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

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

Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice

“…Although both C-terminal and N-terminal regions is thought to be involved in protein interaction, the molecular mechanisms of the observed selfinhibition of GS3 and DEP1 remain elusive [19,30]. As DEP1 plays a crucial role in the understanding of G protein in rice and in rice breeding, a number of studies employing CRISPR/Cas9 technology have been conducted to verified the function of DEP1 [22,31,[38][39][40][41]. The DEP1 CRISPR/Cas9 gene-edited plants with an eliminated C-terminal exhibited an increase in grain number per panicle, reductions in plant height, panicle length, and grain length, and an erect panicle architecture, whereas the plants that had lost both the Gγ and cys-rich domains showed reductions in setting rate and grain number per panicle.…”

“…The plot was 5.4 m 2 and contained 120 plants with 30 cm × 15 cm intervals. The cultivation method and field management were as described previously [38]. We harvested the aboveground parts of 24 plants for each transgenic line at the mature stage (35 days after the full heading stage).…”

In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods

“…Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region, and indica varieties were planted in low latitudes in southern China (Min et al, 2011;Wang et al, 2015). Over the past decades, many elite japonica varieties have been bred for mid latitudes in China.…”

Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF1 Lines Uncover Multiple Heterosis-related Loci

“…The percentage of phenotypic variance calculation explained by each QTL was obtained according to the population variance within the mapping population. The details of the QTL analysis were described in our previous studies [21].…”