Analysis of wheat (<em>Triticum aestivum </em>L.) resistance to cereal cyst nematode <em>Heterodera filipjevi</em> by genome-wide association mapping

Abstract

The cereal cyst nematode <em>Heterodera filipjevi</em> is an important plant parasite causing substantial yield loss in wheat. The use of resistant cultivars is the preferable method to manage this nematode, however, only few resistance sources are identified in cereals and no durable resistant cultivar is available for <em>H. filipjevi</em> in wheat. In this study, a collection of 290 winter wheat accessions was screened for resistance against <em>H. filipjevi</em>. The plants were infected with nematode juveniles and the number of developing females and cysts was counted. One percent of the wheat accessions was ranked as resistant, 16% as moderately resistant, 41% as moderately susceptible, 26% as susceptible, and 15% as highly susceptible. To understand the underlying resistance mechanism, nematode invasion, development, and reproduction were analyzed in one resistant accession Nudakota and three moderately resistant accessions Ekonomka, Katea and Lantian 12 and compared with susceptible accession Bezostaya 1. Invasion rate, and number of females and cysts per plant were significantly lower in Nudakota, Ekonomka, Katea and Lantian 12 compared to Bezostaya 1. The different responses of wheat accessions observed in this study suggested genetic variation within the screened population. Therefore, it was decided to identify relevant quantitative trait loci (QTLs) and genes using genome-wide association studies. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as nematode resistance can be located in the genome. A mapping panel of 161 wheat accessions was genotyped by 90K iSelect SNP bead chip and was analyzed for QTL identification. These accessions were phenotyped in two nematode infection assays under controlled conditions. High variation was revealed in single nucleotide polymorphisms (SNPs) on wheat genomes A, B, and D. Linkage disequilibrium decayed across wheat genome was < 3cM. Population structure and principle component analysis (PCA) revealed a very low genetic differentiation (K = 2, and PCA1 = 6.16%) within the 161 wheat accessions and needed no further corrections. Eleven novel quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL and 7BL were detected using a mixed linear model at false discovery rate (P ≤ 0.01) that explained 43% of total genetic variation. The identified 11 novel QTLs can now be used in resistance breeding via marker-assisted selection. In-silico annotation of flanking sequences of the significant markers identified genes supposed to be involved in biotic and abiotic stresses. Eight of the 11 QTLs on chromosome 1AL, 2AS, 2BL, 3AL and 4AL were linked to putative genes known to be involved in plant-pathogen interactions. Two other QTLs on 3BL and one QTL on 7BL linked to putative genes known to be involved in abiotic stress and plant growth. Five of the QTLs identified on chromosomes 1AL, 2AS, 2BL, 3BL, and 5BL in this study were previously reported to be linked to resistance against <em>H. avenae</em>, while QTL IWB66494 on chromosome 2BL was reported to be linked to resistance against Fusarium head blight. Although the wheat genome is sequenced, annotation of a large number of genes and proteins is still limited. In order to characterize the candidate gene <em>TaAAT</em> we applied a comparative genomics approach and identified the orthologue gene <em>AtAAP6</em> in <em>Arabidopsis thaliana</em>. Nematode infection assays of an <em>AtAAP6</em> mutant Arabidopsis line revealed a significant reduction in average number of females, female size, and female-associated syncytia. Different methods showed that <em>AtAAP6</em> is upregulated in syncytia. We also found a strong expression of <em>TaAAT</em> in infected roots of two susceptible wheat accessions, whereas the expression remained unchanged in infected roots of two resistant accessions. We further analyzed the amino acid sequence of <em>AtAAP6</em> in 3 lowly susceptible and 3 highly susceptible Arabidopsis accessions and found glycine is substituted by alanine on a specific site in the <em>AtAAP</em> ORF in the lowly susceptible accessions. The molecular mechanism by which the exchange of a single amino acid in <em>AtAAP6</em> leads to reduced nematode development needs further investigation.