Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki

Population Genetic Analysis in Persimmons (Diospyros kaki Thunb.) Based on Genome-Wide Single-Nucleotide Polymorphisms

This study investigated the genetic diversity and population structure of a persimmon (Diospyros kaki Thunb., 2n = 6x = 90) collection in South Korea by evaluating 9751 genome-wide single-nucleotide polymorphisms (SNPs) detected using genotyping-by-sequencing in 93 cultivars. The results of neighbor-joining clustering, principal component analysis, and STRUCTURE analysis based on SNPs indicated clear separation between cultivar groups (pollination-constant nonastringent (PCNA, 40 cultivars), pollination-constant astringent (PCA, 19), pollination-variant nonastringent (PVNA, 23), and the pollination-variant astringent type (PVA, 9)) based on the astringency types, while separation between PVA and PVNA-type cultivars was unclear. Population genetic diversity based on SNPs showed that the proportions of polymorphic SNPs within each group ranged from 99.01% (PVNA) to 94.08% (PVA), and the PVNA group exhibited the highest genetic diversity (He = 3.86 and uHe = 0.397). F (fixation index) values were low ranging from -0.024 (PVA) to 0.176 (PCA) with an average of 0.089, indicating a deficiency of heterozygosity. Analysis of molecular variance (AMOVA) and Fst among cultivar groups indicated that variation within individuals was higher than that among the groups. Pairwise Fst values among the groups ranged from 0.01566 (between PVA and PVNA) to 0.09416 (between PCA and PCNA), indicating a low level of cultivar type differentiation. These findings highlight the potential application of biallelic SNPs in population genetics studies of allopolyploids species and provide valuable insights that may have significant implications for breeding and cultivar identification in persimmon.

Genetic Diversity and Association Analysis among Germplasms of Diospyros kaki in Zhejiang Province Based on SSR Markers

In subtropical to temperate regions, persimmon (Diospyros kaki Thunb.) is an economically important fruit crop cultivated for its edible fruits. Persimmons are distributed abundantly and widely in Zhejiang Province, representing a valuable resource for the breeding of new cultivars and studying the origin and evolution of persimmon. In this study, we elucidated the genetic structures and diversity patterns of 179 persimmon germplasms from 16 different ecologic populations in Zhejiang Province based on the analysis of 17 SSR markers. The results show that there was a medium degree of genetic diversity for persimmon found in Zhejiang Province. With the exception of the Tiantai Mountain and Xin’an River populations, we found extensive gene exchange had occurred among the other populations. The 179 D. kaki germplasms from the 16 populations could be separated into three distinct clusters (I, II, and III) with a higher mean pairwise genetic differentiation index (FST) (0.2714). Nearly all samples of Cluster-I were distributed inland. Cluster-II and Cluster-III contained samples that were widely distributed throughout Zhejiang Province including all samples from the coastal populations and the Northeast Plain populations. In addition, we performed association mapping with nine traits (fruit crude fiber content, fruit calcium content, fruit water content, fruit longitudinal diameter, fruit aspect ratio, seed width, seed length, leaf aspect ratio, and number of lateral veins) using these markers. This led to the identification of 13 significant marker–trait associations (MTAs; p < 0.00044, 0.1/228) using a general linear model, of which, six MTAs with a correlation coefficient (R2) >10% were consistently represented in the general linear model with p < 0.00044 in the two models. The genetic structures and diversity patterns of the persimmon germplasms revealed in this study will provide a reference for the efficient conservation and further utilization of persimmon germplasms. The MTAs identified in this study will be useful for future marker-assisted breeding of persimmon.

Genetic divergence in Tunisian castor bean genotypes based on trap markers

In the present study, the representatives of the genus Ricinus communis collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 30 TRAP primers. The efficacy of the TRAP technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 30 primers for TRAP analysis produced 490 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (TRAP 04 x arb 1, TRAP 22 x arb 3 and TRAP 23 x arb 3) to 13 (TRAP 56 x arb 2), and the amplicon size ranged from 100 to 1600 bp. Of the 490 amplified bands, 377 were polymorphic, with an average of 5.71 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for TRAP 10 x arb 1 (0.555) and the highest PIC values were detected for TRAP 44 x arb 2 (0.961) with an average of 0.770. A dendrogram was constructed from a genetic distance matrix based on profiles of the 30 TRAP primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Moreover, functional TRAP markers would be efficiently useful in genetic studies for castor genetic improvement.