Genome-wide Association Analysis And Linkage Analysis Of Pre-harvest Sprouting In Wheat

Wheat is one of the most important economic food crops in China and even in the world.It is also an important ration in people’s daily life.In recent years,with the frequent occurrence of global warming and extreme climate,the harm of pre-harvest sprouting is becoming more and more serious.Pre-harvest sprouting seriously reduces the wheat yield and affect quality.It has been important for wheat breeding to improve the resistance,dig out the resistance sites,screen the related genes and cultivate new varieties resistant to pre-harvest sprouting.However,the genetic mechanism of pre-harvest sprouting is complex,which is a quantitative trait regulated by multiple genes and there are few effective genes / markers related to pre-harvest sprouting.In this study,the 90 K and 50 K SNP chips were used to conduct genome-wide association analysis and linkage analysis of wheat pre-harvest sprouting related traits in 207 wheats(lines)and 309 RIL families constructed by "Berkut×Worrakata".The aim of this study was to find new high-quality genetic loci regulating wheat pre-harvest sprouting traits and to explore new stable and reliable resistance genes.The main results are as follows:1.The results showed that the distribution trend of 207 wheat varieties(lines)in the two environments was similar.Less than 10% of the materials distributed in the resistance grade(0%～30%)and more than70% in the sensitive grade(61%～100%)were distributed.The variation range of germination rate was wide and the average value were high,indicating that the materials with different genetic background showed rich phenotypic variation in both environments,but most of the materials in the natural population had weak resistance to pre-harvest sprouting and had great potential for genetic improvement.Analysis of variance showed that the difference of germination rate between the two environments was very significant(P=0.00001).The results showed that the seven varieties of Chuanmai 107,Zhenmai 168,Zhenmai 6,Kechengmai 1,E’en 5,Miannong 4 and Yangmai 9 were selected,which provided basic materials for further stress resistance breeding and gene mining of pre-harvest sprouting.The results of population structure analysis and principal component analysis showed that the natural population of 207 wheats(lines)could be divided into three subgroups.The genome-wide association study(GWAS)of 207 wheats(lines)was conducted by using 16686 SNPs with uniform distribution covering the wheat genome and mixed linear model(MLM).A total of 34 significant markers(P<0.001)were detected on chromosomes 3A,3B,4A,4B,5D,6A,6B,6D,7B and 7D of wheat.A single locus could explain 5.55%～11.63% of the phenotypic variation.2.The trend of 309 RIL populations resistance to pre-harvest sprouting in four environments was basically same.Both parents and the RIL populations showed higher germination rate,which indicated the resistance was weak.But within RIL populations,The variation range of germination rate was wide,which reflected there was significant difference in RIL families and there was super parent segregation.Analysis of variance showed that there were significant differences in germination rate among genotypes,environments and genotype environment interactions(P = 0.00001).The 50 K SNP microarray was used to analyze the QTL of "Berkut×Worrakata" RIL population.A total of 9 related loci were detected on chromosomes 1AL,1DL,2AL,2AS,2BS,3DS,4BL and 7BL of wheat.a single locus could explain2.67%～6.39% of the phenotypic variation.Except for 4 loci on chromosomes 1DL,2BS,4BL and 7BL,the other 5 alleles were derived from Berkut.3.Comparing the two analysis methods,it was found that the SNP sites and QTLs located on chromosomes 4B and 7B might be the same locus.13 and 8 candidate genes that may be related to the sprouting traits were identified by gene mining of association loci and QTLs with high phenotypic effect value or stable inheritance.The candidate genes for germination are mainly related to seed dormancy,plant hormone biosynthesis and signal transduction.Traes CS3A01G589400 LC and Traes CS7B01G200100 affect seed dormancy by regulating the sensitivity of abscisic acid;The F-box protein encoded by Traes CS6B01G294800 gene plays an important role in plant hormone signal transduction,light signal transduction,flower organ development and other physiological processes;Traes CS3D01G124500 is a biosynthetic pathway of gibberellin(GA)It is the key enzyme in plant growth and development by catalyzing the formation of active GA.These candidate genes can be used as important genes related to pre-harvest sprouting resistance.