Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci.

BACKGROUND: Two 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. RESULTS: In 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. CONCLUSIONS: This 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.

Influence of YKL-40 gene RNA interference on the biological behaviors of endometrial cancer HEC-1A cells.

The present study aimed to investigate the effects of chitinase-3-like protein 1 (YKL-40) gene RNA interference on the biological behaviors and enhanced chemosensitivity of endometrial cancer (EC) HEC-1A cells. YKL-40 small interfering (si)RNA was transduced into EC HEC-1A cells using a lentivirus. The experiment was divided into three groups: The experimental group was transfected with YKL-40 siRNA (si-YKL-40); the mock-treatment group was transfected with transfection reagent only; and the blank control group was left untreated. A reverse transcription-quantitative polymerase chain reaction was performed to investigate the mRNA expression levels of YKL-40. The biological behaviors, including cell proliferation, migration, invasion and apoptosis, were detected by MTT and Transwell assays, and flow cytometry (FCM) analysis, respectively. The results of the present study demonstrated that the mRNA expression levels of YKL-40 were downregulated within HEC-1A cells upon transfection with si-YKL-40 (P<0.05). The proliferative, migratory and invasive abilities of HEC-1A cells were inhibited by si-YKL-40 (P<0.05). The mRNA expression levels of YKL-40 were upregulated within HEC-1A cells following treatment with cisplatin (P<0.05). FCM analysis revealed that the average cellular apoptosis rate increased following the inhibition of YKL-40 gene expression via siRNA (P<0.05). Therefore, the YKL-40 gene may be associated with the proliferative, migratory, invasive and anti-apoptotic ability of HEC-1A cells. YKL-40 downregulation may enhance the sensitivity of human EC HEC-1A cells to chemotherapy.

Deciphering the Environmental Impacts on Rice Quality for Different Rice Cultivated Areas.

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.