Dissecting The Genetic Architecture On Body Weight Traits Of Indigenous Chicken

Body weight is one of the most important economic traits in animal production,which is a typical complex quantitative trait.Comprehensively dissecting the Complex Genetic architecture of Body Weight is a key and difficult question for molecular marker-assisted selection.Genetic architecture describes the characteristics of quantitative trait locus（QTLs）,including the number of QTLs affecting a trait,their positions in the whole genome,their frequencies in each sub-population,the magnitude of the effects and their interactions with others and the environment.QTL database have already recorded a lot of QTLs affecting body weight traits,but only a small number of causal-mutations have been discovered.As most of the researches used F₂ generation,they only took notice of the number of QTLs,their positions and the magnitude of the effects.To clarify the effects of other genetic characteristics of body weight,population used in our research is composed of multiple sub-populations.Chinese indigenous chicken with notably different body weight provided materials for our study.According to the growth curve of multiple breeds in National Chickens Genetic Resources（NCGR,JIANGSU Province）,we selected two low-body weight breeds（Chahua Chicken and Silkie Chicken）and two high-body weight breeds（Langshan Chicken and Beard Chicken）,with 100 samples in each breed.In view of the stratification of population structure,on the one hand,we constructed a mixed linear model（MLM）contained sex,birth weight and breeds as fixed effects,Kinship matrix as random effect,and on the other hand,we used different method for building Kinship matrix in order to increase the accuracy of the results of mapping.We identified 6 independent significant QTLs associated with body weight traits through Genome-wide association study,each QTL can explain 1-2%phenotypic variance.These QTLs distributed on chromosome 2,3,5,9,20 and 27 was repetitive with QTLs mapped in other studies,besides,other researches have already proved that DLK1which is 32Kb upstream of BW_Q5 and GDF5 within the BW_Q20 are functionally associated with body weight traits of chicken.These results showed the number of major QTLs affecting body weight,their positions and the magnitude of the effects,which indicated body weight has a polygenic genetic basis.The haplotype-based association study further confirmed the QTLs above and obtained 7 significant haplotypes,between which BW_Q9 have two outstanding haplotypes with oppsite direction of the effects.Using 100 Recessive White Chicken samples and 4 Red Jungle Fowl samples as control groups,we then observed the proportional distribution and the magnitude of the effects of these haplotypes in each sub-population.The results showed that 4 of them were unique in Beard Chicken,so we inffered that these 4 haplotypes were specific haplotypes affecting body weight in Beard Chicken.QTL on the chromosome 27 had one significant haplotype with the effect of increasing body weight,which was found in each of the 4 sub-populations but took large propotion in high-body weight breeds than in low-body weight breeds,showing an increasing tendency with the increase of average body weight in different sub-population;however,2 haplotypes contained BW_Q9 were prominent,each of the 4 sub-population has one of the 2 significant haplotypes,which has negative effect on body weight,interstingly,Langshan Chicken possesses another significant haplotype with positive effect on body weight.The haplotype unique in Langshan Chicken made it significantly different with Chahua Chicken and Silkie Chicken in body weight.Unlike the other 4QTLs,quantitative trait locus on chromosome 9 and 27 had effects on all breeds,but the frequencies distribution and magnitude of the effects reflected the complexity of genetic architecture.As one of the most important part of genetic architecture,we also evaluated the epistasis effects on body weight.Combine the results of GWAS and vGWAS,10 SNPs were defined as candidate loci for further analysis to find other loci which interact with these candidate loci.We found interactive loci for 4 of these 10 candidate SNPs.Although the experimental population limited a further study for interaction of genes in our study,the candidate intervals with interactive loci contained many genes related to body weight traits,such as ABCD2、NRIP1、KIT and BCHE.Based on the theory of reverse genetics,we validated and renewed the number of QTLs affecting body weight traits by detecting the selective signatures between different breeds.Finally,we got 24 independent selective signatures using XP-EHH and F_ST,which were repetitive with the QTLs associated with body weight found in other researches.In conclusion,the number of QTLs,their positions in the whole genome,their frequencies in each sub-population,the magnitude of the effects and their interactions with others may affect body weight traits at different levels.So,comprehensively dissecting the complex genetic architecture of body weight is of great necessity,which may provide important theoretical basis for characteristic breeding of indigenous chicken.