'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--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.

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 '' 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 (, , , and ), which blocked the Urogen III to Coprogen III conversion, was the primary cause of the yellow phenotype in '' seedlings. Additionally, the down-regulation of () and () genes during the chlorophyll cycle explained the reduced total chlorophyll content in '' and the gradual normalization of the chlorophyll a/b ratio in '' yellow leaves. The expression of (), a key enzyme in chlorophyll degradation, further confirmed that the yellow-to-green transition in '' leaves was linked to chlorophyll degradation processes.

Buckwheat () 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 F 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.

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. and the East Asian subsp. 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. of the Ic type proved to be endemic to Africa, indicating its African origin.

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 ( and ) boosting the content of β-glucan and one gene () 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.

Common bean ( 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.

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, , 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 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, 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 ( L. ssp. ) 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.

Cucumber is one of the most important vegetables in the Japanese market. To facilitate genomics-based breeding, there is a demand for reference genome of Japanese cucumber. However, although cucumber genome is relatively small, its assembly is a challenging issue because of tandem repeats comprising ~30% (~100 Mbp) of the genome. To overcome, we deployed the Oxford Nanopore sequencing that produces long reads with N50 length of >30 kbp. With this technology we achieved a chromosome-level assembly of cv. 'Tokiwa', a founder line of Japanese cucumber represented with the elongated fruit shape and high-crisp texture. Compared to the existing cucumber genomes, the Tokiwa genome is 20% longer and annotated with 10% more genes. The assembly with nanopore long reads also resolved tandem repeats spanning >100 kbp, demonstrating its strength in overcoming repetitive sequences.

"Tanpo", a Japanese rice landrace widely cultivated approximately 120 years ago in Akita Prefecture, exhibits a shorter, wider, thicker, and heavier grain compared to Akitakomachi. Microscopic analysis has revealed that the epidermal cells of Tanpo spikelet hulls are narrower and shorter, with an increased number of cells in the grain width direction, thus resulting in a distinctive grain shape. In a genetic analysis of an F population derived from a cross between Tanpo and Akitakomachi, the Tanpo allele was found to determine the grain shape in a recessive manner. The allele in Tanpo is a loss-of-function allele because it generates a stop codon immediately after the start codon with a 100-bp deletion within the first exon. Because the GW5 protein suppresses glycogen synthase kinase 2 (GSK2), a negative regulator of brassinosteroid (BR) signaling, GW5 deficiency in Tanpo results in reduced BR signaling. As a result, the expansion of epidermal cells was suppressed, while the radial cell division was promoted, which led to thicker and shorter spikelet hulls and, ultimately, the characteristic grain shape of Tanpo. The identification of this unique allele in the Tanpo landrace provides a valuable resource for breeding new rice varieties with unique grain characteristics.

Cassava is an important staple crop in tropical and subtropical regions. Cassava mosaic disease (CMD) is one of the most dangerous diseases affecting cassava production in Africa. Since the first reported in Southeast Asia in 2015, the CMD prevalence has become a concern in Southeast Asia. To combat it, CMD resistance has been introduced from African cassava into Asian elite cultivars. However, efficient DNA markers for the selection of CMD resistance are not available. The locus confers resistance to African cassava mosaic virus via non-synonymous substitutions in the DNA polymerase δ subunit 1 gene (). Here, we developed DNA markers to identify the mutations providing the resistance. We examined the association between the resistance score in CMD-infected fields and the genotypes of hybrids of CMD-resistant and ‑susceptible Asian lines. Our study provides powerful tools to the global cassava breeding community for selecting CMD resistant cassava.

Grain chalkiness decreases the appearance quality (APQ) of rice ( L.) grains and reduces consumer satisfaction. Improving APQ is a crucial issue for both marketing and breeding. Here, we screened chromosome segment substitution lines (CSSLs) with higher APQ to find promising genetic resources. These CSSLs harbor chromosome segments derived from multiple donors in the genetic background of 'Koshihikari', a leading rice cultivar in Japan. Three CSSLs had an increased percentage of perfect grains without panicle weight loss under field conditions across 3 years in Tsukuba city, Ibaraki prefecture, Japan. The positions of reduced chalkiness in grains differed among CSSLs, suggesting the different contribution of the harbored chromosome segments to APQ improvement. There were no significant differences in days to heading, culm length, panicle length, or panicle number in all three CSSLs, but 1000-grain weight was reduced in one. These results identify two promising genetic resources for further improvement of APQ in current cultivars with reduced chalkiness but unaltered heading date and yield traits.

In barley ( L.), many DNA markers have been developed for the selection of traits related to various end-use purposes of breeding. To perform rapid marker-assisted selection of many lines, we developed Kompetitive Allele-Specific PCR (KASP) markers, which can be used for effective automatic genotyping of single nucleotide polymorphisms (SNPs). The KASP primers were designed for 17 SNPs in 14 genes related to important traits. The target allele of all primers tried was identified on the basis of high FAM fluorescence in comparison with that of HEX. To evaluate the suitability of the developed markers in breeding programs, we used them to genotype 62 representative cultivars and lines. Then, using six of the developed markers, we comprehensively analyzed a total of 2,941 lines collected from eight breeding sites with a genotyping success rate of 95.1%-99.8% (mean, 98.6%). All six markers showed differences in allele percentages among breeding programs, and specific allele combinations were observed in all four barley types. Our data will be useful for predicting phenotype segregation and designing cross combinations. The developed KASP marker set can be used for high-throughput genotyping and should make breeding more efficient when combined with an accelerated generation technique.

Resistance breeding for rice blast is an economic strategy for protecting rice crops against this disease. Genes with nucleotide-binding site leucine-rich repeat (NBS-LRR) structures are known to contribute to disease resistance. Here, we identified a candidate resistance gene, named (t), associated with leaf and panicle blasts in an introgression line carrying the chromosome 4 segment of wild rice ( Griff.) backcrossed with the cultivar 'Nipponbare' ( L.). Mapping analysis based on leaf blast severity confirmed that (t) was localized in the 177-kb NBS-LRR cluster region. To identify the (t) sequence, mutant lines were generated by knocking out a candidate NBS-LRR gene in a homozygous line carrying (t), M18, using CRISPR/Cas9-mediated genome editing. Leaf blast resistance was lost in the mutant lines lacking the corresponding Os04g0620950 N-terminal sequence of the M18 line. The result suggested that the counterpart NBS-LRR gene in the M18 line is involved in resistance to leaf blast. (t) showed homology to in the resistant cultivar 'Kahei', and an NBS-LRR gene in the resistant cultivar 'Mine-haruka' carrying (t). These results suggest that the NBS-LRR gene is a candidate gene of (t) and is present on the long arm of chromosome 4.

Strong yellow color, caused by carotenoid accumulation, in semolina flour made from durum wheat ( L. subsp. (Desf.)) is one of the most important traits for pasta production. The first step in the carotenoid biosynthesis pathway, which is catalyzed by phytoene synthase (PSY), is a bottleneck, and allelic variation of in durum wheat produces different yellow pigment contents (YPC) in seeds. Durum wheat carrying leaf rust resistance gene , which was translocated from wheat relative chromosome 7E to durum wheat chromosome 7A, is known to produce high YPC, and the causal gene is presumed to be , which is tightly linked to . In this study, produced higher YPC than alleles, such as , and , in durum wheat. Segregation analysis demonstrated that is located at the locus on chromosome 7A. In a 2-year field test of near-isogenic materials, was accompanied by yield loss with decreases in grain number per spike, test weight and thousand-kernel weight under moisture conditions typical of wheat-growing areas of Japan. Thus, has the potential to contribute high YPC in durum wheat breeding programs, although the applicable cultivation environments are limited.

Polyphenol oxidase (PPO) is a key enzyme contributing to the time-dependent discoloration of wheat products. Developing cultivars with low PPO activity is one way to solve this problem. In this study, we focused on the gene, which has the second highest effect on grain PPO activity after the gene. Utilizing resequencing data, we found that the gene in the common wheat line 'Fukuhonoka-NIL', which exhibits low PPO activity, has an approximately 3 kb deletion in the 3'UTR and a 73 bp deletion in the third exon. The deletion in the third exon indicated that this allele was the allele, previously identified in the wheat D genome progenitor, Coss. Additionally, the allele in 'Fukuhonoka-NIL' had very low expression, suggesting that this allele is non-functional. We developed a new co-dominant DNA marker for distinguishing the , and alleles and demonstrated that F plants homozygous for the allele exhibited significantly lower grain PPO activity. Additionally, we determined that the allele likely originated from ssp. (lineage 1) accessions. The allele has not previously been found in common wheat ( L., AABBDD genome), and thus the DNA marker developed in this study will be helpful for introducing this allele in common wheat breeding programs.

Japanese red or white common bean ( L.) cultivars, used to make sweetened boiled beans, are called "kintoki" beans. Kintoki beans are planted to precede winter wheat for crop rotation in Hokkaido, northern Japan. Therefore, early maturity is an important trait for them. The aim of this study was to map the genomic region associated with days to maturity in kintoki beans by genome-wide association study (GWAS). Significant single nucleotide polymorphisms associated with days to maturity were detected on chromosome 1 (Pv01) by GWAS in 3 years, and the candidate region for early maturity was mapped to a 473-kb region. Sequencing analysis indicated that , a gene, is likely to be responsible for early maturity in kintoki cultivars: the insertion of a cytosine in exon 1 at position 47 644 850 on Pv01 causes a frameshift that creates an early stop codon. Our findings suggest that the loss-of-function mutation of is derived from a leading cultivar, 'Taisho-Kintoki', and is originated from a spontaneous mutation in the oldest kintoki cultivar, 'Hon-Kintoki'. The DNA markers targeting the functional insertion of will be useful for marker-assisted selection in kintoki bean breeding.

Advances in sequencing technologies have enabled the determination of genome sequences of multiple lines within a single species. Comparative analysis of multiple genome sequences reveals all genes present within a species, providing insight into the genetic mechanisms that lead to the establishment of species. Highly accurate pan-genome analysis requires telomere-to-telomere gapless genome assembly, providing an ultimate genome sequence that covers all chromosomal regions without any undetermined nucleotide sequences. This review describes the genome sequencing technologies and sophisticated bioinformatics required for telomere-to-telomere gapless genome assembly, as well as a genetic mapping that can evaluate the accuracy of telomere-to-telomere genome assembly. Pan-genome analyses may contribute to the understanding of genetic mechanisms not only within a single species but also across species.

Barley () is widely cultivated, ranking fourth in cultivation area among cereal crops worldwide. Many wild and cultivated barley accessions have been collected and preserved in crop genebanks throughout the world. Barley has a large genome (~5 Gbp) that has recently been sequenced and assembled at the chromosome level by the international research community. The community also is sequencing accessions representing the diversity of both domesticated and wild barley to provide genome-wide genotyping information for pangenome analysis. Given that the pangenome represents the universe of genome sequences existing in a species, the long-term goal of this project is to obtain high-quality genome sequences of the major barley accessions worldwide. As each accession is annotated, the capacity to explore structural differences is enhanced by the increased understanding of the diversity of the barley genome, which will facilitate efficient development of cultivars for human consumption. This review describes our current knowledge of barley genome diversity and proposes future directions for basic and applied research of the barley pangenome.

Soybean is an ancient crop domesticated from wild soybean ( Sied. & Zucc) in East Asia 6,000-9,000 years ago and has been widely grown as human food and livestock feed in China, Korea, Japan, and the rest of the world since. Global climate change has led to a series of challenges in soybean cultivation and breeding. With the development of high-throughput genomic sequencing technologies, genomic information on soybeans is now more readily available and can be useful for molecular breeding. However, epigenetic regulations on crop development are still largely unexplored. In this review, we summarized the recent discoveries in the regulatory mechanisms underlying soybean adaptations to biotic and abiotic stresses, particularly with respect to histone modifications and microRNAs (miRNAs). Finally, we discussed the potential applications of this knowledge on histone modifications and miRNAs in soybean molecular breeding to improve crop performance in the changing environment.