The cultivated peanut, L., is an important source of edible oil and highly digestible protein. Wild incompatible species outside section Arachis are ideal gene reservoirs for genetic improvement of the peanut crop. Among these, Benth. stands out for its noted resistance to various stresses. Traditional embryo rescue techniques have been fraught with challenges, including time consumption, resource intensiveness, late intervention timing, and limited effectiveness. In this study, we employed three hormone formulations in an innovative embryo rescue approach to facilitate the production of intersectional hybrids. Through this method, hybrid seeds resulting from the crossing of two incompatible species, namely and , with four high-oleic peanut varieties were successfully obtained. Molecular marker analysis and observation of plant characteristics confirmed the hybrid nature of these seeds. This breakthrough represents a significant advancement in expediting the utilization of incompatible wild species in peanut breeding programs. Moreover, the embryo rescue technique showcased in this study holds promise for application in other plant species characterized by postzygotic cross-incompatibility.

'Sanenashi' is a landrace of var. (Iwateyamanashi) with seedless fruit originating from northern Tohoku, Japan. To determine the mechanism of seedless fruit formation, we compared the number of styles in the pistil, fruit, seed set and the pollen tube growth between 'Sanenashi' and the Japanese pear cultivar 'Kosui'. Morphological variations such as short or browning pistils were observed in 64.2% of 'Sanenashi' and 5.9% of 'Kosui'. The initial fruit set rate of 'Sanenashi' was 48.3% at 4 weeks after cross-pollination with pear, and there were no fruit sets with peach pollen and non-pollinated sections at 8 weeks. Although the seed sets of 'Sanenashi' fruit were much lower than that of 'Kosui', 55.3% of viable 'Sanenashi' seeds germinated. Pollen tube growths were observed in the stigma and style of 'Sanenashi', but whether they reached the ovary could not be confirmed. Single sequence repeat (SSR) alleles of F progenies between 'Sanenashi' and pear cultivars were presented by five SSR markers. These results suggest that the seedless fruit formation in 'Sanenashi' corresponds with pseudo-parthenocarpy (stenospermocarpy) because pollination by pear pollen is necessary for the fruit set. However, the results do not fully confirm this hypothesis and require further experiments.

Heading date is a key agronomic trait for adapting rice varieties to different growing areas and crop seasons. The genetic mechanism of heading date in Myanmar rice accessions was investigated using a genome-wide association study (GWAS) in a 250-variety diversity panel collected from different geographical regions. Using the days to heading data collected in 2019 and 2020, a major genomic region associated with the heading date, designated as MTA3, was found on chromosome 3. The linkage disequilibrium block of the MTA3 contained the coding sequence (CDS) of the phytochrome gene but not in its promoter region. Haplotype analysis of the 2-kb promoter and gene regions of revealed the six haplotypes, PHYCHapA, B, C, D, E, and F. The most prominent haplotypes, PHYCHapA and PHYCHapC, had different CDS and were associated with late heading and early heading phenotypes in MIDP, respectively. The difference in CDS effects between the PHYCHapB, which has identical CDS to PHYCHapA, and PHYCHapC was validated by QTL analysis using an F population. The distribution of PHYCHapA in the southern coastal and delta regions and of PHYCHapC in the northern highlands appears to ensure heading at the appropriate time in each area under the local day-length conditions in Myanmar. The natural variation in would be a major determinant of heading date in Myanmar accessions.

The -deficient rice ( L.) mutant (), with a low grain cadmium (Cd) content, was registered as 'Koshihikari Kan No. 1' in Japan. Its agronomic traits are almost identical to those of 'Koshihikari' except for its low Cd content and its susceptibility to brown spot (BS) caused by . To restore BS resistance, we introduced the BS resistance quantitative trait locus (QTL) into it. The resulting isogenic line (IL) had higher resistance to BS than Koshihikari Kan No. 1 while retaining low grain Cd, with no significant difference from Koshihikari in grain yield or quality. This IL, which we named 'Kanto IL 31', can be used for breeding varieties with low Cd content and BS resistance.

The PLATZ (Plant AT rich protein and zinc binding protein) transcription factor, which is a type of plant specific zinc dependent DNA binding protein, participates in regulating the process of plant growth and environmental stress responses. In order to clarify the characteristics of the family genes in birch (), the members of the family were screened and analyzed in this study. Totals of ten genes were identified in birch genome and classified into five groups base on phylogenetic relationship, genes in the same group usually possess a similar motif composition, exon or intron number. These ten genes distributed on eight chromosomes of fourteen chromosomes of birch. In addition, various -elements were distributed in the promoter regions of , especially with abundant MYC, ABRE and MYB, which were reported to be involved in salt stress responses. The RT-qPCR analysis results show that most genes have the higher expression levels in the roots compared to leaves and stems in birch. , , , and are significantly induced expressed response to salt stress. These studies provide a basis for the further functional study of the genes.

Visualizing genotypic data is essential in genetic research and breeding programs as it offers clear representations of genomic information, enhancing understanding of genetic architecture. This becomes especially critical with the emergence of next-generation sequencing (NGS) technologies, which generate vast datasets necessitating effective visualization tools. While traditional tools for graphical genotypes have been groundbreaking, they often lack flexibility and universal applicability. These tools encounter limitations such as user-customized visualization and compatibility issues across different operating systems. In this study, I introduce GenoSee, a novel visualization tool designed to address these shortcomings. GenoSee can handle phased and non-phased variant calling data, offering extensive customization to suit diverse research requirements. It operates seamlessly across multiple platforms, ensuring compatibility, and provides high-quality graphical genotypes. GenoSee facilitates deeper insights into genomic structures, thereby advancing genetic and genomic research, and breeding programs by enhancing accessibility to genetic data visualization.

The progenies of polyploid crops inherit multiple sets of homoeologous chromosomes through various combinations, which impedes the identification of the quantitative trait loci (QTL) governing agronomic traits and the implementation of DNA marker-assisted breeding. Previously, we developed a whole-genome sequencing-based polyploid QTL-seq method that utilizes comprehensively extracted simplex polymorphisms for QTL mapping. Here, we verified the detection of duplex QTLs by modifying the analytical settings to explore the QTLs governing tuber flesh color and starch phosphorus content using tetraploid potato ( L.). The F progenies were obtained from a cross between 'Touya' (TY) and 'Benimaru' (BM). A single TY-derived QTL responsible for yellow flesh color was identified around a β-carotene hydroxylase gene on chromosome 3 using simplex polymorphisms, and a BM-derived QTL associated with decreased starch phosphorus content near a starch synthase II gene on chromosome 2 was detected using duplex polymorphisms. Furthermore, linked DNA markers were developed at the QTL sites. For the latter QTL, plexity-distinguishable markers were developed using quantitative PCR, fragment analysis, and amplicon sequencing. These revealed the allele dosage-dependent effect of the reduced starch phosphorus content. Thus, the polyploid QTL-seq pipeline can explore versatile QTLs beyond simplex, facilitating DNA marker-assisted breeding in various polyploid crops.

Stem length is a crucial agronomic trait in rice breeding. The short stature of rice dwarf mutants is caused by shortening of internodes, resulting in five distinct internode elongation patterns: dn, dm, d6, nl and sh. Several genetic studies have been conducted; however, the genetic mechanisms underlying these internode elongation patterns remain unclear. In this study, we examined two Daikoku dwarf () mutants, T65() and Kin(), which display contrasting internode elongation phenotypes. Anatomical observation revealed that T65() exhibits a dm-type internode elongation pattern due to the lack of the second internode counted from the top, while Kin() shows a dn-type pattern with a relatively elongated second internode. To identify the genetic factors influencing these phenotypes, we conducted a quantitative trait locus (QTL) analysis using two F populations derived from reciprocal crosses between them. The QTL analysis showed that the second internode length is regulated by three QTLs on chromosomes 4, 5, and 6. Epistatic effects were observed through the analysis of F progenies, indicating that the combination of Kin() alleles at these QTLs is associated with an increased second internode length. Furthermore, specific combinations of alleles result in varying degrees of elongation in the second internode, significantly impacting the internode elongation pattern. These findings contribute to a deeper understanding of the genetic factors influencing the internode elongation patterns in rice.

The vascular bundle system in the panicle neck of rice ( L.) connects the culm to the panicle and transports assimilates. The number of vascular bundles in the panicle neck (VBN) is correlated with the diameter of the panicle neck (DPN), but there are few reported QTLs for DPN. We conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross between 'Asominori' and 'IR24' and detected three QTLs-, , and -on chromosomes 5, 6, and 11. The , , and were in the same position as the QTLs for VBN reported in previous studies. Within the RILs, there was a significant positive correlation between DPN and VBN. In segregating populations, each QTL had a distinct effect on both values. Analysis of chromosome segment substitution lines showed that and affected DPN and affected VBN. Through substitution mapping, we narrowed down the region of and to 960 kbp between KNJ8 Indel385 and RM18926, and the region of to 750 kbp between C5 Indel5756 and KNJ8 Indel493. Due to the weak effect of in the 'IR24' genetic background, the location of could not be determined.

Hokkaido-specific malting barley varieties have been developed to improve the grain yield, disease resistance, malting quality, and brewing quality. In this report we describe the breeding and evaluation of brewing quality of a hulled two-row malting barley ( L.) variety 'Satuiku 5 go' lacking lipoxygenase-1 (LOX-1-less). 'Satuiku 5 go' was evaluated in the joint field trials for malting barley in Hokkaido from 2016 to 2018. 'Satuiku 5 go' exhibited 11% higher grain yield and 7.6 cm shorter plant height than the control variety, 'Ryohfu'. However, the disease severity of Fusarium head blight (FHB) in 'Satuiku 5 go' was higher than in 'Ryohfu'. For malting quality, 'Satuiku 5 go' exhibited higher diastatic power, soluble nitrogen content, and fine extract content, and lower wort β-glucan content than 'Ryohfu'. 100-litter pilot scale brewing trials were conducted with 'Satuiku 5 go' and 'Satuiku 2 go' as a control variety, also a LOX-1-less variety, and no clear differences were observed.

This review compiles information on the morphology, historical taxonomic treatments, species origin, gene pool concept, geographical and ecological habitats, and stress tolerance of the azuki bean () and related species. Willdenow (1802) first described the azuki bean in the genus , and Ohwi and Ohashi (1969) finally transferred it to the genus . The genus is currently divided into five subgenera: , , , , and . The subgenus includes the moth bean in section ; the mungbean and black gram in section ; and the azuki bean, rice bean, and creole bean in section . The wild species in section generally possess larger standard petal with more prominent appendage, keel petal with longer pocket, pistil with longer style beak compared with those of species in sections and , and characterized by glabrous mature pod, smooth seed coat, hypogeal germination seed, and cordate primary leaves with petiole. Section currently consists of 13 species. The taxa that cross readily with the azuki beans included in the primary genepool are the wild azuki bean var. , , , , , , and . These wild species are expected to be used as breeding material against biotic and abiotic stresses.

To explore the molecular mechanism behind maize grain quality and use of different gene stacking to improve the nutritional quality of grain, marker-assisted selection (MAS) was used to select three recessive mutant lines containing , along with the double-recessive mutant lines containing , , and . The resulting seeds were taken for transcriptome sequencing analysis 18 days after pollination (DAP). Results: Compared with the recurrent parent genes, in the lysine synthesis pathway, the gene pyramiding lines (, , and ) revealed that the gene encoding aspartate kinase (AK) was up-regulated and promoted lysine synthesis. In the lysine degradation pathway, 'QCL8010_1' () revealed that the gene encoding saccharopine dehydrogenase (LKR/SDH) was down-regulated. In addition, the gene pyramiding lines (, , and ) indicated that the gene encoding 2-oxoglutarate dehydrogenase E1 component (OGDH) was down-regulated, inhibiting the degradation of lysine. In the tryptophan synthesis pathway, the genes encoding anthranilate synthase (AS), anthranilate synthase (APT), and tryptophan synthase (TS) were up-regulated (in , , , and ), and promote tryptophan synthesis. In the tryptophan degradation pathway, it was revealed that the genes encoding indole-3-producing oxidase (IAAO) and indole-3-pyruvate monooxygenase (YUCCA) were down-regulated. These results provide a reference for revealing the mechanism of the , , and with different gene pyramiding to improve grain quality in maize.

Green rice leafhopper (GRH, Uhler) is a serious insect pest of rice in the temperate regions of Asia. Myanmar has a high genetic diversity and is located at the center of the origin of rice. To understand the genetic architecture of GRH resistance in Myanmar rice landraces, a genome-wide association study (GWAS) was performed using a diversity panel collected from diverse geographical regions. Phenotypic variation in GRH resistance was associated with three genomic regions, MTA4, MTA5, and MTA11, located on chromosomes 4, 5, and 11, respectively. MTA4 and MTA5 were adjacent to the known resistance genes and . Analysis of haplotypes and linkage disequilibrium blocks revealed that the haplotypes HapA, HapA, and HapMTA11A mainly explained GRH resistance. Map-based cloning revealed that was highly induced by GRH infestation and conferred resistance by inhibiting the sucking of phloem sap. The distribution of resistance haplotypes revealed that accessions harboring major resistance haplotypes (HapA and HapA) were mainly distributed in Southern Myanmar, and HapMTA11A was mainly responsible for GRH resistance in mountainous areas of Myanmar. Our findings could facilitate the elucidation of the molecular mechanism of GRH resistance and provide essential haplotype-based genetic information for the development of GRH-resistant rice cultivars.

The introgression of heterologous genomes through interspecific hybridization offers a great opportunity to expand the gene pool of crops, thereby broadening the traits that can be targeted for improvement. The introgression of C genomic regions carrying desirable traits from (AACC) into the diploid (AA) via homoeologous recombination (HR) has been commonly used. However, the precise identification of HR sites remains a significant challenge, limiting the practical application of genome introgression via HR in breeding programs. Here, we developed an indicator named 'Dosage-score' from the coverage depth of next-generation sequencing reads. Then, Dosage-score analysis applied to both in BCF individuals obtained by backcrossing to F progeny ( × ) and in the parental lines, and successfully identified the precise HR sites resulting from F meiosis as well as those that were native in the parental genome. Additionally, we introgressed the C6 segment from HR identified by Dosage-score analysis into genome background, revealing gene expression on the added segment without noticeable phenotypic change. The identification of HR by Dosage-score analysis will contribute to the expansion of the gene pool for breeding by introgression of heterologous genomes in crops.

Tomatoes have the highest agricultural production among vegetables in Japan and worldwide. Japanese large-sized fresh-market tomatoes have a unique breeding history that differs from that of other countries, represented by pink-colored and juicy fruits with a good taste and flavor. We performed whole-genome resequencing of 150 Japanese large-sized fresh-market tomato cultivars released from the 1940s to the 2000s to unveil how breeding selection has changed the genome of Japanese tomato cultivars and provide a genomic basis for future Japanese tomato breeding. The genomic population structure of the cultivars was highly correlated with the year of release. Comparison between the agronomic performance and release year of the cultivars reflected trends in recent breeding selection: an increase in fruit sugar content and a decrease in yield performance. Multiple selection signatures were detected on all the tomato chromosomes. One of the selection signatures was related to the introgression of a resistance gene () from a wild relative. Interestingly, some of the putative QTLs detected by genome-wide association studies did not co-localize with the selection signatures, indicating that the genetic diversity of Japanese tomato cultivars still has the potential for genetic improvement of agronomic performance.

Turnip mosaic virus (TuMV) poses a major threat to crops like Chinese cabbage, causing significant economic losses. A viable and effective strategy to manage such diseases is by improvement of genetic-based viral resistance. To achieve this, it is important to have detailed and wide-ranging genetic resources, necessitating genetic exploration. To identify useful TuMV resistant genetic resources, we screened geographically and genetically diverse resources including over 90 accessions from the Tohoku Univ. Seed Bank against eleven TuMV isolates phylogenetically classified into five clusters. Two USA accessions exhibited no or only slight symptoms with no virus protein detected in virus-inoculated and non-inoculated upper leaves, suggesting an extreme resistance to all tested TuMV isolates. Through sequencing and dCAPS analysis of eukaryotic translation initiation factor (eIF4E/eIFiso4E) in the 95 accessions, several amino acid substitutions were observed on the dorsal surface and cap-binding sites of eIF4E/eIFiso4E proteins, with three of them significantly associated with resistance/susceptibility responses. When exploring co-infection using TuMV and cucumber mosaic virus (CMV), the TuMV susceptible accession died, but TuMV resistance was retained in the TuMV resistant accession. It suggested that the broad-spectrum resistance in the two USA accessions is a highly valuable resources for breeding.

Asian rice ( L.) was domesticated from wild rice ( Griff.). During rice domestication, the wild characteristic of seed-shattering behaviour was suppressed, enabling an efficient harvest with increased yield. Rice, a stable food for humans, is one of the most important crops consumed by billions of people, especially in Asian countries. With advances in molecular genetic studies, genes or loci involved in reduced seed shattering via the inhibition of abscission layer formation have been identified. The mutations alone showed no inhibitory effect on abscission layer formation in the wild rice , but their combination enabled a stepwise change in the degree of seed shattering, which may be associated with advances in harvesting tools. In the early stages of rice domestication, the closed panicle formation and slight inhibition of the abscission layer resulted in complementary effects that increased harvesting efficiency. Furthermore, common and distinct loci were found to contribute to reduced seed shattering in groups of rice cultivars, indicating that mutations at seed-shattering loci are important information for tracing the process of rice domestication.

'Hisui no Kaori' is the first lettuce ( L.) cultivar characterized by a sweet fragrance, attributed to 2-acetyl-1-pyrroline with the same compound as in fragrant rice and soybean cultivars, as well as edible leaves and stem. Field cultivation trials established optimal planting distances at 30 cm between seedlings, with a fertilizer requirement of N = 150 kg/ha. 'Hisui no Kaori' exhibited minimal stem burst as well as resistance to soft rot disease, proving easier to cultivate compared with prominent stem-type cultivars. Field cultivation tests at different altitudes and incubator tests revealed that an air temperature exceeding 20°C is pivotal for the development of the sweet fragrance. 'Hisui no Kaori' displayed moderately resistance to Fusarium wilt race 1 and highly resistance to race 2. In lettuce, discoloration is known to occur at the cut surface due to mechanical wounding. In a cut leaf test, 'Hisui no Kaori' was classified as having delayed discoloration. Overall, 'Hisui no Kaori' is expected to contribute to the expanding potential and the increasing market price of lettuce. This work represents a pioneering effort to open up the fragrant type of lettuce.

The awn is a bristle-like appendage that protrudes from the seed tip and plays a critical role in preventing feed damage and spreading habitats in many grass species, including rice. While all wild species in the genus have awns, this trait has been eliminated in domesticated species due to its obstructive nature to agricultural processes. To date, several genes involved in awn development have been identified in wild rice, and which are ancestral species of cultivated rice in Asia and Africa, respectively. However, the responsible genes for awn development have not been identified in other wild rice species even though multiple QTLs have been reported previously. In this study, we identified gene responsible for awn development in two wild rice species, and . encodes a cytochrome P450 enzyme and is homologous to , a known brassinosteroid biosynthesis enzyme in rice. The identification of provides insight into a distinct molecular mechanism underlying awn development that occurs in geographically separated environments.

As an essential grain, oil, and feed crop worldwide, soybean plays a crucial role. Developing high-yielding and high-quality soybean varieties is a critical goal for breeders. The grain weight per plant and 100-grain weight directly impact the soybean yield. This study combined genotypic data from the population with phenotypic data. Based on genome-wide association analysis (GWAS), GLM and MLM analysis models were used to locate the Gm04_21489088, Gm04_15703616, and Gm04_46466250 are loci related to soybean grain weight per plant, and find the Gm09_20334173, Gm04_39518612 and Gm04_39518624 are loci related to 100-seed weight. After performing a reference comparison, we conducted gene annotation and identified candidate genes and , potentially associated with grain weight per plant in soybeans. These genes are primarily involved in protein synthesis and cell differentiation processes. The candidate gene , associated with the 100-grain weight trait, was successfully annotated. The analysis revealed that the gene primarily involves enzyme activity, suggesting its potential role in regulating grain weight. These findings offer valuable insights into the mechanism of soybean yield and serve as a critical theoretical foundation and genetic resource for cultivating new soybean germplasm with high yield. These findings are of immense significance for future research endeavors to achieve high-yielding soybean varieties.

Combining high-throughput genotyping data with the latest wheat genomic information provided more detailed information on the genetic diversity of the Japanese wheat core collection (JWC). Analysis of genomic population structure divided the JWC accessions into three populations: northeast Japan accessions, native and southwest Japan accessions, and modern accessions showing mixed breeding patterns. This indicates that Japanese wheat varieties have a background of native genomes from southwest Japan incorporating valuable genes from various exotic lines, which is supported by the history of Japanese wheat breeding. Association analyses of several agronomic traits have revealed how genes or alleles have been selected in Japanese wheat breeding and how they differ from those in other regions of the world. This analysis of the JWC collection is expected to contribute not only to the elucidation of genetic diversity in Japanese wheat accessions but also to future wheat breeding by providing a new genetic resource.