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.
Highlights
Root lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and pose serious threat to global food security
We explored the overlap of the identified marker-trait associations (MTAs) and the known QTLs from previous studies to locate the novel genomic regions which could be targeted in plant breeding
The restricted maximum likelihood (REML) analysis of the nematode count revealed significant effect of the genotypes which was ascertained by comparing the models wherein batch and replications were considered as random terms
Summary
Root lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and pose serious threat to global food security. 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. All juveniles and adult stages are mobile and can enter and leave the roots They are distributed worldwide and have been reported on wheat cultivation in Syria, Mexico, Canada, Israel, Yugoslavia, Morocco, Iran, India, Turkey, Pakistan, Algeria, Italy, Australia, and USA10. Several of these countries recorded significant wheat yield loss due to the P. thornei infection[11]. Excalibur for P. neglectus resistance was mapped on the chromosome 7AL in a doubled haploid p opulation[40]
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