Genome-wide Association Study For Main Agronomic And Quality Traits In Common Wheat

Wheat is one of the most important crops in China.As the main producing area of wheat in China,the south of Yellow and Huai Valley in China has a large planting area and rich germplasm resources,which plays an important role in wheat production and food security.High-yield breeding has long been the breeding goal of breeders.With the improvement of people’s living standards and the change of grain supply and demand structure,the improvement of quality becomes particularly important.It is of great significance to select and breed wheat varieties with high quality and strong gluten and weak gluten to meet people’s demand for various terminal flour products.Due to the growth characteristics of wheat,large-scale single planting and long-term selection of breeders have led to a decline in wheat genetic diversity,and it is difficult to make breakthroughs in breeding.Modern biological technology and high-throughput genotyping assay technology are developing rapidly.High-density molecular markers are used to genome-wide association study,which provides a theoretical basis for marker-assisted selection and becomes an effective way to tap wheat yield potential and improve wheat flour quality.We investigated 9 agronomic traits and 7 quality traits using 150 wheat cultivars(lines)from the south of Yellow and Huai Valley in China across 4 environments.Genome-wide association(GWAS)was performed using wheat 35 K genotyping assay with 5 association models(Q,PCA,K,PCA+K,Q+K).The purpose of this study was to find the loci significantly associated with the target traits,and to excavate excellent alleles,so as to provide reference for marker-assisted selection.The main results are as follows:1.The genotyped for 150 wheat varieties(lines)was performed by 35 K genotyping assay,and 35143 SNP markers were found.The markers with the minimum allele frequency(MAF)less than 5% and the Miss rate greater than 25% were removed.A total of 9552 high-quality markers with high polymorphism and stable existence were screened out.In total,the polymorphic information content(PIC)of values was between 0.0950 to 0.5000 and the minimum allele frequency(MAF)were between 0.0500 to 0.5000,the PIC of the 3 chromosomes was as follows: A(0.3317)> B(0.3240)> D(0.3100).The length of the physical map was 14541.4 Mb,and the marker density was 1.70 Mb / marker.Both the population structure analysis and the PCA analysis showed that the tested materials could be divided into two sub-populations.Linkage disequilibrium analysis found that the LD decay distances of the A,B,D,and the whole genome were approximately 4.7,8,11,and 6 Mb,respectively.2.Phenotypic identification of 9 agronomic traits and 7 quality traits was carried out under 4 environmental conditions,and the GWAS model was modified for different traits.A total of 935 significant(P≤0.001)marker-trait associations(MTAs)were detected,thereinto,63 SNPs could be detected in two or more environments,among which 21 were associated with agronomic traits and 44 were associated with quality traits,11 SNPs were significantly associated with two or more traits.The single SNP could explain 7.67 % to 40.24 % variation of phenotype.3.The 12 dominant alleles of agronomic traits were found in this study,eight rare favorable alleles accounted for a low proportion in the tested population.For example,AX-94532508-T on chromosome 6A reduced the length of first internode by 2.79 cm.AX-94799632-C on chromosome 5B increased kernel number per spike by 3.22.AX-95152265-C on chromosome 7D increased thousand kernel weight by 4.91 g.AX-95094324-C on chromosome 1A reduced plant height by 3.42 cm.AX-95108722-T on chromosome 2D and AX-94542697-C on chromosome 3A increased spike length by 0.63,and 0.69 cm,respectively.A total of 35 dominant alleles of quality traits were found,and 26 rare favorable alleles accounted for a low proportion in the tested population.For example,AX-94690816-A on chromosome 5A increased wet gluten content by 2.86% and protein content by 1.21%.AX-94445422-T on chromosome 1A and AX-94465394-T on chromosome 2A increased zeleny sedimentation by 2.98 and 4.18.The dough formation time of AX-95683498-C,AX-94693410-T,and AX-94958994-T on chromosome 1D was increased by 0.6,0.61 and 0.61 min,respectively.AX-94571120-T,AX-95236907-A,and AX-94673659-A on chromosome 1A all increased the dough stabilization time by 1.93 min.The water absorption rate of AX-95073002-G,AX-94781832-T,AX-94943787-T,AX-94978347-T,AX-94890987-T,and AX-95085919-T were increased by 3.29,2.72,2.33,2.30,3.32,and 3.06%,respectively.In addition,Five haplotypes significantly affecting dough formation time and dough stabilization time were detected in the genome region of 6807 kb,1848kb,and 6886 kb on chromosome 1A,1B,and 1D.The dominant types of 5 haplotypes accounted for 59.33%,12.67%,16.00%,16.00% and 11.33% of the tested population.4.Fourteen candidate genes that may be related to agronomic traits of wheat were identified.Among them,Traes CS5B02G237200,Traes CS7D02G129700 and Traes CS1B02G426300 may play important roles in plants resistance to biotic and abiotic stress.Traes CS5B02G010800,and Traes CS7D02G436800 may be related to the synthesis and response of hormones in plants.Traes CS2A02G092200 may enhance the cell wall formation of plants.Traes CS5A02G438800 may be involved in chloroplast development.The function of the other seven candidate genes is unknown.Thirty-six candidate genes that may be related to quality traits of wheat were identified.Among them,Traes CS3B02G549000,Traes CS5D02G429000,Traes CS5D02G547400,Traes CS1D02G318800,Traes CS1A02G317900,Traes CS1A02G323000,Traes CS1D02G317200,and Traes CS1B02G426300 may improve plant resistance to external stress.Traes CS5A02G498800,Traes CS1A02G314100,and Traes CS7D02G045800 may be related to cell cycle maintenance and secondary metabolism.Traes CS5A02G438800,and Traes CS1D02G315700 may be involved in some nitrogen reactions in plants.Traes CS1D02G317301,and Traes CS1A02G317311 are high molecular weight glutin subunits,and Traes CS4B02G325300 is involved in abscisic acid mediated reaction with photosensitive pigment.Traes CS5D02G004300 is gene of Pinb-D1,which controls wheat grain hardness.Traes CS1A02G315300,and Traes CS1B02G327200 may be related to cell wall structure.The function of the other seventeen candidate genes is unknown.