Evaluation And Genome-wide Association Study On The Main Agronomic Traits Of Core Collections Of Chinese Pepper (Capsicum Spp.) Germplasm

Pepper(Capsicum spp.)is an annual or perennial plant belonging to the genus Solanaceae.It is one of the worldwide important vegetables and seasonings.In China,its annual cultivation area is about 1.5 million hm2,accounting for about 10% of the vegetable cultivation area.And it is of great significance to supply the annual vegetable market.In this study,core collection of pepper germplasm resources with 349 accessions were evaluated by phenotypic identification and genetic diversity analysis of horticultural traits.Genome-wide re-sequencing of pepper collection were performed to developed SNPs.Using SNP markers analyzed the population structure.312 accessions of Capsicum annuum L.with no population stratification among the population structure were selected for diversity analysis with a two-year phenotypic investigation.Genome-wide association analysis(GWAS)of horticultural traits was performed with whole genomic SNP markers.The main research contents and results are as follows: 1.Analysis of diversity of horticultural traits: Phenotypic investigation and analysis of 48 major horticultural traits of 349 pepper core collections showed that the phenotypic variation of each trait was very rich,and the average coefficient of variation and Shannon’s information index were 39.0% and 1.28;the coefficient of variation of weight per fruit,longest lateral branch length,and number of fruits per plant exceeded 90%;the Shannon’s information index of petiole length and leaf length was 2.10,the highest among all pairs of the characters.Fruit shape,its coefficient of variation and Shannon’s information index are also high.Cluster analysis of horticultural traits divided 349 pepper germplasm resources into eleven groups at a genetic distance of 0.35.Capsicum annuum L.can be distinguished from other pepper materials.The phenotypic differences between the groups are obvious.2.Analysis of population structure of pepper resources: A total of 349 Chinese pepper core collection materials were subjected to a high-average sequencing test with an average sequencing depth of 8.5×.The coverage of whole genome 1×coverage was 90.56% on average,and 4×coverage reached 76.59%.About 20 million SNPs were obtained through screening and filtration,among which the number of SNPs located in the intergenic region was the highest,the average number reached 7,039,123,accounting for 94.8% of the total number of average SNPs;only about 5.2% of the average was located on the gene.Using the developed SNPs markers,349 accessions of pepper were analyzed by phylogenetic tree,principal component analysis and population structure analysis.The results showed that there were obvious population structure in 349 pepper resources.There are two distinct subgroups of pepper,that Capsicum annuum L.resources and Capsicum frutescens L.resources.with the rest of the materials in the middle.C.annuum L.can be clearly layered with other kinds of pepper,but C.frutescens L.are mixed with C.chinense Jacq..This shows that C.chinense Jacq.are more similar to C.frutescens L.In terms of evolution.Among other materials,this shows that the genetic structure of C.annuum L.and C.pubesens Ruiz &Pavon is more similar to that of shrub-like peppers.312 accessions of C.annuum L.were closely related.Their genetic structures were similar,and there was no obvious stratification within the population.It is suitable for genome-wide association analysis.3.Genome-wide association analysis of accessions of C.annuum L.populations: A two-year field survey was conducted on 48 horticultural traits of 312 accessions of C.annuum L..The results showed that,in addition to branching,two-year survey results of other horticultural traits were extremely relevant Significant.Based on the SNP data developed by the whole genome high coverage sequencing,a genome-wide association analysis was performed on the 48 major horticultural traits of 312 accessions of C.annuum L..The results showed that 94 significantly associated SNPs associatedwith 20 horticultural traits such as pungency,and the multiple sites were consistent with previous studies.