On the cover

Typical symptoms of Pythium root and stalk rot caused by Pythium spp. (including P. arrhenomanes) in maize (Zea mays L.). At the yellow ripening stage, the ears of forage maize droop and the aboveground parts wither completely. Longitudinal sections of the stem near the soil surface reveal white fungal mycelium filling the internal tissues, accompanied by light brown decay. The roots exhibit overall browning, with a marked reduction in root volume (This issue, p. 240–250).

(Photos by Dr. Takao Tsukiboshi)

Hybridization generates biodiversity and wide hybridization plays a pivotal role in enhancing and broadening the useful attributes of crops. Hybridization can be achieved through sexual or somatic hybridization between distant species; however, sexual hybridization between intergeneric or inter-subfamily combinations often results in unsuccessful fertilization/embryogenesis due to pre- and/or post-fertilization barriers. In addition, as cytoplasmic organelles are maternally transmitted to the zygote via sexual reproduction, cytoplasmic genome hybridization is rare. Although somatic hybridization offers distinct advantages over sexual hybridization, the isolation and culture of protoplasts are not feasible in most plant species, including vital crops. Recently, allopolyploid wheat–rice or wheat–maize hybrid zygotes were produced by in vitro fertilization (IVF) using isolated wheat, rice, and maize gametes, and these hybrid zygotes developed into wheat cytoplasmic hybrids (cybrids) with wheat–rice or wheat–maize hybrid mitochondria. These indicate that the IVF system with isolated gametes provides a solution to limitations of fertilization barriers and one-way cytoplasmic inheritance in sexual and somatic hybridizations, and that the present rice–wheat cybrid, ^OryzaWheat, and maize–wheat, ^ZeaWheat, will provide a new horizon for the utilization of inter-subfamily genetic resources.

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.

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.

Pythium arrhenomanes Drechsler is a destructive soil-borne pathogen threatening forage maize (Zea mays L.) production worldwide, leading to substantial economic losses due to root and stalk rot (RSR). Developing resistant varieties is the most sustainable and effective management strategy. However, studies analyzing general combining ability (GCA) for disease resistance using genome-wide association study (GWAS) are lacking. This study investigated the genetic architecture of resistance to Pythium RSR using 107 maize inbred lines using GCA for disease resistance as a phenotypic trait, addressing instability of disease expression in inbred lines and targeting additive genetic variance crucial for F₁ hybrid breeding. A GWAS was conducted using 49,187 high-quality single-nucleotide polymorphism (SNP) markers. Five SNPs were significantly associated with resistance GCA that did not form linkage disequilibrium blocks in their vicinity. One SNP on chromosome 9 conferred a beneficial reduction in GCA, indicating an increase in resistance. Four of the five SNPs exhibited an apparent effect and were polymorphic between the resistant ‘Na71’ and susceptible ‘Ho112’ inbred lines, indicating their direct applicability in applied breeding. Overall, these loci are strong candidates for marker-assisted selection, providing a direct route to accelerate the development of forage maize hybrids with enhanced disease resistance and agronomic performance.

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.

The mechanisms of flowering-time (FT) regulation in cultivated chrysanthemum (Chrysanthemum morifolium) are essential for breeders owing to their significant effects on cultivation. The wild diploid Chrysanthemum seticuspe has the same short-day flowering habits as cultivated chrysanthemum. We investigated an F₂ segregating population derived from crosses of accessions with differences in FT for quantitative trait locus (QTL) mapping. Three major QTLs for FT were mapped, each overlapping with QTLs for other flowering traits: one QTL associated with a longer critical daylength and two QTLs linked to the ability to flower rapidly following floral transition under short-day conditions, one of which also contributes to flowering competence at high temperatures. These traits collectively influence the regulation of FT. Altered expression patterns of circadian-clock-related genes in SoS4-4, the early-flowering parental line, suggested altered rhythmicity of the circadian clock. Circadian-clock-related genes and a photoreceptor gene were also found in the FT QTL interval. These genes may be responsible for altering the circadian clock and causing variation in FT by changing the critical daylength.

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 cultivars. 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.

Genomic selection has revolutionized breeding by enabling early identification of superior individuals using genome-wide markers. Over the past decade, new selection and mating strategies leveraging optimization methods have been introduced to improve decision-making in breeding programs. However, optimizing breeding remains challenging when the positions and effects of quantitative trait loci are unknown. We developed a framework that optimizes breeding strategies while updating genomic prediction models during recurrent selection programs. In these programs, selection, crossing, and progeny allocation are repeated across generations under limited population sizes. By updating prediction models at intermediate generations, we re-optimized how progeny are allocated among crosses, i.e., the number of progeny assigned to each cross under a fixed total population size, based on newly accumulated data. Our simulations compared this approach with equal allocation and optimal cross selection methods across various conditions. The optimized allocation strategy significantly outperformed other approaches under moderate to low selection intensities, particularly when combined with model updates. While genetic gains plateaued without updates, our approach with updates enabled continuous improvement through the fourth generation of recurrent selection. The framework showed robustness across different conditions and maintained genetic diversity, confirming its effectiveness under estimated marker effects intended for real-world breeding programs.

Cleistogamy, or closed flowering, has received significant attention in wheat (Triticum aestivum) due to its wide range of applications. A stable cleistogamy system in barley (Hordeum vulgare), regulated by a single gene (cly1), has been successfully utilized in practical breeding. The aim of this study was to establish stable cleistogamy in hexaploid wheat by combining point mutations in the microRNA172 target site of three AP2 homoeologs, which are the wheat orthologs of barley Cly1. Triple mutants carrying the three relevant mutant AP2 alleles successfully exhibited cleistogamy resulting from suppression of lodicule swelling. Further investigation revealed that strong mutant alleles from two homoeologous loci (AP2-B and AP2-D) were necessary and sufficient to induce cleistogamy equivalent to that in barley, which stably suppressed lodicule development. The analysis also demonstrated that the total dosage of mutant AP2 alleles contributed to lodicule suppression and cleistogamy, likely correlating with the gene expression levels. Approaches for resolving the compact spike trait, which is expressed simultaneously with cleistogamy and is disadvantageous in practice, are also discussed.

Target leaf spot (TLS), caused by Corynespora cassiicola, is among the most economically important diseases of cucumber (Cucumis sativus L.). Because of the rising incidence of disease problems, much effort has been put toward resistance breeding. Here, we investigated the inheritance of high TLS resistance in a Japanese–type inbred line. QTL analyses were performed using F₂ and F_2:3 families derived from a cross between the resistant and a susceptible (Beit Alpha–type) inbred line. We evaluated disease severity in F_2:3 families in four independent assays and mapped a total of five TLS-resistance QTLs on chromosome (Chr.) 2, Chr. 5, and Chr. 6. The effect of the two major QTLs on Chr.5, Tls5.1 and Tls5.2, was confirmed through additional assays and verified in different genetic backgrounds. Fine mapping using recombinants in several generations narrowed down Tls5.2 to a 496.8-kb region with 69 genes, several of which are potential candidates involved in plant disease resistance. The newly identified resistance loci may confer more durable resistance when combined with previously characterized resistance genes or loci. Furthermore, molecular markers linked to TLS resistance derived from the Japanese–type inbred line could be effectively used to accelerate breeding for this trait.

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.

Flowering promotion is an essential technique in plant breeding. In plants of the Brassicaceae family, flowering generally requires a prolonged period of low temperature, known as vernalization, which often represents a rate-limiting step in breeding programs. In this study, we identified a phenomenon termed Long-day Induced Vernalization Exclusion (LIVE), in which flowering is triggered under non-conventional long-duration light conditions without the need for vernalization. In Brassica rapa and Raphanus sativus, this phenomenon was observed across many lines under super-long-day conditions, and its induction became increasingly pronounced as the day length extended. LIVE was also induced under a repeating 11-hour light/1-hour dark cycle, suggesting that uninterrupted long day length is not strictly required for LIVE induction. This study reveals that low-temperature treatment can be bypassed through these long-duration light conditions across multiple lines, offering important insights for accelerating flowering in practical breeding.