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.
In order to develop an optimal method for the investigation of relative potencies of dioxin-like compounds using Japanese medaka, the present study conducted five independent early-life stage ...toxicity tests using 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) as the positive control. First, both short- and long-term effects of TCDD were examined to determine sensitive and highly reproducible endpoints. Then, the outcome and threshold of TCDD toxicities under different experimental conditions, e.g., exposure timing and duration, were compared to develop a cost-effective method. Finally, we decided to observe yolk sac/pericardial edema, hatching failure, and mortality of medaka embryos/larvae within a 28-d experimental period, after 6-h exposure to TCDD at 0-d post fertilization. We obtained the LC50 values of TCDD at 28-d post fertilization based on its concentration in water (6.84 ng/L) or in egg (753 pg/g-egg), and the LC50 values were comparable with those reported in the literature. Thus, in our future studies, relative toxic potencies of dioxin-like compounds will be tested using the method established in this study.
Accurate crop pedigree information is essential for breeding programs, especially to make better decisions on the breeding materials to be selected in crossings. As the available tools for ...facilitating pedigree analysis and visualization are insufficient, breeders use a limited pedigree chart to trace the relationships between crop varieties. To resolve this problem, we have developed a web-based pedigree viewer for graph databases, “Pedigree Finder” (https://pedigree.db.naro.go.jp/), that facilitates the effective utilization of pedigree data sets for breeding programs and crop data analysis. For data normalization, the ontologies and data formats used to describe pedigree information have been standardized. Pedigree, genomic, and phenotypic data can be integrated by assigning and applying unique identifiers to different crop varieties. The Resource Description Framework (RDF) was adopted as the data model to enhance commonality and persistence, and an RDF graph was constructed to visualize the pedigree network. This semantic web technology enables advanced search functions and allows for the blending of data sets from disparate sources using an RDF model. “Pedigree Finder” provides an integrated data-driven framework for the appropriate selection of breeding materials, understanding of genetic correlations between phenotypes and pedigrees in breeding programs, and promotion of crop genetics research.
Many papers about rice genes related to yield are published every year, but few of these genes have been used in practical rice breeding. Therefore, we generated or received near-isogenic lines ...(NILs) of nine alleles related to yield in the genetic backgrounds of Japanese rice cultivars, and performed simultaneous comparative cultivation tests. Significant increases in brown rice yield were detected in the NILs for qCTd11Takanari, SD1DGWG, and a combination of TGW6Kasalath and SD1DGWG in the genetic background of ‘Koshihikari’ and a NIL for DEP1Ballila in the genetic background of ‘Akidawara’. These alleles and QTLs may have the genetic potential to improve rice yield, even in the genetic background of Japanese cultivars. On the other hand, an increase in the brown rice yield of NILs for qLIA3Takanari, GPSTakanari, GS3Oochikara, GW2BG1, and GN1ATakanari was not detected in the ‘Koshihikari’ genetic background probably due to small direct effects to increase sink size by these alleles and QTLs or a relative reduction of their source abilities to the total sink sizes increased in these NILs. In addition, analysis using multiple NILs in the ‘Koshihikari’ genetic background showed a negative correlation between panicle weight and panicle number. This indicated that an increase in the number of panicles did not subsequently increase yield because of the tradeoff to reduce the weight of one panicle and the thousand grain weight; this was considered the main reason why GW2BG1, GS3Oochikara, and GN1ATakanari, which were expected to increase sink capacity, did not increase yield. We considered that the alleles increasing sink capacity are not sufficient to increase yield in the genetic background of Japanese cultivars and need to be combined with alleles, such as qCTd11Takanari, expected to improve the source ability by increasing photosynthesis per unit leaf area or alleles to improve canopy structure including SD1DGWG and DEP1Ballila.
Accurate crop pedigree information is essential for breeding programs, especially to make better decisions on the breeding materials to be selected in crossings. As the available tools for ...facilitating pedigree analysis and visualization are insufficient, breeders use a limited pedigree chart to trace the relationships between crop varieties. To resolve this problem, we have developed a web-based pedigree viewer for graph databases, “Pedigree Finder” (https://pedigree.db.naro.go.jp/), that facilitates the effective utilization of pedigree data sets for breeding programs and crop data analysis. For data normalization, the ontologies and data formats used to describe pedigree information have been standardized. Pedigree, genomic, and phenotypic data can be integrated by assigning and applying unique identifiers to different crop varieties. The Resource Description Framework (RDF) was adopted as the data model to enhance commonality and persistence, and an RDF graph was constructed to visualize the pedigree network. This semantic web technology enables advanced search functions and allows for the blending of data sets from disparate sources using an RDF model. “Pedigree Finder” provides an integrated data-driven framework for the appropriate selection of breeding materials, understanding of genetic correlations between phenotypes and pedigrees in breeding programs, and promotion of crop genetics research.
In rice, caryopses located at the base of the panicle have a lower growth rate than those at the tip of the panicle. The former and latter types of caryopses are called inferior and superior ...caryopses, respectively. Taking the different growth rate into consideration, sugar status and the expression of genes encoding carbohydrate-metabolizing enzymes in inferior caryopses were compared with those in superior caryopses. During the first 5 d after flowering, superior caryopses elongated rapidly, but inferior caryopses did not. At this phase, inferior caryopses had a low ratio of hexose to sucrose, high activity of acid invertase and the absence of the expression of the genes encoding the above enzymes except for two isoforms of cell wall invertase, OsCIN4 and INV1, in comparison with superior caryopses. At the start of caryopsis elongation in both superior and inferior caryopses, the hexose/sucrose ratio increased accompanied by gene expression of vacuolar invertase (INV3), sucrose synthase (RSusl) and ADP-glucose pyrophosphorylase (AGP-L2: D50317). Furthermore, the genes related to endospermal starch accumulation were expressed highly with the decrease in the hexose/sucrose ratio after its peak. Based on the comparison of superior and inferior caryopses, the possible mechanism of grain filling in rice is discussed.
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