Rice root genetic architecture

meta-analysis from a drought QTL database

Brigitte Courtois, Nourollah Ahmadi, Farkhanda Khowaja, Adam H. Price, Jean-Francois Rami, Julien Frouin, Chantal Hamelin, Manuel Ruiz

Research output: Contribution to journalArticle

140 Citations (Scopus)

Abstract

During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudochromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.
Original languageEnglish
Pages (from-to)115-128
Number of pages14
JournalRice
Volume2
Issue number2-3
DOIs
Publication statusPublished - Sep 2009

Fingerprint

meta-analysis
quantitative trait loci
rice
drought
drought resistance
drought tolerance
Akaike information criterion
root-shoot ratio
gene
confidence interval
positioning
chromosome
penetration
genome
root shoot ratio
software
genes
chromosomes

Keywords

  • rice
  • drought avoidance
  • root morphology
  • QTLs
  • meta-analysis
  • quantitative trait loci
  • oryza-sativa L.
  • doubled-haploid population
  • recombinant inbred lines
  • heading date
  • candidate genes
  • photoperiod sensitivity
  • epistatic interactions
  • penetrartion ability
  • mapping QLTs

Cite this

Courtois, B., Ahmadi, N., Khowaja, F., Price, A. H., Rami, J-F., Frouin, J., ... Ruiz, M. (2009). Rice root genetic architecture: meta-analysis from a drought QTL database . Rice, 2(2-3), 115-128. https://doi.org/10.1007/s12284-009-9028-9

Rice root genetic architecture : meta-analysis from a drought QTL database . / Courtois, Brigitte; Ahmadi, Nourollah; Khowaja, Farkhanda; Price, Adam H.; Rami, Jean-Francois; Frouin, Julien; Hamelin, Chantal; Ruiz, Manuel.

In: Rice, Vol. 2, No. 2-3, 09.2009, p. 115-128.

Research output: Contribution to journalArticle

Courtois, B, Ahmadi, N, Khowaja, F, Price, AH, Rami, J-F, Frouin, J, Hamelin, C & Ruiz, M 2009, 'Rice root genetic architecture: meta-analysis from a drought QTL database ', Rice, vol. 2, no. 2-3, pp. 115-128. https://doi.org/10.1007/s12284-009-9028-9
Courtois B, Ahmadi N, Khowaja F, Price AH, Rami J-F, Frouin J et al. Rice root genetic architecture: meta-analysis from a drought QTL database . Rice. 2009 Sep;2(2-3):115-128. https://doi.org/10.1007/s12284-009-9028-9
Courtois, Brigitte ; Ahmadi, Nourollah ; Khowaja, Farkhanda ; Price, Adam H. ; Rami, Jean-Francois ; Frouin, Julien ; Hamelin, Chantal ; Ruiz, Manuel. / Rice root genetic architecture : meta-analysis from a drought QTL database . In: Rice. 2009 ; Vol. 2, No. 2-3. pp. 115-128.
@article{60cdc9e0ce3449f794e9ac59e515f326,
title = "Rice root genetic architecture: meta-analysis from a drought QTL database",
abstract = "During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudochromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.",
keywords = "rice, drought avoidance, root morphology, QTLs, meta-analysis, quantitative trait loci, oryza-sativa L., doubled-haploid population, recombinant inbred lines, heading date, candidate genes, photoperiod sensitivity, epistatic interactions, penetrartion ability, mapping QLTs",
author = "Brigitte Courtois and Nourollah Ahmadi and Farkhanda Khowaja and Price, {Adam H.} and Jean-Francois Rami and Julien Frouin and Chantal Hamelin and Manuel Ruiz",
year = "2009",
month = "9",
doi = "10.1007/s12284-009-9028-9",
language = "English",
volume = "2",
pages = "115--128",
journal = "Rice",
issn = "1939-8433",
publisher = "Springer Publishing Company",
number = "2-3",

}

TY - JOUR

T1 - Rice root genetic architecture

T2 - meta-analysis from a drought QTL database

AU - Courtois, Brigitte

AU - Ahmadi, Nourollah

AU - Khowaja, Farkhanda

AU - Price, Adam H.

AU - Rami, Jean-Francois

AU - Frouin, Julien

AU - Hamelin, Chantal

AU - Ruiz, Manuel

PY - 2009/9

Y1 - 2009/9

N2 - During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudochromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.

AB - During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudochromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.

KW - rice

KW - drought avoidance

KW - root morphology

KW - QTLs

KW - meta-analysis

KW - quantitative trait loci

KW - oryza-sativa L.

KW - doubled-haploid population

KW - recombinant inbred lines

KW - heading date

KW - candidate genes

KW - photoperiod sensitivity

KW - epistatic interactions

KW - penetrartion ability

KW - mapping QLTs

U2 - 10.1007/s12284-009-9028-9

DO - 10.1007/s12284-009-9028-9

M3 - Article

VL - 2

SP - 115

EP - 128

JO - Rice

JF - Rice

SN - 1939-8433

IS - 2-3

ER -