Genome Wide Association Study For Cd Content In Grains Of Sweet And Waxy Maize

The wide-spread Cadmium in China,one of the most toxic heavy metal,causes dramatic yield reduce of crops.Cd pollution is now a huge threat to national food security,and also causes the rise of cancer rate of citizens who live around polluted arable land and which causes a huge lost on economy.In this research,171 sweet-waxy maize lines and 90 maize inbred lines were employed and planted in heavy metal polluted arable field in Shifang in 2018.Grains were collected for Cd determination determination.Cd accumulation features were analyzed to screen inbred lines with different accumulation features for phytoremediation crop breeding.Genotyping chip maizeSNP50 K were employed to determinate genotype of the population.We explored SNPs correlated to grain-Cd-accumulation by using Genome Wide Association Study and mined candidate genes by using bioinformatics.Results of this study are as below:1.Descriptive statistics analysis was conducted with grain phenotype data.Result shows that the Cd content in grains are between 0.001 and 1.44mg/kg in Env.1 and between 0.0005 and 3.56mg/kg in Env.2.Sweet-waxy maize accumulated more Cd in grains than that of normal maize notably in Env.1.However,there is no diversity of Cd content in grains between Sweet-waxy maize and normal maize in Env.2.With the rising of Cd stress grains Cd content in Env.1 increased less than grains Cd content in Env.2.By combing 2 environments,22 low-Cd inbred lines and 31 high-Cd inbred lines were screened out and 17CL197 and 17CL68 are the most consistent lines in low-Cd inbred lines and high-Cd inbred lines respectively.2.Axiom? Maize56 K SNP Array chip was employed to identify the genotype of 261 inbred lines.After data quality controlling and consolidation,13448 high quality SNP markers were obtained for genome-wide association analysis.Phylogenetic analysis was performed and the result shows that 261 inbred lines were composed of 3 subgroups.PCA analysis was also performed and the result agrees with the phylogenetic tree.The population genetic structure was analyzed by using Admixture.The result shows that in 90 inbred lines,the numbers of temperate,tropical,mix lines are 45,35,10 respectively,and Q value of 171 sweet-waxy maize account with characteristics of Q value of tropical.3.tassel5.0 was employed to study the association of genotype and phenotype by MLM.Result shows that 21 SNPs are detected at significant level(logP≥4.13).According to physical location of SNPs,MaizeGDB were adopted to screen candidate genes and to investigate the function of candidate genes.Result shows that gene Zm00001d033585 may encode leaf permease.Gene Zm00001d004890 may encode zinc finger(MYND type)family protein and programmed cell death 2 C-terminal domain-containing protein.Gene Zm00001d040183 may encode pfkB-like carbohydrate kinase family protein.Gene Zm00001d014957 may encode Translationally-controlled tumor protein homolog.Gene Zm00001d010375 and Zm00001d009716 may encode ATP-dependent 6-phosphofructokinase and Extra-large G-protein-like protein respectively.7 close-located SNPs were found on chromosome 2(Pos:157292561-165068962bp).3 SNPs were detected in Env2 and 1 SNP was found on chromosome 2 and that is a common SNP marker(AX-86304181,Pos:163564013bp)detected both in Env1 and Env2.According to the LD decay(R2=0.1),Gene HMA2 and HMA3 were both located in the same segment.The result of comparison analysis of Cd content in grains between 2 environments helps researchers to understand Cd accumulating mechanism better and also provides basic materials for further inbred lines screening.The result of cluster and population structure analysis helps researchers to understand the Cd content diversity between different families.The result of Genome-wide association study of Cd content in grains provides theory evidence for further breeding of low-Cd accumulation and high-Cd accumulation materials by using gene editing system.