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.

Bean paste color is one of the most important quality traits in adzuki beans (Vigna angularis). The present study was aimed at identifying quantitative trait loci controlling bean paste color and its associated seed color using recombinant inbred lines (RILs) crossed between cv. ‘Murasakisayaka’ (superior bean paste color) and cv. ‘Erimoshozu’. RILs and parental cultivars were grown over two years and in two locations in Hokkaido, Japan. Seed coat color and boiled bean color were evaluated using the L*C*h color space. A total of 36 PCR-based molecular markers, including 34 insertions/deletions, CAPS, and derived CAPS markers, were developed through re-sequencing data of the parents. Using these DNA markers, seven linkage groups (LGs) covering a total length of 363.6 cM were constructed. The hue angle of the boiled bean (BBH) of the bean paste color of ‘Murasakisayaka’ was consistently lower than that of ‘Erimoshozu’ across four trials. For seed coat color, 2 QTLs for L*, 4 QTLs for C*, and 3 QTLs for h were identified on LGs 3, 4, 7, 8, 10, and 11. For boiled bean color, a single QTL for L*, 3 QTLs for C*, and 4 QTLs for h were identified on LGs 1, 3, 10, and 11. These QTL findings should facilitate gene isolation and breeding application for the improvement of the bean paste quality of adzuki bean cultivars.

For the evaluation of disease susceptibility and overwintering performance in pasture cultivar breeding, 88 RGB vegetation indices, including GRVI, were compared with the breeders’ scores from aerial images taken by an unmanned aerial vehicle (UAV) equipped with a common RGB camera. In the disease severity evaluation, 11 vegetation indices (GRVI, GmR, GmR_2, MGVRI, VARI, GI, RGRI, ExGR, ExR_2, SAVI, and SAVI_2) showed a high correlation (mean of R² ≥ 0.5) with the breeders’ score. Most of the vegetation indices were vegetation indices that were less affected by B. Eight vegetation indices (g, ExG, ExG_2, GLI, CIVE, CIVE_2, RGVBI, and RGBVI) showed a high correlation with the breeders’ score in the overwinterability evaluation. The 8 vegetation indices that correlated well with the overwinterability evaluation were vegetation indices that used all the RGB colors. In addition, a comparison of breeders’ scores in breeding trials of oats, Italian ryegrass, Sudan grass, perennial ryegrass, and red clover with rG, a relative indicator of GRVI, showed a high correlation in the evaluation of grass vigor and degree of winter kill. On the other hand, correlations were low for grass shape and degree of lodging. In addition, regardless of the type of trait, the correlation was low in tests where the evaluation by the breeder itself was difficult. These results suggest that the rG evaluation is suitable for traits evaluated by the size of the plant area in the test area or by the color tone of the entire test area in aerial images taken from the sky.

To enhance the cropping potential of ‘Mizuhochikara’, which has good properties for making rice bread, we developed a new rice cultivar, ‘Emitawawa’, for making rice bread and has early heading. This variety was selected from the progeny derived from crosses among PMF₈4/Momiroman//Mizuhochikara. The heading date of ‘Emitawawa’ was the same as that of ‘Hinohikari’, the leading variety grown in warm regions of Japan, and 7 days earlier than ‘Mizuhochikara’. The ripening date of ‘Emitawawa’ was 8 days later than that of ‘Hinohikari’, and 10 days earlier than ‘Mizuhochikara’. The culm length of ‘Emitawawa’ was 3 cm longer than that of ‘Hinohikari’, the panicle length was 4 cm longer than that of ‘Hinohikari’, and the number of panicles was less than that of ‘Hinohikari’. The plant type was classified as the panicle weight type. The lodging tolerance of ‘Emitawawa’ was stronger than that of ‘Hinohikari’. The grain yield of ‘Emitawawa’ was 40% more than that of ‘Hinohikari’, and the same as that of ‘Mizuhochikara’. The resistance to leaf blast of ‘Emitawawa’ was classified as weak, the resistance to rice stripe disease was susceptible, the resistance to bacterial leaf blight was classified as weak, the sprouting tolerance was classified as moderately strong, and it was sensitive to herbicides that inhibit 4-HPPD. Following cultivation tests in warm and temperate regions, the heading date and ripening date of ‘Emitawawa’ were found to be earlier than those of ‘Mizuhochikara’, and the grain yield was the same or more than that of ‘Mizuhochikara’. The specific loaf volume of 100% rice bread made of ‘Emitawawa’ rice flour was the same as that of ‘Mizuhochikara’. The desirable amylose content (21.3%), low damaged starch content (1.7%), and small particle size distribution affected the specific loaf volume of 100% rice bread. ‘Emitawawa’ is expected to be used for rice bread and is suitable for cultivation in warm and temperate regions in Japan.

Improving soybean yield in Japan is one of the most important goals in soybean breeding. Although the Tohoku region in Japan is one of the largest soybean production areas, the average yield in the region is lower than the national average. The improvement of soybean productivity in the Tohoku region would therefore lead to an overall improvement of soybean productivity in Japan. A reduction in soybean yield has occurred recently in the Tohoku region partly due to pod shattering caused by late harvesting and the soybean cyst nematode (SCN) infecting SCN race 3 resistant varieties. Through marker-assisted selection and back-crossing, we developed two elite lines of soybean, ‘Tohoku 185’ and ‘Tohoku 189’, using the high-yielding variety ‘Fukuibuki’ as a recurrent parent. ‘Tohoku 185’ was developed using ‘Hayahikari’, a variety resistant to pod shattering, as a donor parent, and showed significantly lower pod shattering rates than ‘Fukuibuki’. ‘Tohoku 189’ was developed using ‘To-8E’, a variety resistant to SCN race 1, as a donor parent, and showed resistance to SCN race 1. The following traits were evaluated to confirm whether the agronomic traits of the two developed lines were equivalent to those of ‘Fukuibuki’: time to maturity, lodging, plant height, height of lowest pod-bearing node, yield, 100-seed weight, and seed protein content. Although the yield and 100-seed weight of ‘Tohoku189’ were lower than those of ‘Fukuibuki’ in all examined environments, there were no significant differences in any of these traits between ‘Fukuibuki’ and the two developed lines. The varieties resistant to both pod shattering and SCN race 1 have not yet been developed for the Tohoku region. Although we must consider the effects of the genes controlling SCN race 1 resistance on both the yield and 100-seed weight, it should be possible to develop high-yielding varieties with resistance to both pod shattering and the SCN race 1 by crossing ‘Tohoku 185’ and ‘Tohoku 189’.