| Meloidogyne enterolobii is gradually evolving into the most important root knot nematode pathogen in pepper production in Hainan Province.Breeding disease resistant varieties is the most effective method to control pepper root knot nematode.However,conventional breeding takes a long time,and the identification of disease resistance phenotype is greatly affected by the environment.Therefore,molecular marker assisted breeding is often used to improve breeding efficiency and speed up the breeding process.In this study,272 Capsicum annuum were identified for their resistance to Meloidogyne enterolobii.And GWAS analysis was performed based on the resistance phenotype and genotype data to screen 222 SNP markers significantly associated with Meloidogyne enterolobii resistance.14 candidate genes were identified.This study laid foundation for the breeding of pepper disease-resistant varieties and the exploration of disease resistance mechanism.The main findings are as follows:1.Gall index(GI),eggmass index(EI),disease index(DI),reproduction factor(RF)and reproductive index(RI)were used to identify the resistance phenotype of Meloidogyne enterolobii.Coefficient of variation values of these five phenotypic index were between 0.5 and 2.51.The results of correlation analysis showed that the three indexes closely related to root knot(GI,EI and DI)were highly correlated,and the two indexes closely related to the reproductive ability of root knot nematode(RF and RI)were less correlated with other indexes.The results of principal component analysis showed that the eigenvalues of the five resistance indexes were greater than 1,which could be used as an important index to evaluate the disease resistance of pepper.16 pepper germplasms with strong resistance,such as 06SCa150-S、06SCa52-1、06Ca107M,were selected through the comprehensive evaluation of the membership function of Meloidogyne enterolobii resistance.2.GBS sequencing was performed on 272 pepper materials,and 363,753 SNP and Indel variants were obtained.The SNP densities at different chromosomal locations vary greatly.The number of SNP markers on chromosome P9 is the largest,which is 51612.The distribution of SNP markers on chromosome P8 was the least,with 7541 markers.Using GBS sequencing data to conduct population structure,phylogenetic tree and principal component analysis,it was found that the tested pepper population could be divided into two subgroups.The relationship analysis showed that 93.93% of the materials had a kinship value of-1 to 0.5,and 6.07% of the materials had a kinship value of-1 to 0.5,indicating that the pepper materials used were from a wide range,and the relationship of kinship had relatively little interference to the association analysis.3.Genome-wide association analysis was performed using the filtered 363,753high-quality SNP markers and pepper root-knot nematode resistance indicators.A total of 222 SNP loci significantly associated with resistance were detected,which could explain 3.59%-15.52% of the phenotypic variation.These SNP loci belonged to117 QTLs,of which 21 QTLs were significantly associated with GI;1 QTL was significantly associated with EI;30 QTLs were significantly associated with DI;14QTLs were significantly associated with RF;51 QTLs were significantly associated with RI.4.Gene scan of these 117 resistance-associated QTLs was carried out to detect139 genes.With gene function annotation,a total of 14 genes related to disease resistance were screened out,which can be used as candidate genes for subsequent gene function verification.This study uses the abundant genetic variation information in natural populations to screen and identify the root-knot nematode resistance loci in pepper on the level of whole genome,which will help to enrich the root-knot nematode resistance gene pool of pepper and speed up the process of molecular-assisted breeding for disease resistance.It will also base an important foundation for in-depth analysis of the root-knot nematode resistance mechanism. |
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