Differential expression of Nrat1 is responsible for Al-tolerance QTL on chromosome 2 in rice

Jixing Xia, Naoki Yamaji, Jing Che, Ren Fang Shen, Jian Feng Ma

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Although rice (Oryza sativa) is the most Al-tolerant species among small-grain cereal crops, there is wide genotypic variation in its tolerance to Al toxicity. A number of quantitative trait loci (QTLs) for Al tolerance have been detected, but the responsible genes have not been identified. By using chromosome segment substitution lines, this work found that Nrat1, a gene encoding an Al transporter, is responsible for a QTL previously detected on chromosome 2. Substitution of the chromosome segment containing Nrat1 from Koshihikari (Al-tolerant variety) by that from Kasalath (Al-sensitive variety) decreased Nrat1 expression and Al uptake and tolerance, but increased binding of Al to the cell wall. Nrat1 in Kasalath showed tissue localization similar to Koshihikari in the roots. Although Koshihikari and Kasalath differed in four amino acids in Nrat1 protein, Nrat1 from Kasalath also showed transport activity for Al. Analysis with site-directed mutagenesis revealed that these differences did not affect the Al-transport activity much. Furthermore, there was no correlation between Al tolerance and the open-reading-frame sequence differences in other rice varieties. On the other hand, there was good correlation between Nrat1 expression and Al tolerance; however, sequence comparison of the promoter region up to 2.1kb did not give a clear difference between the Al-tolerant and-sensitive varieties. Taken together, these results indicate that differential expression of Nrat1 is responsible for the QTL for Al tolerance on chromosome 2, although the mechanism controlling Nrat1 expression remains to be examined.

Original languageEnglish
Pages (from-to)4297-4304
Number of pages8
JournalJournal of Experimental Botany
Volume65
Issue number15
DOIs
Publication statusPublished - 2014

Fingerprint

Chromosomes, Human, Pair 2
Quantitative Trait Loci
quantitative trait loci
chromosomes
rice
Chromosomes
grain crops
chromosome substitution
Site-Directed Mutagenesis
Genetic Promoter Regions
Cell Wall
substitution lines
Open Reading Frames
Genes
site-directed mutagenesis
transporters
open reading frames
Amino Acids
Oryza sativa
genes

Keywords

  • Al QTL
  • Al tolerance
  • expression
  • genotypic difference
  • Nrat1
  • Oryza sativa

ASJC Scopus subject areas

  • Plant Science
  • Physiology
  • Medicine(all)

Cite this

Differential expression of Nrat1 is responsible for Al-tolerance QTL on chromosome 2 in rice. / Xia, Jixing; Yamaji, Naoki; Che, Jing; Shen, Ren Fang; Ma, Jian Feng.

In: Journal of Experimental Botany, Vol. 65, No. 15, 2014, p. 4297-4304.

Research output: Contribution to journalArticle

@article{4df28b5080ac4bf084ce3bfd9eaac88f,
title = "Differential expression of Nrat1 is responsible for Al-tolerance QTL on chromosome 2 in rice",
abstract = "Although rice (Oryza sativa) is the most Al-tolerant species among small-grain cereal crops, there is wide genotypic variation in its tolerance to Al toxicity. A number of quantitative trait loci (QTLs) for Al tolerance have been detected, but the responsible genes have not been identified. By using chromosome segment substitution lines, this work found that Nrat1, a gene encoding an Al transporter, is responsible for a QTL previously detected on chromosome 2. Substitution of the chromosome segment containing Nrat1 from Koshihikari (Al-tolerant variety) by that from Kasalath (Al-sensitive variety) decreased Nrat1 expression and Al uptake and tolerance, but increased binding of Al to the cell wall. Nrat1 in Kasalath showed tissue localization similar to Koshihikari in the roots. Although Koshihikari and Kasalath differed in four amino acids in Nrat1 protein, Nrat1 from Kasalath also showed transport activity for Al. Analysis with site-directed mutagenesis revealed that these differences did not affect the Al-transport activity much. Furthermore, there was no correlation between Al tolerance and the open-reading-frame sequence differences in other rice varieties. On the other hand, there was good correlation between Nrat1 expression and Al tolerance; however, sequence comparison of the promoter region up to 2.1kb did not give a clear difference between the Al-tolerant and-sensitive varieties. Taken together, these results indicate that differential expression of Nrat1 is responsible for the QTL for Al tolerance on chromosome 2, although the mechanism controlling Nrat1 expression remains to be examined.",
keywords = "Al QTL, Al tolerance, expression, genotypic difference, Nrat1, Oryza sativa",
author = "Jixing Xia and Naoki Yamaji and Jing Che and Shen, {Ren Fang} and Ma, {Jian Feng}",
year = "2014",
doi = "10.1093/jxb/eru201",
language = "English",
volume = "65",
pages = "4297--4304",
journal = "Journal of Experimental Botany",
issn = "0022-0957",
publisher = "Oxford University Press",
number = "15",

}

TY - JOUR

T1 - Differential expression of Nrat1 is responsible for Al-tolerance QTL on chromosome 2 in rice

AU - Xia, Jixing

AU - Yamaji, Naoki

AU - Che, Jing

AU - Shen, Ren Fang

AU - Ma, Jian Feng

PY - 2014

Y1 - 2014

N2 - Although rice (Oryza sativa) is the most Al-tolerant species among small-grain cereal crops, there is wide genotypic variation in its tolerance to Al toxicity. A number of quantitative trait loci (QTLs) for Al tolerance have been detected, but the responsible genes have not been identified. By using chromosome segment substitution lines, this work found that Nrat1, a gene encoding an Al transporter, is responsible for a QTL previously detected on chromosome 2. Substitution of the chromosome segment containing Nrat1 from Koshihikari (Al-tolerant variety) by that from Kasalath (Al-sensitive variety) decreased Nrat1 expression and Al uptake and tolerance, but increased binding of Al to the cell wall. Nrat1 in Kasalath showed tissue localization similar to Koshihikari in the roots. Although Koshihikari and Kasalath differed in four amino acids in Nrat1 protein, Nrat1 from Kasalath also showed transport activity for Al. Analysis with site-directed mutagenesis revealed that these differences did not affect the Al-transport activity much. Furthermore, there was no correlation between Al tolerance and the open-reading-frame sequence differences in other rice varieties. On the other hand, there was good correlation between Nrat1 expression and Al tolerance; however, sequence comparison of the promoter region up to 2.1kb did not give a clear difference between the Al-tolerant and-sensitive varieties. Taken together, these results indicate that differential expression of Nrat1 is responsible for the QTL for Al tolerance on chromosome 2, although the mechanism controlling Nrat1 expression remains to be examined.

AB - Although rice (Oryza sativa) is the most Al-tolerant species among small-grain cereal crops, there is wide genotypic variation in its tolerance to Al toxicity. A number of quantitative trait loci (QTLs) for Al tolerance have been detected, but the responsible genes have not been identified. By using chromosome segment substitution lines, this work found that Nrat1, a gene encoding an Al transporter, is responsible for a QTL previously detected on chromosome 2. Substitution of the chromosome segment containing Nrat1 from Koshihikari (Al-tolerant variety) by that from Kasalath (Al-sensitive variety) decreased Nrat1 expression and Al uptake and tolerance, but increased binding of Al to the cell wall. Nrat1 in Kasalath showed tissue localization similar to Koshihikari in the roots. Although Koshihikari and Kasalath differed in four amino acids in Nrat1 protein, Nrat1 from Kasalath also showed transport activity for Al. Analysis with site-directed mutagenesis revealed that these differences did not affect the Al-transport activity much. Furthermore, there was no correlation between Al tolerance and the open-reading-frame sequence differences in other rice varieties. On the other hand, there was good correlation between Nrat1 expression and Al tolerance; however, sequence comparison of the promoter region up to 2.1kb did not give a clear difference between the Al-tolerant and-sensitive varieties. Taken together, these results indicate that differential expression of Nrat1 is responsible for the QTL for Al tolerance on chromosome 2, although the mechanism controlling Nrat1 expression remains to be examined.

KW - Al QTL

KW - Al tolerance

KW - expression

KW - genotypic difference

KW - Nrat1

KW - Oryza sativa

UR - http://www.scopus.com/inward/record.url?scp=84905179175&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84905179175&partnerID=8YFLogxK

U2 - 10.1093/jxb/eru201

DO - 10.1093/jxb/eru201

M3 - Article

VL - 65

SP - 4297

EP - 4304

JO - Journal of Experimental Botany

JF - Journal of Experimental Botany

SN - 0022-0957

IS - 15

ER -