A genome-wide association study (GWAS) identifies multiple loci linked with the natural variation for Al

Acid soils limit yields of many important crops including canola (Brassica napus), Australia’s third largest crop. Aluminium (Al3+) stress is the main cause of this limitation primarily because the toxic Al3+ present inhibits root growth. Breeding programmes do not target acid-soil tolerance in B. n...

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Published inFunctional plant biology : FPB Vol. 49; no. 10; pp. 845 - 860
Main Authors Du, Hanmei, Raman, Harsh, Kawasaki, Akitomo, Perera, Geetha, Diffey, Simon, Snowdon, Rod, Raman, Rosy, Ryan, Peter R.
Format Journal Article
LanguageEnglish
Published 27.06.2022
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Abstract Acid soils limit yields of many important crops including canola (Brassica napus), Australia’s third largest crop. Aluminium (Al3+) stress is the main cause of this limitation primarily because the toxic Al3+ present inhibits root growth. Breeding programmes do not target acid-soil tolerance in B. napus because genetic variation and convincing quantitative trait loci have not been reported. We conducted a genome-wide association study (GWAS) using the BnASSYST diversity panel of B. napus genotyped with 35 729 high-quality DArTseq markers. We screened 352 B. napus accessions in hydroponics with and without a toxic concentration of AlCl3 (12 μM, pH 4.3) for 12 days and measured shoot biomass, root biomass, and root length. By accounting for both population structure and kinship matrices, five significant quantitative trait loci for different measures of resistance were identified using incremental Al3+ resistance indices. Within these quantitative trait locus regions of B. napus, 40 Arabidopsis thaliana gene orthologues were identified, including some previously linked with Al3+ resistance. GWAS analysis indicated that multiple genes are responsible for the natural variation in Al3+ resistance in B. napus. The results provide new genetic resources and markers to enhance that Al3+ resistance of B. napus germplasm via genomic and marker-assisted selection.
AbstractList Acid soils limit yields of many important crops including canola (Brassica napus), Australia’s third largest crop. Aluminium (Al3+) stress is the main cause of this limitation primarily because the toxic Al3+ present inhibits root growth. Breeding programmes do not target acid-soil tolerance in B. napus because genetic variation and convincing quantitative trait loci have not been reported. We conducted a genome-wide association study (GWAS) using the BnASSYST diversity panel of B. napus genotyped with 35 729 high-quality DArTseq markers. We screened 352 B. napus accessions in hydroponics with and without a toxic concentration of AlCl3 (12 μM, pH 4.3) for 12 days and measured shoot biomass, root biomass, and root length. By accounting for both population structure and kinship matrices, five significant quantitative trait loci for different measures of resistance were identified using incremental Al3+ resistance indices. Within these quantitative trait locus regions of B. napus, 40 Arabidopsis thaliana gene orthologues were identified, including some previously linked with Al3+ resistance. GWAS analysis indicated that multiple genes are responsible for the natural variation in Al3+ resistance in B. napus. The results provide new genetic resources and markers to enhance that Al3+ resistance of B. napus germplasm via genomic and marker-assisted selection.
Author Diffey, Simon
Raman, Rosy
Kawasaki, Akitomo
Du, Hanmei
Perera, Geetha
Raman, Harsh
Ryan, Peter R.
Snowdon, Rod
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  year: 2009
  ident: FP22073R57
  article-title: A zinc finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice.
  publication-title: The Plant Cell
  doi: 10.1105/tpc.109.070771
– volume: 149
  start-page: 85
  year: 2006
  ident: FP22073R29
  article-title: Incremental crop tolerance to weeds: a measure for selecting competitive ability in Australian wheats.
  publication-title: Euphytica
  doi: 10.1007/s10681-005-9056-5
– volume: 12
  year: 2021
  ident: FP22073R52
  article-title: Aluminum or low pH – which is the bigger enemy of barley? Transcriptome analysis of barley root meristem under Al and low pH stress.
  publication-title: Frontiers in Genetics
  doi: 10.3389/fgene.2021.675260
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Snippet Acid soils limit yields of many important crops including canola (Brassica napus), Australia’s third largest crop. Aluminium (Al3+) stress is the main cause of...
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Title A genome-wide association study (GWAS) identifies multiple loci linked with the natural variation for Al
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