‘Shine Muscat’ is an elite table grape cultivar developed by the National Agriculture and Food Research Or‍ganization in Japan. Recently, the infringement of breeders’ rights in various fruits has become a serious problem in Japan. In this study, a loop-mediated isothermal amplification (LAMP)-mediated cultivar identification method for ‘Shine Muscat’ was developed. We comprehensively analyzed retrotransposon insertion sites using 24 major grape cultivars and identified two insertions, VINE1-Cl160 and VINE1-Cl155, which are unique to ‘Shine Muscat’. LAMP primers targeting VINE1-Cl160 and VINE1-Cl155 were designed, and ‍specific amplifications were confirmed. We also designed a primer set to detect the grape endogenous refer‍ence sequence, UDP-glucose:flavonoid 3-O-glucosyltransferase. To improve rapidness and cost-ef‍fec‍tiveness, we applied single-stranded tag hybridization on a chromatography printed-array strip system, a lateral flow DNA chromatography technology. The developed method was validated with an interlaboratory study. This novel identification method would be particularly useful for border inspections.

Fukumi Fiber, a new six-rowed hull-less barley cultivar, has an extremely high β-glucan content; this is the ‍world’s first cultivar with two genes (wax and amo1) boosting the content of β-glucan and one gene (ant28.2131) suppressing the browning reaction after cooking, to our knowledge. The β-glucan content of pearled barley is 13.2% in Fukumi Fiber, and is approximately three times higher than that of the standard barley cultivar Ichibanboshi and approximately two times higher than that of the waxy cultivars Daishimochi and Kirari-mochi. Fukumi Fiber has a standard plump grain percentage required for a six-rowed hull-less barley cultivars. The yield is over 10% higher than that of Ichibanboshi. Fukumi Fiber is suitable for cultivation in the plains of central and western Japan and was released in 2018. It can be used for cooked pearled barley and various purposes such as confectionery, noodles, and bread. The spread of this cultivar is expected to lead to a stable supply and the expansion of high-value-added domestic waxy barley.

In soybean production, lodging poses a significant challenge to modern mechanized agriculture, such as the use of combine harvesters. Most Japanese varieties are prone to lodging because of the local weather conditions, such as wind and rain, resulting in a decline in productivity. In the United States (US), where mechanized agricultural production systems are prevalent, lodging tolerance (LT) is essential in soybean breeding. We thus used two recombinant inbred-line (RIL) populations developed by crossing major Japanese and modern US varieties for the genetic dissection of LT. One reliable quantitative trait locus (QTL) for lodging angle, qLT13-1, was identified from the first RIL population under two experimental conditions, early and late maturity groups of the first RILs in Ibaraki in 2018, and it accounted for 20.7%–20.9% of the phenotypic variation. An allele at qLT13-1 from a US variety was effective in improving LT under most experimental conditions. In addition, a QTL for LT was valid in the same genetic region of the other RIL populations. The effective allele, qLT13-1 is thus expected to be important for improving LT in soybean breeding, particularly in Japanese varieties.

In this study, we mapped quantitative trait loci (QTLs) associated with heading date and grain quality traits in a novel set of 44 chromosome segment substitution lines (CSSLs) derived from closely related rice (Oryza sativa L. ssp. japonica) cultivars ‘Yukihikari’ (good grain quality) and ‘Joiku462’ (superior eating and high grain appearance qualities). Days to heading (DTH), apparent amylose content (AAC), protein content (PC), thousand brown-grain weight (TBGW), brown grain length (BGL), brown grain width (BGWI), brown grain thickness (BGT), and the contents of 12 mineral elements (S, P, Mg, Ca, K, Mo, Cu, Zn, Mn, Fe, Sr, and Si) in polished rice were evaluated in 44 CSSLs grown in two different environments. We identified 78 QTLs, including 8, 7, 8, 8, 19, 10, and 10 for DTH, AAC, PC, TBGW, BGL, BGWI, and BGT, respectively, and 2, 1, 3, and 2 for S, Mo, Cu, and Zn contents, respectively. Several QTLs were observed in the same region, forming 17 clusters on chromosomes 1–10. These QTLs can facilitate gene isolation and breeding to develop rice cultivars with optimum heading time and improved grain quality.

Buckwheat (Fagopyrum esculentum) is a heterostylous self-incompatible crop that requires outcrossing for seed formation. Pollen parents influence the traits of seeds in many plants, but their influence in buckwheat is unknown. Here, we crossed self-incompatible (SI) and self-compatible (SC) lines with different rutin contents. The average rutin contents of SI leading cultivars were all 0.15–0.21 mg/g, and a SI high rutin content line that we had developed was 0.6 mg/g, although it has wide range SDs (0.12–0.41). On the other hand, the average rutin contents of SC lines were 0.01–0.06 mg/g, with stable SDs (0.02–0.03). In crosses between high- and low-rutin parents, the average rutin content of F₁ seeds was significantly lower than that of the high-rutin parent and higher than that of the low-rutin parent, indicating that the pollen parent influences the rutin content in seeds of buckwheat. RNA-seq analysis confirmed that alleles of several genes encoding enzymes involved in rutin synthesis derived from pollen parents were expressed during seed formation.

Common bean (Phaseolus vulgaris L.) is one of the most abundantly consumed legume crops as foods worldwide. In many African countries, this crop is an important staple food because of its rich nutrients. The Great Lakes region of Central Africa, which includes Rwanda, the nation with the highest per capita consumption of common beans worldwide, is known to be a center of common bean diversity in Africa. Increasing the amount of iron and zinc in common bean for biofortification has been a key breeding goal in Rwanda and other countries. In this study, using 192 accessions, including local landraces from Rwanda, breeding materials, released varieties, and others, we performed genome wide association studies (GWAS) to determine the loci governing those traits in addition to other agronomic traits. We identified a locus that was strongly associated with seed zinc concentration and candidate genes. The information might be a great help for marker-assisted breeding of this trait in common bean.

Snap bean leaves are the primary site of photosynthesis. Mutant leaf color provides valuable tools for investigating leaf color changes, their role in photosynthesis, and pigment metabolic pathways. In this study, we found that the seedling leaves of ‘ytg-2’ exhibited a yellow phenotype characterized by reduced chlorophyll content compared with ‘A18’. Blockage of the uroporphyrinogen III (Urogen III) to the fecal porphyrinogen III (Coprogen III) synthesis pathway primarily affected the synthesis of chlorophyll intermediate metabolites. As the plants matured, their leaves transformed from yellow to light green, accompanied by an increase in the total chlorophyll content. Transcriptome analysis revealed that the significantly down-regulated expression of four genes in the HemE gene family (Phvul.008G059400.1, Phvul.010G110900.1, Phvul.008G147200.1, and Phvul.010G069500.1), which blocked the Urogen III to Coprogen III conversion, was the primary cause of the yellow phenotype in ‘ytg-2’ seedlings. Additionally, the down-regulation of POR (Phvul.004G113000.1) and NOL (Phvul.004G163900) genes during the chlorophyll cycle explained the reduced total chlorophyll content in ‘ytg-2’ and the gradual normalization of the chlorophyll a/b ratio in ‘ytg-2’ yellow leaves. The ex‍pression of PAO (Phvul.004G163900.1), a key enzyme in chlorophyll degradation, further confirmed that the yellow-to-green transition in ‘ytg-2’ leaves was linked to chlorophyll degradation processes.

Melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9 mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp. melo and the East Asian subsp. agrestis were characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence. In South Asia, in addition to the Europe/US and East Asian types, re‍combinant types between the two types were detected and accounted for 34.8% of South Asian melon. The finding of such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types. As to Momordica popular in South Asia, seed length was intermediate between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp. agrestis of the Ic type proved to be endemic to Africa, indicating its African origin.