| Wheat is an important food crop in China.Cultivation of high-yield and high-quality wheat plays an important role in maintaining China's food security.Therefore,in this study,543 wheat cultivars distributed in 10 provinces and cities in northern China's winter wheat region and foreign were used as materials to reveal QTLs associated with agronomic traits and quality traits using 90 K SNP markers.The main contents are as follows:1.A total of 543 wheat materials with extensive genetic backgrounds were used to identify 31 agronomic traits(plant height,spike length,1000-grain weight,etc.)and quality traits(protein content,wet gluten content,and starch content)in wheat in six environments.All the traits showed significant variation,ranging from 0.88% to41.37%.The average value of the 31 traits showed a continuous distribution and showed a normal distribution and the 31 traits had high general heritability.2.The gene chip contains a total of 81,587 SNPs that cover the whole wheat genome.For the detected SNP genotyping results,quality control was performed with a genotype heterozygosity of less than 50%,a detection rate of greater than 90%,and a minimum allele frequency(MAF)of less than 5%.After that,11140 SNP markers were used for follow-up analysis,which mean MAF was 0.18,and which mean value of PIC was 0.27.543 wheat materials were divided into 3 subpopulations and the genetics similarity coefficient were calculated using NTSYSpc 2.11 a software.The range of genetic similarity coefficient between the 543 wheat cultivars ranged from0.3699 to 0.9965 with an average of 0.5943.The range of the genetic similarity coefficient between the varieties in the subgroup I was from 0.4832 to 0.9965 with an average value of 0.6828.The range of the genetic similarity coefficient between the varieties in the subgroup II was from 0.4550 to 0.9964 with an average of 0.6135.The range of genetic similarity coefficient between the varieties in the subgroup? was0.3599~0.9410 with an average of 0.5786.The linkage disequilibrium analysis was performed using 11140 SNP markers distributed on 21 chromosomes.Among the 3wheat genomes,A genome decayed fastest,D genome followed,and B genome decayed most slowly.3.The best linear unbiased prediction(BLUP)was performed on the trait datameasured in 6 environments of 543 wheat cultivars to eliminate the errors caused by the environment.After that,the BLUP data and all the trait data in the six environments were used at the same time.In addition,GLM,GLM+PCA,MLM+K and MLM+PCA+K were used to perform genome-wide association analysis on 31 traits.In 6 environments,31 traits and 4 models simultaneously mapped 164 SNP loci,of which 124 loci related to agronomic traits and 81 loci related to quality traits;using BLUP data,31 traits and 4 models simultaneously mapped 55 SNP loci,of which 25 loci related to agronomic traits and 30 loci related to quality traits.4.A BLAST search was performed against the International Wheat Genome Sequencing Consortium database(IWGSC)using the sequences of the significant SNP markers identified by GWAS.When SNP marker sequence and a wheat contig from the IWGSC were 100% identical,the sequence was extended to 10 kb for each marker using the IWGSC BLAST results.The extended sequence was used to perform a BLAST search against the National Center for Biotechnology Information(NCBI)database to identify flanking genes.Using 543 wheat varieties with rich genetic background distributed in 10 provinces and cities in northern China's winter wheat region,90 K SNP markers were used to reveal QTLs significantly associated with agronomic traits and quality traits.The genetic relationship and population structure of Chinese winter wheat at the level of DNA were clearly identified,and SNP sites closely related to the target traits were discovered to provide a theoretical basis for favorable gene mining and breeding of new wheat varieties. |
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