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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.
Highlights
Rice is the only cereal crop solely cultivated for human consumption, in addition to being the staple food crop for more than half of the world’s population [1]
The indica and japonica rice are reported to have a large genetic variation [3,4], which could be explained in part by the evolutionary genetic differentiation and the independent domestication processes of both rice subspecies investigated through comparative genomic studies [5]
A recent report supported that the indica and japonica subspecies differ in their ability to assimilate nitrate (NO3 ), and have a differential nitrogen use efficiency (NUE) [8]
Summary
Rice is the only cereal crop solely cultivated for human consumption, in addition to being the staple food crop for more than half of the world’s population [1]. The indica and japonica rice are reported to have a large genetic variation [3,4], which could be explained in part by the evolutionary genetic differentiation and the independent domestication processes of both rice subspecies investigated through comparative genomic studies [5]. To distinguish the genetic variation between indica and japonica rice subspecies, the resistance to potassium chlorate (KClO3 ) is commonly used as a reliable strategy, and has been shown to be effective [6,7]. A recent report supported that the indica and japonica subspecies differ in their ability to assimilate nitrate (NO3 ), and have a differential nitrogen use efficiency (NUE) [8]. Gao and colleagues [9] identified nitrate reductase (OsNR2) as the Agriculture 2020, 10, 360; doi:10.3390/agriculture10080360 www.mdpi.com/journal/agriculture
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