Th1_Identifying Core Regions of the O. sativa Genome Controlling
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Transcript of Th1_Identifying Core Regions of the O. sativa Genome Controlling
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Identifying Core Regions of the O. sativa Genome Controlling
Root Architecture
Erin E. Sparks PhDPhilip Benfey Laboratory
Duke UniversityDurham, NC, USA
Tuesday, 22nd October 2013
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Root System Architecture (RSA) Influences Plant Function in Changing Environmental
Conditions
RSAthe Spatial Organization
of Roots in the Soil
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How can we modify roots to improve agriculture?
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Iyer-Pascuzzi et al. 2010
Moroberekan Nipponbare
Basmati 217 TeqingIR64 Carolina Gold
CaiapoJeffersonLemont
Iyer-Pascuzzi et al., Plant Physiology 2010
Oryza sativa Cultivars have Diverse RSAs
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Imaging time: 5 minutes / plant
Identify Core Regions of the Genome Controlling RSA in Rice
High-throughput Root Imaging System
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Digital Phenotypingautomatic 2-D and 3-D trait extraction
GiA-Roots – Galkovskyi et al. BMC Plant Biology 2012; Iyer-Pascuzzi, Symonova, et al. Plant Physiology 2010, & unpublished
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Identifying Core Regions of the Genome Controlling RSA in Rice
Balaupland Indica
Azucenatropical Japonica
Bala x Azucena Recombinant Inbred Lines (RILs) were
phenotyped at d12, d14 and d16
Adam Price, Aberdeen, UK
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AzucenaBala RIL 001 RIL 002 RIL 003
Root Traits are Segregating in the Bala x Azucena RIL Population
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89 Univariate QTLs Clustered at 11 Loci
Topp et al., PNAS, 2013
Successful Identification of Core Regions of the Genome Controlling RSA in Rice
Positive allele = Bala
Positive allele = Azucena
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Topp et al., PNAS, 2013
Thomas Mitchell-Olds, Jill Anderson, Cheng-Ruei Lee
Multivariate QTLs Give Rise to Distinctive RSAbased on 9 traits over 3 time points
Bala allele
Azucena allele
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Current & Future Directions
-Generation of additional genetic markers by Multiplexed Shotgun Genotyping (Andolfatto, et al., 2011)
-Fine mapping and RNA-sequencing to identify differentially expressed genes underlying the QTL intervals
-Introgression the genomic regions into additional cultivars to assay yield under specific nutrient-limited conditions
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Genetic Control of RSA Changes in Response to Limited Nutrients
100% N 1% N
Azucena
low Nitrogen
high Nitrogen
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Core Regions
Controlling Root
System Architecture are
Candidates Targets for
Crop Improvement
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Chris Topp (Donald Danforth Plant Science Center, USA)
Anjali Iyer-Pascuzzi (Purdue University, USA)
• Tom Mitchell-Olds (Duke, USA) • Joshua Weitz (Georgia Tech, USA)• Herbert Edelsbrunner (IST, Austria)• Leon Kochian (Cornell, USA)
Acknowledgements
Funding: NSF AT2010, NIH R01, NIH P50, GBMF/HHMI
Benfey Lab 2013
Collaborators