This review summarizes the current status and future prospects of using genomic information for wheat breeding. Wheat has the largest genome among all major crops (~16 Gb), thus requiring a sophisticated approach to collect and utilize genomic information compared to other crops. In this review, we first describe the conventional methods of marker-assisted selection in wheat breeding. We discuss results from studies using DNA markers, such as those breaking the tight linkage between disease resistance and undesired quality traits. Although marker-assisted selection has achieved some success, breeding efficiency cannot be easily improved using this technique alone because several important traits, such as yield, are governed by a large number of genes. Recently-developed tools for genetic analysis, such as next-generation sequencing, are being increasingly used in wheat research. Therefore, we outline the history and current status of wheat genome resources, including reference genome sequencing, databases, analysis tools, and genotyping platforms. Further, we discuss the prospects for wheat breeding based on these resources. This review highlights the importance of incorporating new technologies to breed wheat varieties with high yield and quality.
The development of new cultivars exhibiting high levels of disease resistance and superior quality is critical for vegetable production. Recent advances in genomics and DNA sequencing technologies have facilitated the identification of sequence variants associated with specific phenotypes. This has enabled the development of novel and improved DNA markers for integration into marker-assisted selection (MAS). The application of MAS has significantly enhanced the efficiency of stacking loci responsible for disease resistance and quality characteristics. This paper provides an overview of recent research findings related to DNA markers and their applications in breeding in Japan, focusing primarily on vegetables from Brassicaceae, Solanaceae, Cucurbitaceae, and Allium, as well as strawberries.
In response to recent environmental and geopolitical changes, Japan requires rice cultivars with high adaptability and production efficiency. Advances in rice genomics have enabled precise genetic mapping and the use of DNA markers for efficient selection. Marker-assisted selection (MAS) reduces labor and environmental influences, and co-dominant markers allow accurate genotyping. When combined with backcrossing, MAS enables rapid pyramiding of multiple traits. Marker-assisted breeding has been widely applied to improving elite cultivars across Japan. This review highlights the practical applications of DNA markers in rice breeding programs in Japan. Specifically, we examine how molecular markers have been used to improve resistance to diseases and pests, improve grain quality, strengthen tolerance to abiotic stresses, and support the selection of agronomically important quantitative traits such as heading date and yield. We also provide an overview of a practical approach to accelerating breeding through MAS and generation advancement for efficient trait stacking. Finally, we present future perspectives on expanding the use of molecular markers to further improve the efficiency and precision of rice breeding.
Tomato plants are susceptible to a wide range of viruses, including those belonging to the genus Tobamovirus, which pose enormous threats to tomato cultivation worldwide. This article reviews a genomics-based breeding strategy applied for the rapid discovery and introgression of the newly identified HREZ resistance gene, which provides high-resistance to the recently emerged Tobamovirus fructirugosum (Tomato Brown Rugose Fruit Virus (ToBRFV)). From the identification of a novel viral tomato pathogen in 2015, an applied breeding strategy allowed us to launch a series of 18 tomato varieties within a time span of seven years.
Following the recent global progress in the establishment of soybean genomic resources, DNA marker technologies have been actively implemented in soybean breeding programs in Japan, thereby enhancing the efficiency of varietal improvement and facilitating the successive release of cultivars developed through the application of DNA markers. In particular, DNA markers developed for the selection of useful traits, such as pod-shattering resistance and bacterial leaf pustule resistance present in foreign germplasms, have facilitated the precise introgression of only the desired alleles from genetically divergent foreign germplasms into Japanese backgrounds. By increasing selection efficiency and shortening breeding cycles, these advances have substantially contributed to the recent improvements in Japanese soybean breeding. The present review consolidates findings on genetic variations identified in Japanese cultivars and breeding materials, which have been investigated for the development of such DNA markers, and from knowledge expected to contribute to future soybean breeding in Japan.
Tea, made from the tea plant (Camellia sinensis L.), is one of the most widely consumed beverages worldwide. Traditional breeding methods have contributed to the development of cultivars with desirable traits; however, these breeding approaches are time-consuming and constrained by the limited genetic diversity of tea plants. Despite the significant impact of genomic information on crop breeding, its application in tea plants has remained limited. Recently, the rapid accumulation of genomic resources for tea plants has enabled the research development for markers-assisted selection and genomic selection in tea breeding. These genomics-based approaches are positioned as complementary methods to phenotypic selection. In this review, we summarize the advancements in breeding technologies for tea in Japan and highlight future directions for genomics-based tea breeding.
Vigna riukiuensis is one of the most salt-tolerant species within the genus Vigna, yet intraspecific variation in its salt tolerance remains uncharacterized. In this study, we evaluated 61 accessions of V. riukiuensis under 200 mM NaCl using effective quantum yield (Y(II)) as an indicator of salt tolerance. Accessions were classified into five clusters, showing substantial variation that accessions in the tolerant group maintained Y(II) for four weeks whereas those in the sensitive group lost Y(II) in a week. We repeated the Y(II)-based classification for a subset of accessions and the results generally reproduced that of the first evaluation. In addition, we measured Na+ and K+ allocation in roots, stems and leaves and found the pattern of Na+ allocation greatly varied even within the most tolerant accessions whereas the pattern of K+ allocation, not the Na+/K+ ratio, showed a minor correlation with salt tolerance. Interestingly, JP254554 restricted Na+ transport from roots to leaves, but it did not develop Casparian strips even under salt stress. This study provides the first comprehensive assessment of intraspecific variation in V. riukiuensis, identifying promising donor accessions for breeding, and highlighting various unknown mechanisms to be elucidated in the future.
Monitoring genome structure provides a great advantage for efficiently and accurately advancing breeding. However, genotyping using DNA markers distributed across the genome is time-consuming and labor-intensive for breeders. Here, we developed a graphical user interface application, "WGG: Whole Genome Genotyping", enabling rapid and easy visualization of genome structures based on single nucleotide polymorphisms (SNPs) detected by resequencing with next-generation sequencing short reads. The accuracy of WGG is enhanced by selecting SNPs from parental resequencing data and determining the majority genotype within each genomic region. As proof of principle, we efficiently developed near-isogenic lines in rice by monitoring genome backgrounds with WGG in intermediate generations. The identification of residual donor regions with WGG facilitated their elimination using DNA markers designed at these loci. Furthermore, we confirmed the applicability of WGG in rice recombinant inbred lines and heterozygous plants, Brassica rapa. In addition, WGG was confirmed to run smoothly on a standard desktop PC even with sufficient sequencing data, making it practical for breeders. WGG will be a powerful tool for visualizing genome structures in breeding intermediate generations, enabling whole-genome selection that will accelerate breeding in diverse crops.
Stink bugs are major insect pests that damage rice after heading, causing pecky rice and sterility, which significantly reduce grain quality and yield. We identified a major quantitative trait locus (QTL) for stink bug resistance derived from the resistant donor variety'Milyang 44' and explored DNA markers useful for marker-assisted selection in rice breeding. QTL analysis using an F5 population (n = 94) identified a major QTL, qSBR11, on chromosome 11, which explained 28.46% of phenotypic variance in Pecky Rice Index. Fine mapping of the BC1F3 and BC5F3 populations narrowed the candidate region of qSBR11 to approximately 616 kbp. In the validation experiments, individuals selected using the marker C5_indel9205 located within this candidate region showed significantly reduced pecky rice rate. Additionally, the marker genotype was highly consistent with phenotypes of 22 tested varieties, and genomic analysis of 685 accessions from TASUKE+ in the Rice Annotation Project Database showed that the resistant allele was rare in japonica culti- vars. Therefore, that qSBR11 is a promising target for breeding japonica rice. This study identified a major QTL for stink bug-induced pecky rice resistance and demonstrated the utility of a reliable DNA marker for practical breeding.
Utilizing genetic information is a promising strategy to accelerate crop breeding. The identification of many causative genes in rice, even for polygenic traits, enables us to take on the challenge of predicting yield-related traits by using allele information. However, phenotyping has been a bottleneck in such analyses. Historical breeding data constitute a valuable source of yield-related phenotypic data. Here, we used a subset of 19,218 records drawn from 225,163 records in the rice historical phenotype dataset maintained by the National Agriculture and Food Research Organization. We evaluated the heritability of seven yield-related traits explained by 26 agronomically important genes and the accuracies of the models' predictions. These genes constituted a portion of the total genetic effect, but the effects of the genetic background were also significant. In some traits, the model based on the agronomically important genes proved more accurate than that based on whole-genome polymorphisms. We also estimated the effects of genes that contribute to yield. This paper presents the possibilities and challenges of utilizing historical breeding data, and important information on how to utilize allele information in future breeding.
The use of genetic variations in Asian cultivated rice is essential for crop improvement. Advanced technologies and accumulated genome information support this effort to ensure sustainable production under changing environmental conditions. Grain length and grain width are important agronomic traits in rice. Extensive studies have revealed their complex genetic control. To further clarify the genetic basis of grain length and grain width in rice, we constructed a comprehensive catalog of QTLs for these traits based on QTL analysis of advanced backcross populations from crosses between a japonica rice cultivar 'Koshihikari' and 12 diverse donor cultivars. It comprised 469 QTLs (average 39.1 QTLs per donor) and provided estimates of allelic effects within a uniform japonica genetic background. To validate and delimit QTLs, we used sub-CSSLs-a set of plant materials with one or no segregating regions from these donors in a homogeneous genetic background. New QTLs were validated by genetic mapping in three chromosomal regions previously unreported in other mapping populations. Our results underscore the diversity and complexity of genetic control of grain length and grain width in Asian cultivated rice, and these insights will facilitate more precise genetic improvement of rice grain traits.
Wheat yellow mosaic (WYM) disease, caused by the wheat yellow mosaic virus (WYMV), significantly affects wheat production. Three WYMV pathotypes-I, II, and III-have been identified in Japan, each with a distinct geographical distribution and pathogenicity. To investigate the historical and geographical distribution of infection-resistant wheat varieties in Japan and the relevant genetics, we comprehensively evaluated the response to WYMV pathotypes and the genotypes conferring resistance in accessions of the Japanese wheat core collection. In the experimental fields harboring WYMV, most of the varieties that showed stable resistance were breeders lines; only a few were traditional varieties. Resistant accessions are particularly prevalent in northern Japan. These results suggest that resistant varieties have been developed through modern breeding, in which crossbreeding with foreign varieties has played a major role. Resistance-conferring genes on the chromosome 2DL and 5AL appeared to have been introduced during this breeding process, and the 5AL locus became widely distributed in Japanese varieties. Through genome-wide association studies, we identified a novel resistance-conferring locus on chromosome 7AS. Furthermore, the resistant haplotype on 7AS confers robust resistance to pathotype I when combined with the haplotype carried on 5AL. The results of this study contribute to the understanding of resistance-associated genetics in the context of WYM disease, highlighting the potential of particular genomes to confer robust and durable resistance in breeding efforts.
Optimizing heading date to suit local conditions is key to maximizing yield potential. 'Haruka Nijo', a two-rowed barley (Hordeum vulgare L.) cultivar developed for the Kyushu region of Japan, is early-heading and has superior yield performance compared to the standard cultivar 'Nishinohoshi'. To identify genomic regions associated with early-heading in 'Haruka Nijo', we conducted analysis of quantitative trait loci (QTLs) using recombinant progeny of 'Haruka Nijo' × 'Nishinohoshi' (heading date difference: 2.4-6.0 days). A stable QTL, designated QHD.HN-5H, was detected near the centromere of chromosome 5H. This QTL explained 30.3-46.1% of the phenotypic variance and consistently conferred 2-5 days earlier heading across three seasons. Pedigree analysis indicated that the QHD.HN-5H region in 'Haruka Nijo' likely originated from the Tohoku six-rowed cultivar 'Haganemugi' and was probably co-introduced into Kyushu cultivars together with the Barley yellow mosaic virus resistance gene rym3. Whole-genome sequencing and Gene Ontology analysis identified non-synonymous differences between 'Haruka Nijo' and 'Nishinohoshi' in five heading-related genes within the QTL region. Four of these genes shared identical genotypes between 'Haganemugi' and 'Haruka Nijo', supporting their candidacy. These findings provide new breeding tools to adapt the heading date of barley to the climate and cultivation environment.
Cottonseeds are rich in proteins with high nutritional value. In this study, a genome-wide association study involving six methods was performed to dissect the genetic architecture of the cottonseed protein content (CPC) in Upland cotton (Gossypium hirsutum L.). The CPC exhibited typical characteristics of a quantitative trait. The six methods revealed 1, 4, 4, 31, 10, and 30 CPC-related quantitative trait nucleotides (QTNs), among which 17 were detected by at least two methods. Notably, TM40095 on A12 and TM59869 on D06 were detected by three methods, thus being considered stable QTNs. Five QTN-by-environment interactions (QEIs) and 29 QTN-by-QTN interactions (QQIs) were detected. The regions flanking the SNPs of two stable QTNs, five QEIs, and four significant QQIs included 49, 174, and 269 candidate genes, respectively. A functional enrichment analysis indicated that 12 and 48 non-redundant genes related to the two stable QTNs and five QEIs, respectively, were associated with significantly enriched functions. Moreover, eight protein (gene)-protein (gene) interactions were predicted. According to RNA-seq expression data, GH_D06G1049 (related to QTNs) and GH_A06G1663, GH_D13G0601, and GH_A05G0236 (related to QEIs) were preferentially expressed in multi- ple ovule tissues, suggesting that they may contribute to seed protein synthesis and accumulation. These findings provide new clues regarding the genetic basis of CPC and may accelerate the molecular breeding of cotton with ideal protein content.
We developed a new reddish-purple fleshed sweetpotato (RFSP) cultivar, 'Sakurahonoka', with high yield for processing use. Released in 2025, the most distinctive characteristic of Sakurahonoka is its flesh color. The dominant aglycone (anthocyanidin-moiety) of anthocyanin (aglycone) in Sakurahonoka is pelargonidin, which distinctly varied from the purple-fleshed sweetpotato (PFSP) cultivars, whose dominant aglycones were peonidin or cyanidin. Sakurahonoka demonstrated a higher marketable root yield than the two major PFSP cultivars in the Kyushu region of Japan: 'Ayamurasaki' and 'Murasakimasari'. Additionally, Sakurahonoka showed a higher resistance to sweetpotato foot rot disease than Ayamurasaki. Furthermore, the color of Sakurahonoka processed as fried chips and steamed paste was unique and brighter than that of the PFSP cultivars. Food manufacturers have found that Sakurahonoka is suitable as an ingredient in fried chips and boiled-diced sweetpotato. It can be processed into a paste; however, its steamed sweetpotato is fibrous and requires effort to be strained. Thus, Sakurahonoka is an epoch-making RFSP that improves the color variation in sweetpotato-processed foods.
In Brassicaceae crops such as cabbage and turnip, which are harvested for their vegetative organs, floral induction can reduce the eating quality of these organs. Therefore, developing late-flowering varieties that are insensitive to vernalization is a key breeding objective. However, a major challenge in breeding these cultivars lies in the contradiction between the late-flowering trait and the need to induce flowering for crossing. To address this, we developed a flowering induction technique using grafting, in which gibberellin-induced elongated internodes are used as scions and grafted onto the flower stalk of Brassica rapa cv. 'CHOY SUM EX CHINA 3', which constitutively expresses FLOWERING LOCUS T (FT), as the rootstock. This method is applicable even to rosette-type Brassicaceae plants with short internodes. Histological and radioisotope analyses confirmed the reconnection of vascular bundles and the functionality of component transport across the graft junction. Additionally, gibberellin treatment was found to promote flowering in the presence of FT, most likely through an activation of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3, a gene known to promote floral meristem development. This rapid flowering system offers a practical strategy for accelerating the breeding of late-flowering Brassicaceae crops.
The National Agriculture and Food Research Organization (NARO) is advancing "Citrus Breeding 2.0" to produce diverse, high-quality hybrid citrus cultivars more efficiently by integrating genomic prediction, genome-wide association studies (GWAS), and pedigree data. Reduced representation sequencing (RRS) methods, such as RAD-Seq, ddRAD-Seq, and GRAS-Di, facilitate large-scale, cost-effective genotyping; however, variable loci hinder cross-platform comparisons, limiting model reuse and GWAS follow-up. Therefore, we developed an Augmented Estimation of Unified Genotype (AEUG) workflow that converts RRS-derived genotypes into a unified set of predefined loci using a whole-genome resequencing reference panel that shares a common haplotype with target populations. Although Beagle-based wholegenome imputation achieved only 61.3-83.6% accuracy, genomic prediction for 17 fruit traits remained virtually unchanged after conversion, demonstrating the robustness of the workflow. The alignment of loci with ancestry informative markers for four pure citrus species also enabled the estimation of the ancestral origin of the trait-associated genomic regions. The AEUG workflow facilitates the integration and reuse of heterogeneous genotype datasets, enhances prediction accuracy, and enables ancestry-informed GWAS interpretation to accelerate citrus genomic breeding.
'Harushizuka' is a novel late-maturing satsuma mandarin (Citrus unshiu Marcow.) cultivar developed through heavy-ion irradiation-induced mutagenesis. The S1152 line, selected from a nucellar seedling of the 'Aoshima unshu' cultivar for superior fruit quality, was irradiated with both carbon and neon ions. Mutations in fruit shape, color, and peel characteristics were observed in the neon-ion-irradiated group. From this group, we isolated the 'Harushizuka' cultivar, which exhibits delayed fruit coloring. The harvest season for 'Harushizuka' is approximately one month later than that of regular C. unshiu, allowing for a more spread-out harvesting period. To develop DNA markers for cultivar protection and identification, we performed whole-genome mutation analysis of 'Harushizuka' and its original cultivar 'Aoshima unshu'. Two mutations were identified: a 30-bp deletion and a 20-bp insertion. The PCR assay targeting the deletion successfully differentiated 'Harushizuka' from 21 other C. unshiu cultivars. Our findings demonstrate that whole-genome mutation analysis is a powerful tool for developing DNA markers, even in citrus cultivars with low genetic diversity caused by bud mutations or nucellar embryogenesis. The established marker enables rapid and accurate identification of 'Harushizuka', contributing to the protection of breeders' rights and the prevention of unauthorized propagation.
Fusarium head blight (FHB) is a severe disease that affects wheat production. 'Sumai 3' has been used as the FHB resistance genetic resource, and DNA markers linked to known quantitative trait loci (QTL) located on 3BS, 6BS, 5AS, or 2DL have been used to detect the 'Sumai 3'-derived allele. We first developed a near-isogenic line (NIL) of a Japanese cultivar, 'Kitahonami', with 'Sumai 3' FHB resistant allele at the 2DL-located QTL by recurrent backcrossing. Although the 'Sumai 3' allele improved resistance to FHB, it reduced yield and thousand-grain weight (TGW) to unacceptable levels. During the genotype of FHB-resistant QTL in FHB-resistant breeding lines K-1932 and K-1976, we found both lines have a novel allele at the 2DL-located QTL introduced from 'Asakaze'. We confirmed the co-segregation between the FHB resistance phenotype and the novel 'Asakaze'-derived allele in the three breeding populations. Furthermore, we developed two sets of NILs, with and without the 'Asakaze'-derived allele, and examined the FHB resistance, yield, and TGW. The results show that the 'Asakaze'-derived allele improved FHB resistance similar to the 'Sumai 3'-derived allele. Surprisingly, the 'Asakaze'-derived allele did not negatively affect yield and TGW, contrary to the 'Sumai 3'-derived allele. Wheat breeders can improve FHB resistance without reducing yield and TGW using the 'Asakaze'-derived QTL allele.
