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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.    Electronic supplementary material  The online version of this article (10.1186/s12915-018-0572-x) contains supplementary material, which is available to authorized users.

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