基于全基因组关联分析筛选林甸鸡胸肌保水性相关候选基因

doi:10.3864/j.issn.0578-1752.2026.18.017

摘要/Abstract

摘要：

【背景】鸡肉保水性是评价肉品质的重要指标，直接影响肉质嫩度、多汁性、加工损失和商品价值。林甸鸡作为我国东北地区优质地方鸡种，具有抗逆性强、肉质风味良好等特点，但其胸肌保水性的遗传基础尚不清晰。【目的】基于全基因组关联分析（GWAS）解析林甸鸡胸肌保水性的遗传机制，挖掘相关分子标记与候选基因，为分子育种提供理论依据。【方法】以441只150日龄林甸鸡公鸡为试验材料，采集翅静脉血液后对试验鸡进行屠宰，并分离左侧胸肌，测定滴水损失、蒸煮损失和压榨损失。采用10×全基因组重测序获取基因型数据，经FASTP质控、BWA比对、GATK变异检测和PLINK筛选获得高质量SNP集合。利用主成分分析评估群体结构，并将显著主成分作为协变量纳入模型。基于GEMMA软件分别构建线性混合模型与多性状线性混合模型开展单性状与多性状GWAS分析，并采用Bonferroni校正确定全基因组显著性阈值。对显著SNP上下游40 kb区域内基因进行注释，并结合GO注释和KEGG富集分析，系统解析候选基因的生物学功能及调控网络。【结果】林甸鸡胸肌滴水损失、蒸煮损失和压榨损失均值分别为2.92%、20.14%和18.73%，并且三者表型均呈近似正态分布。相关性分析显示，三项保水性指标间均呈极显著正相关，其中滴水损失与压榨损失相关系数为0.996（P<0.001），蒸煮损失与压榨损失相关系数为0.975（P<0.001），滴水损失与蒸煮损失相关系数为0.964（P<0.001）。单性状GWAS共鉴定到28个与保水性指标显著相关的SNP位点，其中与滴水损失显著相关的7个SNP位点注释到ADTRP和EXT1；与蒸煮损失显著相关的7个SNP位点注释到SLC25A21、CMPK1、CIB2和DPY19L3；与压榨损失显著相关的14个SNP位点注释到PCDH9、NUDT13、CDH2和CALN1等6个基因。针对3个保水性指标开展多性状GWAS分析，一共鉴定到28个与胸肌保水性显著相关的SNP，注释到ILDR1、EXT1、SLC25A21等9个基因。整合两种分析结果发现，EXT1、CMPK1、SLC25A21和CDH2在单性状与多性状GWAS中均被筛选出来。功能富集分析表明候选基因主要富集于核苷酸代谢过程、细胞间黏附调控、糖胺聚糖生物合成—硫酸乙酰肝素/肝素通路、核苷酸代谢通路及细胞黏附分子等功能条目和信号通路。【结论】通过单性状GWAS与多性状GWAS联合分析，筛选到EXT1、CMPK1、SLC25A21和CDH2与林甸鸡胸肌保水性相关，上述基因可作为改善林甸鸡胸肌保水性的重要候选基因。

关键词: 林甸鸡, 胸肌保水性, 全基因组关联分析, 单核苷酸多态性位点, 候选基因

Abstract:

【Background】Water-holding capacity of chicken meat is an important index to evaluate meat quality, which directly affects meat tenderness, juiciness, processing loss and commodity value. As a high-quality local chicken breed in Northeast China, Lindian chicken is characterized by strong stress resistance and good meat flavor, but the genetic basis of its breast muscle water-holding capacity traits is still unclear.【Objective】The purpose of this study was to analyze the genetic mechanism of breast muscle water-holding capacity in Lindian chicken based on genome-wide association analysis (GWAS), and to explore relevant molecular markers and candidate genes, so as to provide a theoretical basis for molecular breeding.【Method】In this study, a total of 441 male Lindian chickens at 150 days of age were used. Blood samples were collected from the wing vein, after which the chickens were slaughtered and the left pectoral muscles were collected for the measurement of drip loss, cooking loss, and pressing loss. Genotype data were obtained by 10 × whole genome resequencing, and a high-quality SNP set was obtained by FASTP quality control, BWA alignment, GATK variant calling and PLINK screening. Principal component analysis was used to evaluate the population structure, and significant principal components were incorporated into the model as covariates. Based on GEMMA software, linear mixed model and multivariate linear mixed model were used for single-trait and multi-trait GWAS, respectively, and Bonferroni correction was used to determine the genome-wide significance threshold. The genes in the 40 kb region upstream and downstream of the significant SNPs were annotated, and combined with GO annotation and KEGG enrichment analysis, the biological functions and regulatory networks of candidate genes were systematically analyzed.【Result】The average drip loss, cooking loss and pressing loss of breast muscle of Lindian chicken were 2.92 %, 20.14 % and 18.73 %, respectively, and the phenotypes of the three were approximately normally distributed. Correlation analysis showed that there was a significant positive correlation between the three water-holding capacity traits. The correlation coefficient between drip loss and pressing loss was 0.996 (P < 0.001), the correlation coefficient between cooking loss and pressing loss was 0.975 (P < 0.001), and the correlation coefficient between drip loss and cooking loss was 0.964 (P < 0.001). A total of 28 SNPs significantly associated with water-holding capacity were identified by single-trait GWAS, of which 7 SNPs significantly associated with drip loss were annotated to ADTRP and EXT1 genes. Seven SNPs significantly associated with cooking loss were annotated to SLC25A21, CMPK1, CIB2 and DPY19L3 genes. The 14 SNPs significantly associated with pressing loss were annotated to 6 genes, including PCDH9, NUDT13, CDH2 and CALN1. A total of 28 SNPs significantly associated with breast muscle water-holding capacity were identified and annotated to 9 genes such as ILDR1, EXT1, and SLC25A21. Combining the two analysis results, it was found that EXT1, CMPK1, SLC25A21 and CDH2 were identified in both single-trait and multi-trait GWAS. Functional enrichment analysis showed that candidate genes were mainly enriched in functional items and signaling pathways such as nucleotide metabolism, intercellular adhesion regulation, glycosaminoglycan biosynthesis-heparan sulfate / heparin pathway, nucleotide metabolism pathway and cell adhesion molecules.【Conclusion】In this study, combined single-trait and multi-trait GWAS identified EXT1, CMPK1, SLC25A21 and CDH2 as candidate genes associated with breast muscle water-holding capacity in Lindian chickens. These genes may serve as important candidate genes for improving breast muscle water-holding capacity in Lindian chicken breeding.

Key words: lindian chicken, breast muscle water-holding capacity, genome-wide association study, SNPs, candidate genes

孙长胜, 王旭, 牟芳, 白雪, 宿志勇, 王宇祥, 李玉茂, 张文鹏, 栾鹏, 王宁, 冷丽. 基于全基因组关联分析筛选林甸鸡胸肌保水性相关候选基因[J]. 中国农业科学, 2026, 59(18): 4183-4194.

SUN ChangSheng, WANG Xu, MU Fang, BAI Xue, SU ZhiYong, WANG YuXiang, LI YuMao, ZHANG WenPeng, LUAN Peng, WANG Ning, LENG Li. Genome-Wide Association Study Identifies Candidate Genes Associated with Breast Muscle Water-Holding Capacity in Lindian Chickens[J]. Scientia Agricultura Sinica, 2026, 59(18): 4183-4194.

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胸肌保水性指标 Breast muscle water-holding capacity trait	样品数量 Number of samples	最大值 Max	最小值 Min	平均值 Mean	标准差 SD	变异系数 CV (%)
滴水损失Drip loss (%)	413	7.15	0.29	2.92	1.27	43
蒸煮损失Cooking loss (%)	412	31.18	6.32	20.14	4.22	21
压榨损失Pressing loss (%)	412	35.28	2.21	18.73	5.77	31

保水性指标 Water-holding capacity index	染色体 Chromosome	位置 Position	等位基因 Genotype	MAF	Beta	P值 P value	基因 Gene	功能区域 Functional region
滴水损失 Drip loss	2	62675771	G/A	0.080	1.02	6.09×10^-7	ADTRP	内含子Intron
	2	62681511	T/C	0.058	1.18	1.64×10^-7	ADTRP	3′UTR
	2	62681846	G/C	0.059	1.08	6.73×10^-7	ADTRP	3′UTR
	2	135004833	G/A	0.324	0.53	4.26×10^-7	EXT1	内含子Intron
	2	135004849	G/A	0.325	0.53	3.16×10^-7	EXT1	内含子Intron
蒸煮损失 Cooking loss	5	36471798	C/T	0.266	2.05	2.38×10^-7	SLC25A21	内含子Intron
	5	36472098	C/G	0.267	1.97	5.42×10^-7	SLC25A21	内含子Intron
	8	21669313	A/G	0.060	3.64	7.70×10^-8	CMPK1	外显子Exon
	10	3865806	A/G	0.232	-1.92	6.97×10^-7	CIB2	内含子Intron
	11	9481641	G/C	0.198	2.07	7.58×10^-7	DPY19L3	内含子Intron
压榨损失 Pressing loss	1	159485028	A/T	0.113	-4.50	9.48×10^-8	PCDH9	内含子Intron
	6	11889674	C/T	0.270	-2.85	4.81×10^-7	NUDT13	内含子Intron
	9	9677460	T/C	0.137	-3.75	9.62×10^-7	DNER	外显子Exon
	9	9684053	T/C	0.133	-3.90	4.71×10^-7	DNER	内含子Intron
	9	14827644	C/T	0.233	3.04	9.90×10^-7	FYTTD1	内含子Intron
	9	14828049	A/G	0.203	3.38	3.30×10^-7	FYTTD1	内含子Intron
	9	14828371	T/A	0.199	3.44	1.43×10^-7	FYTTD1	内含子Intron
	9	14828634	C/A	0.206	3.22	4.83×10^-7	FYTTD1	外显子Exon
	9	14829028	G/A	0.205	3.29	3.56×10^-7	FYTTD1	外显子Exon
	9	14829103	T/C	0.204	3.31	4.59×10^-7	FYTTD1	外显子Exon
	10	14641961	G/C	0.066	-5.50	7.49×10^-7	CDH2	外显子Exon
	19	1421788	T/C	0.126	-4.02	5.26×10^-7	CALN1	外显子Exon
	19	1421822	T/C	0.124	-4.12	2.81×10^-7	CALN1	外显子Exon

染色体Chromosome	位置Position	等位基因Genotype	MAF	Beta	P值P value	基因Gene	功能区域Functional region
1	83511182	C/G	0.054	6.38×10^-2	8.77×10^-7	ILDR1	内含子Intron
2	135035915	C/G	0.228	-3.73×10^-1	8.97×10^-7	EXT1	外显子Exon
5	36471533	A/G	0.292	1.02	7.02×10^-7	SLC25A21	内含子Intron
5	36471798	C/T	0.267	1.09	2.23×10^-7	SLC25A21	内含子Intron
5	36472098	C/G	0.268	1.13	7.71×10^-7	SLC25A21	内含子Intron
5	36546467	C/T	0.499	9.64×10^-1	1.12×10^-7	MIPOL1	内含子Intron
8	21669313	A/G	0.060	1.16	1.95×10^-7	CMPK1	外显子Exon
10	13036134	G/A	0.426	7.56×10^-1	4.59×10^-8	ABHD2	外显子Exon
10	13036139	G/A	0.429	7.15×10^-1	1.17×10^-7	ABHD2	外显子Exon
10	13036165	G/A	0.443	6.54×10^-1	4.50×10^-7	ABHD2	外显子Exon
10	13036430	T/C	0.429	6.45×10^-1	8.04×10^-7	ABHD2	外显子Exon
10	13036909	T/C	0.433	6.79×10^-1	3.25×10^-7	ABHD2	外显子Exon
10	13037648	A/G	0.476	-7.34×10^-1	1.75×10^-7	ABHD2	外显子Exon
10	13044147	G/A	0.374	6.46×10^-1	8.12×10^-7	ABHD2	外显子Exon
10	13044332	T/G	0.369	6.64×10^-1	2.57×10^-7	ABHD2	外显子Exon
10	13044836	C/T	0.480	5.98×10^-1	1.44×10^-7	ABHD2	外显子Exon
10	13051936	C/T	0.457	-6.66×10^-1	2.72×10^-7	ABHD2	外显子Exon
10	13053118	A/G	0.328	-7.22×10^-1	8.55×10^-7	ABHD2	外显子Exon
10	13088937	T/A	0.473	7.27×10^-1	4.77×10^-7	MFGE8	内含子Intron
10	13089070	G/C	0.473	7.12×10^-1	8.82×10^-8	MFGE8	内含子Intron
10	13092789	G/A	0.480	6.79×10^-1	2.91×10^-7	MFGE8	内含子Intron
10	13390772	G/A	0.296	8.68×10^-1	2.74×10^-7	NTRK3	内含子Intron
10	14641858	C/T	0.477	-8.64×10^-1	4.40×10^-7	CDH2	内含子Intron
10	14681952	T/G	0.216	-1.08	3.38×10^-7	CDH2	3′UTR