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. We find that a 4 bp InDel in one of the 14-3-3 family genes, GF14h, preferentially changes the germination rate of rice under optimum temperature conditions. The GF14h protein constitutes a transcriptional regulatory module with a bZIP-type transcription factor, OREB1, and a florigen-like protein, MOTHER OF FT AND TFL 2, to control the germination rate by regulating abscisic acid (ABA)-responsive genes. The GF14h loss-of-function allele enhances ABA signalling and reduces the germination rate. This allele is found in rice varieties grown in the northern area and in modern cultivars of Japan and China, suggesting that it contributes to the geographical adaptation of rice. This study demonstrates the complicated molecular system involved in the regulation of seed germination in response to temperature, which has allowed rice to be grown in various geographical locations.

Genome-wide association studies (GWASs) are used to detect quantitative trait loci (QTLs) 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. In this study, we conducted a GWAS using phenotypic data of temperate japonica rice (Oryza sativa) varieties from a public database. The GWAS using the legacy data detected several known agriculturally important genes, indicating reliability of the legacy data for GWAS. By comparing the GWAS using legacy data (L-GWAS) and a GWAS using phenotypic data that we measured (M-GWAS), we detected reliable QTLs for agronomically important traits. These results suggest that a L-GWAS is a strong alternative to replicate tests to confirm the reproducibility of QTLs detected by an M-GWAS. In addition, because legacy data have often been accumulated for many traits, it is possible to evaluate the pleiotropic effect of the QTLs identified for the specific trait that we focused on with respect to various other traits. This study demonstrates the effectiveness of using legacy data for GWASs and proposes the use of legacy data to accelerate genomic breeding.

Plants recognize environmental information as external signals, which they use to coordinate developmental processes for their survival and reproduction. In the agricultural production of rice, the primary staple crop worldwide, soil nitrogen (N) is an important environmental factor. Heading date, a key trait for rice quality and yield, is modulated by N fertilisation; however, the molecular mechanisms underlying N-dependent flowering regulation remain unclear. Here, we conduct a genome-wide association study using differences in heading dates of Japanese rice cultivars grown under different N conditions. We identify Hd6, which is known to be involved in photoperiodic flowering regulation, as a key signalling component in the phenotypic variation observed under various N conditions. Further analyses using near-isogenic lines reveal that not only Hd6 but also Hd2 and Hd1 are required for the delayed flowering caused by N fertilisation. We also discover that Hd6 regulates floral inducer genes by stabilizing Hd2 through phosphorylation in response to N conditions and that the Hd6-Hd2 module can counteract the transcriptional regulation of Hd1. This study elucidates the molecular pathway directly linking N responses to flowering regulation in rice, providing insights for novel breeding and cultivation strategies.

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. Genome‐wide association studies (GWAS) identified Hd1, Hd16, and Hd18 as the major genes controlling days to heading in the population. However, we suspected that this highly bred population might exhibit genomic stratification, which could lead to spurious or false correlations in the GWAS. Thus, we also conducted correlation and partial correlation analyses, which uncovered another key heading date gene, Hd17, that GWAS failed to detect because of its linkage disequilibrium with the major effect gene Hd16. Examination of haplotype frequencies across different breeding periods revealed that the early‐heading Hd16 (Hd16(E)) and late‐heading Hd17 (Hd17(L)) were increasingly co‐selected in the Hd1 functional population. Varieties carrying this Hd16(E)/Hd17(L) combination exhibited days to heading in the range of 70–80, which corresponds to the peak temperature and sunshine period and is also optimal for grain quality and yield components in the Fukui environment. The present study highlights that it is imperative to remain vigilant for Type I (false positives) and Type II (false negatives) errors when performing GWAS on highly bred populations and to implement appropriate countermeasures by accounting for gene‐by‐gene interactions established through the breeding process. We also discuss the effectiveness of Hd16(E), which is not used outside Japan for subtle days to heading control but is widely used in Japan at certain latitudes.

Objective: To identify individual characteristics related to the development of pulmonary tuberculosis (PTB) among residents in the Airin area (Airin), Osaka City, Japan. Methods: We conducted a retrospective case-control study of individual characteristics potentially related to the development of PTB by comparing PTB patients and residents without tuberculosis (TB) in Airin. The following binominal data of characteristics were compared: age (< 65 or > 65); body mass index (BMI) (< 18.5 or > 18.5); diabetes mellitus (diagnosed or not diagnosed); smoking (currently smoking any amount or not smoking); and alcohol use (currently drinking any amount or not drinking). Results: We compared the individual characteristics of 192 PTB patients notified from January 2015 to December 2018 and 190 residents of supportive houses who attended a health education programme from April 2016 to March 2018. Univariable analysis showed that the following characteristics were significantly related with PTB: BMI < 18.5 (odds ratio [OR]: 6.54, 95% confidence interval [CI]: 3.58–11.97, P < 0.001) and current alcohol use (OR: 1.88; 95% CI: 1.24–2.85, P = 0.003). Multivariable analysis showed similar results: BMI < 18.5 (adjusted odds ratio [aOR]: 6.90, 95% CI: 3.72–12.79, P < 0.001) and current alcohol use (aOR: 2.15, 95% CI: 1.36–3.42, P = 0.001). Discussion: Undernutrition and alcohol use are individual characteristics associated with PTB among residents in Airin, Osaka City. To strengthen the TB control programme further, it is suggested to develop new programmes for primary prevention.

The first aim of this study was to evaluate the association between time spent living near a contaminated area and concentration of arsenic (As) compounds in the urine among study subjects. The second aim is to assess the association between consumption of various foods or beverages and As concentration in urine among them. Urine sampling was performed on 177 persons who voluntarily participated in the survey in May 2014. The median value of the sum of inorganic As (iAs) and total As (tAs) compounds was used for us to divide into two groups, such as the high and low iAs and high and low tAs groups. We analyzed data separately in two-age strata of age group A (the subjects <18 years old), and age group B (the subjects ≥18 years old). A multivariate analysis was performed with the logistic regression model to adjust for potential confounding variables. No link between time spent living near a contaminated area and urinary As concentration was observed in our study. For age group B, frequently drinking beer was significantly associated with risk of being in the high tAs group (p = 0.008). Compared to not drinking beer, odds ratios (95 % confidence intervals) of drinking beer <1 or 2 times per week, and drinking beer ≥3 or 4 times per week were 3.09 (1.32–7.24) and 3.00 (1.02–8.80), respectively, after adjusting for age, sex, and smoking index. Frequent consumption of beer may be associated with high tAs in age group B