ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice (O. sativa)

Juan D. Arbelaez, Lyza G. Maron, Timothy O. Jobe, Miguel A. Piñeros, Adam N. Famoso, Ana Rita Rebelo, Namrata Singh, Qiyue Ma, Zhangjun Fei, Leon V. Kochian, Susan R. McCouch

Research output: Contribution to journalArticle

Abstract

Transcription factors (TFs) regulate the expression of other genes to indirectly mediate stress resistance mechanisms. Therefore, when studying TF-mediated stress resistance, it is important to understand how TFs interact with genes in the genetic background. Here, we fine-mapped the aluminum (Al) resistance QTL Alt12.1 to a 44-kb region containing six genes. Among them is ART1, which encodes a C2H2-type zinc finger TF required for Al resistance in rice. The mapping parents, Al-resistant cv Azucena (tropical japonica) and Al-sensitive cv IR64 (indica), have extensive sequence polymorphism within the ART1 coding region, but similar ART1 expression levels. Using reciprocal near-isogenic lines (NILs) we examined how allele-swapping the Alt12.1 locus would affect plant responses to Al. Analysis of global transcriptional responses to Al stress in roots of the NILs alongside their recurrent parents demonstrated that the presence of the Alt12.1 from Al-resistant Azucena led to greater changes in gene expression in response to Al when compared to the Alt12.1 from IR64 in both genetic backgrounds. The presence of the ART1 allele from the opposite parent affected the expression of several genes not previously implicated in rice Al tolerance. We highlight examples where putatively functional variation in cis-regulatory regions of ART1-regulated genes interacts with ART1 to determine gene expression in response to Al. This ART1–promoter interaction may be associated with transgressive variation for Al resistance in the Azucena × IR64 population. These results illustrate how ART1 interacts with the genetic background to contribute to quantitative phenotypic variation in rice Al resistance.

Original languageEnglish (US)
Article numbere00014
JournalPlant Direct
Volume1
Issue number4
DOIs
StatePublished - Jan 1 2017
Externally publishedYes

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R Factors
Aluminum
genetic background
aluminum
Transcription Factors
rice
transcription factors
Genes
gene
Genetic Background
Oryza
Gene Expression
stress resistance
gene expression
isogenic lines
Gene expression
stress tolerance
allele
Alleles
alleles

Keywords

  • abiotic stress
  • acid soils
  • aluminum
  • QTL mapping
  • rice
  • transcriptional regulation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Plant Science

Cite this

ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice (O. sativa). / Arbelaez, Juan D.; Maron, Lyza G.; Jobe, Timothy O.; Piñeros, Miguel A.; Famoso, Adam N.; Rebelo, Ana Rita; Singh, Namrata; Ma, Qiyue; Fei, Zhangjun; Kochian, Leon V.; McCouch, Susan R.

In: Plant Direct, Vol. 1, No. 4, e00014, 01.01.2017.

Research output: Contribution to journalArticle

Arbelaez, JD, Maron, LG, Jobe, TO, Piñeros, MA, Famoso, AN, Rebelo, AR, Singh, N, Ma, Q, Fei, Z, Kochian, LV & McCouch, SR 2017, 'ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice (O. sativa)', Plant Direct, vol. 1, no. 4, e00014. https://doi.org/10.1002/pld3.14
Arbelaez, Juan D. ; Maron, Lyza G. ; Jobe, Timothy O. ; Piñeros, Miguel A. ; Famoso, Adam N. ; Rebelo, Ana Rita ; Singh, Namrata ; Ma, Qiyue ; Fei, Zhangjun ; Kochian, Leon V. ; McCouch, Susan R. / ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice (O. sativa). In: Plant Direct. 2017 ; Vol. 1, No. 4.
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abstract = "Transcription factors (TFs) regulate the expression of other genes to indirectly mediate stress resistance mechanisms. Therefore, when studying TF-mediated stress resistance, it is important to understand how TFs interact with genes in the genetic background. Here, we fine-mapped the aluminum (Al) resistance QTL Alt12.1 to a 44-kb region containing six genes. Among them is ART1, which encodes a C2H2-type zinc finger TF required for Al resistance in rice. The mapping parents, Al-resistant cv Azucena (tropical japonica) and Al-sensitive cv IR64 (indica), have extensive sequence polymorphism within the ART1 coding region, but similar ART1 expression levels. Using reciprocal near-isogenic lines (NILs) we examined how allele-swapping the Alt12.1 locus would affect plant responses to Al. Analysis of global transcriptional responses to Al stress in roots of the NILs alongside their recurrent parents demonstrated that the presence of the Alt12.1 from Al-resistant Azucena led to greater changes in gene expression in response to Al when compared to the Alt12.1 from IR64 in both genetic backgrounds. The presence of the ART1 allele from the opposite parent affected the expression of several genes not previously implicated in rice Al tolerance. We highlight examples where putatively functional variation in cis-regulatory regions of ART1-regulated genes interacts with ART1 to determine gene expression in response to Al. This ART1–promoter interaction may be associated with transgressive variation for Al resistance in the Azucena × IR64 population. These results illustrate how ART1 interacts with the genetic background to contribute to quantitative phenotypic variation in rice Al resistance.",
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AU - Maron, Lyza G.

AU - Jobe, Timothy O.

AU - Piñeros, Miguel A.

AU - Famoso, Adam N.

AU - Rebelo, Ana Rita

AU - Singh, Namrata

AU - Ma, Qiyue

AU - Fei, Zhangjun

AU - Kochian, Leon V.

AU - McCouch, Susan R.

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AB - Transcription factors (TFs) regulate the expression of other genes to indirectly mediate stress resistance mechanisms. Therefore, when studying TF-mediated stress resistance, it is important to understand how TFs interact with genes in the genetic background. Here, we fine-mapped the aluminum (Al) resistance QTL Alt12.1 to a 44-kb region containing six genes. Among them is ART1, which encodes a C2H2-type zinc finger TF required for Al resistance in rice. The mapping parents, Al-resistant cv Azucena (tropical japonica) and Al-sensitive cv IR64 (indica), have extensive sequence polymorphism within the ART1 coding region, but similar ART1 expression levels. Using reciprocal near-isogenic lines (NILs) we examined how allele-swapping the Alt12.1 locus would affect plant responses to Al. Analysis of global transcriptional responses to Al stress in roots of the NILs alongside their recurrent parents demonstrated that the presence of the Alt12.1 from Al-resistant Azucena led to greater changes in gene expression in response to Al when compared to the Alt12.1 from IR64 in both genetic backgrounds. The presence of the ART1 allele from the opposite parent affected the expression of several genes not previously implicated in rice Al tolerance. We highlight examples where putatively functional variation in cis-regulatory regions of ART1-regulated genes interacts with ART1 to determine gene expression in response to Al. This ART1–promoter interaction may be associated with transgressive variation for Al resistance in the Azucena × IR64 population. These results illustrate how ART1 interacts with the genetic background to contribute to quantitative phenotypic variation in rice Al resistance.

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