| To reveal the structure and extent of genetic variation in germplasm collections is essential for conservation and utilization of cultivated plants. Previous studies of pepper genetic diversity of our country had the small test materials and the low representation, and detailed insights into genetic structure and diversity of our country are largely missing. In this study we have fingerprinted the total national Genebank pepper accessions（1904）with 29 highly polymorphic SSR markers distributing evenly in genome. We analysised the population structure, geographical distribution, genetic relationships and fruit characteristics of different genetic populations. We started functional genes mining of pepper resources, and analysised gene diversity of pvr2 gene. We researched the botanical classification of local pepper varieties “shuanla”and“que la”in Yunnan.The main contents and results in our study are as follows:（1）Genetic diversity of the pepper resource. We have fingerprinted 1904 national Genebank pepper accessions with 29 highly polymorphic SSR markers. The gene diversity index and polymorphism information index respectively range from 0.016 to 0.883, 0.02 to 0.87, and respectively the average was 0.486 and 0.46. 29 SSR markers generated 459 alleles. Out of the 459 SSR alleles, 86 displayed a frequency of more than 5% in the total sample and hence were classified as ‘common’ alleles, while 81 displayed frequencies between 1% and 5% that were denoted as ‘less common’ alleles. Out of the 292 remaining alleles, 159 were denoted as ‘rare alleles’ with frequencies between 0.1% and 1% and 133 as ‘very rare’ alleles with frequencies smaller than 0.1%. That 64% of the observed alleles showed a frequency of less than 1% in the mega-collection suggested that this collection represents the bio-diversity of pepper broadly. Analysises of population genetic structure, neighbor-joining tree and principal component showed that there are two different pepper genetic groups in China and admixtures are mostly located in between two populations. Group 1 contains 1411 accessions, characterized by triangular and horn shaped peppers. Its geographical distribution mainly concentrated in the southern region in our country, such as Hunan, Hubei, Sichuan, Yunan and Guizhou. Group 2 contains 493 accessions, characterized by large fruited peppers with blocky or rectangular shape, mainly distributed in the northern regions, such as Heilongjiang, Jilin, Liaoning and Hebei.（2）Construction of core collections. M（M method） and R（Random method） predicted the optimal sample size of core germplasm. Two sampling methods showed that M score is higher than R, no matter how sample size change, M method sampling alleles is significantly efficienter than R method. M method was used to extract respectively 10, 20, 40, 80 and 160 samples. Five sample sizes of core collection captured 28%, 50%, 57% and 69% alleles of raw materials. Considering the practicability of core collection, we selected characteristic accessions in different regions. The final core collection of 344 accessions（supplementary material）captured 81% of the SSR, including all common alleles, 80（81）less common alleles, 138（159）rare alleles and 68（133）vary rare alleles. Out of the 344 accessions, 227 from group 1 and 117 from group 2. Its genetic diversity index and PIC indexwere 0.527 and 0.5 respectively, higher than those of raw materials（0.486,0.46）. Using 29 SSR markers to analyze the neighbor-joining tree,result show that the final primary core accessions evenly distributed in raw materials and had high representative. East China（6）, southwest（5） and northwest（5） regions had abundant variation. Southern part of China had the least variants than other regions（3）.（3）Analysis of pvr2 gene polymorphism. Five exons of pvr2 gene（eukaryotic translation initiation 4E） of 1904 pepper accessions from National Vegetable Germplasm Bank in China was sequenced and researched on the diversity. We detected 16 sense mutation sites, 25 genotypes and named the 17 newly discovered pvr2 alleles as pvr223pvr239. Germplasm from foreign countries had 13 kinds variations. There were 18 types of variation in domestic resources. East China had the most genotypes（9） and there were least genotypes（5） in south of China. The differences of genotypes between regions were mainly concentrated in a few resources. M strategy algorithm was used to construct the core collection that contained 25 materials based on 16 mutation locis.（4）The research of botanical classification of local pepper varieties “shuanla”and“que la”. Based on 90 accessions of pepper genetic germplasms, phylogenetic analysis of “shuan la”“que la”was carried out using genetic structure and molecular clustering based on 29 SSR makers evenly distributed over 12 chromosomes and using horticultural characters. The results show that “shuanla” belongs to C.chinese and “que la” belongs to C.frutescenson in botanical classification. |
PDF Full Text Request