How have breeders adapted rice flowering to the growing region?

Flowering time is a crucial rice trait that influences its adaptation to various environments, cropping schedules, and agronomic characteristics. Rice breeders have exploited spontaneous mutations in heading date genes to regulate the flowering time. In the present study, we investigated how breeders in Fukui Prefecture regulated days to heading while developing promising rice varieties.

Targeting Tumor-Associated Macrophages with the Immune-Activating Nanomedicine for Achieving Strong Antitumor Activity with Rapid Clearance from the Body.

Toll-like receptors (TLRs) are a class of pattern recognition receptors (PRRs) crucial for the detection of infections and activation of downstream signaling pathways that lead to the production of pro-inflammatory cytokines and interferons. The TLR pathway is an attractive actively studied target pathway. Because of their strong immunostimulatory activity, TLRs are thought to be a "double-edged sword" for systemic treatment, even in the cancer field.

Redefining awn development in rice through the breeding history of Japanese awn reduction.

The study challenges the conventional understanding of awn loss as a domestication syndrome, showing instead that many awned varieties continued to be widely grown in Japan until the early twentieth century and that selection for awn reduction was active at that time, demonstrating that awn loss is not a domestication syndrome but "a trait that emerged during crop improvement". Although selection for awnless mutants was carried out independently using different types of awned cultivars in the early twentieth century in Japan, awn loss was caused by the mutation in This suggests that a single mutant haplotype of was conserved in the genomes of different cultivars and subsequently selected within each line to meet the demand for awnless varieties. The study also conducts phylogenetic analyses of in 48 grass plants, revealing its unique involvement in awn formation in rice while potentially playing a different role in the domestication of other grass plants.

Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences.

In the early 1900s, mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.

Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice.

Enhancing leaf photosynthetic capacity is essential for improving the yield of rice (Oryza sativa L.). Although the exploitation of natural genetic resources is considered a promising approach to enhance photosynthetic capacity, genomic factors related to the genetic diversity of leaf photosynthetic capacity have yet to be fully elucidated due to the limitation of measurement efficiency.

Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice.

Improving grain quality is a primary objective in contemporary rice breeding. Japanese modern rice breeding has developed two different types of rice, eating and sake-brewing rice, with different grain characteristics, indicating the selection of variant gene alleles during the breeding process. Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding, we conducted genome scans for divergence, genome-wide association studies, and map-based cloning.

Effective use of legacy data in a genome-wide association studies improves the credibility of quantitative trait loci detection in rice.

Genome-wide association studies (GWASs) are used to detect quantitative trait loci (QTL) using genomic and phenotypic data as inputs. While genomic data are obtained with high throughput and low cost, obtaining phenotypic data requires a large amount of effort and time. In past breeding programs, researchers and breeders have conducted a large number of phenotypic surveys and accumulated results as legacy data.

Effects of irrigation on root growth and development of soybean: A 3-year sandy field experiment.

Increasing the water use efficiency of crops is an important agricultural goal closely related to the root system -the primary plant organ for water and nutrient acquisition. In an attempt to evaluate the response of root growth and development of soybean to water supply levels, 200 genotypes were grown in a sandy field for 3 years under irrigated and non-irrigated conditions, and 14 root traits together with shoot fresh weight and plant height were investigated. Three-way ANOVA revealed a significant effect of treatments and years on growth of plants, accounting for more than 80% of the total variability.

Genome-wide association study identifies a gene responsible for temperature-dependent rice germination.

Environment is an important determinant of agricultural productivity; therefore, crops have been bred with traits adapted to their environment. It is assumed that the physiology of seed germination is optimised for various climatic conditions. Here, to understand the genetic basis underlying seed germination, we conduct a genome-wide association study considering genotype-by-environment interactions on the germination rate of Japanese rice cultivars under different temperature conditions.

Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza.

Proper anther and pollen development are important for plant reproduction. The plant hormone gibberellin is important for anther development in rice, but its gametophytic functions remain largely unknown. Here, we report the functional and evolutionary analyses of rice gibberellin 3-oxidase 1 (OsGA3ox1), a gibberellin synthetic enzyme specifically expressed in the late developmental stages of anthers.

Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons.

It is generally believed that rice landraces with long culms are susceptible to lodging, and have not been utilized for breeding to improve lodging resistance. However, little is known about the structural culm strength of landraces and their beneficial genetic loci. Therefore, in this study, genome-wide association studies (GWAS) were performed using a rice population panel including Japanese rice landraces to identify beneficial loci associated with strong culms.

Making the 'Green Revolution' Truly Green: Improving Crop Nitrogen Use Efficiency.

Traditional breeding for high-yielding crops has mainly relied on the widespread cultivation of gibberellin (GA)-deficient semi-dwarf varieties, as dwarfism increases lodging resistance and allows for high nitrogen use, resulting in high grain yield. Although the adoption of semi-dwarf varieties in rice and wheat breeding brought big success to the 'Green Revolution' in the 20th century, it consequently increased the demand for nitrogen-based fertilizer, which causes severe threat to ecosystems and sustainable agriculture. To make the 'Green Revolution' truly green, it is necessary to develop new varieties with high nitrogen use efficiency (NUE).

Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections.

We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified.

Evolution of GA Metabolic Enzymes in Land Plants.

Gibberellins (GAs) play key roles in various developmental processes in land plants. We studied the evolutionary trends of GA metabolic enzymes through a comprehensive homology search and phylogenetic analyses from bryophytes to angiosperms. Our analyses suggest that, in the process of evolution, plants were able to acquire GA metabolic enzymes in a stepwise manner and that the enzymes had rapidly diversified in angiosperms.

Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles.

Panicle architecture directly affects crop productivity and is a key target of high-yield rice breeding. Panicle length strongly affects panicle architecture, but the underlying regulatory mechanisms are largely unknown. Here, we show that two quantitative trait loci (QTLs), PANICLE RACHIS LENGTH5 (Prl5) and PRIMARY BRANCH LENGTH6 (Pbl6), independently regulate panicle length in rice.

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin.

Allosteric regulation is protein activation by effector binding at a site other than the active site. Here, we show via X-ray structural analysis of gibberellin 2-oxidase 3 (GA2ox3), and auxin dioxygenase (DAO), that such a mechanism maintains hormonal homeostasis in plants. Both enzymes form multimers by interacting via GA and indole-3-acetic acid (IAA) at their binding interface.

Genome-wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure.

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified.

GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture.

Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture.