqi LI, Yu HUANG, Qigui WANG, Haiwei WANG, Chaowu YANG, Lingbin LIU. Screening Candidate Genes for Ovarian Development and Constructing Regulatory Network in Nesting Chickens by Transcriptome and Proteome[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(11): 4950-4967.

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基因Gene	上游引物(5′→3′) Forward primer	下游引物(3′→5′) Reverse primer	产物长度/bp Product length
FN1	CACCTACCCCCAGTTCACAC	TGGATGTTGTGTGTCTGCCT	109
COL1A1	GCCAAGACGAAGACATCCCA	GGCAGTTCTTGGTCTCGTCA	156
SGK2	GCCAAACGCAAGAGTGATGG	TCTCCGAGGTCTGGAAGGAG	169
CASTOR1	CTGTGTCCTCACACTGGACC	AACGTGATGGAGCTGGGTTC	129
ACAT1	GGTTCTGATGACCACGGAGG	GAATCTTGGGAACAGCGTGC	131
MMP10	CTCTATGGACCCCCAAGGGA	TGGGTGCCATTTCTGTTGGT	121
β-actin	CTGTGCCCATCTATGAAGGCTA	ATTTCTCTCTCGGCTGTGGTG	132

基因Gene	描述Description	log₂(FC)	P-value
TTLL11	Tubulin polyglutamylase TTLL11 isoform X4	10.500 841 88	1.458 15×10^-5
VPREB3	Pre-b lymphocyte 3	6.516 213 893	0.000 819 366
AICDA	Activation induced cytidine deaminase	5.560 132 636	0.001 782 563
Aldh3b1	Aldehyde dehydrogenase family 3 member b1	5.347 768 100	0.000 477 674
CXCL13	C-x-c motif chemokine ligand 13	4.643 001 006	0.010 083 317
CHIR-B2	Gallus gallus immunoglobulin-like receptor chir-b2	4.070 460 591	0.000 434 750
MR1	F10 alpha chain-like isoform x1	3.665 580 961	0.016 924 252
PAX5	Paired box 5	3.554 588 852	0.034 263 113
CXCR5	C-x-c motif chemokine receptor 5	3.372 478 676	0.000 260 851
SLC6A18	Solute carrier family 6 member 18	3.145 381 031	0.000 118 215
CD79B	Cd79b molecule	3.030 284 866	5.085 67×10^-5
RGS13	Regulator of g-protein signaling 13	3.000 836 587	0.014 083 046
BPTF	Bromodomain phd finger transcription factor, partial	2.964 106 33	0.000 817 016
pol	Uncharacterized protein loc106895380	2.701 115 657	0.040 790 927
sebox	Paired box protein 6 homolog	2.626 303 296	0.000 660 700
RGS20	Regulator of g-protein signaling 20	2.588 546 838	0.000 265 790
Tnr	Fibrinogen-like protein 1-like protein	2.567 345 957	4.961 03×10^-5
SLC22A18	Solute carrier family 22 member 18	2.460 845 463	0.000 527 036
GSX2	Gs homeobox 2-like	2.448 250 869	0.012 140 053
POU2AF1	Pou class 2 associating factor 1	2.421 874 929	0.002 290 982

基因Gene	描述Description	log₂(FC)	P-value
CYP2AB1	Cytochrome P450, family 2, subfamily AB, polypeptide 1	-5.805 985 902	1.147 4×10^-151
ACTC1	Actin alpha cardiac muscle 1	-4.874 610 515	1.073 13×10^-7
ALB	Albumin	-4.060 938 705	4.069 68×10^-6
UMOD	Uromodulin	-4.015 674 232	6.976 03×10^-8
ZP3	Zona pellucida sperm-binding protein 3	-3.809 355 324	5.409 94×10^-10
COL8A1	Collagen type Ⅷ alpha 1 chain	-3.743 850 285	3.122 75×10^-9
ACTA1	Actin alpha 1, skeletal muscle	-3.444 999 220	6.556 52×10^-10
MMP13	Matrix metallopeptidase 13	-3.430 684 692	7.028 18×10^-5
TAGLN	Transgelin	-3.213 487 543	2.005 09×10^-11
MYL4	Myosin, light chain 4, alkali; atrial, embryonic	-3.204 401 269	2.002 51×10^-13
FAM189A2	Family with sequence similarity 189 member A2	-3.123 454 143	5.063 02×10^-7
INHA	Inhibin alpha subunit	-3.115 492 881	7.802 8×10^-5
MMP10	Matrix metallopeptidase 10	-3.045 843 231	1.819 7×10^-27
ACTG2	Actin, gamma 2, smooth muscle, enteric	-2.980 748 271	1.992 53×10^-9
CNN1	Calponin 1	-2.957 732 234	3.116 93×10^-23
SFRP4	Secreted frizzled related protein 4	-2.826 452 510	1.254 79×10^-19
COL4A1	Collagen type Ⅳ alpha 1 chain	-2.821 702 234	1.732 3×10^-25
VCAN	Versican	-2.761 868 293	4.999 09×10^-36
COL4A2	Collagen type Ⅳ alpha 2 chain	-2.702 337 677	1.318 83×10^-21
ACTA2	Actin, alpha 2, smooth muscle, aorta	-2.687 926 646	1.802 76×10^-6

KEGG通路KEGG pathway	差异表达基因、差异表达蛋白DEGs, DEPs	基因数Gene number
Focal adhesion	MYLK、COMP、FN1、ITGA8、THBS1、COL4A2、MYL9、COL4A1、TNC、COL1A1、ACTN1、FLNA	12
ECM-receptor interaction	COMP、FN1、ITGA8、THBS1、SDC1、COL4A2、COL4A1、TNC、COL1A1	9
PI3K-Akt signaling pathway	COMP、SGK2、FN1、ITGA8、THBS1、COL4A2、EIF4E1B、COL4A1、TNC、COL1A1	10

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