Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea

Authors: DESGROUX, AURORE - Institut National De La Recherche Agronomique (INRA); L'ANTHOENE, VIRGINE - Institut National De La Recherche Agronomique (INRA); ROUX-DUPARQUE, MARTINE - Institut National De La Recherche Agronomique (INRA); RIVIERE, JEAN-PHILLIPE - Institut National De La Recherche Agronomique (INRA); AUBERT, GREGOIRE - Institut National De La Recherche Agronomique (INRA); TAYEH, NADIM - Institut National De La Recherche Agronomique (INRA); MOUSSART, ANNE - Institut National De La Recherche Agronomique (INRA); MANGIN, PIERRE - Institut National De La Recherche Agronomique (INRA); VETEL, PIERRICK - Institut National De La Recherche Agronomique (INRA); PIRIO, CHRISTOPHE - Institut National De La Recherche Agronomique (INRA); McGee, Rebecca; Coyne, Clarice - Clare; BURSTIN, JUDITH - Institut National De La Recherche Agronomique (INRA); BARANGER, ALAIN - Institut National De La Recherche Agronomique (INRA); MANZANARES-DAULEUX, MARIA - Institut National De La Recherche Agronomique (INRA); BOURION, VIRGINIE - Institut National De La Recherche Agronomique (INRA); PILET-NAYEL, MARIE-LAURE - Institut National De La Recherche Agronomique (INRA)

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2016
Publication Date: 2/20/2016
Citation: Desgroux, A., L'Anthoene, V., Roux-Duparque, M., Riviere, J., Aubert, G., Tayeh, N., Moussart, A., Mangin, P., Vetel, P., Pirio, C., Mcgee, R.J., Coyne, C.J., Burstin, J., Baranger, A., Manzanares-Dauleux, M., Bourion, V., Pilet-Nayel, M. 2016. Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea. BMC Genomics. 17:124.

Interpretive Summary: Aphanomyces euteiches is a soil borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. A few studies reported gene regions (QTL) controlling resistance to A. euteiches in pea by linkage mapping. Confidence intervals of QTL remained large and often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to validate and refine confidence intervals of Aphanomyces resistance QTL previously reported, as well as identify new resistance gene regions, by genome wide association study. An Aphanomyces collection of 175 pea lines, enriched in germplasm derived from resistant sources previously studied, was evaluated for resistance to A. euteiches in field infested nurseries and with two strains in under controlled conditions. The collection was also genotyped with 13,204 functional gene polymorphisms (SNPs). Genome-wide association analysis detected a total of 52 genomic regions (QTL) small size-intervals associated with resistance to A. euteiches. The analysis validated six of the seven main Aphanomyces resistance QTL previously reported and detected new resistance loci. It identified SNPs associated with resistance gene locations (QTL) with much higher resolution than previously. The analysis also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of best alleles (form of the gene) in highest resistant lines for use by breeders. Previous linkages between resistance alleles and late-flowering alleles undesired for dry pea breeding were mostly confirmed but the linkage between loci controlling resistance and colored flowers was broken due to the high resolution of the analysis. This study brings valuable markers, haplotypes and germplasm to increase levels of partial resistance to A. euteiches for use in applied pea breeding programs.

Technical Abstract: Genome-wide association mapping has recently emerged as a valuable approach to refine genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. A few studies reported QTL controlling resistance to A. euteiches in pea by linkage mapping. Confidence intervals of QTL remained large and often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to validate and refine confidence intervals of Aphanomyces resistance QTL previously reported, as well as identify new resistance loci, by genome wide association study. An Aphanomyces collection of 175 pea lines, enriched in germplasm derived from resistant sources previously studied, was evaluated for resistance to A. euteiches in field infested nurseries over nine environments and with two strains in climatic chamber. The collection was also genotyped using 13,204-SNPs from the GenoPea Infinium® BeadChip recently developed. Genome-wide association analysis detected a total of 52 QTL small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven main Aphanomyces resistance QTL previously reported and detected novel resistance loci. It identified SNPs associated with resistance QTL with much higher resolution than previously. The analysis also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of best haplotypes in highest resistant lines. Previous linkages between resistance alleles and late-flowering alleles undesired for dry pea breeding were mostly confirmed but the linkage between loci controlling resistance and colored flowers was broken due to the high resolution of the analysis. A high frequency of putative candidate genes underlying resistance loci encoded stress-related protein functions and suggested various QTL functions hypothesis. This study brings valuable markers, haplotypes and germplasm to increase levels of partial resistance to A. euteiches in pea breeding. It also provides an analytical approach and relevant results about comparative analysis of association and linkage analysis of polygenic resistances in plants.