Genetic Analysis Of Complex Traits With Genetic Effects Of Additive,Dominance,Epistasis,and Gene-environment Interactions

Genome-wide association studies(GWAS)have become a widely accepted strategy for dissecting genetic architectures of complex traits in humans,plants,and animals.To define and score a phenotype in many individuals,the GWAS provides a powerful tool to recombine association trait back to its underlying genetics.With the convenience of next-generation sequencing technology,high dense single nucleotide polymorphism(SNP)arrays and DNA re-sequencing have been generated for different organisms.In quantitative genetics,it is well known that complex traits are controlled by multiple genes.epistasis,and gene × environment interactions effects.Dominance,epistasis,and gene ×environment interactions effects might have influences on complex traits that are being ignored in most of the GWAS.Ignoring these effects is one of the major causes of missing heritability of GWAS.In this study,heritability was estimated for dominance,epistasis,and location specific interaction effects of ear traits of maize NAM population.Analyses were performed by using a mixed linear model approach implemented in OTXNetwork.For NAM population full genetic model includes additive,dominance,epistasis and location-specific genetic effects.For MESA population the mixed linear based full genetic model includes additive,dominance,epistasis,and ethnic-specific genetic effects.In this study,the genetic architecture of maize ear traits and body surface area(BSA)of the MESA population was dissected that provide new insight about the traits.For maize ear traits,dominance and dominance-related epitasis effects contributed significantly to the estimated heritability.Location-specific genetic effects are also important variants of maize ear.Only a few pleiotropic loci were identified that mentions different sets of genes are controlling the ear traits.Superior line and superior hybrid were predicted by utilizing association analysis results.The full genetic model helps to understand the genetic basis of ear traits,and provides a roadmap for location-specific marker-assisted selection that may be useful to breeders for traits enhancement to increase crop production.Monte-Carlo simulation study reveals the importance of analyzing gene-environment interaction for plant complex traits.Ignoring gene-environment interaction could cause lower detection power and high false discovery rate(FDR).Moreover,it can cause of misleading heritability estimation of genetic effects.Genetic analysis of BSA identified genes associated with several diseases related to obesity.BSA is controlled by genetic and ethnic-specific genetic effects of multiple loci.Base and cofactor models estimated mostly similar total heritability,where heterozygous genotypes play important roles in controlling phenotypic variations.Lifestyle cofactors also influence on casual loci to control phenotypic variations.Bioinformatics analysis showed that the candidate genes have a relationship with calcium compounds or BSA related diseases.This study explored the complex genetic mechanisms of BSA in different ethnic groups and evaluated the influence of lifestyle cofactors on the genetic level,which could be useful in designing personalized medicine.