On the cover

In conventional breeding systems, different varieties are crossed, and individuals exhibiting desirable traits are repeatedly selected from the resulting progeny. The complexity of this process is largely determined by the life cycle and reproductive mode of each crop. However, beyond these biological constraints, DNA marker-assisted selection (MAS) provides an effective approach to enhancing breeding efficiency across a wide range of species. MAS is now routinely employed in rice breeding in Japan, and a substantial number of varieties developed through this approach are widely cultivated (This issue, p. 3–26).

(A. Goto: Institute of Crop Science, NARO)

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.

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.

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.

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.

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.

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 whole-genome 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.