基于组学数据筛选康乐黄鸡16周龄体重候选基因与关键通路

doi:10.11843/j.issn.0366-6964.2025.10.011

摘要/Abstract

摘要：

旨在挖掘康乐黄鸡16周龄体重相关功能基因及关键信号通路，以期为地方鸡种出栏体重性状的选种选育提供依据。本研究以434只康乐黄鸡为研究对象，采用“京芯1号”55K SNP芯片对康乐黄16周龄体重进行全基因组关联分析(genome-wide association study, GWAS)，筛选显著关联SNP(single nucleotide polymorphism)位点。共检测到13个显著关联SNPs，分别位于3号染色体(81 641 565 bp)、4号染色体(1 860 041、33 409 710、33 716 131、33 925 946 bp)、6号染色体(23 563 123、35 324 210 bp)、11号染色体(15 294 113、15 346 007 bp)、12号染色体(2 503 065、2 504 749 bp)以及18号染色体(1 994 686、2 307 607 bp)，筛选到825个候选基因。基因功能注释结果表明，运动活动过程为最显著富集的生物学过程，细胞间紧密连接、糖胺聚糖降解和新陈代谢途径等17个通路为显著性富集通路(P < 0.05)。结合前期转录组测序数据、文献综述，初步确定KCNQ5、P2RY10、ITM2A、RBPMS、PGAM1、CYP17A1、BNIP3、ATMIN、BCO1、TNNC1、GNAI2、MYH1F、MYH1A、MYH10、PIK3R5可作为康乐黄鸡16周龄体重的重要候选基因。神经活性配体-受体相互作用信号通路、新陈代谢途径信号通路、心肌细胞肾上腺素能信号传导通路和细胞间紧密连接信号通路为关键通路。本研究初步确定13个SNPs、15个关键候选基因以及4条关键通路与康乐黄鸡16周龄体重显著关联，这些结果为康乐黄鸡生长性状的分子标记辅助育种提供理论依据和技术支撑。

关键词: 康乐黄鸡, SNP, 全基因组关联分析, 体重性状, 候选基因, 基因通路

Abstract:

This study aimed to identify functional genes and key signaling pathways related to body weight at 16 weeks of age in Kangle yellow chickens based on omics data, in order to provide a basis for the selection and breeding of local chicken breeds for market weight traits. To detect SNPs significantly associated with body weight at 16-week in 434 Kangle yellow chickens, genome-wide association study (GWAS) was performed using the "Jingxin No. 1" 55K SNP chip. A total of 13 potential SNPs significantly associated with target traits were detected, located on chromosome 3 (81 641 565 bp), chromosome 4 (1 860 041 bp, 33 409 710 bp, 33 716 131 bp, 33 925 946 bp), chromosome 6 (23 563 123 bp, 35 324 210 bp), chromosome 11 (15 294 113 bp, 15 346 007 bp), chromosome 12 (2 503 065 bp, 2 504 749 bp) and chromosome 18 (1 994 686 bp, 2 307 607 bp). The 825 candidate genes near SNP sites were screened. Gene function annotation analysis showed the most significant enrichment of biological processes was motor activity. The significant enrichment of 17 KEGG pathways were found, including tight junction, glycosaminoglycan degradation and metabolic pathways (P < 0.05). Combined with previous transcriptomic sequencing data, and published literature, KCNQ5, P2RY10, ITM2A, RBPMS, PGAM1, CYP17A1, BNIP3, ATMIN, BCO1, TNNC1, GNAI2, MYH1F, MYH1A, MYH10, and PIK3R5 were preliminarily identified as important candidate genes for body weight traits at 16 weeks of age in Kangle yellow chickens. Neuroactive ligand-receptor interaction, metabolic pathway, adrenergic signaling in cardiomyocytes and tight junction were key pathways. In this study, 13 SNPs, 15 key candidate genes and 4 key pathways were preliminarily identified related to the body weight at 16-week of Kangle yellow chicken. These results provided theoretical basis and technical support for molecular marker-assisted breeding of growth traits in Kangle yellow chickens.

Key words: Kangle yellow chicken, SNP, GWAS, body weight traits, candidate gene, gene pathway

中图分类号:

S831.2

马荆鄂, 万书星, 雷文静, 章英枝, 俞梓萱, 刘梓阁, 许继国. 基于组学数据筛选康乐黄鸡16周龄体重候选基因与关键通路[J]. 畜牧兽医学报, 2025, 56(10): 4889-4902.

MA Jing'e, WAN Shuxing, LEI Wenjing, ZHANG Yingzhi, YU Zixuan, LIU Zige, XU Jiguo. Identification of Candidate Genes and Key Pathways Associated with Body Weight at 16 Weeks of Age in Kangle Yellow Chickens Based on Omics Data[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(10): 4889-4902.

图/表 7

图 1

表 1

表 2

图 2

图 3

图 4

表 3

关键候选基因功能分析"

基因 Gene	染色体 Chromosome	区域/bp Position	功能 Function
TMEM30A	3	80 772 707~80 786 202	TMEM30A在小鼠骨骼肌再生中有重要作用^[28]
KCNQ5	3	81 552 966~81 817 022	猪生长相关候选基因^[29]
P2RY10	4	1 435 115~1 442 506	与阳原驴体尺性状和延边牛生长性状相关^[30-31]
ITM2A	4	1 468 932~1 477 914	参与德州驴骨骼肌的生长和发育^[32]
TBX22	4	1 505 219~1 510 388	Wnt信号通路通过TBX22调节鸡胚上颌骨形态发生和生长^[33]
PHKA1	4	1 863 361~1 879 695	可能参与调节鸡肉早期生长^[34]
SH3D19	4	33 241 343~33 322 918	与斑马鱼胚胎发育、体节发生相关^[35]
RBPMS	4	34 740 148~34 745 550	对于斑马鱼心脏发育具有重要调控作用^[36]
PGAM1	6	23 308 079~23 310 457	参与藏羊细胞增殖以及精子发生^[37]
BTRC	6	23 789 857~23 907 913	与鸡生长性状相关^[11]
CYP17A1	6	24 341 475~24 343 952	参与鸡卵泡和睾丸的生长和发育^[38-39]
SLK	6	25 039 625~25 086 733	与成人肌肉发育有关^[40]
EBF3	6	35 109 889~35 223 910	与鸡胚骨骼发育有关^[41]
BNIP3	6	35 758 032~35 763 615	与动物肌肉发育有关^[42]
ATMIN	11	15 376 764~15 396 951	对于小鼠正常肾脏发育至关重要^[43]
BCO1	11	15 458 803~15 472 637	参与调节鸡成肌细胞的增殖^[44]
CDH13	11	15 966 410~16 399 105	调节牛早期生殖发育^[45]
KCNG4	11	16 658 646~16 675 825	与俄罗斯原住民卡拉柴山羊臀部高度、体长和胸围相关^[46]
TNNC1	12	975 844~981 282	调控鹌鹑肌肉分化和生长性能^[47]
MUSTN1	12	1 237 476~1 240 740	与鸡、鸭肌肉发育有关^[48-49]
GNAI2	12	3 602 465~3 612 992	为绵羊生长相关基因^[50-51]
MYH1F	18	407 274~424 973	在家禽肌肉生成中起关键作用^[52]
MYH1A	18	458 828~477 172	海扬黄鸡生长发育的候选基因^[53]
MYH10	18	1 725 821~1 818 952	可能参与调节鸡肉组织早期生长^[34]
PIK3R5	18	1 984 538~2 033 615	与绵羊体型特征相关的基因^[54]
ARHGAP44	18	2 210 621~2 231 195	调控猪的腰肌面积^[55]

表 3

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染色体 Chromosome	物理位置/bp Position	P值 P-value	基因型(个体数) Genotype (Number)	基因型频率 Genotype frequency	16周龄体重(平均值±标准差)/g Body weight at 16 weeks (Mean±standard deviation)
3	81 641 565	4.00×10^-8	CC (386)	0.970	790.73±138.97^a
			TC (12)	0.030	920.83±80.26^b
4	1 860 041	2.88×10^-9	CC (376)	0.945	968.09±135.34^a
			TC (21)	0.053	988.10±177.89^a
			TT (1)	0.002	1 000^b
4	33 409 710	2.83×10^-6	CC (385)	0.967	970.78±138.95^a
			TC (13)	0.033	923.08±86.86^b
4	33 716 131	2.83×10^-6	GG (385)	0.967	970.78±138.95^a
			AG (13)	0.033	923.08±86.86^b
4	33 925 946	2.83×10^-6	TT (385)	0.967	970.78±138.95^a
			CT (13)	0.033	923.08±86.86^b
6	23 563 123	6.00×10^-7	GG(8)	0.020	969.74±138.33^a
			AG (390)	0.980	943.75±107.35^b
6	35 324 210	7.68×10^-8	AA (1)	0.002	1 000^a
			AC (21)	0.053	973.81±111.93^b
			CC (376)	0.945	968.88±139.30^ab
11	15 294 113	3.48×10^-7	TT(386)	0.969	970.73±138.45^a
			CT(12)	0.031	920.83±105.00^b
11	15 346 007	3.48×10^-7	CC(386)	0.969	970.73±138.45^a
			TC(12)	0.031	920.83±150.00^b
12	2 503 065	1.79×10^-12	GG(2)	0.005	950±50^a
			GT(10)	0.027	995±145.69^b
			TT(358)	0.968	968.65±137.86^c
12	2 504 749	1.79×10^-12	AA(358)	0.968	968.65±137.86^a
			CA(10)	0.027	995±145.69^b
			CC(2)	0.005	950±50^c
18	1 994 686	1.30×10^-7	TT(387)	0.972	970.80±138.14^a
			CT(11)	0.028	913.64±113.00^b
18	2 307 607	5.84×10^-9	AG(8)	0.020	925±129.90^a
			GG(390)	0.980	970.13±137.84^b

引物名称 Primer name	SNP位置/bp Position	方向 Direction	引物序列(5′→3′) Primer sequence	退火温度/℃ Temperature	片段长度/bp Length
1	Chr3:81 641 565	Forward	CATGCAAAGCACCGAACTCC	60	233
		Reverse	AGAAAAGCGCTCCAGTGTCT
2	Chr4:1 860 041	Forward	CTGGGTCCCTATATCCACATACATT	61	418
		Reverse	GCCAGCTGGACAAAAGCCTG
3	Chr4:33 409 710	Forward	TAAAGTTGAGGTGCTTGACC	55	322
		Reverse	TGGACAGTTACACAGAACAT
4	Chr4:33 716 131	Forward	GGACATTTGCACACACCGTT	60	280
		Reverse	TTGCTTGCTCCTGCTAGCTC
5	Chr4:33 925 946	Forward	TACGTTCAGAGTGACGTTTGTATG	60	393
		Reverse	CTTCAAGCCAGGATGGAGCAT
6	Chr6:23 563 123	Forward	GTGAACGTGTCAGCCAACTG	60	372
		Reverse	GCCTGAAGACAAGCGCATAG
7	Chr6:35 324 210	Forward	GTTGGCAATGGGGTGTTTGA	59	280
		Reverse	CCTGGGTTCTGGGCTAACTT
8	Chr11:15 294 113	Forward	CATATCAGCACCCCAAGCCTC	60	297
		Reverse	TGCAGAAAACACCTACAGCTTC
9	Chr11:15 346 007	Forward	ATCTCAGCCACAGTGGTCCT	61	235
		Reverse	AGTATGGGGGCAGTTTGGGA
10	Chr12:2 503 065	Forward	TTTCCAGTTGTTCCAGCTGAC	59	295
		Reverse	TGCCAACCTGAAAGGTCTTCT
11	Chr12:2 504 749	Forward	GTGCCTTGAGCTAGCATTGTG	61	523
		Reverse	TTTCAGACATGCCGTGCGTT
12	Chr18:1 994 686	Forward	GCTCACATCATGCAGAGAAACA	60	534
		Reverse	CCAGGCCAAGACACTGGAAG
13	Chr18:2 307 607	Forward	TGTCAAAGCCAACTCCCTCTT	60	339
		Reverse	GACAGCGTCACTTCCCACG

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