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

BMC Biology
Xiukun LiQuan Xu

Abstract

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. 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. This study provides information on the suitable environmental conditions, and genetic background, for functional g...Continue Reading

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Citations

May 31, 2019·Journal of Experimental Botany·Gopal MisraNese Sreenivasulu
Sep 8, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Qishen GuZhiying Ma
Mar 20, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yue CuiQuan Xu
May 6, 2021·The Plant Genome·Lekha T PazhamalaRajeev K Varshney
Jun 3, 2021·International Journal of Molecular Sciences·Piengtawan TappibanJinsong Bao

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Methods Mentioned

BETA
genotyping
RNA-seq
transgenic
RNA Extraction
PCR

Software Mentioned

Highmaps
SOAPsnp
Augustus
InterProScan
SNAP
DF
MITE
Quiver
GeMoMa
PILER

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