Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi

Abstract

The cyst nematode Heterodera filipjevi is a plant parasite causing substantial yield loss in wheat. Resistant cultivars are the preferred method of controlling cyst nematodes. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as resistance to pathogens can be located. Therefore, a genome-wide association study of 161 winter wheat accessions was performed with a 90K iSelect single nucleotide polymorphism (SNP) chip. Population structure analysis grouped into two major subgroups and first principal component accounted 6.16% for phenotypic diversity. The genome-wide linkage disequilibrium across wheat was 3 cM. Eleven quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL, and 7BL were identified using a mixed linear model false discovery rate of P < 0.01 that explained 43% of total genetic variation. This is the first report of QTLs conferring resistance to H. filipjevi in wheat. Eight QTLs on chromosomes 1AL, 2AS, 2BL, 3AL, 4AL, and 5BL 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.

Dissecting the Genetic Complexity of Fusarium Crown Rot Resistance in Wheat

“…The process of effective recombination events in A and B genomes might have resulted from the historical development of hexaploid wheat and its domestication process 2,33 . Consistent with our previous findings, A and B genomes have higher polymorphism than D genome 19,24 . Würschum et al 34 reported similar finding of few SNPs to be located on the D genome of 172 European winter wheat cultivars 34 .…”

“…The flanking sequences of the significant markers were blasted against gene models of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, IWGSC, the Institute for Genomic Research (TIGR) Wheat genome annotation, and National Center for Biotechnology Information (NCBI). The genes/proteins were selected based on significant hit and lowest expect e-value 24 . The wheat transcriptome assemblies from MAS Wheat dataset 71 were downloaded and the full open reading frame (ORF) at significant marker locations were identified.…”

“…GWAS utilizes linkage disequilibrium to dissect the genetic architecture of complex traits by correlating phenotypes to genotypes. It has been used earlier to identify QTLs that are involved in plant responses to soil borne pathogens in a large set of unrelated wheat accessions 19,24 . Detection of QTLs tightly linked to gene/s that control FCR resistance are the pre-requisite for marker assisted breeding.…”

Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back

“…The study revealed three DArT markers for four novel H. avenae resistance QTL. In a separate study, resistance to H. filipjevi was revealed in winter wheat accessions from the International Wheat Improvement Program using the 90K SNP platform [57]. Resistance was based on counts of cysts and females in root and soil samples, and was associated with 11 QTL.…”

Activity profiling of barley vacuolar processing enzymes provides new insights into the plant and cyst nematode interaction

“…The rye cyst nematode ( H. filipjevi ), like other CCNs, is an obligate biotrophic sedentary endoparasite, mainly infesting barley and wheat (Dababat and Fourie, ). As a result of H. filipjevi feeding on roots of infected plants the grain yield losses may reach up to 50% (Pariyar et al , ). The infective second‐stage juvenile (J2) of CCN damages the host root cell wall using its stylet and hydrolytic enzymes synthesized in oesophageal glands and secreted through the stylet orifice.…”