Saponins are a diverse group of secondary metabolites widely distributed in plants. Some saponins in soybean seeds have medicinal properties, but the terminal acetylated sugar at the C-22 position of group A saponins in seed hypocotyls causes a bitter and astringent taste. We used cultivated and wild soybean accessions classified into four different group A saponin phenotypes, including non-acetylated A0-αg and deacetyl-Af, as parents to obtain four F₂ populations and a population of recombinant inbred lines to test their genetic relationship. The gene controlling the phenotype of the group A saponins in each line was mapped near the simple sequence repeat marker Satt336 on soybean chromosome 7 (linkage group M). An allelism test of the A0-αg and deacetyl-Af variants revealed no segregation of Aa and Ab phenotypes in the progeny, although the genes controlling the two phenotypes have been assigned to two different loci, Sg-1 and Sg-2. These results suggest that the four group A saponin phenotypes are controlled by multiple alleles at the single locus Sg-1.

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Gentians (Gentiana triflora, G. scabra) are one of the most important ornamental plants, however, repellent odor emitted from their flowers makes them undesirable in indoor floral utilization. It is necessary to understand the component of their flower scent for breeding of new cultivars without repellent odor. Floral scent compounds of gentians were analyzed by the method of Head Space-Solid Phase Micro Extraction with GC-MS (HS-SPME/GC-MS). The level of scent emission from gentian flowers increased with the age of the flower and reached a maximum at three days after anthesis and decreased thereafter. Their flowers emitted volatiles throughout the day, and the amounts were higher at night than during the day. A total of 98 compounds were detected in 13 genotypes examined, and quantitative and qualitative variations were found. Of these compounds, several kinds of lilac aldehydes (terpenoids) were only detected in G. scabra. The results of principal component analysis showed that cultivars/lines classified in the same species were grouped with each other. Of the 13 genotypes, Ashiro-no-Natsu emitted the most abundant volatiles and has strong unpleasant odor. 2-Methylbutanoic acid is considered to be one of the major constituents responsible for the unpleasant odor of gentians.

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The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is a serious insect pest of cultivated rice (Oryza sativa L.) in temperate East Asia. Six GRH-resistance genes (Grh1, Grh2, Grh3, Grh4, Grh5, and Grh6) and one quantitative trait locus (QTL; qGRH4) have been identified. We selected near-isogenic lines (NILs) carrying Grh1, Grh2, Grh4, Grh5, Grh6, and qGRH4 with the japonica genetic background (Taichung 65 cultivar) by means of marker-assisted selection using new simple sequence repeat markers flanking the GRH-resistance genes and QTL. We also developed three pyramided lines (PYLs; Grh2/Grh6-PYL, Grh4/Grh6-PYL, and Grh5/qGRH4-PYL) using each NIL that carried a GRH-resistance gene or QTL. The NILs, PYLs, and donor parents were evaluated by using an antibiosis test. The resistance of Grh1-NIL and Grh5-NIL did not differ significantly from those of the donor parents, whereas the resistances of Grh2-NIL and Grh6-NIL were significantly lower than those of the donor parents. Grh4-NIL and qGRH4-NIL were highly susceptible. The resistance levels of the pyramided lines for Grh2 and Grh6, Grh4 and Grh6, and Grh5 and qGRH4 demonstrated a gene pyramiding effect that significantly increased their resistance. The developed NILs and PYLs should be useful genetic resources for rice improvement and deployment of the resistance genes.

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There are two types of seed coat cracking that are controlled genetically in soybean: Type I with irregular cracks and Type II with net-like cracks. This study was conducted to determine the genetic basis of Type II cracking using DNA markers. A F₂ population and F₃ lines derived from a cross between Uzuramame with black seed coats having net-like cracking, and a Clark mutant line with black seed coats were used in this study. Degree of cracking in each seed was scored by cracking index (no cracking, 0 to severe cracking, 4) and was averaged per plant (average cracking index, ACI). One morphological and 189 SSR markers were analyzed and assigned to 31 linkage groups spanning 2463 cM. Two QTLs for ACI (ncr1 and ncr2) were identified in molecular linkage group C1 with a distance of about 62 cM. The ncr1 and ncr2 had LOD scores of 5.90 and 8.61, accounting for 16.0 and 32.4% of phenotypic variation, respectively. The alleles from Uzuramame at the QTLs conferred increased ACI. The effects of QTLs identified in the F₂ population were confirmed in the F₃ lines. No epistatic interaction was observed between the QTLs.

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Diversity among Iranian melon landraces of Groups Flexuosus and Dudaim was studied by analyzing morphological and physiological traits and by random amplified polymorphic DNA (RAPD). Thirty-one morphological and physiological traits showed significant variation among accessions. Some Flexuosus accessions had typical morphological characters of elongated fruit shape, light skin color, ribs on fruit skin and non-sweet flesh. Characters distinct from in typical accessions, such as short fruits, dark green skin color, five carpels, sweet flesh, were especially in ribless accessions. Cluster analysis of morphological and physiological characters divided Iranian melon into seven groups. Dudaim (cluster VII) was clearly separated from Flexuosus, in which typical (cluster I) accessions and atypical accessions (clusters III-VI) were grouped separately. The diversity index shown by RAPD was 0.201 in 25 Flexuosus accessions and was rich in genetic diversity. Cluster analysis using RAPD divided Flexuosus accessions into eight subclusters, and clarified genetic similarity between Iranian melon accessions and reference accessions of large-seed type (Groups Inodorus and Cantalupensis). These results may suggest that large-seed Flexuosus, Inodorus and Cantalupensis are not differentiated genetically, probably due to spontaneous inter-group hybridization.

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The free amino acid (FAA) concentration of rice is becoming an increasingly important grain quality factor because of its apparent influence on the organoleptic acceptability of cooked rice. To determine the variability of this character among rice cultivars the FAA profiles of 49 cultivars were determined using Pico-Tag method. Among these 13 cultivars were selected to determine variation in FAA accumulation pattern after 24-hour germination treatment. The results show significant variation in the concentrations of total as well as individual FAAs among cultivars. There were also significant differences between indica- and japonica-type cultivars in the concentrations of some FAAs. The ratio of the total concentration of aspartate-derived to glutamate-derived FAAs (A/G ratio) evaluated for the japonica group (0.68) was significantly lower than that for the indica group (1.07). This suggests that typically, japonica-type rice grains tend to accumulate more Glu-derived than Asp-derived FAAs. Other results show a decline in the A/G ratios of both groups in response to germination treatment, with the indica group exhibiting a more rapid response. These results appear to suggest key differences in the FAA accumulation patterns of japonica- and indica-type rice grains especially with respect to the contents of aspartate-derived and glutamate-derived amino acids.

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Controlling the grain number in rice panicles is essential for increasing the yield potential. Because this trait depends on some complicated panicle branching structures, we prepared a newly developed software, PASTAR (PAnicle STructure Analyzer for Rice) and PASTA Viewer, to automatically extract values of the length and number of various branches and grain number from scanned photographic images of panicles. Furthermore, PASTA Viewer could draw panicle branching patterns based on actually measured values. Using this image analyzing method, we analyzed some extra numerous grain rice cultivars and performed quantitative trait locus (QTL) analysis for 18 panicle traits in the F₂ segregated population derived from a cross between a japonica rice cultivar, Koshihikari, and an extra numerous grain cultivar, NP-6, classified as a “New Plant Type”. The results revealed that QTLs enhanced by NP-6 alleles for some panicle traits were concentrated on a few regions of chromosomes 1, 6 and 8, although some single QTLs were also detected in various chromosomal regions. This suggests that the NP-6 panicle and extra numerous grain traits are predominantly controlled by a few gene loci acting pleiotropically, along with some partially effective panicle structure genes.

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Traits that contribute to fruit texture are important targets for genetic improvement in cucumber, and the knowledge of the combining abilities of parental genotypes is crucial to conducting systematic breeding of new F₁ hybrid cultivars that possess a desired fruit texture. We estimated the general combining ability (GCA) and specific combining ability (SCA) of fruit texture traits related to fruit firmness and crispness. We produced a diallel set of 28 F₁ hybrids by crossing eight cucumber genotypes in a half-diallel mating design. We obtained quantitative scores of fruit texture by means of mechanical measurement and analyzed them by Griffing’s combining ability analysis to estimate the GCA and SCA effects of the parental genotypes. The GCA effect was of more significance than the SCA effect in determining hybrid performance. Estimates of the GCA effects were highly significant for most parental genotypes and were highly correlated with actual performance of parental genotypes. Because of this close correlation between GCA effect and actual fruit texture traits exhibited by the parents, we demonstrated that all traits could be effectively pre-selected at the level of parental genotype.

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The brown planthopper (BPH) resistance gene bph4 has previously been assigned on the short arm of rice chromosome 6. However, the map position of the gene could not be determined. To detect the bph4 locus, 15 polymorphic simple sequence repeat (SSR) markers covering genetic distance of 0.0–63.4 cM on chromosome 6 were used to survey 15 BPH resistant (R) and susceptible (S) individuals from each of the 95 and 78 F₂ populations derived from crosses of TN1/Babawee and Babawee/KDML105, respectively. One SSR marker, RM586, was associated with the R and S from the F₂ populations. Additional markers surrounding the RM586 locus were examined to define the location of bph4. From the genetic linkage map and QTL analysis of 95 and 78 F₂ individuals, the bph4 locus was mapped at the same chromosomal region of Bph3 between two flanking markers RM589 and RM586. Markers linked to the resistance gene explained 58.8–70.1% of the phenotypic variations and can be used for marker-assisted selection in BPH-resistant breeding programs. In addition, our experiment provides evidence that a recessive gene could behave as a dominant gene under different genetic backgrounds.

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We crossed a doubled haploid line of the turnip Brassica rapa cv. ‘Iyo-hikabu’, which is pigmented with anthocyanin, with a Chinese cabbage inbred line, ‘Y54’, which lacks anthocyanin pigmentation. The presence and absence of anthocyanin pigmentation was segregated 79: 27 in the F₂ population, suggesting monogenic control. A bulked segregant analysis was conducted with random amplified polymorphic DNA (RAPD) markers. A total of 480 primers were used to screen a pair of bulked DNA samples of the F₂ plants. We found five RAPD markers closely linked to the pigmentation locus. A partial linkage map around the pigmentation locus was constructed with four RAPD markers, two simple sequence repeat (SSR) markers, and one cleaved amplified polymorphic sequence (CAPS) marker. A 0.84-kb fragment amplified by a random primer, OPU10, was cloned, sequenced, and then converted into a CAPS marker (OPU10C). This CAPS marker was mapped at a distance of 4 cM from the pigmentation locus in the partial linkage map and was also mapped in linkage group R07 of the previously reported reference map of B. rapa. This locus is independent of the previously reported anthocyanin-regulating anl locus mapped in R09. We named the locus Anp. The locus will be useful in plant breeding and genome characterization in B. rapa.

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For molecular breeding of mushrooms, understanding the mechanism of fruiting body formation by gene expression level is one of vital approaches. To identify the genes controlling traits of fruiting body and determine functions of their genes, the position of candidate genes should be combined with QTL analyses data. As primarily step to analyze the mechanism of fruiting body formation of Lentinula edodes, we located 12 loci containing specifically or abundantly expressed genes during fruiting body formation stage onto a linkage map of L. edodes. Two mapped genes were completely cosegregated from the mfbC gene, and an expressed sequence tag (EST) marker, LEEST359, respectively. In addition, other 2 genes were suggested to be closely located on the genome of L. edodes, because the 2 genes completely cosegregated each other. As a whole, 12 genes isolated from primordia and specifically or abundantly expressed during fruiting body formation were studded all over the genome of L. edodes, and mapped to 8 linkage groups.

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Recent advances in DNA marker technologies have increased the use of single nucleotide polymorphism (SNP) as a genetic marker. We developed SNPs in Paraserianthes falcataria and arranged them for multiplexed DNA typing using single nucleotide primer extension (SNuPE). Seventeen sequence characterized amplified regions (SCARs) were developed from random amplified polymorphic DNA (RAPD). In 12 SCARs of them, a SNP which possessed high heterozygosity was selected, and three sets of multiplexed SNuPE analysis system with 4 SNPs were constructed. Estimating the discrimination power (DP) revealed that set A had the highest DP (0.968), followed by set B and set C. The ability to discriminate could be almost 100% (1.000 of DP) when all sets were used. This SNuPE system provides a practicable method for individual identification of this forest tree species.

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Genic male sterility (GMS) has been widely used as a tool for hybrid seed production in chili pepper (Capsicum annuum L.). Little work has been done on the development of molecular markers linked to pepper GMS genes, which are generally controlled by a recessive nuclear gene. In this study, we developed a DNA marker linked to paprika GMS using bulked segregant analysis (BSA) and an amplified fragment length polymorphism (AFLP) technique. Two F₂ populations were made by selfing commercial F₁ varieties of ‘Mirage’ and ‘Fiesta’ and subjected to BSA-AFLP using 256 primer combinations. Among five reproducible polymorphic primer combinations, an AFLP marker Egat/Mcgg was converted to a codominant cleavage amplified polymorphic sequence (CAPS) marker. This marker, named PmsM1-CAPS, is located about 2 to 3 cM from the ms locus. Although PmsM1-CAPS was not correlated with GMS in ‘MiniBell’ because it was a different GMS gene, the marker was found to be useful in screening for male sterility, as tested in F₂ progenies from ‘Helsinki’ and F₃ families derived from the F₁ varieties used in this study.

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