‘Somei-yoshino’ (Yoshino cherry, Prunus × yedoensis) is the most popular flowering cherry cultivar in Japan. In order to confirm the clonal status of this cultivar, which is one of the most important issues, genotypes of different individuals were investigated using 21 microsatellite markers. Of the 52 individuals examined, including 47 old trees planted from the late 19th to the early 20th century that had been collected from various locations in Japan, 50 showed an identical genotype. The other two were assumed to be the offspring of this cultivar. These results showed that ‘Somei-yoshino’ is a clone from a single tree. The genealogy of six other cultivars belonging to the same hybrid species was examined using the same method. The results were congruent with the documentation of their genealogy. ‘Mishima-zakura’ and ‘Shouwa-zakura’ were found to be the offspring of ‘Somei-yoshino’, while ‘Amagi-yoshino’, ‘Izu-yoshino’, ‘Mikado-yoshino’ and ‘Perpendens’ were not directly related to ‘Somei-yoshino’.
The wild progenitor (Oryza rufipogon) of Asian rice (Oryza sativa) shows a wide range of variations in life-history traits, forming an annual-perennial continuum. A conspicuous feature of an annual type of wild rice is represented by its adaptability to disturbed habitats, and its short stature with many tillers and a prostrate growth habit. The present study was carried out to examine the genetic differentiation between wild annual and cultivated (Japonica type) rice strains by quantitative trait locus (QTL) analysis. In total, 20 adaptive and/or domestication-related traits were evaluated in recombinant inbred lines (RILs). A total of 28 putative QTLs were detected across the genome. Six QTLs responsible for plant architecture were located on the short arm of chromosome 7. The near-isogenic line with the region containing the QTL cluster confirmed that the QTLs exerted a significant effect on the plant architecture in the genetic background of cultivated rice. A similar QTL cluster was also found in another annual strain of a different origin, suggesting that the QTL cluster might be predominant in annual wild rice. Furthermore, a QTL for tolerance to disturbance (simulated trampling) was detected within the region of the cluster on chromosome 7. These results are discussed in relation to their ecological significance in wild annuals of rice.
Septoria leaf blotch, powdery mildew and yellow and brown rusts are major wheat diseases characterized by a worldwide distribution. The level of genetic resistance against these diseases is low in durum wheat (Triticum turgidum) germplasm, while some wheat relatives, such as crested wheatgrass (Agropyron cristatum), are resistant. In an attempt to incorporate resistance genes into durum wheat, crosses were carried out between durum wheat and a fertile allotetraploid (2n = 4x = 28; DDPP) previously obtained from a cross between diploid wheat (T. tauschii) and crested wheatgrass (A. cristatum). The plants were backcrossed twice to durum wheat and studied for their reaction to the diseases. The genomic constitution of all the backcross derivatives from these crosses were analyzed by fluorescence in situ hybridization (FISH) using both total genomic DNA of A. cristatum and the pAs1 repetitive DNA sequence isolated from T. tauschii. All of them retained chromosomes or chromosome segments of A. cristatum. All the analyzed plants were immune to septoria leaf blotch and powdery mildew and showed a high level of resistance to yellow and brown rusts.
Tocopherols, known as members of vitamin E, are the major lipophilic antioxidants in soybean. Since soybean seeds contain a low concentration of α-tocopherol (α-Toc), the tocopherol isoform with the highest vitamin E activity, some breeding efforts have been implemented to increase the α-tocopherol content in the seeds. In the present study, we used F2 seed and F2 plant (F3 seeds) populations derived from a cross between a variety with a high α-tocopherol content, Keszthelyi A.S. (α-Toc 20–30%) and a Japanese cultivar, Ichihime (α-Toc < 10%) for genetic analysis of the high α-tocopherol concentration. There was no significant correlation between the α-tocopherol and total tocopherol contents in the F2 plant (F3 seeds) population, suggesting that the α-tocopherol and total tocopherol contents were regulated independently in the seeds. Therefore, it may be possible to increase the α-tocopherol concentration without affecting the total tocopherol content. Broad-sense heritability value for the α-tocopherol concentration trait was estimated to be 0.645 in the F2 seeds, suggesting that the α-tocopherol concentration trait was highly heritable. Chi-square goodness-of-fit test for evaluating the relationship between genotype of certain SSR markers and the α-tocopherol concentration showed that the Sat_243 and Sat_167 markers (linkage group K) were significantly associated with the α-tocopherol concentration (P < 0.05). These markers could be used for marker-assisted selection to breed soybean cultivars with high α-tocopherol concentrations. Analysis of the F2 seeds and the F2 plants (F3 seeds) for tocopherol composition showed that there was a significantly negative correlation between the α-tocopherol and γ-tocopherol concentrations, suggesting that the activity of γ-tocopherol methyltransferase, the enzyme that converts γ-tocopherol to α-tocopherol, is high in individuals with a high α-tocopherol concentration.
Cultivated barley (Hordeum vulgare L.) is well known as one of the most widely cultivated crops in the world and as an extensively studied plant species in the field of genetics. In recent years, despite its very large genome size (ca. 5,000 Mb), the research resources needed for barley genomic studies have become available, including a large number of expressed sequence tags (ESTs). These have been widely used for barley genome analyses, such as DNA marker-generation and the construction of microarrays. However, the availability of a large-insert genomic library, which is also essential for genomic studies, has been relatively limited in the barley research community. We described here the construction and characterization of a barley bacterial artificial chromosome (BAC) library, using the Japanese malting barley variety ‘Haruna Nijo’. The BAC library consisted of 294,912 clones arrayed in 768 384-well microtiter plates. The average size of each cloned insert was estimated to be 115.2 kb, with approximately 0.5% of the clones lacking inserts. Chroloplast DNAs were present in about 1.7% of the library. Thus, the genomic coverage of the ‘Haruna Nijo’ BAC library was estimated to be about 6.6 genome-equivalents. In order to rapidly identify specific BAC clones, we developed a screening strategy that combined PCR analysis of pooled BAC DNAs with colony hybridization. Using this screening scheme, we investigated the genomic coverage of this BAC library, using 13 locus-specific ESTs and a sequence-tagged site marker. By screening the whole library with individual markers, we identified an average of 5.1 clones per marker. This screening scheme also enabled us to rapidly construct a physical contig spanning a region of approx. 190 kb around the HvBRI1 locus, where the mutation responsible for the semi-dwarf plant type ‘uzu’ is located. These results indicate that the ‘Haruna Nijo’ BAC library will be useful for barley genomic studies.
A linkage map was constructed using PCR-based markers developed from barley expressed sequence tags (ESTs) for recombinant inbred (RI) lines (F10) derived from a cross between Triticum monococcum L. strain KT3-5 and T. boeoticum Boiss. strain KT1-1. Among the primer sets of 2,695 barley ESTs, 242 EST markers were integrated into the frame of a previously constructed diploid wheat linkage map with 96 RFLP markers. The total map length comprising barley EST, previously mapped RFLP and morphological markers was 1,038.1 cM, and the average distance between two adjacent loci was 3.1 cM. The linkage map showed saturation with the barley EST markers by covering extended telomeric regions and increasing the resolution compared with the previous RFLP map. Order of barley ESTs on the diploid wheat linkage map mostly showed a collinearity to that on the barley linkage map constructed previously, although the long arms of the homoeologous linkage groups 4 and 5 showed structural changes between diploid wheat and barley. Phenotypes of nine quantitative traits were scored for the diploid wheat RI lines and their parents. Composite interval mapping enabled to detect 24 quantitative trait loci for the traits. Thus, barley ESTs could become powerful tools to reveal homoeologous relationships between barley and wheat chromosomes, and valuable resources to develop genetic markers for wheat genomes.
To identify the chromosomal regions controlling the occurrence of undesirable white-back kernels (WBK) in rice under growth conditions at high temperatures, we performed a quantitative trait locus (QTL) analysis in F6 recombinant inbred lines (RILs). We constructed a linkage map using 106 simple sequence repeat (SSR) markers from 107 RILs derived from a cross between the japonica cultivar ‘Chiyonishiki’, which shows a high incidence of WBK at high temperatures, and the japonica cultivar ‘Koshijiwase’, which is tolerant to high temperatures and displays a low incidence of WBK. Each RIL was exposed to high temperatures in a greenhouse during the ripening period (from heading to maturity). The number of heat-damaged kernels was counted to obtain the rates of WBK in each RIL. Four putative QTLs for the occurrence of WBK–qWK1-1, qWK1-2, qWK2 and qWK8–were detected near the SSR markers RM8068 and RM5501 on chromosome 1, RM5916 on chromosome 2, and RM2680 on chromosome 8, respectively. The Koshijiwase alleles at the qWK1-2, qWK2 and qWK8 loci decreased the incidence of WBK and showed additive effects. qWK1-2 explained 15.0% of the total phenotypic variance, while qWK1-1, 8.8%, qWK2, 9.3%, and qWK8, 9.2%.
The widespread adoption of the high-yielding semi-dwarf rice variety, IR8, led to the “green revolution” in Asia in the 1960s. The short stature of this variety is due to a loss-of-function of the SD1 gene that encodes a GA20 oxidase-2 (GA20ox-2) which catalyzes late steps of gibberellin biosynthesis. In this study, we investigated how widely sd1 mutations have been employed in the generation of semi-dwarf varieties of rice. Genetic and molecular analyses revealed that the sd1 allele of IR8 has been used in the production of japonica varieties. Sequence analysis of the SD1 locus of 57 semi-dwarf varieties showed that at least 7 sd1 alleles have been used in the breeding of semi-dwarf rice varieties in China, USA and Japan. The utilization of such a high number of different alleles all controlling the same target trait highlights that mutations in GA20ox-2 induce an agronomically advantageous architecture in rice.
The level of self-incompatibility (SI) directly influences the purity of F1 seed produced by using an SI system. Using insect-pollination test, we performed diallel analysis to determine the levels of SI of 6 inbred lines of Brassica rapa L. differing in their rates of pod set. Each of 3 lines with a high level of SI (Ka1-22, Ka1-3 and Ch1-504) appeared to have different modes of inheritance. To clarify these in detail, we performed 4 × 4 diallel analysis using each of these 3 lines together with 3 other lines (Ko1-303, Ha1-400 and Ha1-10). The crosses with Ka1-22 showed an incomplete dominance and non-significant correlation between the proportion of dominant alleles of the parents (Vr + Wr) and the parental values (Pr), suggesting that Ka1-22 possesses dominant genes controlling the high level of SI. The crosses with Ch1-504 showed significant correlation between Vr + Wr and Pr, suggesting that Ch1-504 possesses recessive genes controlling the high level of SI. The crosses with Ka1-3 showed epistatic effects and specific combining effects. This study is the first to define strictly the genetic diversity controlling a high level of SI. Breeders must be careful in selecting the breeding material, because the mode of inheritance of the level of SI could differ in lines showing a high level of SI.
In order to clarify the characteristics of the photoperiod-insensitive genes Ppd-B1 and Ppd-D1 carried by the Japanese wheat cultivars, we produced near-isogenic lines (NILs) and investigated their effects on apical development. The NIL ‘H(A)’ was produced by backcrossing the Japanese photoperiod-sensitive cultivar ‘Haruhikari’ as a recurrent parent and the insensitive cultivar ‘Saitama 27’ (Ppd-D1) as a nonrecurrent parent. The other three NILs ‘H(B)’, ‘H(C)’ and ‘H(D)’ were produced using the insensitive cultivar ‘Fukuwasekomugi’ (Ppd-B1 Ppd-D1) as another nonrecurrent parent. Genetic analysis of the photoperiod response showed that ‘H(A)’, ‘H(B)’, ‘H(C)’ and ‘H(D)’ carried Ppd-D1, Ppd-D1, Ppd-B1 and Ppd-B1 Ppd-D1, respectively. Ppd-B1 and Ppd-D1 were incompletely dominant and exhibited an interaction, the former displaying a stronger effect on insensitivity to photoperiod. The analysis of apical development indicated that both Ppd-B1 and Ppd-D1 had significant effects on accelerating double-ridge initiation and on the following spike development under a short photoperiod.
The National Institute of Genetics (NIG), Mishima, Japan, maintains 1,725 accessions of 20 wild species of the genus Oryza, which have been collected from tropical and subtropical areas all over the world and covering all species in the genus except for O. schlechteri Pilger. A core collection of 282 accessions was chosen to represent the genetic spectrum of the whole NIG collection. The genome sizes of 39 accessions of Oryza core collection, covering all 20 species and 9 genome types, were measured based on both flow cytometry and microscopic observation. Most accessions showed good correspondence with respect to genome size within the same species and genome type, but showed significant differences between different genome types. In contrast to other species, however, CC, CCDD and HHJJ species showed significant variation within the same genome type. The total somatic chromosome length and ploidy level were also investigated for several accessions, and they correlated well with the DNA content. In this study, a simple flow cytometric analysis provided reliable results for genome size evaluation, and in addition, the genome size of five species was newly determined. Thus the DNA content, which is the simplest reliable indicator of genome variability, should be a good means of monitoring for evaluation and identification of Oryza germplasm.