Shinya Kanzaki

Phylogenetic relationships of Mangifera species revealed by ITS sequences of nuclear ribosomal DNA and a possibility of their hybrid origin

Abstract. The phylogenetic relationships among 14 Mangifera L. species of Thailand were analyzed by comparing sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA). Parsimony and neighbor joining (NJ) analyses revealed that the common mango (M. indica L.) was closely related to M. laurina Bl., M. sylvatica Roxb., and M. oblongifolia Hook. f. Mangifera foetida Lour. and M. odorata Griff. were also related to M. indica in both parsimonious and NJ trees, although these two species are classified into a different subgenus (subgenus Limus) from the subgenus Mangifera to which M. indica belongs. ITS sequence analysis revealed that several species have nucleotide additivity (two different nucleotides at the same locus) at several sites in the ITS region. Also, M. indica had several polymorphisms among cultivars. This finding may suggest a possibility of hybrid origin of Mangifera species, although Mangifera species are all assumed to be diploid having chromosome number of 2n=2x=40.

Sequence analyses of the ITS regions and the matK gene for determining phylogenetic relationships of Diospyros kaki (persimmon) with other wild Diospyros (Ebenaceae) species

To elucidate the relationships among Diospyros kaki and species closely related in previous studies, the nuclear ribosomal internal transcribed spacer (ITS) DNA sequence and the chloroplast matK gene were sequenced and compared with those of nine Diospyros species from Thailand, four species from temperate regions, and one species of southern Africa, D. lycioides. Maximum parsimony, maximum likelihood, and neighbor joining analyses of the matK and ITS data sets revealed that D. kaki is closely related to two diploid species, D. oleifera and D. glandulosa. D. kaki, D. glandulosa, and D. oleifera were placed differently in the trees obtained from ITS and matK data sets, suggesting that hybridization and/or introgression may have occurred during the development of these species. D. kaki was not found to be closely related to D. ehretioides, a diploid species from Thailand. These results differed from a prior analysis of this genus performed with chloroplast DNA (cpDNA) restriction site mutations in 3.2- and 2.1-kb amplified sequences. The results supported Ng’s hypothesis that D. glandulosa and D. kaki may share a common ancestor. D. oleifera was also closely associated with D. kaki.

Quantitative real-time PCR to determine allele number for the astringency locus by analysis of a linked marker in Diospyros kaki Thunb.

Persimmon (Diospyros kaki Thunb.) is a polyploidy fruit tree species of economic importance to East Asia. Natural astringency loss is an important trait in persimmon breeding programs. Quantitative real-time PCR was used to determine the number of AST/ast alleles for fruit astringency in persimmon (D. kaki Thunb.). To this end, the cultivar Jiro was transformed with one or two copies of a gene encoding NADP-dependent sorbitol-6-phosphate dehydrogenase (S6PDH), which was used as a standard for measuring the allele number of a sequenced marker tightly linked to the recessive ast locus for nonastringency. Primers for markers linked to the AST or ast allele were then used to measure the AST to ast ratio directly in the progeny of a full-sib cross. From determination of the AST to ast ratio and the results of the S6PDH copy number, the number of AST and ast alleles at the AST/ast locus was estimated. This research supported the hypothesis that D. kaki is a hexaploid with six AST and/or ast alleles. In addition to the determination of the allelic status of the AST locus, the application of real-time PCR for confirmation of the ploidy level and allelic composition of target genes in autopolyploids or allopolyploids was demonstrated.

Diospyros species in Thailand: Their distribution, fruit morphology and uses

Diospyros species distributed widely in Thailand were classified into four ecotypes, according to their habitat; constantly humid area, alternately dry and wet area, mountainous cool area and all area. Some of them inhabit near dwelling areas or in the paddy field in the village. The young fruit is covered with dense pubescence in most species. The size, shape, and color of mature fruit greatly vary greatly with the species. In most species, the mature fruit has a soft pulp and hard skin. The fruit of six species has been used for dying. Four species produce edible fruits, with color and flavor favorable for breeding of edibleDiospyros species. The fruit of some species contains some chemicals useful as fish poisoning or of medicines, although the active components have not yet been identified. The edible fruit contained many tannin cells, but the fruit used as fish poisoning and medicines had only a few.

Phylogenetic relationships between the jackfruit, the breadfruit and nine other Artocarpus spp. from RFLP analysis of an amplified region of cpDNA

Abstract The phylogenetic relationships among eleven Artocarpus species, including two economically important species, the jackfruit (A. heterophyllus Lamk) and the breadfruit (A. altilis Fosberg), were estimated by comparing 30 restriction-site mutations in an amplified region of chloroplast DNA (cpDNA). Neighbor-joining and parsimony analyses were performed on the data to identify the relationships. The jackfruit and chempedak (A. integer Merr.) were monomorphic and therefore indistinguishable for all restriction sites. This confirmed the close relationship between these two species. The breadfruit and A. elasticus formed a monophyletic group with strong support from both neighbor-joining and parsimony analyses, indicating the possibility that the breadfruit was derived from A. elasticus or its close relatives. In general, our results were in agreement with the conventional classifications in Artocarpus species except for the position of A. chaplasha.

Phylogenetic relationships of the common durian (Durio zibethinus Murray) to other edible fruited Durio spp. by RFLP analysis of an amplified region of cpDNA

SummaryPhylogenetic relationships among seven species of the genus Durio, of which four produce edible fruits including the common durian (D. zibethinus), were investigated from RFLP analysis of PCR products from a variable region of cpDNA. The target region of cpDNA was reliably amplified from all Durio species tested, using total DNAs extracted by a modified CTAB method of Doyle and Doyle (1987) followed by an additional purification step. When restriction fragment polymorphisms of amplified products were examined with 19 restriction endonucleases (AseI, BamiiI, BfaI, DraI, EcoRI, EcoRV, HindIII, KpnI, MspI, RsaI, SeaI, ScrFI, SalI, SmaI, SspI, StyI, TaqI, XbaI, XhoI), RFLPs were observed with 14 endonucleases. However, since all Durio species tested had length mutation on this amplified region of cpDNA, the most parts of diversities from 14 endonucleases were caused by the length mutations among species. Considering length mutation among species, a total of seven site mutations were detected as well as...

Relationships among Asian persimmon cultivars, astringent and non-astringent types

A molecular marker analysis for Asian persimmon cultivar relationships and pollination status was conducted with 496 amplified fragment length polymorphism (AFLP) markers and 146 cultivars of Asian origin. Cultivars from China, Korea, and Japan were evaluated for marker composition and pollination status, which strongly influences fruit characteristics. Separation of Chinese, Korean, and Japanese cultivar groups and pollination type by neighbor-joining clustering, multidimensional scaling, and STRUCTURE was only weakly supported and not genetically significant. Significant differences for cultivar origin and pollination status were found for analysis of molecular variance (AMOVA), but most of the variation was among cultivars, not classification groups. All of the cultivar groups were genetically similar at the molecular level with most polymorphism due to individual cultivar differences.