基于组学数据筛选康乐黄鸡8周龄体质量相关基因

doi:10.7668/hbnxb.20195294

摘要/Abstract

摘要：

旨在基于组学数据筛选与康乐黄鸡8周龄体质量性状相关的重要候选基因,为康乐黄鸡生长性状的分子标记辅助育种提供理论基础,为完善地方鸡种分子选育方法、加快品种选育进展提供关键的基础数据。以434只康乐黄鸡为研究对象,测定8~22周龄体质量,采用基因芯片技术对康乐黄鸡8周龄体质量性状进行全基因组关联分析,筛选显著关联SNP位点。寻找位于每个显著SNP周围2 Mb区域内的候选基因,对候选基因进行GO和KEGG功能分析。结合前期转录组测序数据、文献数据,筛选与康乐黄鸡8周龄体质量性状相关的关键候选基因。共检测到2个显著关联SNPs,分别位于2号染色体(131 485 613 bp)和4号染色体(60 413 848 bp),筛选到118个候选基因。基因功能注释结果表明,视黄酸代谢过程为最显著富集的生物学过程,脂肪酸降解、酪氨酸代谢和药物代谢-细胞色素P450等12个通路为显著性富集通路。初步确定基因OXR1、RSPO2、EIF3E、TRHR、BMPR1B、ADH1C、MTTP、LAMTOR3、PPP3CA、PDLIM3可作为康乐黄鸡8周龄体质量性状的关键候选基因。研究初步确定了2个与康乐黄鸡8周龄体质量性状显著关联的SNP位点,以及10个关键候选基因。

关键词: 康乐黄鸡, SNP, 全基因组关联分析, 体质量, 候选基因, 基因通路

Abstract:

The purpose of this study is to screen candidate genes related to the body weight at 8 weeks age of Kangle yellow chicken based on the omics data,and provide the theoretical foundation for molecular marker-assisted breeding of growth traits in Kangle yellow chickens.It also provides key basic data for improving molecular breeding methods for high-quality broilers and accelerating,the progress of breed selection.To detect SNPs significantly associated with body weight traits at 8 weeks age of Kangle yellow chickens,the body weight was measured from 8 to 22 weeks of age of 434 Kangle yellow chickens.Genome-wide association study(GWAS)was performed using the gene chip technology.Genes in the candidate regions with 2 Mb windows surrounding each significant SNP were found for GO and KEGG function analysis.Combined with the data of transcriptomic sequencing and published literature,key candidate genes related to the body weight at 8 weeks age of Kangle yellow chicken were screened.Two potential SNPs significantly associated with target traits were detected,located on chromosome 2(131 485 613 bp)and chromosome 4(60 413 848 bp).A total of 118 candidate genes were screened near SNP sites.Gene function annotation analysis showed the most significant enrichment of biological processes was retinoic acid metabolism.The significant enrichment of 12 KEGG pathways was found,including fatty acid degradation,tyrosine metabolism and drug metabolism-cytochrome P450.OXR1, RSPO2,EIF3E,TRHR,BMPR1B, ADH1C, MTTP, LAMTOR3, PPP3CA and PDLIM3 were preliminarily identified as key candidate genes for body weight traits at 8 weeks age of Kangle yellow chickens.Two SNPs and 10 key candidate genes were preliminarily identified related to the body weight at 8 weeks age of Kangle yellow chicken.

Key words: Kangle yellow chicken, SNP, GWAS, Body weight, Candidate gene, Gene pathway

马荆鄂, 陈玉洁, 雷文静, 许桥, 许继国, 许晶, 饶友生. 基于组学数据筛选康乐黄鸡8周龄体质量相关基因[J]. 华北农学报, 2025, 40(1): 224-231. doi: 10.7668/hbnxb.20195294.

MA Jinge, CHEN Yujie, LEI Wenjing, XU Qiao, XU Jiguo, XU Jing, RAO Yousheng. Identification of Genes Associated with Body Weight at 8 Weeks Age in Kangle Yellow Chickens Based on Omics Data[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(1): 224-231. doi: 10.7668/hbnxb.20195294.

http://www.hbnxb.net/CN/Y2025/V40/I1/224

图/表 10

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性状 Trait	统计量/只 Statistical magnitude	最大值/g Maximum value	最小值/g Minimum value	平均值/g Mean	标准差 Standard deviation	变异系数/% Coefficient of variation	相关系数 Correlation coefficient
8周龄体质量 Weight at 8 weeks	414	650	187	479.23	51.40	10.73	1.000
10周龄体质量 Weight at 10 weeks	414	800	400	582.13	63.93	10.98	0.835^**
12周龄体质量 Weight at 12 weeks	413	950	500	703.87	78.65	11.17	0.265^**
14周龄体质量 Weight at 14 weeks	406	1 200	600	818.23	98.70	12.06	0.291^**
16周龄体质量 Weight at 16 weeks	404	1 500	650	790.17	138.34	14.26	0.233^**
22周龄体质量 Weight at 22 weeks	413	1 800	900	1 282.20	174.96	13.64	0.124^*

性状 Trait	统计量/只 Statistical magnitude	最大值/g Maximum value	最小值/g Minimum value	平均值/g Mean	标准差 Standard deviation	变异系数/% Coefficient of variation	相关系数 Correlation coefficient
8周龄体质量 Weight at 8 weeks	414	650	187	479.23	51.40	10.73	1.000
10周龄体质量 Weight at 10 weeks	414	800	400	582.13	63.93	10.98	0.835^**
12周龄体质量 Weight at 12 weeks	413	950	500	703.87	78.65	11.17	0.265^**
14周龄体质量 Weight at 14 weeks	406	1 200	600	818.23	98.70	12.06	0.291^**
16周龄体质量 Weight at 16 weeks	404	1 500	650	790.17	138.34	14.26	0.233^**
22周龄体质量 Weight at 22 weeks	413	1 800	900	1 282.20	174.96	13.64	0.124^*

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	体质量/g Body weight
2	131 485 613	8.48×10^-6	CC (26)	0.16	429.04±67.12a
			CG (155)	0.38	476.67±53.08b
			GG (207)	0.51	487.41±44.74b
4	60 413 848	1.12×10^-5	CC (164)	0.40	465.90±49.79a
			TC (199)	0.49	485.08±49.79b
			TT (45)	0.11	501.04±52.89c

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	体质量/g Body weight
2	131 485 613	8.48×10^-6	CC (26)	0.16	429.04±67.12a
			CG (155)	0.38	476.67±53.08b
			GG (207)	0.51	487.41±44.74b
4	60 413 848	1.12×10^-5	CC (164)	0.40	465.90±49.79a
			TC (199)	0.49	485.08±49.79b
			TT (45)	0.11	501.04±52.89c

引物名称 Primer name	SNP位置/bp SNP position	引物序列(5'—3') Primer sequence(5'—3')	退火温度/℃ Annealing temperature	片段长度/bp Fragment length
1	Chr2:131 485 613	F:ACATGACGGCAAGGTAACGTA	60	268
		R:CCAGAGCACACACACTCCTC
2	Chr4:60 413 848	F:AGCCAATGTCCAAGCATACCA	60	314
		R:GGTGGCATTGCAGCACTATTC

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