On the cover

Japanese morning glory (Ipomoea nil) is a short-day plant. A single-base deletion (SBD) in the coding region of InCO/IhCO causes a frameshift mutation, which is presumed to result in a loss of function in the TKS allele, inco-1. Accessions carrying inco-1 tend to flower earlier than those carrying InCO-2. Based on its geographical distribution, the SBD in inco-1 may have contributed to the expansion of I. nil, originally native to tropical regions of the Americas, into temperate regions of Asia. The photograph below the world map shows the cultivation of I. nil accessions maintained by the National BioResource Project (NBRP) (This issue, p. 339–348).

(T. Kuboyama: College of Agriculture, Ibaraki University)

Japanese morning glory (Ipomoea nil), a short day plant, has been used for studying flowering times. Here, quantitative trait loci (QTL) analysis for days from sowing to flowering (DTF) of F₂ between I. nil var. Tokyo Kokei Standard (TKS) and I. hederacea line var. Q65, an early flowering variety, revealed seven QTLs: QTL Ipomoea Flowering 1–7 (qIF1–7). The position of qIF3, which had the most significant effect among the seven QTLs, corresponds with that of I. nil (or I. hederacea) CONSTANS (InCO/IhCO) in the linkage map. There is a single-base InDel in the coding sequence of InCO/IhCO. The single-base deletion (SBD) causes a frame-shift mutation and loss of function in TKS allele (inco-1). I. nil accessions bearing inco-1 tend to flower early, similarly to rice varieties bearing the loss of function allele of CO ortholog, hd1. The TKS allele of qIF3 reduces DTF and corresponds with the inferred effect of inco-1. Based on the distribution of inco-1, a hypothesis was proposed that the SBD in inco-1 might have played an important role in the expansion of Japanese morning glories, originally native to the tropical regions of the Americas, into temperate Asia.

Visible-near infrared hyperspectral analysis is widely used for plant characterization and evaluation of agricultural products and food quality. On the other hand, it has remained un-certain whether this technique has a sufficient potential for evaluation of biological complexity during the growth of crop plants. In the present study, using a spectrometer and hyperspectral camera placed in a laboratory environment, we carried out continuous hyperspectral profiling of leaves derived from four rice cultivars grown under two field conditions. Combined analysis with transcriptome data revealed that the hyperspectral profile had potential to predict the degree of expression of developmentally regulated genes. In addition, principal component analysis of hyperspectral imaging data made it possible to detect growth-stage dependent dynamics and to distinguish differences between subspecies as well as field conditions by selecting an adequate pretreatment method. Furthermore, we obtained hyperspectral data for brown rice grains of recombinant inbred lines derived from a cultivar with high temperature tolerance during the ripening stage and with a good grain appearance. We then performed quantitative trait locus analysis using the extracted principal component scores and trait values related to grain appearance to explore the possibility of using spectral analysis for genetic studies.

To identify QTLs controlling the eating quality of ‘Akidawara’, ‘Satojiman’, and ‘Ikuhikari’ rice, we performed a genome-wide association mapping analysis using two breeding populations in 2013 and 2014 derived from crosses between these and another parental line. Through sensory tests by a trained panel, we evaluated five components of the eating quality of cooked rice. Fifty-eight QTLs for these components were detected in breeding lines in 2013 (seven regions of chromosome [chr.] 1, 4, and 11) and 2014 (ten of chr. 1, 2, 4, 8, 9, and 11). The Akidawara, Satojiman, or Ikuhikari alleles at these QTLs increased eating quality. QTLs on the short arm of chr. 4, the middle of the long arm of chr. 4, the distal end of the long arm of chr. 4, and the short arm of chr. 11, were identified in both years. The genetic effects of the Satojiman alleles at QTLs on the distal end of the long arm of chr. 4 and on the short arm of chr. 11 were confirmed by analysis of two chromosome segment substitution lines containing a Satojiman segment in the ‘Koshihikari’ background in 2016 and 2017, in which the Satojiman alleles increased the level of eating quality of Koshihikari.

The brown planthopper (Nilaparvata lugens (Stål); BPH) is a serious insect pest of rice (Oryza sativa L.). Host plant resistance is an effective means of controlling this pest; up to date at least 46 BPH resistance genes have been identified. However, BPH can overcome resistance conferred by single resistance genes. Therefore, it is necessary to detect new and durable resistance genes. Here, we identified quantitative trait loci (QTLs) for BPH resistance from the wild rice Oryza nivara (Sharma et Shastry) IRGC 89073. Using backcrossed populations derived from IRGC 89073 × the susceptible ‘Taichung 65’, we detected two resistance QTLs, qBPH4 on chromosome 4 and qBPH11 on chromosome 11. qBPH11 was validated in the BC₃F₂ population. A near-isogenic line carrying qBPH11 showed significant resistance to BPH in antibiosis, antixenosis, MSST, and honeydew tests. These results suggest that IRGC 89073 harbors valuable genetic resources that could enhance BPH resistance in rice breeding programs, particularly through pyramiding strategies using marker-assisted selection.

Mapping quantitative trait loci (QTLs) is one of the major goals of quantitative genetics; however, identifying the interactions between QTLs (i.e., epistasis) remains challenging. Recently developed machine learning methods, such as deep learning and gradient boosting, are transforming the real world. These methods could advance QTL mapping methodologies because of their high capability for capturing complex relationships among features. One problem with applying such complex models to QTL mapping is the evaluation of feature importance. In this study, XGBoost, a popular gradient tree boosting algorithm, was applied for QTL mapping in biparental populations with Shapley additive explanations (SHAPs). SHAP is a local (i.e., instance-wise) importance index with the desired properties as feature importance indices. The SHAP-assisted XGBoost (SHAP-XGB) was compared with conventional methods, including composite interval mapping (CIM), multiple interval mapping (MIM), inclusive CIM (ICIM), and BayesC, using simulations and rice heading date data. SHAP-XGB performed comparably to CIM, MIM, ICIM, and BayesC in mapping main QTL effects and was superior to MIM, ICIM, and BayesC in mapping QTL interaction effects. As SHAP can evaluate local importance, interactions between markers can be visualized by plotting SHAP interaction values for each instance (plant/line). These results illustrated the strength of SHAP-XGB in detecting and interpreting epistatic QTLs and suggest the possibility that SHAP-XGB complements conventional methods.

Grain amaranth is a promising alternative food grain owing to its nutrient-rich composition and ability to grow under poor environmental conditions. In this study, we aimed to identify quantitative trait loci (QTLs) associated with key morphological and phenological traits using an F₂ population of Amaranthus hypochondriacus derived from two commercial cultivars, Golden and Pygmy Torch. Nine traits were evaluated across three cultivation trials, and single nucleotide polymorphism (SNP) genotyping conducted using double digest restriction site-associated DNA sequencing analysis. Genetic linkage maps were constructed based on SNP markers, and QTL analysis independently conducted for each trial. Three linkage maps were constructed, spanning 5640, 5970.3, and 6960.2 cM, respectively. In total, 12 QTLs were associated with the nine traits detected on Chr. 4, 6, 9, 10, and 16 in at least two cultivations, with QTL regions of the five traits overlapping on Chr. 4. Notably, seven QTLs (AhPH6, AhSTD4, AhNN4, AhBI4, AhHC16, AhIFC16, and AhSCC9) related to important morphological traits were consistently detected in all three cultivation trials. The study results provide valuable genetic insights for the improvement of A. hypochondriacus and suggest the possibility of using molecular markers for the selection of important traits to establish breeding programs more efficiently.

Ovule number per ovary (ONPO) directly determines seed quantity in plants. In this study, two radish (Raphanus sativus L.) accessions exhibiting marked phenotypic variation in ONPO and seed number per pod (SNPP) were selected to generate bi-parental populations for quantitative trait locus (QTL) analysis. Additionally, genome-wide association studies (GWAS) on ONPO using 206 radish accessions were conducted. Through an integrated analysis of QTL mapping and GWAS results, a major common QTL was identified spanning a 0.6 Mb region on the terminal of chromosome 5. Based on genomic position, gene ontology, and expression analyses, RsFLK was highlighted as the primary candidate, along with two other selected genes RsSGT and RsEMB3004. Subsequent comparison of the RsFLK promoter sequences in the parental lines revealed unique InDels that may affect its expression, potentially contributing to the high-ONPO. These findings provide new insights into the genetic regulation of ovule number in radishes.

Rice is one of the world’s most widely cultivated field crops and a short-day adapted plant. It possesses a complex genetic regulatory mechanism for heading date determination. Gemdjah Beton (GB) is an Indonesian rice cultivar that takes approximately 17 weeks to flower after being transplanted into a rice field in Japan. We isolated early-heading mutant line GB-10 (flowers around two to three weeks earlier than GB in the field). Under long-day (LD) conditions, GB-10 flowered approximately two weeks earlier than GB. Under short-day conditions, the heading date between GB-10 and GB plants shows no apparent difference. In agreement with the heading date, Hd3a and RFT1 expressions show around a 10-time relative transcript quantity difference under LD conditions in GB-10 compared to GB. Interestingly, Ghd7 expression was significantly reduced in GB-10, which may trigger the Hd3a and RFT1 activation. A bulk segregation analysis indicated that a single nucleotide variant on chromosome 7 was genetically linked to the early heading phenotype of GB-10 lines. Taken together, we reported the successful isolation of GB-10 as an early-heading mutant.

The isolated rice mutant, designated lowac2, exhibited low amylose content. Whole-genome resequencing and single-nucleotide polymorphism (SNP) fragment analysis revealed that a mutation in the gene encoding the C₂H₂ zinc-finger protein in the long-arm terminal of Chromosome 6 was responsible for this low amylose phenotype. An SNP from G to A was observed in the 5ʹ splice junction of intron11, resulting in the production of a protein lacking the C-terminal. Mutation of the C₂H₂ zinc-finger protein specifically affected the splicing efficiency of intron1 in Waxy^b (Wx^b). This reduced the levels of granule-bound starch synthase I, which is encoded by Wx^b. Mutations in lowac2 increased the mRNA expression levels of several starch biosynthetic enzymes, especially starch synthase IIa and starch branching enzyme I. This was consistent with the presence of amylopectin with reduced short glucan chains in lowac2 seeds compared to wild-type seeds. Furthermore, the crossed lines possessing a gene combination between Wx^a from indica variety and lowac2 also showed a decrease in amylose content and Wx^a expression; however, this did not affect splicing in Wx^a. The new allele of the C₂H₂ zinc-finger protein found in this study affects both Wx genes differently.

In this study, 49 ABD-type synthetic hexaploid wheat germplasm resources grown on the Qinghai-Tibet Plateau in 2022–2024 were measured for important agronomic traits. Clustering and principal component analyses were applied to classify and compare relevant indicators for a comprehensive evaluation. The aim was to identify outstanding synthetic hexaploid wheat germplasm and establish a new germplasm resource foundation for the breeding and improvement of new wheat varieties in the Qinghai-Tibet Plateau and other regions with similar climatic conditions. The coefficient of variation for important agronomic traits ranged from 1.63% to 22.02%, with the highest coefficients of variation observed for spike stem node length, plant height, and thousand-grain weight. Cluster analysis revealed that the 49 synthetic hexaploid wheat germplasm resources could be divided into eight major clusters. Among them, the quality traits of the accessions belonging to clusters Ⅴ exhibited excellent performance, while the accessions with outstanding yield-related traits were concentrated in clusters Ⅲ and Ⅷ. Using the gray relational analysis method for comprehensive evaluation, the five germplasm resources with the highest scores were ABD-SHW-15 (64.53), ABD-SHW-6 (64.39), ABD-SHW-5 (63.70), ABD-SHW-14 (63.18), and ABD-SHW-38 (62.33).

Structural variants (SVs) are genomic mutations that are typically 50 bp or larger. Given their larger scale compared to single nucleotide polymorphisms and small insertions and deletions, SVs are expected to be associated with various traits in several crops and fruit species. They can also be used to identify plant cultivars. However, it is challenging to detect SVs using short-read next-generation sequencing (NGS), which, until recently, has been the mainstream method, due to its short read length compared to SVs. In recent years, long-read NGS, which generates reads exceeding the length of SVs, has made SV detection more feasible. To take advantage of this, we developed LAYLA (Large indel AnalYzer for muLti-sAmple), a pipeline program designed to comprehensively detect and visualize SVs across multiple samples using long-read data. Here, we applied LAYLA to 13 citrus founder cultivars used in Japanese breeding and Citrus unshiu Marc. We identified SVs at 59,983 positions in the reference genome. This analysis revealed both common and cultivar-specific SVs. Furthermore, we designed primers targeting nine selected SVs and conducted experimental validation, confirming the presence of SVs detected by LAYLA. In the future, LAYLA can be applied to other plant species to detect SVs.

The brown planthopper (Nilaparvata lugens (Stål); BPH) is a serious pest of rice (Oryza sativa L.). Host plant resistance is an effective means of controlling it; at least 46 BPH resistance genes have been identified. However, BPH can overcome resistance genes, so we need to detect more genes. To find new BPH resistance genes in Oryza rufipogon, we analysed quantitative trait loci (QTLs) associated with BPH resistance. Using 161 backcross recombinant inbred lines derived from O. rufipogon accession W0630, we identified eight loci associated with resistance. qBPH5 and qBPH6, on chromosomes 5 and 6, were validated in F₂ and F_2:3 populations derived from crosses between O. sativa japonica variety ‘Nipponbare’ and the inbred lines. BPH resistance of a line carrying both QTLs was higher than that of lines carrying just one. Pyramiding improved resistance and can be used in breeding BPH-resistant rice.

We developed a new sweetpotato cultivar, ‘Miyaakari’, for confectionery processing. It was released in 2023. Herein we observed that Miyaakari shows a significantly higher yield compared to two major sweetpotato cultivars in Japan, ‘Kokei No. 14’ and ‘Beniharuka’. Miyaakari has a higher carotenoid content than Kokei No. 14 and Beniharuka, and the flesh color of heat-cooked Miyaakari sweetpotato is bright yellow. The quality of heat-cooked Miyaakari sweetpotato (i.e., hardness and sweetness) is more stable during storage compared to Beniharuka. These characteristics are suitable for food processing. Indeed, a primary food manufacturer concluded that Miyaakari is suitable for ingredients of paste and diced food products. Miyaakari will thus both contribute to an increased production of ingredients for confectionery processing and improve the quality of sweetpotato sweets.