GWAS Analysis Of Plant Architecture And Spike Traits And Screening Of Excellent Germplasms In Wheat

As the largest grain ration crop of the word,the contradiction between wheat supply and demand is becoming increasingly acute.The increase in wheat production is directly related to national food security.The study of plant architecture and spike traits has become an important direction for wheat breeding in China and even the world to seek breakthroughs.In this study,210 wheat germplasm were used as materials and excellent germplasm were screened based on phenotype identification.The SNP/InDel markers were called according to the results of RNAsequencing.Using these markers and the phenotypic data of 20 plant architecture and spike traits,we conducted geneome-wide associaton study(GWAS).The main results are as follows:(1)We identified 20 plant architecture and spike phenotypic traits of 210 wheat germplasm and conducted correlation analysis.The number 20 excellent germplasms were selected for each of the eight traits,flag leaf area,top second leaf area,thousand grain weight,grain number per spike,spike number,angle between flag leaf base and the main stem,angle between top second leaf base and the main stem,and plant height.Of these,11 varieties,S229,Xinong979,Zhongmai895,Gao38,Han6172,Hongmai30,Jimai38,Linxuan49,Youbaomai,Yumai70 and Zhoumai21,showed excellent on 3～4 traits.The range of phenotypic variation for each trait is 8.68 to 46.13%,indicated that the phenotypic variation were widespread for each trait.The correlation analysis showed that the most correlations were significant betweem the traits.(2)Transcriptome sequencing was performed usisng 210 test materials.A total of 3115.35 Gb clean reads were obtained.The average Q30 of sequencing data was more than 87%,the GC content was 48.60～56.48%,the average was 54%,the unique comparison rate was71.40～86.74%,and the average comparison rate was more than 80%.Using the Chinese Spring genome IWGSC v2.1 as a reference sequence for alignment,a total of 3254126 original mutation sites were obtained.After filtering according to MAF≥10% and U≤50%,the 144310 markers,including 11631 InDel and 132679 SNP were remained.For the 21 chromosomes of wheat,3B chromosome has the most markers of 13264,including 12212 SNPs and 1052 InDel;4D chromosome markers has the least markers of 525,including 469 SNPs and 56 InDel.There are 55351,75487 and 13472 markers for A,B and D sub-genomes,respectively.(3)The genome-wide association study for plant architecture traits showed that a total of1379 markers significantly associated with the traits,which were distributed on all the 21 chromosomes and could explain 5.50～18.98% of phenotypic variation.Among them,306,143,55,72,220,252,78,104,134,141,109,50,and 29 markers were significantly associated with plant height,stem diameter,flag leaf length,top second leaf lenght,flag leaf width,top second leaf width,flag leaf length-width ratio,top second leaf length-width ratio,angle between flag leaf base and the main stem,angle between top second leaf base and the main stem,flag leaf area,top second leaf area,and spike number,respectively.The genome-wide association study foe spike traits showed that a total of 665 markers were significantly associated with the traits,which were distributed on all the 21 chromosomes,and could explain 5.61～18.23% of phenotypic variation.Among them,92,172,114,77,91,69,and 106 markers were significantly associated with spike length,total spikelet number per spike,sterile spikelet number per spike,fertile spikelet number per spike,thousand grain weight,grain number per spike,and grain number per spikelet,respectively.The GWAS results showed that 105 pleiotropic markers were found to be significantly associated with three or more traits simultaneously.(4)The 1961 markers were annotated to genes.The results showed that a total of 865 candidate genes were preliminarily obtained.Of these,609 genes were associated with plant architecture traits,including 128 genes of plant height,63 genes of stem diameter,28 genes of flag leaf length,40 genes of top second leaf length,93 genes of flag leaf width,102 genes of second leaf width,35 genes of flag leaf length-width ratio,59 genes of top second leaf lengthwidth ratio,73 genes of angle between flag leaf base and the main stem,62 genes of angle between top second leaf base and the main stem,57 genes of flag leaf area,25 genes of top second leaf area,and 17 genes of spike number.A number of 294 genes were associated with spike traits,including 40 genes of spike length,75 genes of total spikelet number per spike,57 genes of sterile spikelet number per spike,41 genes of fertile spikelet number per spike,47 genes of thousand grain weight,35 genes of grain number per spike,and 39 genes of grains number per spikelet.The 105 pleiotropic markers were annotated to 44 genes.