Hiroyuki Iketani

Simple Sequence Repeat-Based Comparative Genomics Between Brassica rapa and Arabidopsis thaliana: The Genetic Origin of Clubroot Resistance

An SSR-based linkage map was constructed in Brassica rapa. It includes 113 SSR, 87 RFLP, and 62 RAPD markers. It consists of 10 linkage groups with a total distance of 1005.5 cM and an average distance of 3.7 cM. SSRs are distributed throughout the linkage groups at an average of 8.7 cM. Synteny between B. rapa and a model plant, Arabidopsis thaliana, was analyzed. A number of small genomic segments of A. thaliana were scattered throughout an entire B. rapa linkage map. This points out the complex genomic rearrangements during the course of evolution in Cruciferae. A 282.5-cM region in the B. rapa map was in synteny with A. thaliana. Of the three QTL (Crr1, Crr2, and Crr4) for clubroot resistance identified, synteny analysis revealed that two major QTL regions, Crr1 and Crr2, overlapped in a small region of Arabidopsis chromosome 4. This region belongs to one of the disease-resistance gene clusters (MRCs) in the A. thaliana genome. These results suggest that the resistance genes for clubroot originated from a member of the MRCs in a common ancestral genome and subsequently were distributed to the different regions they now inhabit in the process of evolution.

Isolation and characterization of microsatellites in Brassica rapa L.

Abstract.We report here the isolation and characterization of microsatellites, or simple sequence repeats (SSRs), in Brassica rapa. The size-fractionated genomic library was screened with (GA)15 and (GT)15 oligonucleotide probes. A total of 58 clones were identified as having the microsatellite repeats, and specific primer pairs were designed for 38 microsatellite loci. All primer pairs, except two, amplified fragments having the sizes expected from the sequences. Of the 36 primer pairs, 35 amplified polymorphic loci in 19 cultivars of B. rapa, while monomorphism was observed in only one primer pair. A total of 232 alleles was identified by the 36 primer pairs in 19 cultivars of B. rapa, and these primer pairs were examined also in nine Brassicaceae species. Most of the 36 primer pairs amplified the loci in the Brassicaceae species. Segregation of the microsatellites was studied in an F2 population from a cross of doubled-haploid lines DH27 × G309. The microsatellites segregated in a co-dominant manner. These results indicate that the microsatellites isolated in this study were highly informative and could be useful tools for genetic analysis in B. rapa and other related species.

Phylogenetic relationships among Japanese flowering cherries (Prunus subgenus Cerasus) based on nucleotide sequences of chloroplast DNA

Flowering cherries are classified into Prunus subgenus Cerasus (family Rosaceae). Nine species and some varieties originated in Japan were used in this study. Phylogenetic relationships among Japanese taxa were analyzed by four chloroplast regions using 46 individuals from 16 taxa. Eighteen haplotypes were distinguished. P.pendula f. ascendens and P. cerasoides formed a clade which is distantly related to other Japanese taxa. These two species were morphologically different from other taxa. All Japanese taxa except for P. pendula f. ascendens formed another clade. All taxa in this clade except for P. maximowiczii showed very similar sequences. However, these taxa could be identified by many morphological characters. Even now, based on previous work, it is thought that interspecific hybridization frequently occurs in flowering cherries. We conclude from the current study, Japanese flowering cherries have experienced complicated speciation arising from hybridization.

Genetic structure of East Asian cultivated pears (Pyrus spp.) and their reclassification in accordance with the nomenclature of cultivated plants

By use of Bayesian statistical inference and allelic data for 18 microsatellite loci, we analyzed the genetic structure of Chinese, Korean, and Japanese pear cultivars and of native populations of Pyrus ussuriensis. Although Japanese pear cultivars had a simple genetic structure, Chinese and Korean pear cultivars were admixures of Japanese pear and native P. ussuriensis from the Asian continent. Genetic differentiation between groups of native populations and those of cultivars was high, but cultivars were not well differentiated from each other. Chinese and Korean cultivars, which have traditionally been classified as either P. ussuriensis, P. bretschneideri, or P. pyrifolia, were much closer to Japanese cultivars, which have traditionally been classified as P. pyrifolia, than to native P. ussuriensis. We propose a new classification of cultivars by using the Group concept in accordance with the International Nomenclature for Cultivated Plants, namely, the Pyrus Ussurian pear group, the Pyrus Chinese white pear group, the Pyrus Chinese sand pear group, and the Pyrus Japanese pear group.

MINIMAL MARKER: AN ALGORITHM AND COMPUTER PROGRAM FOR THE IDENTIFICATION OF MINIMAL SETS OF DISCRIMINATING DNA MARKERS FOR EFFICIENT VARIETY IDENTIFICATION

DNA markers are frequently used to analyze crop varieties, with the coded marker data summarized in a computer-generated table. Such summary tables often provide extraneous data about individual crop genotypes, needlessly complicating and prolonging DNA-based differentiation between crop varieties. At present, it is difficult to identify minimal marker sets--the smallest sets that can distinguish between all crop varieties listed in a marker-summary table--due to the absence of algorithms capable of such characterization. Here, we describe the development of just such an algorithm and MinimalMarker, its accompanying Perl-based computer program. MinimalMarker has been validated in variety identification of fruit trees using published datasets and is available for use with both dominant and co-dominant markers, regardless of the number of alleles, including SSR markers with numeric notation. We expect that this program will prove useful not only to genomics researchers but also to government agencies that use DNA markers to support a variety of food-inspection and -labeling regulations.

Introgression and Long-Term Naturalization of Archaeophytes into Native Plants - Underestimated Risk of Hybrids

Alien plants pose problems in the conservation of biodiversity, especially by invasion and successive mal-effects on local ecosystem and biodiversity (Pysek et al., 1995; Ellstrand, 2003; Nentwig, 2007). Even if they are only in cultivation, they could affect by hybridization, vector of diseases and pests and other factors. Since an alien plant is defined as one whose distribution has expanded out of its native range under human influence, the history of alien plants begins with human migration, especially in association with agriculture. As most have spread with active migration since the Age of Discovery, alien plants can be delineated into archaeophytes (introduced before the Age of Discovery) and neophytes (introduced since) (Pysek et al., 2002; Preston et al., 2004).

Genetic structure and diversity of the wild Ussurian pear in East Asia.

The Ussurian pear is the most important cultivated pear in the northern part of China. Cultivated Ussurian pears are considered to have derived from Pyrus ussuriensis Maxim. which is native to the northeast of China. In Japan, two varieties of P. ussuriensis, P. ussuriensis var. aromatica and var. hondoensis are native to the northern area and the central area of the main island respectively. In order to reveal the origin of Pyrus ussuriensis var. aromatica distributed in the northern area of main island of Japan, more than 40 explorations have been performed in Japan and in China, and more than 30 natural habitats were recognized. These natural habitats are at risk of extinction because of human development and forest degradation caused by climate change. Population structure and genetic diversity of P. ussuriensis in China and P. ussuriensis var. aromatica in Japan have been investigated using both morphological and molecular markers in order to define appropriate conservation units, and to provide a good focus for conservation management. Distant evolutionary relationships between P. ussuriensis Maxim. in China and P. ussuriensis var. aromatica in Japan inferred from population genetic structure and phylogenetic analysis are also discussed.

Native fruit tree genetic resources in Japan

The diversity of climate, from subarctic to subtropical, and the complex geological history of Japan have produced a rich biodiversity. The flora includes several hundred species of native woody plants with edible fleshy fruits or nuts. People have eaten them from prehistoric times until about a half century ago. In Hokkaidō and the Ryūkyū Islands nut species had an important role in the diet, but fleshy fruits were also eaten until recently. Only Castanea crenata and a few minor species became domesticated as edible fruit trees in pre-modern times. Recently, Vitis coignetiae, Lonicera caerulea, Akebia quinata, Akebia trifoliata, Stauntonia hexaphylla, and Actinidia arguta have entered small-scale cultivation. The conservation of the germplasm of many of these native species, both in situ and ex situ, is precarious.