Background: Rice (Oryza sativa L.) is cultivated in a wide range of climatic conditions, and is one of mankind's major staple foods. The interaction of environmental factors with genotype effects major agronomic traits such as yield, quality, and resistance in rice. However, studies on the environmental factors affecting agronomic traits are often difficult to conduct because most environmental factors are dynamic and constantly changing. Results: A series of recombinant inbred lines (RILs) derived from an indica/japonica cross were planted into four typical rice cultivated areas arranging from latitude N22°to N42°. The environmental data from the heading to mature (45 days) stages were recorded for each RIL in the four areas. We determined that light, temperature, and humidity significantly affected the milling quality and cooking quality overall the four areas. Within each area, these environmental factors mainly affected the head rice ratio, grain length, alkali consumption, and amylose and protein content. Moreover, the effect of these environmental factors dynamically changed from heading to mature stage. Compared to light and humidity, temperature was more stable and predictable, and night temperature showed a stronger correlation efficiency to cooking quality than day temperature, and the daily temperature range had contrary effects compared to day and night temperature on grain quality. Conclusions: The present study evaluated the critical phase during the grain filling stage by calculating the dynamic changes of correlation efficiency between the quality traits and climate parameters. Our findings suggest that the sowing date could be adjusted to improve rice quality so as to adjust for environmental changes.

BackgroundTwo of the most widely cultivated rice strains are Oryza sativa indica and O. sativa japonica, and understanding the genetic basis of their agronomic traits is of importance for crop production. These two species are highly distinct in terms of geographical distribution and morphological traits. However, the relationship among genetic background, ecological conditions, and agronomic traits is unclear.ResultsIn this study, we performed the de novo assembly of a high-quality genome of SN265, a cultivar that is extensively cultivated as a backbone japonica parent in northern China, using single-molecule sequencing. Recombinant inbred lines (RILs) derived from a cross between SN265 and R99 (indica) were re-sequenced and cultivated in three distinct ecological conditions. We identify 79 QTLs related to 15 agronomic traits. We found that several genes underwent functional alterations when the ecological conditions were changed, and some alleles exhibited contracted responses to different genetic backgrounds. We validated the involvement of one candidate gene, DEP1, in determining panicle length, using CRISPR/Cas9 gene editing.ConclusionsThis study provides information on the suitable environmental conditions, and genetic background, for functional genes in rice breeding. Moreover, the public availability of the reference genome of northern japonica SN265 provides a valuable resource for plant biologists and the genetic improvement of crops.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0572-x) contains supplementary material, which is available to authorized users.

We determined the effects of biochar on starch properties and the activities of enzymes and expression levels of genes related to starch in two Japonica rice cultivars. The two rice varieties were subjected to five biochar treatments (0, control; and 5, 10, 20, and 40 t/hm2). In both rice varieties, the content of apparent amylose and resistant starch were lower in biochar treatments than in the control. The proportion of fa chains was higher and that of fb3 chain was lower in the biochar treatments than in the control. Starch viscosity and cooking taste quality were improved by the biochar treatments. In both rice varieties, the activity of granule-bound starch synthase was significantly decreased by biochar treatments, and the activities of soluble starch synthase, starch branching enzyme, and starch debranching enzyme were significantly increased. The transcript levels of genes encoding starch synthases and starch branching enzymes were significantly increased by biochar treatments. We conclude that biochar at a dose of 5–10 t/hm2 can regulate the activity of starch-related enzymes, and this affects the type, content, and fine structure of starch. Therefore, the addition of biochar to soil can improve the viscosity and taste quality of rice starch.