We examined the role of the hull, seed coat and embryo in the effect of qLG-9, as a first step to elucidate the mechanism(s) responsible for seed longevity in rice. The effects of the other proposed QTLs for seed longevity, qLG-2 and qLG-4, were also investigated. We used chromosome segment substitution lines (CSSLs) derived from a cross between a japonica variety (Koshihikari) and an indica variety (Kasalath) to isolate each QTL. To examine the seed longevity, a germination test was performed after an aging treatment. Both in unhulled and hulled seeds, qLG-9 (located on chromosome 9) increased the seed longevity, unlike qLG-2 and qLG-4 (located on chromosomes 2 and 4, respectively). A germination test using unhulled seeds of the reciprocal crosses between Koshihikari and SL226, the CSSL harboring qLG-9, failed to reveal a maternal effect from the hull or seed coat on the longevity. Thus, it was assumed that the increased seed longevity conferred by qLG-9 was associated primarily with embryonic and/or endospermic factors.
Rice cultivars show a wide range of variation in stele and xylem structures of the root as well as in root thickness (RTH). We identified quantitative trait loci (QTLs) for stele and xylem structures of the root by using 117 F3 lines from a cross between the lowland rice cultivar IR64 (thin roots) and the upland rice cultivar Kinandang Patong (thick roots). QTL analysis was performed using genotype data consisting of 197 DNA markers in F2 plants and phenotype data of the F3 plants. Stele transversal area (STA), total area and number of late metaxylem vessels (MXA and MXN) and RTH were measured in basal cross sections of nodal roots. A total of 10 QTLs, 2 for STA, 4 for MXA, 2 for MXN and 2 for RTH, were detected on chromosomes 1, 2, 3, 9 and 10. The Kinandang Patong allele at all QTLs showed a positive additive effect on each trait, except for one QTL for MXA on chromosome 10. The phenotypic variance explained by each QTL ranged from 8.7% to 23.9%. A QTL for MXA on chromosome 9 showed the largest effect (23.9%) on total phenotypic variance. Although one QTL for STA, detected on chromosome 2, was mapped near a QTL for RTH, the other QTLs for stele and xylem structures did not map to the same chromosomal regions as the QTLs for RTH. We conclude that stele and xylem structures might be controlled by several genetic factors different from the QTLs for RTH.
Nucleotide sequence variations of the trnK/matK region were investigated in cultivated and wild radish species and related Brassica species. Two insertions/deletions and 9 substitutions were detected among the Raphanus accessions. The value of the nucleotide diversity (π) was found to be higher in cultivated radish (0.00184) than in the wild species (0.00134). Based on the nucleotide diversity, the phylogenetic relationships of Raphanus and its related species were inferred by constructing a Neighbor-Joining tree. Raphanus species and Brassica barrelieri formed a sister clade located between the Rapa/Oleracea group and the Nigra group of Brassica. These results were in complete agreement with those obtained by Warwick and Black. The placement of Raphanus species at this position showed the existence of a paraphyletic relationship among the Brassica species. Each of the three varieties of cultivated radish, R. sativus var. sativus (European small radish), var. hortensis (East Asian big radish) and var. niger (black radish), belonged to a different cluster of the phylogenetic tree, suggesting the existence of independent multiple origins of these varieties. Based on the phylogenetic tree, problems related to the identification of the wild ancestral species of cultivated radish and original birthplaces of cultivated radish varieties were discussed.
We constructed a framework map of the edible mushroom Lentinula edodes (shiitake mushroom) using tetrad analysis. The map is based on the segregation of 264 randomly amplified polymorphic DNA (RAPD) markers, 14 structural genes, 1 expressed sequence tag (EST) marker, 2 mating factors (matA and matB), and 8 sequence-characterized amplified regions (SCARs) among 92 basidiosporic strains in 23 tetrads. We identified 11 linkage groups on a support interval of a minimal LOD score of 3.0 and a maximum distance of 25 centimorgans (cM). The length of the 11 linkage groups (LGs) ranged from 157.2 cM to 24.4 cM, and they covered a distance of 908.8 cM. One of the quantitative trait loci controlling the vegetative growth rate on potato dextrose agar (PDA) for L. edodes was detected between the markers D18CCA-360t and S08-1000c on LG2.
We investigated and compared the relationships between the earliness of head formation and developmental characteristics of cabbage cultivars grown in spring (sown in early spring, harvested in early summer) and autumn (sown in summer, harvested in late autumn). In both seasons, earliness of head formation, namely the duration of the period to attain the target head weight from transplanting, was highly correlated with the leaf position at which head formation started (LPH): the lower the LPH value, the earlier head formation. This result suggests that a low LPH value is necessary for early-head-forming cultivars. However, the LPH value in some cultivars varied with the growing season, showing a significant genotype (G) × environment (E) interaction. To determine whether this G × E interaction might influence the use of LPH as a selection criterion, we analyzed the developmental pattern of the leaf shape. In cultivars with LPH values that largely differed between the two seasons, the leaves were longer up to a higher leaf position and widened later in the spring than in autumn, mainly because of delayed shortening of the petiole. We thus characterized the complex nature of early head-forming in spring, and suggested that LPH was a useful selection criterion for the development of early head-forming spring cultivars.
The internodes of deepwater rice can elongate in response to rises in water level. This unique character allows deepwater rice to survive severe flooding during the monsoon season in South and Southeast Asia. Our previous quantitative trait locus (QTL) analysis of a deepwater rice cultivar (Oryza sativa) detected QTLs on chromosomes 1, 3 and 12. In this study, we produced three nearly isogenic lines (NILs) possessing each of the three QTLs by backcross introduction of each chromosomal region into a non-deepwater rice cultivar. The NILs showed internode elongation under deepwater conditions, and we were able to demonstrate the existence of the QTLs and to evaluate the effect of each QTL. Using progenies of the NILs, we mapped all QTLs between molecular markers. Comparison of the location of the most effective QTL between the rice cultivar (O. sativa) and a wild rice species (O. rufipogon) indicated that the QTL on chromosome 12 is common and is the most important QTL for internode elongation in deepwater condition.
Deepwater rice (floating rice) can survive under flooded conditions because of their floating ability. We conducted genetic analysis to elucidate the genetic control of floating ability by using an F2 and BC3F2 populations derived from a cross between deepwater and non-deepwater rice varieties. Internode elongation is the most important trait responsible for this adaptation, and is characterized by two factors: timing of the initiation of elongation and the rate of elongation. The position of the lowest elongated internode (LEI) and the rate of internode elongation (RIE) were used to measure floating ability. Two QTLs for LEI were detected on chromosomes 3 (qLEI3) and 12 (qLEI12). For RIE, two QTLs were detected on chromosomes 1 (qRIE1) and 12 (qRIE12). We confirmed the genetic effects and map positions of qLEI3, qLEI12 and qRIE12 by using BC3F2 populations. Characterization of near-isogenic lines of qLEI3, qLEI12 and qRIE12 revealed that the LEI and RIE are at least partly controlled by different genetic pathways. Observation of near-isogenic lines suggested that the introgressed segment of qLEI12 and qRIE12 of chromosome 12 affected the deepwater-responsive elongation.
Genetic factors controlling root shape and red pigmentation on the surface of the hypocotyl (upper part of root) were investigated using a molecular linkage map based on an F2 population derived from a cross between two radish cultivars, ‘Huang-he hong-wan’ and ‘Utsugi-gensuke’. One hundred and ninety-eight segregating markers (169 AFLPs, 28 Brassica SSRs and one SLG-CAPS) were located on 14 linkage groups (LGs) at a LOD threshold value of 5.0. The mapping position of Brassica SSRs revealed that frequent genomic rearrangements occurred between the Brassica and Raphanus genomes. Three quantitative trait loci (QTLs) for root shape with LOD values of 2.42, 3.22 and 2.88 were identified on LGs 3, 8 and 9, respectively. These three QTLs accounted for 42.4% of the phenotypic variance when joined together. Analysis of QTL(s) for root diameter revealed the presence of two QTLs on LG4 and LG8. The QTL on LG8 was considered to control root thickening and to affect the root shape. For hypocotyl pigmentation, a QTL which exerted a large genetic effect with a LOD value of 9.58, was recognized on LG 11 and accounted for 43.8% of the phenotypic variance.
Pod dehiscence (shattering) is a major source of yield loss in mechanical harvest of soybean. To develop a marker-assisted selection system for a major quantitative trait locus (QTL) controlling pod dehiscence, designated as qPDH1, we confirmed the usefulness of flanking markers and the effect of qPDH1 under different genetic backgrounds. The progeny of a residual heterozygous line for the genomic region around qPDH1 was screened for four flanking markers to obtain various recombinants in the vicinity of the QTL. The analysis of the relationship between the pod dehiscence degree and the graphical genotype of these lines confirmed the presence of qPDH1 in the region between the SSR markers, Sat_366 and Sat_093, on linkage group J. At these marker loci, the alleles from a Thai cultivar, SJ2, the donor of the shattering resistance, were inherited by most of the shattering-resistant, SJ2-derived cultivars and were distinct from those of the shattering-susceptible cultivars tested. The effect of the allele from SJ2 at qPDH1 was confirmed by association tests under four genetic backgrounds derived from crosses with three susceptible cultivars in the northern to southwestern regions of Japan and a susceptible accession of Indonesian origin at three locations. These results suggest that the allele from SJ2 at qPDH1 and the linked markers could be widely used for the improvement of the shattering resistance in soybean.
Petunia axillaris complex and P. integrifolia complex consist of three subspecies (ssp. axillaris, ssp. parodii and ssp. subandina) and two species (P. integrifolia and P. inflata), respectively. Since these taxa within each complex can only be distinguished by the flower morphology, it would be useful to discriminate them by DNA markers. In this study, we sequenced the 19th intron and the 20th exon of the PolA1 gene, a single gene encoding the largest subunit of RNA polymerase I, and showed clear differences between P. axillaris complex and P. integrifolia complex, and also among all the taxa within each complex. These sequence variations will be promising to develop PCR-based markers to discriminate taxa within P. axillaris complex and P. integrifolia complex.
To select suitable genetic resources for scent breeding, we qualitatively and quantitatively analyzed floral scent emitted from 9 wild Gladiolus species. Dynamic headspace collection was performed and scent compounds emitted from the wild species were analyzed using gas chromatography-mass spectrometry, resulting in detection of twenty scent compounds. The analyzed species were divided into 4 groups;—Linalool/Benzenoid group, Nerol group, Ionone group or Ocimene/Caryophyllene group. Based on the kind and amount of scent compounds we selected G. orchidiflorus, G. recurvus, G. tristis and G. watermeyeri as potential genetic resources for fragrance. Temporal changes in emissions were investigated in 3 promising species that were selected. G. orchidiflorus emitted the maximum amount of scent compounds between 10:00 and 14:00 while the maximum output of G. recurvus and G. tristis was between 18:00 and 22:00. This differential release of scent compounds during the day is an important character to select for, in addition to the quality and quantity of scent compounds, in breeding program for Gladiolus.