| Triticum aestivum L is an allohexaploid crop(2n=6x=42,AABBDD)with a large(16-17Gb)and complex genome.Wheat is one of our main grain crops,its yield directly affects national food security.However,with the increase of population,the decrease of arable land,the emergence of adverse stress and different kinds of heavy metal pollution and other problems,wheat yield has been more and more seriously affected,so it is particularly important to improve wheat yield.In this study,660K SNP chip was used to conduct genome-wide association analysis of 1000-grain weight of 493 wheat materials with abundant genetic variation in 1000-grain weight.The main results are as follows:(1)Population structure and genetic relationship analysis of wheat varieties.493 wheat materials from different places belonged to natural population.The results of population structure detection showed that when K=29,the Cross-validation error value was the smallest.The phylogenetic identification results showed that most of the materials used in this study were far from each other.These results indicate that this population material is suitable for subsequent association analysis.(2)Identification of grain weight of wheat varieties.The frequency distribution histograms of 1000- grain weight of 493 experimental materials in 5 different environments(17HN,17SX,17SD,17XP,18XP)all conform to normal distribution,which is suitable for subsequent genome-wide association analysis.The 1000-grain weight of Pindong 34,Zhenmai 168,Xuke 718,Chuanmai 36 and Jiaomai 266 were higher in multiple environments.The average 1000-grain weight of 17XP environment is the smallest,and the coefficient of variation is the largest.(3)Genome-wide association analysis of wheat variety populations.In the genome-wide association analysis,it was found that the quantile-quantile plot under 18XP environment was high,and the 1000-grain weight data of some varieties were missing.Through the genotype filling,population structure analysis,principal component analysis and standardized processing of phenotypic data,it was found that the general linear model GLM based on principal component analysis was more suitable for 493 materials.A total of 128 SNP loci related to 1000-grain weight were detected on chromosomes 1A,1B,2B,3A,3B,4B,4D,5A,5B,6D,7B and 7D by genome-wide association analysis,and the phenotypic variation explanation rate(R~2)of single association loci was 2.87%-11.31%.Among them,AX110471449 on chromosome 4B,AX110944993 on chromosome 5A,AX108816050 on chromosome 5B,AX95145294,AX111511481 and AX89503835 on chromosome 7B,AX108772300,AX109666241,AX110576947,AX111184541,AX111832758 and AX111843581 on chromosome 7D were detected in at least four environments.Genome-wide association analysis of wheat variety populations.In the genome-wide association analysis,it was found that the quantile-quantile plot under 18XP environment was high,and the 1000-grain weight data of some varieties were missing.Through the genotype filling,population structure analysis,principal component analysis and standardized processing of phenotypic data,it was found that the general linear model GLM based on principal component analysis was more suitable for 493 materials.A total of 128 SNP loci related to 1000-grain weight were detected on chromosomes 1A,1B,2B,3A,3B,4B,4D,5A,5B,6D,7B and 7D by genome-wide association analysis,and the phenotypic variation explanation rate(R~2)of single association loci was 2.87%-11.31%.Among them,AX110471449 on chromosome4B,AX110944993 on chromosome 5A,AX108816050 on chromosome 5B,AX95145294,AX111511481 and AX89503835 on chromosome 7B,AX108772300,AX109666241,AX110576947,AX111184541,AX111832758 and AX111843581 on chromosome 7D were detected in at least four environments.(4)Prediction of thousand-grain weight candidate genes.Perform gene annotation analysis on 12 stable genetic loci,among which 5 SNP loci(AX110471449 marker,AX110944993 marker,AX108772300,AX111843581,AX109666241 marker)are located in the inter gene region,and their functions need further research.A total of 7 candidate genes for grain weight were identified:Traes CS5B02G028200(related to the binding domain of plant calmodulin binding proteins),Traes CS7B02G066400LC(related to hexose synthesis and metabolism),Traes CS7D02G108700(responsible for catalyzing the redox steps of various metabolic activities in the organism),Traes CS7D02G110900(located on the plasma membrane and participating in the biosynthesis process of heme)Traces CS7D02G11000(formation of transcription elongation factor complexes),Traces CS7B02G650400LC(related to plant transporter synthesis),and Traces CS7B02G387700(altering downstream gene expression by regulating transcription factor activity).(5)Haplotype block analysis.Through haplotype block analysis of 12 stable genetic loci,except for the AX108772300 and AX111843581 marker loci on 7D,there were no LD blocks present.Among them,the 7B chromosomes AX89503835 and AX111511481 are located in the same block interval of approximately 83 kp,while the 7D chromosomes AX111184541,AX111832758,and AX109666241 are located in the same block interval of approximately 392 kp.(6)Analysis of superior allelic variation.By performing excellent allelic variation analysis on 12 SNP loci stably associated with thousand grain weight,it was found that variant loci A and G on chromosome5A(AX110944993)did not significantly improve wheat yield in all four environments.The remaining 11 markers achieved significant increases in wheat yield in multiple environments,with the highest being AX111843581-C on chromosome 7D,which increased thousand grain weight by 5.194 g,The lowest was AX111511481-G on chromosome 7B,which increased the 1000 grain weight by 2.933 g.(7)Gene expression analysis.Through gene expression analysis of various growth cycles in wheat, it was found that the Traes CS5B02G028200,Traes CS7D02G110900,and Traes CS7B02G066400LC genes were expressed at all stages of wheat,while the other four genes(Traes CS7B02G387700,Traes CS7D02G11000,Traes CS7D02G108700,and Traes CS7B02G650400LC)were almost not expressed.In GO annotation analysis,Traes CS7D02G110900 gene is mainly involved in heme O biosynthesis in cellular respiration,which is related to the activity of proheme IX farnesyl transferase;Traes CS7D02G11000 gene is related to chromatin mediated transcriptional maintenance and transcriptional extension of RNA polymerase II promoter in biological process,;The Traes CS5B02G028200 gene is mainly related to microtubules in cell components;The Traes CS7D02G108700 gene is associated with plant-based allergic reactions in biological processes.This study detected a total of 12 stable genetic loci related to thousand grain weight,among which the loci on chromosomes 4B(AX110471449),5A(AX110944993),5B(AX108816050),and 7B(AX111511481,AX95145294,and AX89503835)were far from the previous research results and may be new loci.These loci provide a theoretical basis for wheat assisted selection breeding and quality improvement at the molecular level,laying the foundation for exploring and developing functional genes that enhance wheat yield characteristics. |
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