Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (18): 4183-4194.doi: 10.3864/j.issn.0578-1752.2026.18.017

• ANIMAL SCIENCE·VETERINARY SCIENCE • Previous Articles    

Genome-Wide Association Study Identifies Candidate Genes Associated with Breast Muscle Water-Holding Capacity in Lindian Chickens

SUN ChangSheng(), WANG Xu, MU Fang, BAI Xue, SU ZhiYong, WANG YuXiang, LI YuMao, ZHANG WenPeng, LUAN Peng, WANG Ning, LENG Li()   

  1. Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province/College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030
  • Received:2025-12-29 Accepted:2026-08-11 Online:2026-09-16 Published:2026-09-20
  • Contact: LENG Li

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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

Table 1

Statistical results of phenotypic values for breast muscle water-holding capacity traits in Lindian chicken"

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

Fig. 1

Frequency distribution histogram of phenotypic values for breast muscle water-holding capacity traits in Lindian chicken A: Frequency distribution histogram of drip loss; B: Frequency distribution histogram of cooking loss; C: Frequency distribution histogram of pressing loss"

Fig. 2

Scatterplot of principal component analysis of population genetic structure in Lindian chicken"

Table 2

Group principal component analysis"

PC 1 2 3 4 5 6 7 8 9 10
P值P value 0.010 0.065 0.075 0.063 0.160 0.176 0.262 0.172 0.163 0.586

Fig. 3

Manhattan plot and Q-Q plot from the single-trait GWAS for Lindian chicken breast muscle water-holding capacity A: Manhattan plot and Q-Q plot from GWAS of drip loss; B: Manhattan plot and Q-Q plot from GWAS of cooking loss; C: Manhattan plot and Q-Q plot from GWAS of pressing loss"

Table 3

Information on significant SNPs annotated to candidate genes for Lindian chicken breast muscle water-holding capacity trait"

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

Fig. 4

Correlation heat map of Lindian chicken breast muscle water-holding capacity traits"

Fig. 5

Manhattan plot and Q-Q plot from the multi-trait GWAS for Lindian chicken breast muscle water-holding capacity"

Table 4

Significant SNPs annotated to candidate genes in the multi-trait GWAS"

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

Fig. 6

GO biological function annotation"

Fig. 7

KEGG pathway enrichment analysis"

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