Genome-wide association mapping for root cone angle in rice

Mathilde Bettembourg,Emilie Thomas,Emmanuel Guiderdoni,Christophe Perin,Anne Dievart,Julien Frouin,Alain Audebert,Nourollah Ahmadi,Brigitte Courtois,Audrey Dardou

doi:10.1186/s12284-017-0184-z

Abstract

BackgroundPlant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years.ResultsTo find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/−50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes.ConclusionsThe present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.

Highlights

Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil
Structure was analyzed on each panel using the program Structure (Pritchard et al 2000), and the results suggested the existence of 4 subpopulations (I1 to I4) in the indica panel (Lafarge et al, 2017) and 6 subpopulations (J1 to J6) in the japonica one (Courtois et al 2013)
The mean root cone angle of the two repeated controls (IR64 and Azucena) was similar in the two experiments, with slightly higher values in the experiments involving the japonica panel; this similarity enabled a comparison of the distribution of frequency between the two panels (Fig. 3)

Summary

Introduction

Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Roots are organs that play several essential roles in plants. Roots are needed to uptake soil water and mineral nutrients and anchor plants to the ground. Several ideotypes of root architecture have been proposed depending on the relative importance given to these different roles. For nutrient uptake, ideotypes differing in root depth, number and angle were recommended for immobile. Root ideotypes should integrate functional parameters such as water and nutrient use efficiency and plasticity in addition to root architecture, as suggested by Ahmadi et al (2014). In rice, which can be grown under fully anaerobic conditions (irrigated ecosystems), fully aerobic conditions (upland ecosystems) and conditions alternating between aerobic and anaerobic

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Conclusion