We examined the origins of 120 cultivars of Primula sieboldii, a popular Japanese pot plant with a cultivation history of more than 300 years. In an assignment test based on the microsatellite allelic composition of representative wild populations of P. sieboldii from the Hokkaido to Kyushu regions of Japan, most cultivars showed the highest likelihood of derivation from wild populations in the Arakawa River floodplain. Chloroplast DNA haplotypes of cultivars also suggested that most cultivars have come from genets originating in wild populations from the same area, but, in addition, that several are descended from genets originating in other regions. The existence of three haplotypes that have not been found in current wild populations suggests that traditional cultivars may retain genetic diversity lost from wild populations.

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In the present study, we investigated salt tolerance heredity in wild soybean, Glycine soja Sieb & Zucc., and compared the salt tolerance quantitative trait locus (QTL) of G. soja with that of Glycine max (L.) Merr. An F₂ population (n = 225) derived from a cross between the salt sensitive soybean cultivar Jackson (PI548657) and a salt-tolerant wild soybean accession (JWS156-1) was used. Evaluation of salt tolerance in the seedling stage was carried out in hydroponic culture with half-strength Hoagland and Arnon nutrient solution containing 120 mM NaCl. Visual ratings of symptoms based on leaf scorching and chlorophyll content (SPAD value) were taken for each plant 20 days after salt treatment. Both traits showed continuous distribution; however, salt-tolerant plants (i.e. plants with a high salt tolerance rating (STR) and SPAD value) were predominant. QTL analysis revealed a major salt-tolerant QTL with a large dominant effect, which accounted for 68.7% of the total variance of the STR scale, on the soybean linkage group N. Our results indicated that the salt tolerance QTL confers a large dominant effect over salt sensitivity and that the salt tolerance QTL is conserved in both wild and cultivated soybeans.

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Soybean contains about 20% oil in seeds and it is therefore currently an important oil seed crop. Considering the fatty acid composition which constitutes the soybean lipid, the concentration of linolenic acid is less than 10%. On the other hand, wild soybean contains about twice the linolenic acid concentration and half as much lipid content as that of soybean. Based on these differences in the lipid content and linolenic acid concentration between soybean and wild soybean, a genetic study on the fatty acid concentration and lipid content using G. max × G. soja populations was carried out. These traits showed normal distribution and were highly heritable in F₂ and RIL populations; moreover; a negative correlation was shown between these traits. In addition, a QTL for the lipid content and linolenic acid concentration was detected in the same position near SSR marker Satt384 on LG E, suggesting that the factors controlling the lipid content might be partly shared by those of the linolenic acid concentration. Further elucidation of the regulatory aspects of these traits will provide information that could lead to the improvement of fatty acid composition and lipid content of soybean seeds.

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Heading date is the major factor in the regional and seasonal adaptation of rice cultivars. Although many genes controlling heading date have been identified using several mapping populations, it is not clear which previously identified genes contribute to the variation of heading date in particular regions. However, great effort is needed to identify quantitative trait loci (QTLs) among rice cultivars in rice breeding programs in a particular region because they are genetically closely related. In this study, we identified QTLs controlling heading date in 3 F₂ populations among rice cultivars in Hokkaido, the northernmost region of Japan. The segregations of heading date were continuous in all populations. For QTL analysis in populations with genetically close relationships, we used SSR markers located near the known QTLs for the heading date. Three QTLs for the heading date, qDTH3, qDTH-6-1, and qDTH6-2, were detected on chromosomes 3 and 6. The relationships between the three QTLs identified in this study and the known QTLs are discussed.

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Polyembryony, in which zygotic and apomictic embryos develop concurrently in a seed, is widespread in Citrus. To obtain further genomic information about the previously characterized map position of the polyembryony locus, the relationship among linkage maps from 3 different hybrid populations was determined using common markers flanking the polyembryony locus. By mapping the polyembryony locus with cleaved amplified polymorphic sequence (CAPS) markers in a F180 × ‘Harumi’ population, the polyembryony locus was detected in a high-density marker region co-segregated to marker Mf0086. By screening a bacterial artificial chromosome (BAC) library with marker Mf0086, two contigs reflecting the polyembryony and monoembryony haplotype were constructed. The single nucleotide polymorphism (SNP) markers detected on these contigs were mapped on the nearest position to the polyembryony locus in linkage group 1 of ‘Miyagawa wase’ and ‘Harumi’. The highly conserved marker lineage in the flanking regions of the polyembryony locus in these polyembryonic cultivars of different parentage suggested that the genomic region of the polyembryony locus might have a common structure in a wide range of Citrus cultivars.

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The five floral characters, i.e., number of pollen grains per flower, pollen grain diameter, anther length, number of ovules per flower and pollen-ovule ratio (P/O), were studied on 119 strains of 53 species in Brassica and allied genera with respect to the breeding system. There were large variations in all five characters among species, especially the number of pollen grains, number of ovules per flower and P/Os showed larger variations. The values range widely from 23–24 × 10⁴ of Eruca spp. to 0.3 × 10⁴ of Diplotaxis viminea and from 19800 of Hutera rupestris to 100 of D. viminea in the number of pollen grains and P/Os, respectively. The P/O was significantly correlated to the energy cost per flower. Both indices were closely related with the breeding system of species. The lowest P/Os and the smallest energy costs were found in the obligate autogamous species, while the xenogamous species showed higher and larger, but more fluctuating P/Os and energy costs. In the facultative autogamous amphidiploid species in Brassica crops, both P/Os and energy costs per flower were similar to those of xenogamous species; however, P/Os were lower than their xenogamous parental species. The relationships of P/Os with natural selection are also discussed.

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We performed genetic analysis of lutein content using three progeny populations from crosses between soybean variety and wild soybean strains with high lutein content. A few F₂ seeds derived from a soybean line, Toiku241 × a wild accession, B09092 showed almost equal lutein content to that of the wild soybean parent, B09092. The high values of the broad-sense heritability estimated in F₂ seed generations and the highly positive correlation between the two generations of RILs from a soybean line, TK780 × a wild accession, B01167, indicated that lutein content is a heritable trait. There was no significant correlation between lutein content and seed weight in F₃ seeds from cv. Toyomusume × a wild accession, GD50344. Flowering time was positively correlated with lutein content in the three populations. We identified xanthophylls, such as neoxanthin, violaxanthin and antheraxanthin, in addition to the major lutein in wild soybean strains. Xanthophyll content in progeny populations from interspecific crosses showed highly positive correlations with lutein content, suggesting that the high lutein trait of the wild soybean might be implicated in the biosynthesis and/or accumulation of xanthophylls during seed filling.

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The genetic diversity and relationships among 127 Japanese apricot (Prunus mume Siebold et Zucc.) germplasms, including 56 fruiting and 55 flower-ornamental cultivars derived from Japan, 8 germplasms from China, 7 germplasms from Taiwan and 1 germplasm from Thailand were assessed by SSR markers. Thirty-nine out of 58 SSR markers developed from peach and apricot could produce one or two amplified fragments in Japanese apricot, suggesting transferability across species. Fourteen SSR markers showing clear amplification and high polymorphisms were chosen for further analysis. A total of 155 putative alleles were observed in Japanese apricot for 14 SSR loci with an average value of 11.1. The values of observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 0.29 to 0.88 (mean value of 0.61) and 0.32 to 0.92 (mean value of 0.68), respectively. A phenogram for 127 Japanese apricot and 3 apricot germplasms showed 3 major clusters, 1) Bungo group of Japanese apricot and apricot, 2) germplasms from Taiwan and Thailand, 3) fruiting and flower-ornamental germplasms derived from Japan and China. In the present study, definite genetic differences were not found between fruiting and flower-ornamental groups, which supported the hypothesis that fruiting cultivars have been selected from flower-ornamentals.

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Nangouhi, a vegetatively propagated cultivar of hinoki cypress (Chamaecyparis obtusa), includes several vegetatively propagated clones with commercial uses. The genetic diversity, relationships, and origin of Nangouhi were evaluated using ten highly polymorphic microsatellite markers and compared with those of natural hinoki populations. In terms of their genetics, Nangouhi clones appeared to be more closely related to each other than to natural populations. Parentage analysis indicated that clone N14, which is commonly found in the grounds of old shrines and temples, is a parent of 11 of the other clones, of which N6 and N13 had genotypes identical to N14 at eight and seven loci, respectively. These clones could have been produced by crossing N14 and genetically related individuals. Assignment tests were used to determine the genetic origin of Nangouhi clones using 25 natural hinoki populations as a reference. The possible sources of most of the clones were the Hikosan population in Kyushu and the Besshiyama population in Shikoku; however, several clones could not be assigned to any natural population. Crosses between Nangouhi and genetically unrelated plus tree clones and recurrent selection from the possible source populations are recommended for future breeding of Nangouhi.

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To establish a marker-assisted selection system for the eating quality of cooked rice, we performed quantitative trait locus (QTL) analysis using 188 recombinant inbred lines (RILs) derived from crosses of two japonica cultivars, ‘Sakihikari’ and ‘Nipponbare’. The former has excellent eating quality with strong stickiness whereas the latter is less sticky. We evaluated the stickiness of cooked rice using a sensory test, as well as amylose content (AC), amylographic characteristics (AM), and days-to-heading of RILs, which affect stickiness, in 2005, 2006 and 2007, and used them for QTL analysis. Six QTLs for stickiness were identified on chromosomes 1, 3 (two QTLs), 6, 7 and 8. Of these, qST3-1 on the short arm of chromosome 3 was detected throughout the three-year experiments but the others were detected in one year only. We also mapped two QTLs for AC, 19 QTLs for AM, and three QTLs for days-to-heading. Stickiness of RILs was significantly correlated with AM, and several QTLs for AM were detected in the same QTL regions for stickiness. These results thus suggested that AM was important for the stickiness of RILs. The obtained QTL information is useful to identify DNA markers tightly linked to genes controlling eating quality.

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To reveal the genetic regions controlling eating quality of japonica rice and to establish a system for marker-assisted selection (MAS), we conducted a QTL analysis for eating quality of Koshihikari, a leading cultivar in Japan. We used a recombinant inbred population consisting of 92 lines derived from a cross between two closely related japonica cultivars, Moritawase (low eating quality) and Koshihikari. We evaluated overall eating quality (OE), glossiness (GL), taste (TA), stickiness (ST), and hardness (HD) of the lines over 3 years by sensory tests. QTL analysis revealed 43 QTLs on 16 regions across all chromosomes except chromosome 5. QTLs on chromosomes 1, 3, 6, 7, and 10 were detected in multiple years. The Koshihikari alleles at 37 QTLs increased the eating quality. Further QTL analysis revealed 8 QTLs for textural characteristics of cooked rice and 3 for the amino acid ratio of polished rice. Those on chromosomes 1, 3, 6, and 7 were located near the QTLs for eating quality.

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To identify the chromosomal regions controlling the eating quality of Koshihikari rice, we performed a quantitative trait locus (QTL) analysis using two backcross inbred lines (BILs): N-BILs (79 lines derived from a cross of Nipponbare/Koshihikari//Nipponbare) and K-BILs (89 lines derived from a cross of Nipponbare/Koshihikari//Koshihikari). We evaluated several components of the eating quality of cooked rice, namely glossiness, taste, stickiness, hardness, and overall evaluation, based on sensory tests by a trained panel, and amylose and protein contents. Ten QTLs for these components were detected in N-BILs (two regions of chromosome [chr.] 3 and one of chr. 11), and six in K-BILs (chr. 3 and chr. 6). Each QTL explained 11.6% to 32.0% of the total phenotypic variance. QTLs at the distal end of the short arm of chr. 3 were commonly identified in both BILs. The Koshihikari alleles at these QTLs increased eating quality. The genetic effect of the Koshihikari alleles was confirmed by analysis of a chromosome segment substitution line containing a Koshihikari segment of the short arm of chr. 3 in the Nipponbare background.

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Elevating the oleic acid content of soybean (Glycine max (L.) Merr.) is a major focus of breeding programs. Previously, we created two high-oleic-acid soybean mutants, M23 and KK21, by X-irradiation. We expected them to have modifications in genes encoding microsomal omega-6 fatty acid desaturase. The objectives of this study were to evaluate which members of the GmFAD2 gene family contribute to oleic acid production during seed maturation, to characterize the mutant genes, and to establish molecular markers for breeding of high-oleic-acid soybeans. Three GmFAD2 genes were expressed in developing seeds; the gene products of GmFAD2-1a and GmFAD2-1b were more active than that of GmFAD2-2a during seed development. We identified different nucleotide modifications in GmFAD2-1a in M23 and KK21. Using nuclease-cleaved DNA fragment-length polymorphisms, we developed a novel molecular marker to distinguish between KK21 mutant and wild-type alleles. This information could be useful for improving soybean oil quality by using the mutant genes from M23 or KK21, and for screening novel high-oleic-acid soybean mutants.

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To improve the efficiency of breeding cucumber in China, we previously mapped QTL for most fruit- and flower-related traits of this species. Here, we mapped QTLs for six plant architecture traits including lateral branch number (LBN), lateral branch total length (LBTL), main-stem length (MSL), internode length (INL), main-stem diameter (MSD), and petiole length (PL) were detected in greenhouse environments. In total, 14 QTLs were identified for the six traits (LBN, 3; LBTL, 2; MSL, 3; INL, 2; MSD, 2; and PL, 2) with additive heritability of individual QTL ranging from 1.6% to 29.5%. Five QTLs for four traits (LBN, LBTL, MSL, and INL) were observed to have significant (P ≤ 0.05) QTL × environment interaction effects. The broad-sense heritability for the six traits ranged from 8.5% to 47.0%. The QTL information presented in this research, together with the data in our previous study on the fruit- and flower-related traits, will facilitate the breeding of elite cucumber cultivars by marker-assisted selection in China.

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To establish a routine procedure for SNP marker development, the previously reported T_m-shift SNP genotyping procedure was validated and extensively improved. The effect of introducing mismatched nucleotides into allele-specific primers, using alternative fluorescent dyes, and varying the DNA polymerase species on SNP discrimination was examined at more than 100 known SNP loci in a solanaceous crop, eggplant. As a result, it has been shown that a success rate over 80% can be achieved with T_m-shift SNP genotyping using directional trials with automatically designed primer sets and a routine protocol for the reaction condition tests.

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The sweet potato, Ipomoea batatas (L.) Lam., is the third most important root crop in the world after the potato and cassava. In particular, the sweet potato is not only an important crop in tropical, subtropical and temperate regions, but also an efficient biomass-producing plant for starch. The sweet potato is widely recognised as being prone to infection by sweet potato feathery mottle virus (SPFMV). Generally, SPFMV is transmitted by aphids (Myzus persicae), and the infected tuberous roots are used for vegetative propagation. However, neither the transmission of SPFMV using the aphid transmission test nor the aphid transmit theory itself has been established for sweet potato. The present study establishes a testing method for the aphid transmission of SPFMV and evaluates viral resistance in transgenic sweet potatoes. As a result of some examinations, we establish a testing method for resistance to SPFMV by aphid transmission in sweet potato. Furthermore, we evaluated the resistance to SPFMV in transgenic sweet potato using the improved aphid transmission method, and determined higher levels of resistance to SPFMVs in transgenic sweet potatoes. These results suggest that transgenic sweet potatoes show resistance to SPFMVs in the field.

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Genomic DNA sequences homologous to the nucleotide binding site (NBS)-leucine-rich repeat (LRR) genes were mapped for Italian ryegrass (Lolium multiflorum Lam.) by using previously published disease resistance gene analogs (RGAs). The RGAs were cloned by means of a nested polymerase chain reaction (PCR) approach with degenerate primers designed from conserved regions of the NBS domain of plant disease resistance genes (R-genes), and primer pairs for specific sequence-tagged sites (STS) were subsequently designed for efficient generation of the RGA fragments. To map the RGA clones on the Italian ryegrass genetic map, an F₁ mapping family was used for the detection of restriction-site polymorphisms of the RGA fragments. Out of 50 RGA fragments, 11 detected genetic polymorphism in the F₁ family. Polymorphic marker loci data were used for linkage analysis with JoinMap version 3.0. The linkage analysis revealed that 10 of the 11 RGAs were mapped in seven linkage groups constructed with amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and expressed sequence tag (EST)-derived cleaved amplified polymorphic sequence (CAPS) markers. This information will be useful for the development of new genetic markers linked to genes associated with disease resistance.

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Cucumber (Cucumis sativus L.) is an important vegetable crop grown worldwide, but the number of available and mapped simple-sequence repeat (SSR) markers is insufficient for construction of an SSR-based genetic linkage map. To improve this situation, we developed SSR markers from SSR-enriched genomic libraries for C. sativus. We sequenced 2304 clones, and obtained 101 primer pairs which showed clear amplification and polymorphism among genotypes in either C. sativus or Cucumis melo (melon). In C. sativus, all were amplified and 91 were polymorphic among the three genotypes that we analyzed. In C. melo, 41 were polymorphic among the three genotypes that we analyzed, but 32 were not amplified. In addition to the SSRs developed in this study, we used SSRs and sequence-characterized amplified regions (SCARs) reported previously in cucumber and melon to construct the first SSR-based linkage map of cucumber. The map now comprises 120 SSRs and 6 SCARs. It contains 22 markers from previous cucumber maps and 8 linkage groups, and spans a distance of 625.7 cM. The present map is the most comprehensive one in terms of the number of SSR markers and will therefore be highly useful in future cucumber genetic studies.

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