QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea

Authors: HAMON, CÉLINE - Institut National De La Recherche Agronomique (INRA); Coyne, Clarice - Clare; McGee, Rebecca; LESNÉ, ANGÉLIQUE - Institut National De La Recherche Agronomique (INRA); ESNAULT, ROBERT - Institut National De La Recherche Agronomique (INRA); MANGIN, PIERRE - Institut National De La Recherche Agronomique (INRA); HERVÉ,, MARIE - Institut National De La Recherche Agronomique (INRA); LE GOFF, ISABELLE - Institut National De La Recherche Agronomique (INRA); DENIOT, GWENAËLLE - Institut National De La Recherche Agronomique (INRA); ROUX-DUPARQUE, MARTINE - Institut National De La Recherche Agronomique (INRA); MORIN, GÉRARD - Institut National De La Recherche Agronomique (INRA); MCPHEE, KEVIN E. - North Dakota State University

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2013
Publication Date: 3/16/2013
Citation: Hamon, C., Coyne, C.J., Mcgee, R.J., Lesné, A., Esnault, R., Mangin, P., Hervé,, M., Le Goff, I., Deniot, G., Roux-Duparque, M., Morin, G., Mcphee, K. 2013. QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea. Biomed Central (BMC) Plant Biology. 13:45. doi:10.1186/1471-2229-13-45

Interpretive Summary: Information regarding the diversity of genes controlling a specific plant disease resistance is required for improving genetic resistance to pathogens. Economic levels of resistance to Aphanomyces root rot, due to Aphanomcyces euteiches, one of the most damaging pathogen of pea worldwide, was previously described in individual mapping populations. However, the diversity of resistance genes to A. euteiches was unknown. We applied sophisticated statistics (meta-analysis) of Aphanomyces root rot resistance genes in the four main pea sources of resistance and compared their genetic map locations with genes controlling morphological or phenological traits. Using this analysis, we increased the confidence in the gene localization four-fold. Seven highly consistent gene regions were identified. Seven resistance were in the same regions as genes for other economic traits; for earliness, plant height, leaf type, flower and seed color. Fortunately, most resistance genes (alleles) were not linked to desired developmental alleles for dry pea breeding. This research identified seven DNA markers which will be highly useful in Marker-Assisted-Selection for increasing resistance in pea breeding programs.

Technical Abstract: More knowledge about diversity of Quantitative Trait Loci (QTL) controlling polygenic disease resistance in natural genetic variation of crop species is required for durably improving plant genetic resistances to pathogens. Polygenic partial resistance to Aphanomyces root rot, due to Aphanomcyces euteiches, one of the most damaging pathogen of pea worldwide, was previously dissected in individual mapping populations but no data is available about the diversity of resistance QTL to A. euteiches in pea natural genetic variation. We performed a meta-analysis of Aphanomyces root rot resistance QTL in the four main pea sources of resistance known to date and compared their genomic localization with genes/QTL controlling morphological or phenological traits. Meta-analysis, conducted from 244 individual QTL reported previously from three mapping populations and in this study from a fourth mapping population resulted in the identification of 27 meta-QTL for resistance to A. euteiches. Confidence intervals of meta-QTL were reduced in average by four-fold compared to mean confidence intervals of independent individual QTL. A moderately low number of 11 consistent meta-QTL, highlighting 7 highly consistent genomic regions, was identified. Seven resistance meta-QTL, including 6 of the highly consistent genomic regions, colocalized with 6 meta-QTL identified in this study for earliness and plant height, and with 3 morphological genes (Af, A, R). Most alleles contributing to resistance did not cosegregate with desired developmental alleles for dry pea breeding. QTL meta-analysis provided an overview of the moderately low diversity of loci controlling partial resistance to A. euteiches in four main pea sources of resistance. It helped to point out seven highly consistent genomic regions useful in Marker-Assisted-Selection for increasing resistance, to suggest reduced confidence intervals at several main QTL regions and to identify cosegregations between resistance and morphological/phenological alleles