Genome-wide association study in hexaploid wheat identifies novel genomic regions associated with resistance to root lesion nematode (Pratylenchus thornei)

Abstract

Root lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and thus pose serious threat to global food security. Reliance on fumigants (such as methyl bromide) and nematicides for crop protection has been discouraged due to environmental concerns. Hence, alternative environment friendly control measures like finding and deployment of resistance genes against Pratylenchus thornei are of significant importance. In the present study, genome-wide association study (GWAS) was performed using single-locus and multi-locus methods. In total, 143 wheat genotypes collected from pan-Indian wheat cultivation states were used for nematode screening. Genotypic data consisted of > 7K SNPs with known genetic positions on the high-density consensus map was used for association analysis. Principal component analysis indicated the existence of sub-populations with no major structuring of populations due to the origin. Altogether, 25 significant marker trait associations were detected with − log10 (p value) > 4.0. Three large linkage disequilibrium blocks and the corresponding haplotypes were found to be associated with significant SNPs. In total, 37 candidate genes with nine genes having a putative role in disease resistance (F-box-like domain superfamily, Leucine-rich repeat, cysteine-containing subtype, Cytochrome P450 superfamily, Zinc finger C2H2-type, RING/FYVE/PHD-type, etc.) were identified. Genomic selection was conducted to investigate how well one could predict the phenotype of the nematode count without performing the screening experiments. Prediction value of r = 0.40 to 0.44 was observed when 56 to 70% of the population was used as a training set. This is the first report where GWAS has been conducted to find resistance against root lesion nematode (P. thornei) in Indian wheat germplasm.

Genome-Wide Association Study of Root-Lesion Nematodes Pratylenchus Species and Crown Rot Fusarium culmorum in Bread Wheat

“…Of these, the ones on chromosomes 4A and 5B were previously reported by Mulki et al [ 20 ]. In a similar study, Kumar et al [ 40 ] reported significant MTAs, on chromosomes 1B, 1D, 3B, and 6B, explaining 23% to 26% of the total phenotypic variation. The SNP marker S4B_539004405 was obtained in both repeats of CR under growth room conditions.…”

Asymptotic tests for Hardy–Weinberg equilibrium in hexaploids

“…Results from our procedure can provide insight into the evolutionary forces that act on the genomes of hexaploids and can also be used to detect genotyping errors in marker data. As the first step of molecular breeding in hexaploids, genome-wide association studies (GWAS) have been increasingly used as a routine approach for studying the genetic architecture of agriculturally important traits [ 32 – 34 ]. Our aHWE testing procedure provides valuable assistance for the quality control of markers and the evolutionary inference of any significant loci detected from GWAS.…”

Discovery of resistance to Pratylenchus neglectus among P. thornei‐resistant Iranian landrace wheats and the introgression of both resistances into advanced breeding lines

“…Many quantitative trait loci (QTLs) for P . thornei resistance have been reported in wheat (Kumar et al, 2021; Schmidt et al, 2005; Zwart et al, 2010). Several studies have reported QTLs associated with P .…”

“…RLNs are best managed through the incorporation into commercial crop cultivars of both genetic tolerance, that is the ability of a plant to minimize yield loss when grown in nematode-infested soil, and genetic resistance, that is the ability of a plant to inhibit nematode reproduction. Many quantitative trait loci (QTLs) for P. thornei resistance have been reported in wheat (Kumar et al, 2021;Schmidt et al, 2005;Zwart et al, 2010). Several studies have reported QTLs associated with P. neglectus resistance (Dababat et al, 2016;Mulki et al, 2013;Zwart et al, 2010); however, the QTLs often explained only a low proportion of genetic variation or they required validation in a genetically diverse panel or appropriate breeding populations before being suitable for use in marker-assisted selection (MAS).…”