Identification And Genome-wide Association Analysis Of Fusarium Crown Rot Resistance In Chinese Endemic Wheat

Wheat（Triticum aestivum L.）is one of the three major food crops in the world.Wheat Fusarium crown rot（FCR）is a fungal soil-borne disease caused by Fusarium infecting the base of wheat stem,which seriously harms wheat production and causes wheat yield reduction and economic losses in many countries and regions around the world.Therefore,it is urgent for researchers to strengthen the screening of resistant germplasm and genetic research of wheat stem rot.Tibetan semiwild wheat,Yunnan hulled wheat,Xinjiang rice wheat,and Sichuan white wheat are unique germplasm resources in China,with rich agronomic traits and genetic diversity.In this study,209 Chinese endemic wheat were identified for resistance to FCR by soaking inoculation in greenhouse at seedling stage,and the accessions with stable resistance were identified.Genome-wide association study（GWAS）was carried out by combining the obtained phenotypic data with genotype data to obtain QTL closely linked to FCR resistance.The haplotype analysis was carried out using the identified major stable QTL to explore the feasibility of gene polymerization to improve the resistance to wheat FCR;The peak SNP in QTL were transformed into available kompetitive allele-specific PCR（KASP）primers,which were verified in the constructed validation population;By homologous annotation and expression analysis,candidate genes related to stem rot resistance were predicted.The specific research results are as follows:1.Identify the resistance of 209 Chinese endemic wheat to FCR,6 stable resistant accessions were selected,and laid a material foundation for subsequent research.209 Chinese endemic wheat were identified for four times.Pearson correlation analysis showed that the four repeated data reached a significant level（P<0.01）,and the correlation coefficient was between 0.71 and 0.81.The results showed that most of the accessions were highly susceptible to FCR（DI>30）.Among them,6 accessions showed stable resistance to FCR（DI≤30.0）,and 3 accessions reached stable medium resistance（10<DI≤20.0）.Among the 6 accessions,except for 2 accessions belonging to Yunnan hulled wheat and Xinjiang rice wheat,the other 4 accessions were Tibetan semiwild wheat,and 3 moderately resistant wheat were also Tibetan semiwild wheat.2.Ten QTL related to FCR resistance were identified by GWAS,and confirmed that gene pyramiding of major resistance QTL could enhance wheat FCR resistanceGWAS was carried out using 37452 high-quality polymorphic markers combined with phenotypic data.A total of 105 significant associated SNP were identified,which were distributed in 10 QTL regions,of which 4 QTL（Qfcr.sicau.2A-1,Qfcr.sicau.2A-3,Qfcr.sicau.5A,and Qfcr.sicau.7D）could explain more than 10%of the phenotypic variation and were considered to be major QTL.The remaining 6 minor QTL could explain5.72-9.28%phenotypic variation.Using different excellent haplotype combinations of major QTL and phenotypic data for gene pyramiding analysis,the results showed that 16accessions contained 4 resistant haplotypes,and the DI values ranged from 16.88 to 64.64,with an average of 44.95.The DI of these 16 accessions was 9.35-31.61%lower than that of accessions without or with 1-3 resistant haplotypes.3.Based on the functional annotation and expression analysis of the genes in the major QTL region,a total of 22 genes related to FCR were identified.Several highly reliable genes in the four major QTL regions were further predicted and analyzed from two aspects of functional annotation and expression analysis.From the functional annotation direction,12 disease resistance related genes were further predicted with Arabidopsis and rice as background plants.In terms of expression analysis,based on the previously reported RNA-seq data of Fusarium graminearum infected wheat,a total of10 genes related to FCR response were predicted.The above 22 genes were identified as candidate genes for FCR resistance.4.The KASP marker tracking Qfcr.sicau.2A-1 was genotyped in the verification population,which proved that it could improve disease resistance by 17.78%under different genetic backgrounds.Using the peak SNP marker in the major QTL,it was successfully transformed into KASP marker,in which a KASP marker developed for Qfcr.sicau.2A-1 and Qfcr.sicau.7D could successfully classify the FCR resistant and susceptible materials in Chinese endemic wheat.The KASP marker developed based on Qfcr.sicau.2A-1 can be successfully genotyped in the F₆RIL population constructed with the resistant material"Yutian rice wheat"and the susceptible material"Chinese Spring".The T-test was carried out by using the typing results combined with the phenotypic data identified by inoculation.The results showed that the DI value of accessions containing resistant alleles was significantly lower than that of materials containing susceptible alleles（P<001）.The difference of DI between materials containing two different alleles was 17.78%.