Abstract
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.
Highlights
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
The de novo assembly of the Shennong 265 (SN265) genome will serve as a reference for the discovery of genes and structural variations that contribute to the increase in rice production in super rice varieties in northern China
Population sequencing and linkage map construction In order to construct the linage map, the Recombinant inbred lines (RILs) derived from the cross between SN265 and R99, along with the parents, were sequenced on an Illumina HiSeq2500 platform
Summary
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. To improve understanding of the genetic mechanism of hybrid super rice, the genomes of two elite indica rice varieties, namely, Zhenshan 97 and Minghui 63, have been assembled [4]. The de novo assembly of the SN265 genome will serve as a reference for the discovery of genes and structural variations that contribute to the increase in rice production in super rice varieties in northern China
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