| Egg production performance is an economically significant trait for both egg-and meat-type poultry.Improving egg production performance not only improves the breed-supplying capacity and reduce the costs,but also increases production capacity and economic benefits of commercial lines.Egg production traits are quantitative traits with low heritability,controlled by micro-effective polygenes.These traits are primarily influenced by various factors such as genetics,environment,and nutrition.In the past,phenotypic selection methods have been often used to improve egg production in poultry.However,egg production performance has approached its limit after nearly a century,making it difficult to achieve greater breakthroughs using cross improvement and phenotypic selection methods.Especially for waterfowl,due to the poor understanding of biological characteristics such as water preference and courtship,combined with the lack of individual cage rearing and artificial insemination techniques,within-population phenotypic selection method has been long adopted for waterfowl breeding,making it difficult to understand the individual phenotypic variations and the underlying molecular regulatory mechanisms.With the development of omics technology,it has provided a new method for improving egg production traits in poultry.In this study,the G-strain of Tianfu Nong Hua Ma ducks were reared in individual cages.Phenotypic data such as the egg-laying numbers from the first egg age to 300 days’age for each individual were recorded daily,and the population coefficient variation in the egg production and egg weight were then analyzed.Genome-wide association study(GWAS)was used to screen differences in the molecular genetic basis for egg production traits.Transcriptomic sequencing was applied to screen key candidate genes involved in the HPG axis and egg yolk and egg white formation responsible for differences in egg production and egg weight.Finally,the integrated analysis of GWAS and transcriptomic data was carried out to explore the key candidate genes that regulating duck egg production and egg weight differences,as well as their molecular regulatory mechanisms.These findings were expected to provide a theoretical basis for molecular assisted breeding and genome-wide breeding of duck egg production performance.The main experimental results were listed as follows:1.Analysis of egg production performance among G-strain.The age of first egg age was 162d,the egg number at 300 days of age was 112.69,and accumulated average egg weight at 300 days of age was 77.43 g,with the coefficients of variation of 6.32%,26.13%and 9.82%,respectively.The time of egg production was mainly concentrated during the 22:00～6:00 and 6:00～8:00 periods,which accounted for60.33%and 31.93%in G-strain,respectively.Correlation analysis showed extremely significant positive correlations between the proportion of individuals laying during the 22:00-6:00 period and egg number and weight at 300 days of age(R~2=0.181,P<0.01).2.GWAS analysis of duck egg number and egg weight among the G line based on genome-wide SNP information.The egg number trait was associated with 747significant SNPs loci,including three loci of major effects and four finely mapped candidate genes such as TENM1.We annotated 66 candidate genes with SNPs loci significantly associated with at least three egg production phenotypes.Egg weight trait was associated with 829 significant SNPs loci,including 1 locus of major effect and 7 finely mapped candidate genes,such as DPYD.We annotated 48 candidate genes with SNPs loci significantly associated with at least 4 egg weight phenotypes.3.Screening of candidate genes and their regulatory pathways for egg production difference based on the HPG axis.Comparing differences in the transcriptomes of the HPG axis related tissues,including hypothalamus,pituitary,ovarian stroma and F5follicle membrane between high-and low egg production groups,543,759,670 and 181differentially expressed genes(DEGs)were screened,respectively.Cluster analysis and protein interaction analysis showed that VEGFC,SPARC,BMP2,THBS1,ADAMTS15 genes cluster to a significant level and were located in the core of the PPI network,and may be important candidates for regulating duck egg production.The neuroactive-ligand receptor interaction pathway is a pathway that significantly enriches DEGs in various tissues of the HPG axis,and may be involved in regulating duck egg production.4.Screening candidate genes associated with the formation of egg yolk and egg white and their regulatory pathways for egg weight differences using the transcriptome and metabolome sequencing technologies.High-and low egg weight duck individuals were screened to develop multi omics assays.733,82,and 74 DEGs were screened from the main tissues involved in egg yolk formation,including the liver,F1 follicular membrane,and F5 follicular membrane,respectively.FASN,HSPA2,HSPA8,and BAG3 may be important candidate genes for regulating egg weight differences.The DEGs in liver were significantly enriched in pathways involved in adipocytokine signaling,fatty acid metabolism related pathways.The DEGs in follicular membrane of F1 and F5 were significantly enriched in neuroactive ligand receptor interaction,Gn RH signaling pathway.591 DEGs were screened from the magnum that is main tissues involved in egg white formation.HSP90AA1,HSPA8,and protein processing in the endoplasmic reticulum pathway,may be an important candidate gene and molecular pathway for regulating egg weight differences.The combined analysis of transcriptome and metabolome showed that arginine and proline metabolism were important molecular pathways involved in the differential regulation of egg weight.5.Identification of key candidate genes for duck egg production and egg weight by the combined analysis of GWAS and transcriptomic sequencing.By selecting the common candidate genes identified by GWAS analysis and DEGs screening,we obtained a total of 31 key candidate genes associated with egg number difference,which were mainly enriched in the phenylalanine metabolism pathway.We also obtained a total of 29 key candidate genes associated with egg weight difference,which were mainly enriched in the cell adhesion molecule pathway.In conclusion,this study revealed the individual variations of egg production and egg weight among the G line population as well as the molecular genetic mechanisms.These findings provide a theoretical reference for molecular assisted breeding and genome-wide selection of duck egg production and egg weight traits. |
