Linkage Mapping And Association Analysis For Plant Architecture Related Traits Of Maize

At present,the urgent problem in maize prodution practice is to enhance the resistance of maize stalk lodging and cultivate the varieties which are suitable for mechanical harvest.Plant architecture related traits directly affect the density-tolerance and lodging resistance propperty of maize.Therefore,it is of great practical significance to dissect the maize plant architecture related traits genetic mechanism.In this study,a recombinant inbred lines?RIL?population derived from a cross of X178 and NX531 and a collection of Mini-core germplasm with abundant genetic basis were used as experimental materials.High-density SNP markers were employed to analyzethe linkage mapping and genome wide association mapping?GWAS?of plant architecture related traits in Baoding and Xinji.The main results are as follows:1.A total of 93 QTLs,which were distributed on all the chromosomes,were detected by linkage mapping for the whole 17 Plant architecture related traits like plant height,ear height and leaf angle.Phenotypic contribution of these QTLs varied from 0.60%to 28.72%,and genetic distance varied from 0.83cM to 64.30cM.Further more,45 QTLs explained more than 10%of the phenotypic variation,and the genetic distance of 10 QTLs was less than 5cM.The intervals of qEHX3 and qEHB3 were overlapped on Chr3,and the physical distance for two peak positions was only 2.99Mb.Meanwhile,qLNAEB1-2 and qLNAEX1were also found partially overlapping on Chr1,and the physical distance for two peak positions was only 3.14Mb.Further more,a total of 10 QTL intervals were found controlling several different traits in two trial positions,of which the highest peak position were co-locus.2.Using the optimal Q model,when setting the threshold of assessing significant markers to P<1.2×10^-5,a total of 49 significant associated SNP,which distributed on all chromosomes,were detected for all traits in two environments by genome wide association mapping.All the detected SNPs explained phenotypic variation ranged from1.36%to70.10%,among which,38 SNPs contributed more than 10%of the phenotypic variation.Meanwhile,correction values for all traits were obtained by the method of Best Linear Unbiased Prediction?BLUP?,afterwards,GWAS were applied for the correction values and24 significant SNPs were detected distributed on chromosome 1?2?3?4?5?6?8 and 10.Comprehensively comparing the mapping results of Baoding,Xinji and BLUP,chr3₁94055187 was found always significantly associated with leaf width.By searching the 63 candidate genes of a locus detected,61 candidate genes were found,33 of which have been functional noted.3.Comparing of the results for linkage mapping and association mapping,there were 6common locis.The candidate genes analysis of these important QTLs showed that GR MZM2G129513 encode malate dehydrogenase 6;GRMZM2G180596 encode putative HVA22-like protein g;GRMZM2G038384 encode reticulon.In conclusion,the use of high-density bin-map linkage maps together with association analysis of SNP markers to analyze the genetic basis of plant architecture related traits could give highly reliable results,and small QTL confidence intervals,which could help to further exploreeffectively candidate genes of target traits.