On the cover

The landrace ‘Sanenashi’ is thought to have originated from Iwateyamanashi (Pyrus ussuriensis var. aromatica). The fruit was favored not only for its taste and fragrance, but also for its small seedless core, which made it easy to eat. Despite being seedless, the variety has been preserved for over 300 years by grafting. Even today, more than 20 trees can be found in each town of Iwate Prefecture in Japan (This issue, p. 427–434).

(S. Mitsuhashi: Food Resources Education and Research Center, Faculty of Agriculture, Kobe University)

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 PLATZ family genes in birch (Betula platyphylla), the members of the PLATZ family were screened and analyzed in this study. Totals of ten BpPLATZ genes were identified in birch genome and classified into five groups base on phylogenetic relationship, BpPLATZ 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 cis-elements were distributed in the promoter regions of BpPLATZs, 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. BpPLATZ3, BpPLATZ5, BpPLATZ6, BpPLATZ7 and BpPLATZ8 are significantly induced expressed response to salt stress. These studies provide a basis for the further functional study of the BpPLATZ genes.

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 (Solanum tuberosum L.). The F₁ 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.

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 indica 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 PhyC but not in its promoter region. Haplotype analysis of the 2-kb promoter and gene regions of PhyC 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 F₂ 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 PhyC would be a major determinant of heading date in Myanmar accessions.

‘Sanenashi’ is a landrace of Pyrus ussuriensis var. aromatica (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 F₁ 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.

The cultivated peanut, Arachis hypogaea L., is an important source of edible oil and highly digestible protein. Wild incompatible Arachis species outside section Arachis are ideal gene reservoirs for genetic improvement of the peanut crop. Among these, A. glabrata Benth. stands out for its noted resistance to various stresses. Traditional in vitro 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 in situ embryo rescue approach to facilitate the production of intersectional Arachis hybrids. Through this method, hybrid seeds resulting from the crossing of two incompatible species, namely A. glabrata and A. paraguariensis, 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 Arachis species in peanut breeding programs. Moreover, the in situ embryo rescue technique showcased in this study holds promise for application in other plant species characterized by postzygotic cross-incompatibility.

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 (d1) mutants, T65(d1-1) and Kin(d1-7), which display contrasting internode elongation phenotypes. Anatomical observation revealed that T65(d1-1) exhibits a dm-type internode elongation pattern due to the lack of the second internode counted from the top, while Kin(d1-7) 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 F₂ 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 F₃ progenies, indicating that the combination of Kin(d1-7) 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.

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 OsNRAMP5-deficient rice (Oryza sativa L.) mutant (osnramp5-2), 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 Bipolaris oryzae. To restore BS resistance, we introduced the BS resistance quantitative trait locus (QTL) bsr1 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.