Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (21): 4356-4366.doi: 10.3864/j.issn.0578-1752.2024.21.014

• ANIMAL SCIENCE·VETERINARY SCIENCE • Previous Articles     Next Articles

Dissecting the Genetic Architecture of Yolk Ratio with Single-Step Genome-Wide Association Study

GUO Jun(), QU Liang, SHAO Dan, MA Meng, DOU TaoCun, LU Jian, HU YuPing, WANG XingGuo, WANG Qiang, LI YongFeng, GUO Wei, TONG HaiBing()   

  1. Jiangsu Institute of Poultry Science, Yangzhou 225125, Jiangsu
  • Received:2024-04-19 Accepted:2024-06-07 Online:2024-11-01 Published:2024-11-10
  • Contact: TONG HaiBing

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Abstract:

【Objective】 Genome-wide association study (GWAS) was used to dissect the genetic architecture of yolk ratio in the 60-week-old hens, with the aim of discovery and utilization of the excellent genetic resources of local chickens and establishing the foundation for the breeding layer to meet market demand. 【Method】 The phenotypic data was collected from the resource population of Jiangsu Institute of Poultry Science. The F2 population was used in this study, Dongxiang green-shelled chickens and White Leghorn were used as parents respectively, and the F1 and F2 generations were obtained through reciprocal crosses. The data set included age at the first egg, shank length, body weight, egg size, Haugh unit, and yolk ratio. Blood samples in F2 generation were collected, and 1 534 hens were genotyped using 600K gene microarray. SNPs data was quality controlled. Missing data was imputed by Beagle software. After data cleaning steps such as removing outliers from the phenotypic data, one-way analysis of variance was used to test the factors that affected the phenotypic value, and these factors enrolled in the fixed effects. The genetic parameters and variance components were determined with multivariate animal model by using pedigree relationship matrix. On the other hand, the genetic relationship matrix was set up with the pedigree and genomic data. Heritabilities were calculated with univariate animal model, and genetic correlation coefficients were determined with bivariate animal model. The BLUPF90 software was used to obtain the SNP effect value, and postGSf90 was used to obtain the P-value and weight corresponding to the SNP. Therefore, the significant SNPs related to the yolk ratio was obtained with GWAS method. Chromosome heritability and haplotype block size were calculated for the yolk ratio. 【Result】The yolk ratio of Dongxiang blue shelled chicken was significantly higher than that of White Leghorn. Fixed effects included the combination of laying batch-generation-breed level. Using the hybrid genetic relationship matrix, the heritability on the yolk ratio and egg size were 0.348±0.041 and 0.500±0.038, respectively. The genetic correlation coefficients between yolk ratio and egg size and Haugh unit were -0.463±0.075 and -0.165±0.111, respectively. Using the pedigree genetic relationship matrix, heritability on yolk ratio and egg size were 0.387±0.052 and 0.465±0.052, respectively. The genetic correlation coefficients between yolk ratio and egg size and Haugh unit were -0.405±0.091 and -0.166±0.121, respectively. The inflation factor on the yolk ratio association analysis was 1.007, indicating that no stratified structure was detected in the resource population. There was a locus on chicken chromosome 22 that was significantly associated with the yolk ratio, which was supported by additional SNPs. This QTL explained 2.18% of the phenotypic variance, and the haplotype block size reached 71 kb. In addition, the potential SNP was also detected on chromosome 2. Chromosome heritability analysis showed that the yolk ratio was controlled by small-effect polygenes, and the heritability was directly proportional to the number of genes harbored by the chromosome. 【Conclusion】The weighted single-step GWAS method was used to analyze the genetic architecture of yolk ratio at 60 weeks of age, and the ADAM9 gene was identified to associate with the yolk ratio. Compared with the pedigree genetic relationship matrix, the hybrid genetic relationship matrix reduced Mendelian sampling errors and obtained more accurate genetic parameters.

Key words: yolk ratio, heritability, genetic architecture, genetic correlation, single-step GWAS

Fig.1

Box-plot on egg quality and performance of resource population"

Table 1

Heritabilities and genetic correlations estimated on resource population"

开产日龄
AFE		 体重
Body weight		 蛋重
Egg size		 哈氏单位
Haugh unit		 胫长
Shank length		 蛋黄比率
Yolk ratio
开产日龄
AFE		 0.417±0.040
0.374±0.052		 0.227±0.072 0.235±0.081 0.122±0.107 0.099±0.094 -0.021±0.097
体重
Body weight		 0.112±0.098 0.692±0.031
0.673±0.048		 0.439±0.059 -0.083±0.090 0.677±0.054 -0.100±0.080
蛋重
Egg size		 0.050±0.107 0.423±0.078 0.500±0.038
0.465±0.052		 -0.403±0.101 0.304±0.085 -0.463±0.075
哈氏单位
Haugh unit		 0.166±0.122 -0.123±0.106 -0.028±0.116 0.254±0.038
0.294±0.049		 0.059±0.058 -0.165±0.111
胫长
Shank length		 -0.059±0.133 0.628±0.071 0.298±0.101 -0.050±0.122 0.373±0.040
0.378±0.050		 0.050±0.098
蛋黄比率
Yolk ratio		 -0.052±0.114 0.013±0.097 -0.405±0.091 -0.166±0.121 0.248±0.109 0.348±0.041
0.387±0.052

Fig. 2

Associated analysis on yolk ratio: QQ plot The abscissa is the expected negative log-transformed P value and the observed negative log-transformed P value"

Table 2

Candidate gene associated with yolk ratio"

染色体
Chromosome		 物理位置*
Physical position		 候选基因
Candidate gene		 SNP位置
Location within gene		 碱基替换
Base substitute		 单倍型片段长度
Length of block（kb）		 解释表型方差比例
Proportion phenotypic variance (%)		 P值
LRT P-value
22 2608650 ADAM9 第11内含子
Intron Ⅺ		 A/G 71 2.18 6.21×10-7

Fig. 3

Associated analysis on yolk ratio: Manhattan plot"

Fig. 4

Regression on heritability and chromosome genes Green circles stand for the chromosome number, and 29 and 30 represent the two largest linkage groups. Grey area around the blue line is the 95% confidence level interval for prediction from the linear model"

Fig. 5

Linkage disequilibrium on candidate gene Number filled in diamond cell stand for the estimates of D′value. The marker with blue star is the significant SNP"

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