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

Root System Architecture (RSA) Influences Plant Function in Changing Environmental

Conditions

RSAthe Spatial Organization

of Roots in the Soil

How can we modify roots to improve agriculture?

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

Imaging time: 5 minutes / plant

Identify Core Regions of the Genome Controlling RSA in Rice

High-throughput Root Imaging System

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 Plant Physiology 2010, & unpublished

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

AzucenaBala RIL 001 RIL 002 RIL 003

Root Traits are Segregating in the Bala x Azucena RIL Population

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

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

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

Genetic Control of RSA Changes in Response to Limited Nutrients

100% N 1% N

Azucena

low Nitrogen

high Nitrogen

Core Regions

Controlling Root

System Architecture are

Candidates Targets for

Crop Improvement

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