Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

Abstract

The oomycete Phytophthora infestans causes late blight, the most relevant disease of potato (Solanum tuberosum) worldwide. Field resistance to late blight is a complex trait. When potatoes are cultivated under long day conditions in temperate climates, this resistance is correlated with late plant maturity, an undesirable characteristic. Identification of natural gene variation underlying late blight resistance not compromised by late maturity will facilitate the selection of resistant cultivars and give new insight in the mechanisms controlling quantitative pathogen resistance. We tested 24 candidate loci for association with field resistance to late blight and plant maturity in a population of 184 tetraploid potato individuals. The individuals were genotyped for 230 single nucleotide polymorphisms (SNPs) and 166 microsatellite alleles. For association analysis we used a mixed model, taking into account population structure, kinship, allele substitution and interaction effects of the marker alleles at a locus with four allele doses. Nine SNPs were associated with maturity corrected resistance (P , 0.001), which collectively explained 50% of the genetic variance of this trait. A major association was found at the StAOS2 locus encoding allene oxide synthase 2, a key enzyme in the biosynthesis of jasmonates, plant hormones that function in defense signaling. This finding supports StAOS2 as being one of the factors controlling natural variation of pathogen resistance.

Detection of epistatic interactions in association mapping populations: an example from tetraploid potato

“…In addition, no full sibs were included in the set. Further details of the germplasm set are described elsewhere (Pajerowska-Mukhtar et al, 2009).…”

“…The clones of our study were evaluated for field resistance to late blight during the years 2004 to 2006, with two replications per year at one to two locations as described by Pajerowska-Mukhtar et al (2009). The plots were inoculated with a mixture of two complex field isolates of P. infestans.…”

“…Furthermore, PM was evaluated in uninfected plants grown under standard phytosanitary regimes in comparison with standard potato varieties of known maturity type, using a 1-to-9 scale (1, very late; 9, very early maturing). From AUDPC and PM, maturity-corrected resistance (MCR) was calculated (Pajerowska-Mukhtar et al, 2009). …”

“…For 21 markers, the allele dosage was scored based on relative band intensities. Furthermore, 22 candidate loci (Table 1) selected on the basis of (i) colocalization with known QTL for resistance to P. infestans or other pathogens, (ii) close linkage with R genes or R gene-like sequences and/or (iii) coding for a gene with known function in pathogen resistance were custom-sequenced as described previously by Pajerowska-Mukhtar et al (2009). Single-nucleotide polymorphisms and insertion/deletion Epistatic interactions and association mapping B Stich and C Gebhardt polymorphisms (InDels) detected from sequence alignments are designated in the following sections as molecular markers.…”

HAPLO-ASP: Haplotype Inference Using Answer Set Programming

“…We have studied the decision version of HIPPG and presented it in ASP. We have tested HAPLO-ASP on some real data for cultivated potato genes (described in [11]), and obtained promising results as in [9].…”