Spatial Effects and GWA Mapping of Root Colonization Assessed in the Interaction Between the Rice Diversity Panel 1 and an Arbuscular Mycorrhizal Fungus

Hazel E. Davidson, Roshi Shrestha, Thomas Cornulier, Alex Douglas, Tony Travis, David Johnson, Adam H. Price (Corresponding Author)

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Abstract

If water saving methods of rice management are to be adopted, the interaction between rice plants and arbuscular mycorrhizal (AM) fungi will grow in agronomic significance. As yet there are very few studies on the interaction between rice and AM fungi and none on host genetics. A subset 334 cultivars from the Rice Diversity Panel 1 were grown in 250 L boxes filled with phosphorus (P) deficient aerobic soil without addition, with added rock phosphate and with rock phosphate and the AM fungus Rhizophagus irregularis. Statistical analysis of position of plants revealed a positive effect of their neighbors on their dry weight which was stronger in the presence of rock phosphate and even stronger with rock phosphate and AM fungi. A weak but significant difference in the response of cultivars to AM fungus treatment in terms of shoot dry weight (SDW) was revealed. Neighbor hyphal colonization was positively related to a plant’s hyphal colonization, providing insights into the way a network of AM fungi interact with multiple hosts. Hyphal colonization ranged from 21 to 89%, and 42% of the variation was explained by rice genotype. Colonization was slightly lower in aus cultivars than other rice subgroups and high in cultivars from the Philippines. Genome wide association (GWA) mapping for hyphal colonization revealed 23 putative quantitative trait loci (QTLs) indicating there is an opportunity to investigate the impact of allelic variation in rice on AM fungal colonization. Using published transcriptomics data for AM response in rice, some promising candidate genes are revealed under these QTLs being a calcium/calmodulin serine/threonine protein kinase at 4.9 Mbp on chromosome 1, two ammonium transporters genes at 24.6 Mbp on chromosome 2 and a cluster of subtilisin genes at 1.2 Mbp on chromosome 4. Future studies should concentrate on the biological significance of genetic variation in rice for AM colonization.
Original languageEnglish
Article number633
Number of pages14
JournalFrontiers in plant science
Volume10
DOIs
Publication statusPublished - 17 May 2019

Fingerprint

mycorrhizal fungi
chromosome mapping
rice
genome
rock phosphate
cultivars
chromosomes
quantitative trait loci
genes
subtilisin
calmodulin
transcriptomics
Philippines
transporters
statistical analysis
concentrates
calcium
phosphorus
genetic variation
shoots

Keywords

  • Oryza sativa
  • Rhizophagus irregularis
  • common mycorrhizal network
  • GWA mapping
  • Glomus intraradices
  • QTL

Cite this

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title = "Spatial Effects and GWA Mapping of Root Colonization Assessed in the Interaction Between the Rice Diversity Panel 1 and an Arbuscular Mycorrhizal Fungus",
abstract = "If water saving methods of rice management are to be adopted, the interaction between rice plants and arbuscular mycorrhizal (AM) fungi will grow in agronomic significance. As yet there are very few studies on the interaction between rice and AM fungi and none on host genetics. A subset 334 cultivars from the Rice Diversity Panel 1 were grown in 250 L boxes filled with phosphorus (P) deficient aerobic soil without addition, with added rock phosphate and with rock phosphate and the AM fungus Rhizophagus irregularis. Statistical analysis of position of plants revealed a positive effect of their neighbors on their dry weight which was stronger in the presence of rock phosphate and even stronger with rock phosphate and AM fungi. A weak but significant difference in the response of cultivars to AM fungus treatment in terms of shoot dry weight (SDW) was revealed. Neighbor hyphal colonization was positively related to a plant’s hyphal colonization, providing insights into the way a network of AM fungi interact with multiple hosts. Hyphal colonization ranged from 21 to 89{\%}, and 42{\%} of the variation was explained by rice genotype. Colonization was slightly lower in aus cultivars than other rice subgroups and high in cultivars from the Philippines. Genome wide association (GWA) mapping for hyphal colonization revealed 23 putative quantitative trait loci (QTLs) indicating there is an opportunity to investigate the impact of allelic variation in rice on AM fungal colonization. Using published transcriptomics data for AM response in rice, some promising candidate genes are revealed under these QTLs being a calcium/calmodulin serine/threonine protein kinase at 4.9 Mbp on chromosome 1, two ammonium transporters genes at 24.6 Mbp on chromosome 2 and a cluster of subtilisin genes at 1.2 Mbp on chromosome 4. Future studies should concentrate on the biological significance of genetic variation in rice for AM colonization.",
keywords = "Oryza sativa, Rhizophagus irregularis, common mycorrhizal network, GWA mapping, Glomus intraradices, QTL",
author = "Davidson, {Hazel E.} and Roshi Shrestha and Thomas Cornulier and Alex Douglas and Tony Travis and David Johnson and Price, {Adam H.}",
note = "The majority of the research reported here is an output of EU project “EURoot” (FP7-KBBE-2011-5 Grant Agreement No. 289300) project. RS’s contribution was funded by FACCE-JPI NET project “GreenRice” (Sustainable and environmental friendly rice cultivation systems in Europe) and was funded by the BBSRC award BB/M018415/1.",
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T1 - Spatial Effects and GWA Mapping of Root Colonization Assessed in the Interaction Between the Rice Diversity Panel 1 and an Arbuscular Mycorrhizal Fungus

AU - Davidson, Hazel E.

AU - Shrestha, Roshi

AU - Cornulier, Thomas

AU - Douglas, Alex

AU - Travis, Tony

AU - Johnson, David

AU - Price, Adam H.

N1 - The majority of the research reported here is an output of EU project “EURoot” (FP7-KBBE-2011-5 Grant Agreement No. 289300) project. RS’s contribution was funded by FACCE-JPI NET project “GreenRice” (Sustainable and environmental friendly rice cultivation systems in Europe) and was funded by the BBSRC award BB/M018415/1.

PY - 2019/5/17

Y1 - 2019/5/17

N2 - If water saving methods of rice management are to be adopted, the interaction between rice plants and arbuscular mycorrhizal (AM) fungi will grow in agronomic significance. As yet there are very few studies on the interaction between rice and AM fungi and none on host genetics. A subset 334 cultivars from the Rice Diversity Panel 1 were grown in 250 L boxes filled with phosphorus (P) deficient aerobic soil without addition, with added rock phosphate and with rock phosphate and the AM fungus Rhizophagus irregularis. Statistical analysis of position of plants revealed a positive effect of their neighbors on their dry weight which was stronger in the presence of rock phosphate and even stronger with rock phosphate and AM fungi. A weak but significant difference in the response of cultivars to AM fungus treatment in terms of shoot dry weight (SDW) was revealed. Neighbor hyphal colonization was positively related to a plant’s hyphal colonization, providing insights into the way a network of AM fungi interact with multiple hosts. Hyphal colonization ranged from 21 to 89%, and 42% of the variation was explained by rice genotype. Colonization was slightly lower in aus cultivars than other rice subgroups and high in cultivars from the Philippines. Genome wide association (GWA) mapping for hyphal colonization revealed 23 putative quantitative trait loci (QTLs) indicating there is an opportunity to investigate the impact of allelic variation in rice on AM fungal colonization. Using published transcriptomics data for AM response in rice, some promising candidate genes are revealed under these QTLs being a calcium/calmodulin serine/threonine protein kinase at 4.9 Mbp on chromosome 1, two ammonium transporters genes at 24.6 Mbp on chromosome 2 and a cluster of subtilisin genes at 1.2 Mbp on chromosome 4. Future studies should concentrate on the biological significance of genetic variation in rice for AM colonization.

AB - If water saving methods of rice management are to be adopted, the interaction between rice plants and arbuscular mycorrhizal (AM) fungi will grow in agronomic significance. As yet there are very few studies on the interaction between rice and AM fungi and none on host genetics. A subset 334 cultivars from the Rice Diversity Panel 1 were grown in 250 L boxes filled with phosphorus (P) deficient aerobic soil without addition, with added rock phosphate and with rock phosphate and the AM fungus Rhizophagus irregularis. Statistical analysis of position of plants revealed a positive effect of their neighbors on their dry weight which was stronger in the presence of rock phosphate and even stronger with rock phosphate and AM fungi. A weak but significant difference in the response of cultivars to AM fungus treatment in terms of shoot dry weight (SDW) was revealed. Neighbor hyphal colonization was positively related to a plant’s hyphal colonization, providing insights into the way a network of AM fungi interact with multiple hosts. Hyphal colonization ranged from 21 to 89%, and 42% of the variation was explained by rice genotype. Colonization was slightly lower in aus cultivars than other rice subgroups and high in cultivars from the Philippines. Genome wide association (GWA) mapping for hyphal colonization revealed 23 putative quantitative trait loci (QTLs) indicating there is an opportunity to investigate the impact of allelic variation in rice on AM fungal colonization. Using published transcriptomics data for AM response in rice, some promising candidate genes are revealed under these QTLs being a calcium/calmodulin serine/threonine protein kinase at 4.9 Mbp on chromosome 1, two ammonium transporters genes at 24.6 Mbp on chromosome 2 and a cluster of subtilisin genes at 1.2 Mbp on chromosome 4. Future studies should concentrate on the biological significance of genetic variation in rice for AM colonization.

KW - Oryza sativa

KW - Rhizophagus irregularis

KW - common mycorrhizal network

KW - GWA mapping

KW - Glomus intraradices

KW - QTL

UR - http://www.mendeley.com/research/spatial-effects-gwa-mapping-root-colonization-assessed-interaction-between-rice-diversity-panel-1-ar

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DO - 10.3389/fpls.2019.00633

M3 - Article

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JO - Frontiers in plant science

JF - Frontiers in plant science

SN - 1664-462X

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