Difference between revisions of "IC4R001-GWAS-2011-21829395"

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==The Background of This Project==
 
==The Background of This Project==
While rice (Oryza sativa) is significantly more Al tolerant than other cereals, no genes underlying Al tolerance in rice have been reported. Using genome-wide association(GWA) and bi-parental QTL mapping, we investigated the genetic architecture of Al tolerance in rice. Japonica varieties were twice as Al tolerant as indica and aus varieties. Overall, 57% of the phenotypic variation was correlated with subpopulation, consistent with observations that different genes and genomic regions were associated with Al tolerance in different subpopulations. Four regions identified by GWA co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified quantitative trait loci(QTL). Haplotype and sequence analysis around the candidate gene, Nrat1, identified a susceptible haplotype explaining 40% of the Al tolerance variation within the aus subpopulation and three non-synonymous mutations within Nrat1 that were predictive of Al sensitivity. Using Indica 6 Japonica mapping populations, we identified QTLs associated with transgressive variation where alleles from a susceptible indica or aus parent enhanced Al tolerance in a tolerant japonica background. This work demonstrates the importance of subpopulation in interpreting and manipulating complex traits in rice and provides a roadmap for breeders aiming to capture genetic value from phenotypically inferior lines.
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* While rice (Oryza sativa) is significantly more Al tolerant than other cereals, no genes underlying Al tolerance in rice have been reported. Using genome-wide association(GWA) and bi-parental QTL mapping, we investigated the genetic architecture of Al tolerance in rice. Japonica varieties were twice as Al tolerant as indica and aus varieties. Overall, 57% of the phenotypic variation was correlated with subpopulation, consistent with observations that different genes and genomic regions were associated with Al tolerance in different subpopulations. Four regions identified by GWA co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified quantitative trait loci(QTL). Haplotype and sequence analysis around the candidate gene, Nrat1, identified a susceptible haplotype explaining 40% of the Al tolerance variation within the aus subpopulation and three non-synonymous mutations within Nrat1 that were predictive of Al sensitivity. Using Indica 6 Japonica mapping populations, we identified QTLs associated with transgressive variation where alleles from a susceptible indica or aus parent enhanced Al tolerance in a tolerant japonica background. This work demonstrates the importance of subpopulation in interpreting and manipulating complex traits in rice and provides a roadmap for breeders aiming to capture genetic value from phenotypically inferior lines.
  
 
==Plant Culture & Treatment==
 
==Plant Culture & Treatment==

Revision as of 08:38, 21 June 2016

Project Title

Genetic Architecture of Aluminum Tolerance in Rice( Oryza sativa ) Determined through Genome-Wide Association Analysis and QTL Mapping

The Background of This Project

  • While rice (Oryza sativa) is significantly more Al tolerant than other cereals, no genes underlying Al tolerance in rice have been reported. Using genome-wide association(GWA) and bi-parental QTL mapping, we investigated the genetic architecture of Al tolerance in rice. Japonica varieties were twice as Al tolerant as indica and aus varieties. Overall, 57% of the phenotypic variation was correlated with subpopulation, consistent with observations that different genes and genomic regions were associated with Al tolerance in different subpopulations. Four regions identified by GWA co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified quantitative trait loci(QTL). Haplotype and sequence analysis around the candidate gene, Nrat1, identified a susceptible haplotype explaining 40% of the Al tolerance variation within the aus subpopulation and three non-synonymous mutations within Nrat1 that were predictive of Al sensitivity. Using Indica 6 Japonica mapping populations, we identified QTLs associated with transgressive variation where alleles from a susceptible indica or aus parent enhanced Al tolerance in a tolerant japonica background. This work demonstrates the importance of subpopulation in interpreting and manipulating complex traits in rice and provides a roadmap for breeders aiming to capture genetic value from phenotypically inferior lines.

Plant Culture & Treatment

  • Plants were grown hydroponically in a growth chamber as described by Famoso et al. [8]. Al tolerance was determined based on relative root growth (RRG) after three days in Al (160 m M Al 3+ ) or control solution. The hydroponic solution used in this study was chemically designed and optimized for rice Al tolerance screening; for a detailed comparison of the phenotypic procedures employed in this work compared to previously published rice Al tolerance work see Famoso et al. (2010). To obtain uniform seedlings, 80 seeds were germinated and the 30 most uniform seedlings were visually selected and transferred to a control hydroponic solution for a 24 hour adjustment period. After the 24 hour adjustment period, root length was measured with a ruler and the 20 most uniform seedlings were selected and distributed to fresh control solution (0 uM Al 3+ ) or Al treatment solution (160 uM Al 3+ ). Plants were grown in their respective treatments for ,72 hours and the total root system growth was quantified using an imaging and root quantification system as described by Famoso et al.(2010). The mean total root growth was calculated for Al treated and control plants and RRG was calculated as mean growth (Al)/mean growth (control). The 373 genotypes screened for Al tolerance and used in the association analysis are part of a set of 400 O. sativa genotypes that have been genotyped with 44,000 SNPs as described by Zhao et al. [65].

Research Findings

  • Two immortalized QTL mapping populations were analyzed for Al tolerance. One consisted of 134 recombinant inbred lines (RIL) derived from the cross IR64/Azucena , and the other was comprised of 78 backcross inbred lines (BIL) derived from the cross Nipponbare/Kasalath//Nipponbare. These popula- tions were used to evaluate Al tolerance using three different indices of relative root growth (RRG), (1) longest root growth (LRG-RRG), (2) primary root growth (PGR-RRG) and total root growth (TRG-RRG) (see Materials and Methods for details). The phenotypic distribution was approximately normal for each population, no matter which root screening index was used. The QTL mapping populations allowed us to determine which of the three root evaluation methods would be most useful for evaluating the diversity panel as a whole.

Labs working on this Project

  • Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
  • Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
  • Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Cornell University, Ithaca, New York, United States of America

Corresponding Author

Susan R. McCouch(srm4@cornell.edu)