Assessing the importance of genotype x environment interaction for root traits in rice using a mapping population II: conventional QTL analysis

Keith MacMillan, K. Emrich, H. -. P. Piepho, Christopher Mullins, Adam Huw Price

Research output: Contribution to journalArticle

81 Citations (Scopus)

Abstract

Modifying plant root systems is considered a means of crop improvement targeted to low-resource environments, particularly low nutrient and drought-prone agriculture. The identification of quantitative trait loci (QTLs) for root traits has stimulated marker-assisted breeding to this end, but different QTLs have been detected in different populations of the same species, and importantly, in the same population when grown in different experimental environments. The presence of QTL x environment interaction is implicated, and this must be characterised if the utility of the target QTLs is to be realised. Previous attempts to do this suffer from a lack of control over replicate environments and inadequate statistical rigour. The Bala x Azucena mapping population was grown in two replicate experiments of four treatment environments, a control, a low light, a low soil nitrogen and a low soil water treatment. After a 4 weeks growth, maximum root length, maximum root thickness, root mass below 50 cm, total plant dry mass, % root mass and shoot length were measured. A summary of the overall results is presented in an accompanying paper. Here, QTL analysis by composite interval mapping is presented. A total of 145 QTLs were detected, mapping to 37 discrete loci on all chromosomes. Superficial evidence of QTL x E (great difference in LOD score) was tested by single-marker analysis which confirmed QTL x E for five loci representing only five individual trait-loci interactions. Some loci appeared to be stable across environments. Some QTLs were clearly more or less active under low light, low nitrogen or drought. A few notable loci on chromosomes 1, 2, 3, 5, 7 and 9 are briefly discussed. Also discussed are some remaining statistical shortcomings that will be addressed in another companion paper.

Original languageEnglish
Pages (from-to)953-964
Number of pages11
JournalTheoretical and Applied Genetics
Volume113
Issue number5
DOIs
Publication statusPublished - Sep 2006

Keywords

  • ORYZA-SATIVA L.
  • CONTRASTING MOISTURE REGIMES
  • MOLECULAR MARKERS
  • LOCI
  • MORPHOLOGY
  • ARCHITECTURE
  • WATER
  • IDENTIFICATION
  • CROSSES
  • LINKAGE

Cite this

Assessing the importance of genotype x environment interaction for root traits in rice using a mapping population II: conventional QTL analysis. / MacMillan, Keith; Emrich, K.; Piepho, H. -. P.; Mullins, Christopher; Price, Adam Huw.

In: Theoretical and Applied Genetics, Vol. 113, No. 5, 09.2006, p. 953-964.

Research output: Contribution to journalArticle

@article{fe3ad14bae8c4da282da140f533a1979,
title = "Assessing the importance of genotype x environment interaction for root traits in rice using a mapping population II: conventional QTL analysis",
abstract = "Modifying plant root systems is considered a means of crop improvement targeted to low-resource environments, particularly low nutrient and drought-prone agriculture. The identification of quantitative trait loci (QTLs) for root traits has stimulated marker-assisted breeding to this end, but different QTLs have been detected in different populations of the same species, and importantly, in the same population when grown in different experimental environments. The presence of QTL x environment interaction is implicated, and this must be characterised if the utility of the target QTLs is to be realised. Previous attempts to do this suffer from a lack of control over replicate environments and inadequate statistical rigour. The Bala x Azucena mapping population was grown in two replicate experiments of four treatment environments, a control, a low light, a low soil nitrogen and a low soil water treatment. After a 4 weeks growth, maximum root length, maximum root thickness, root mass below 50 cm, total plant dry mass, {\%} root mass and shoot length were measured. A summary of the overall results is presented in an accompanying paper. Here, QTL analysis by composite interval mapping is presented. A total of 145 QTLs were detected, mapping to 37 discrete loci on all chromosomes. Superficial evidence of QTL x E (great difference in LOD score) was tested by single-marker analysis which confirmed QTL x E for five loci representing only five individual trait-loci interactions. Some loci appeared to be stable across environments. Some QTLs were clearly more or less active under low light, low nitrogen or drought. A few notable loci on chromosomes 1, 2, 3, 5, 7 and 9 are briefly discussed. Also discussed are some remaining statistical shortcomings that will be addressed in another companion paper.",
keywords = "ORYZA-SATIVA L., CONTRASTING MOISTURE REGIMES, MOLECULAR MARKERS, LOCI, MORPHOLOGY, ARCHITECTURE, WATER, IDENTIFICATION, CROSSES, LINKAGE",
author = "Keith MacMillan and K. Emrich and Piepho, {H. -. P.} and Christopher Mullins and Price, {Adam Huw}",
year = "2006",
month = "9",
doi = "10.1007/s00122-006-0357-4",
language = "English",
volume = "113",
pages = "953--964",
journal = "Theoretical and Applied Genetics",
issn = "0040-5752",
number = "5",

}

TY - JOUR

T1 - Assessing the importance of genotype x environment interaction for root traits in rice using a mapping population II: conventional QTL analysis

AU - MacMillan, Keith

AU - Emrich, K.

AU - Piepho, H. -. P.

AU - Mullins, Christopher

AU - Price, Adam Huw

PY - 2006/9

Y1 - 2006/9

N2 - Modifying plant root systems is considered a means of crop improvement targeted to low-resource environments, particularly low nutrient and drought-prone agriculture. The identification of quantitative trait loci (QTLs) for root traits has stimulated marker-assisted breeding to this end, but different QTLs have been detected in different populations of the same species, and importantly, in the same population when grown in different experimental environments. The presence of QTL x environment interaction is implicated, and this must be characterised if the utility of the target QTLs is to be realised. Previous attempts to do this suffer from a lack of control over replicate environments and inadequate statistical rigour. The Bala x Azucena mapping population was grown in two replicate experiments of four treatment environments, a control, a low light, a low soil nitrogen and a low soil water treatment. After a 4 weeks growth, maximum root length, maximum root thickness, root mass below 50 cm, total plant dry mass, % root mass and shoot length were measured. A summary of the overall results is presented in an accompanying paper. Here, QTL analysis by composite interval mapping is presented. A total of 145 QTLs were detected, mapping to 37 discrete loci on all chromosomes. Superficial evidence of QTL x E (great difference in LOD score) was tested by single-marker analysis which confirmed QTL x E for five loci representing only five individual trait-loci interactions. Some loci appeared to be stable across environments. Some QTLs were clearly more or less active under low light, low nitrogen or drought. A few notable loci on chromosomes 1, 2, 3, 5, 7 and 9 are briefly discussed. Also discussed are some remaining statistical shortcomings that will be addressed in another companion paper.

AB - Modifying plant root systems is considered a means of crop improvement targeted to low-resource environments, particularly low nutrient and drought-prone agriculture. The identification of quantitative trait loci (QTLs) for root traits has stimulated marker-assisted breeding to this end, but different QTLs have been detected in different populations of the same species, and importantly, in the same population when grown in different experimental environments. The presence of QTL x environment interaction is implicated, and this must be characterised if the utility of the target QTLs is to be realised. Previous attempts to do this suffer from a lack of control over replicate environments and inadequate statistical rigour. The Bala x Azucena mapping population was grown in two replicate experiments of four treatment environments, a control, a low light, a low soil nitrogen and a low soil water treatment. After a 4 weeks growth, maximum root length, maximum root thickness, root mass below 50 cm, total plant dry mass, % root mass and shoot length were measured. A summary of the overall results is presented in an accompanying paper. Here, QTL analysis by composite interval mapping is presented. A total of 145 QTLs were detected, mapping to 37 discrete loci on all chromosomes. Superficial evidence of QTL x E (great difference in LOD score) was tested by single-marker analysis which confirmed QTL x E for five loci representing only five individual trait-loci interactions. Some loci appeared to be stable across environments. Some QTLs were clearly more or less active under low light, low nitrogen or drought. A few notable loci on chromosomes 1, 2, 3, 5, 7 and 9 are briefly discussed. Also discussed are some remaining statistical shortcomings that will be addressed in another companion paper.

KW - ORYZA-SATIVA L.

KW - CONTRASTING MOISTURE REGIMES

KW - MOLECULAR MARKERS

KW - LOCI

KW - MORPHOLOGY

KW - ARCHITECTURE

KW - WATER

KW - IDENTIFICATION

KW - CROSSES

KW - LINKAGE

U2 - 10.1007/s00122-006-0357-4

DO - 10.1007/s00122-006-0357-4

M3 - Article

VL - 113

SP - 953

EP - 964

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

SN - 0040-5752

IS - 5

ER -