| Albumen height and Haugh unit which represent the fresh of egg play an important role in egg quality.Eggshell color,mottled egg,and egg shell index which represent the appearance of egg are related to consumer choice.In order to study the genetic architecture of albumen height and Haugh unit,egg shell color,mottled egg and egg shape index,genome-wide association study was performed using 600 K SNP array based on an F2 resource population generated from Dongxiang Blue Shell Chicken and Single Comb White Leghorn.The aim of our study was to analyze the genetic mechanism of egg quality trait and provide reference for molecular marked selection.The main experiments are as follows:The genetic parameter of albumen height and Haugh unit was calculated by multi-trait animal model based on WOBAT software.The change regulation of mottled egg was measured and the correlation with temperature and humidity,egg quality was analyzed.The preparation of F2 population data was genotyped by Affymetrix 600 SNP array,quality control was carried out by APT and PLINK software,genotype imputation was imputed by BEAGLE software;The significant association SNP loci were conducted using mixed linear model in GEMMA software;Linkage disequilibrium(LD)between significant loci located in same region were calculated by Haploview;Gene annotation was performed by BioMat,gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG);Genetic parameter based on SNP and SNP effect was calculated by GCTA software;Phenotype of different genotype was calculated.Part one:Genetic parameter and genome-wide association for albumen traitThe albumen height and Haugh unit from parent,F1 and F2 generation were measured from the age at first egg to 72 weeks old by ORKA Egg Analyzer;The genetic parameters of albumen quality from three generation were calculated by multi-trait animal model;The trend and genetic parameter based on SNP were calculated and GWAS method was applied to analyze the genetic architecture of albumen quality.The results are as follows:1.The value of albumen height and Haugh unit from Dongxiang Blue Shell parent generation were 3.81±0.83mm and 65.50±7.47,respectively.The value from White Leghon parent were 5.25±0.88mm and 70.80±7.83,respectively.The value of albumen height and Haugh unit from F1 generation were higher than that from F1 generation.There were significantly difference of albumen height and Haugh unit between Dongxiang Blue Shell and White Leghon Chicken in three generation.2.The fixed effect and the parental variety effect were included in the multi-trait animal model.The heritability of albumen height and Haugh unit from F1 generation was 0.17-0.30 and 0.14-0.30,respectively.The heritability of albumen height and Haugh unit showed moderate to low,genetic progress would be gained by long term selection.3.The heritability of albumen height spanned from 0.15 to 0.35 based on SNP.The heritability of albumen height on 32 weeks old showed the largest.The phenotypic correlation between albumen height and Haugh unit showed high positive correlation,while the genetic correlation between them showed low.4.We obtained significant SNPs located on chromosome 1(GGA1),GGA2,GGA4 and GGA7 by univariate GWAS model.The most important region on GGA4 affected albumen in many weeks age;only 1 SNP was obtained related to Haugh unit on 44 weeks old.5.We found that QTL located on GGA4 was the most important region affecting albumen height by multivariate GWAS.Two genes,NCAPG and FGFBP1 were considered as potential candidates.Other candidate genes KPNA3,THSD7B,CDC25A and WDR48 may be promising candidate genes affecting albumen quality in partial weeks old.Part two:Genome-wide association study for eggshell colorEgg shell color was measured by spectrophotometer with L a b color space system including 11 weeks point(age at first egg,32,36,40,44,48,52,56,60 and 72 weeks old).Phenotype and genetic parameters of pink and green egg shell colors were calculated,respectively.Univariate and multivariate GWAS were performed to analyze egg shell color.The results are as follows:1.The shell colors of pink egg and green egg both showed L value increased as the hens aged,adverse a value decreased,while the change of b value display irregular.Correlation coefficient between L value and a value or b value in pink egg showed extremely significant negative;Correlation coefficient between L value and a value in green egg showed extremely positive,while the correlation coefficient between L value and b value showed extremely significant negative.2.The SNP heritability of pink eggshell ranged from 0.32 to 0.82,displaying a moderate and high heritability.The genetic correlation coefficient between color value in different weeks were all more than 0.5.The SNP heritability of green eggshell ranged from 0.23 to 0.71,most genetic correlation coefficients were also more than 0.5.3.The major region affecting pink egg shell color located at 10.3-13.0 Mb on GGA20.Several candidate genes SLC35C2,PCIF1 and SLC12A5 were obtained.The minor effect QTL region located on GGA1,GGA6,GGA9,GGA12 and GGA15.Eleven candidate genes such as MTMR3,SLC35E were obtained.4.The major effect QTL affecting green eggshell color located at 61.1-68.5 Mb on GGA1.Candidate genes PIK3C2G,ABCC9,ITPR2,RAD52,TTLL12,SLCO1C1 and SLCO1A2 were obtained.The secondary effect QTL located at 19.2-23.4 Mb on GGA9.Candidate genes RARRES1 and TM4SF4 were obtained.5.The process of synthesis,transport and deposition between pink and green egg shell color may partly share the same regulatory mechanism and another part show unique genetic regulation.Moreover,organic anion-transporting polypeptide family(OATP)play an important role in the shell color regulation.Part three:Influence factors and genome-wide association study for mottled eggshellThe influence of storage time,temperature and humidity and egg quality on mottled egg were analyzed.The mottled egg with pink and green color on the lay day and the storage time of 7 days were performed by GWAS.The results are as follows:1.The mottled egg became more severe as the storage days.The temperature and humidity affect the mottled egg.The thinner color of the pink egg showed the more mottled it was,while the darker of the green egg showed the more mottled it was.2.The mottled egg in green is more serious than that in green.The SNP heritability of mottled egg in pink and green on the lay day was 0.13 and 0.18,respectively.And the SNP heritability of storage 7 days in the two type eggs was 0.54 and 0.61,respectively.3.The number of significant loci affect the pink mottled egg on the lay day was 7,which mainly located at 24.1-24.3Mb on GGA5 and 21.9-22.1Mb on GGA21.There were no significant SNPs related to mottled egg on storage 7 days.Suggestive loci located on GGA3,5,7,11,14 and 18 were obtained association with mottled eggs on storage 7 days.Candidate genes of SLC35C1,VPS18,SSU72,VWA1,and ZNF507 were obtained.4.A total of 3 SNPs were detected that related to green mottled egg on the lay day.These loci mainly located at 129.9-130.5 Mb on GGA2 and 49.4 Mb on GGA5.The regions affect mottled eggs on storage 7 days mainly distributed at 19.2 and 80.1 Mb on GGA2,33.3Mb on GGA15,and 0.86 Mb on GGA17.Candidate genes of SLC25A32,RIMS2,HTR1B,RIMBP2,LYPLAL1 and DIO3 were obtained.Part four:Genome-wide association study for eggshell indexThe egg shape index was calculated from the length and breadth that were measured from age at first egg to 72 weeks old;the change of egg shape index was analyzed.The genetic parameter was calculated and GWAS method was applied to analyze the genetic architecture of egg shape index.The results are as follows:1.The value of egg shape index in most weeks was less than 1.30,and the coefficient of variation increased as the hens aged.2.The SNP heritability of egg shape index ranged from 0.17 to 0.37,showing a moderate and low heritability;the correlation coefficient showed more than 0.8 except age at first egg,the phenotype correlation was more than 0.4.3.Significant or suggestive loci located at 67.1 Mb on GGA1,47.2 Mb on GGA3 and 16 Mb and 62.8-63.8 Mb on GGA4 were related to egg shape index in 32 and 48 weeks old.A total of 25 suggestive loci located on GGA1,GGA2,GGA4 and GGA17 were obtained by multi trait GWAS.Candidate genes of ZDHHC2,SCG2,COG5,ABCC9,UST and GPR107 were obtained. |
PDF Full Text Request