Genome Wide Association Analysis Of Genetic Loci Associated With Canopy Structure In Maize

The dry matter yield of maize is affected by many factors,especially the source sink relationship.The distribution of maize canopy leaf type will seriously affect its photosynthetic efficiency.Therefore,it is of great significance to study the correlation of maize leaf type after anthesis.In this study,genome wide association study（GWAS）was carried out to compare the genetic basis of upper,middle and lower leaves of maize canopy in vertical space,providing new insights for the analysis of genetic basis of canopy related traits.In this paper,266 inbred varieties with rich genetic resources were planted in Chongzhou,Sichuan and Jinghong of Yunnan in 2019 and in Chongzhou,Sichuan and Xiangyang,Hubei in 2020.The correlation between leaf area and leaf orientation value of the top two leaves of the canopy and the three leaves of the middle and lower panicles of the canopy,as well as the duration of flowering,20 days,30 days and 40days after flowering were studied The phenotype of green trait was identified.Using Excel software to analyze the performance data,we found that the phenotypic data basically conform to the normal distribution.Based on previous studies,the population structure was divided into two subgroups:subtropical and temperate,and the linkage disequilibrium（LD）was 100k bp when r²=0.2.Using tassel 5 software,genome-wide association analysis was performed between the genotypes with 47000 single nucleotide polymorphisms（SNPs）after screening by using tassel 5 software.At significant level–lg（p）≥4.8,38 SNPs were screened out which were significantly associated with traits in multiple environments.According to the physical location of SNP and LD_（r）2=0.2=100kbp,the corresponding quantitative trait locus（QTL）was deduced.Based on the physical location of QTL on chromosome,candidate genes were screened from maize GDB website,and their functions were annotated.The candidate genes in upper,middle and lower leaves of canopy were compared in vertical space,the results are as follows:1.For the upper and middle leaves of the canopy,the candidate genes GRMZM2G083328 and GRMZM2G083394,which affect the length of the top two leaves and upper ear leaves,are DCD domain protein genes located in bin8.03 region.The candidate gene NBCS8 of SNP13033,which affects the leaf height of the top two leaves and the leaf height at ear position,is the gene of adenine/guanine permeating enzyme azg2 or nucleotide cation transporter 8.2.For the middle and lower leaves of canopy,the candidate gene KRP3,which affects the length of leaf at ear and under ear,as well as the leaf area of upper and lower leaves,is a kinesin related gene,which is located in bin8.06 region.The mutation of CYP27,a candidate gene for QTL corresponding to the length of ear leaf and under ear leaf,will cause leaf injury,which is located in bin2.06 region of chromosome.b ZIP47 is a transcription factor gene in b ZIP family,which is located in bin7.04 region.CPX2,a candidate gene for QTL corresponding to leaf height and leaf orientation of ear leaf and lower leaf,is constitutively expressed in maize and may catalyze chlorophyll synthesis.NIT1,a possible QTL candidate gene,which affects the angle between ear leaf and leaf under ear,may be very important in the transformation of Ian to IAA in developing grains and seedlings.3.Rld2,a candidate gene of QTL,which affects the orientation value of the last two leaves,is usually expressed in the apical meristem of bud tip,which affects the performance of leaf orientation value.The candidate gene LG4,which affects the QTL corresponding to the leaf height of the last two leaves,will transform the leaf tissue into a region with sheath like characteristics,thus forming a finger like invasion of the leaf,causing the normal leaf tongue to disappear or shift.Te1,a potential QTL candidate gene affecting leaf area at ear position,may lead to plant type and inflorescence differences in maize.