Identification of a Novel QTL for Chlorate Resistance in Rice (Oryza sativa L.)

Abstract

Chlorate resistance analysis is an effective approach commonly used to distinguish the genetic variation between Oryza sativa L. ssp. indica and japonica, and predict the nitrogen use efficiency (NUE). This study aimed at investigating the response of a doubled haploid (DH) population derived from anther culture of 93-11 × Milyang352 exposed to 0.1% potassium chlorate (KClO3) at the seedling stage. The results revealed that the parental rice lines 93-11 (indica) and Milyang352 (japonica) showed distinctive phenotypic responses. The parental line 93-11 scored highly sensitive (0% survival) and Milyang352 scored resistant (66.7% survival) 7 days after treatment. The DH lines reflected the differential phenotypic response observed in parental lines. Interestingly, we identified a novel quantitative trait locus (QTL) for chlorate resistance on chromosome 3 (qCHR-3, 136 cM, logarithm of the odds—LOD: 4.1) using Kompetitive Allele-Specific PCR (KASP) markers. The additive effect (−11.97) and phenotypic variation explained (PVE; 14.9%) indicated that the allele from Milyang352 explained the observed phenotypic variation. In addition, shoot growth showed a significant difference between parental lines, but not root growth. Moreover, in silico analysis identified candidate genes with diverse and interesting molecular and physiological functions. Therefore, this study suggested that the QTL qCHR-3 harbors promising candidate genes that could play a role in the regulation of nitrogen metabolism in rice.

New Insights into the Transcriptional Regulation of Genes Involved in the Nitrogen Use Efficiency under Potassium Chlorate in Rice (Oryza sativa L.)

“…The results revealed that 26 lines and 59 lines carried the indica alleles of NR and NRT, respectively ( Figure S2 ). These introgression lines amplified the expected band size of 200 bp for the indica allele of nitrate reductase, and 165 bp specific to the indica allele of nitrate transporter, respectively, on chromosomes 2 and 10, as reported earlier [ 24 ]. The indica alleles of the NR and NRT were previously suggested to explain the differences in the nitrogen use efficiency between indica and japonica rice varieties.…”

“…Prior to germination, rice seeds were sterilized with 0.7% nitric acid (HNO 3 ) (CAS: 7697-37-2, Lot No. 2016B3902; Junsei Chemical Co. Ltd., Tokyo, Japan) overnight to break the dormancy [ 24 ], followed by incubation for 48 h at 27 °C to induce germination. Germinated seeds were grown in 50-well trays containing an enriched soil, and placed in a greenhouse until three-leaf stage.…”

“…In our recent study, a novel quantitative trait locus (QTL) for chlorate resistance was identified, and candidate genes were proposed to be associated with chlorate resistance in rice [ 24 ]. A study conducted by Gao and his colleagues [ 25 ] supported that the indica allele of nitrate reductase ( OsNR2 ) is the major component for the nitrogen biological cycle, and confers a high nitrogen use efficiency (NUE) compared to the japonica allele [ 26 ].…”

“…Potassium chlorate has been shown to induce stress in plants [ 24 , 32 , 33 ]. Generally, when plants are exposed to an environmental stimulus, they generate reactive oxygen species (ROS) [ 34 , 35 ] and reactive nitrogen species (RNS) [ 36 ].…”

Combined Linkage Mapping and Genome-Wide Association Study Identified QTLs Associated with Grain Shape and Weight in Rice (Oryza sativa L.)

“…The frequency distribution, the Quantile-Quantile (Q-Q) plots, the correlation between traits, the principal component analysis of all phenotypes of the mapping population, the pairwise kinship matrix [86], and heat map, were generated using the hist, qqplotr, data functions (only for correlation analysis in Microsoft Excel 2016), ggplot2, tidiverse, cluster, and factoextra (for heat map only) R packages in RStudio [87,88].…”