Comparative Genome-Wide-Association Mapping Identifies Common Loci Controlling Root System Architecture and Resistance to Aphanomyces euteiches in Pea.

Aurore Desgroux,Gilles Boutet,Alain Baranger,Judith Burstin,Marie-Laure Pilet-Nayel,Henri Miteul,Gwenola Le Roy,Maria Manzanares-Dauleux,Grégoire Aubert,Véronique Aubert,Valentin N Baudais,Gérard Duc,Henri De Larambergue,Virginie Bourion

doi:10.3389/fpls.2017.02195

Abstract

Combining plant genetic resistance with architectural traits that are unfavorable to disease development is a promising strategy for reducing epidemics. However, few studies have identified root system architecture (RSA) traits with the potential to limit root disease development. Pea is a major cultivated legume worldwide and has a wide level of natural genetic variability for plant architecture. The root pathogen Aphanomyces euteiches is a major limiting factor of pea crop yield. This study aimed to increase the knowledge on the diversity of loci and candidate genes controlling RSA traits in pea and identify RSA genetic loci associated with resistance to A. euteiches which could be combined with resistance QTL in breeding. A comparative genome wide association (GWA) study of plant architecture and resistance to A. euteiches was conducted at the young plant stage in a collection of 266 pea lines contrasted for both traits. The collection was genotyped using 14,157 SNP markers from recent pea genomic resources. It was phenotyped for ten root, shoot and overall plant architecture traits, as well as three disease resistance traits in controlled conditions, using image analysis. We identified a total of 75 short-size genomic intervals significantly associated with plant architecture and overlapping with 46 previously detected QTL. The major consistent intervals included plant shoot architecture or flowering genes (PsLE, PsTFL1) with putative pleiotropic effects on root architecture. A total of 11 genomic intervals were significantly associated with resistance to A. euteiches confirming several consistent previously identified major QTL. One significant SNP, mapped to the major QTL Ae-Ps7.6, was associated with both resistance and RSA traits. At this marker, the resistance-enhancing allele was associated with an increased total root projected area, in accordance with the correlation observed between resistance and larger root systems in the collection. Seven additional intervals associated with plant architecture overlapped with GWA intervals previously identified for resistance to A. euteiches. This study provides innovative results about genetic interdependency of root disease resistance and RSA inheritance. It identifies pea lines, QTL, closely-linked markers and candidate genes for marker-assisted-selection of RSA loci to reduce Aphanomyces root rot severity in future pea varieties.

Highlights

Plant architecture has often been reported to play a role in modifying organ susceptibility to pathogens or pests, by favoring mechanisms leading to infection escape or increased tolerance (Ney et al, 2013)
The pea-Aphanomyces collection is representative of the genetic and phenotypic variability identified or created in pea for resistance vs. susceptibility to A. euteiches. It includes: (i) 58% resistant or susceptible lines derived from a French recurrent-selection based breeding program, (ii) 28% partially resistant pea recombinant inbred line (RIL) or wild and germplasm lines derived from INRA and USDA Aphanomyces research programs, and (iii) 14% susceptible spring or winter pea varieties grown in Europe
This study was based on a genome wide association (GWA) approach, using a collection of 266 pea lines established from previous collections including contrasted lines for plant architecture traits and Aphanomyces root rot resistance

Summary

Introduction

Plant architecture has often been reported to play a role in modifying organ susceptibility to pathogens or pests, by favoring mechanisms leading to infection escape or increased tolerance (Ney et al, 2013). Spatial disease avoidance was shown to result from a combination of architectural features with unfavorable effects on disease development and severity (Tivoli et al, 2013). Combining plant genetic resistance with the architectural traits that are the most unfavorable to diseases would be a strategy of interest for reducing epidemics. Most reports of exploiting plant architecture effects to limit disease development were carried out on the aerial parts of the plant. Few studies have identified and used root architecture traits in breeding to limit root disease development, probably due to the difficulty in evaluating the effects of both disease and plant architecture on the root compartment (Downie et al, 2015)

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