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

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.

Delineation of Genotype-by-Environment interactions for identification and validation of resistant genotypes in mungbean to root-knot nematode (Meloidogyne incognita) using GGE biplot.

Susceptibility to root-knot nematodes (Meloidogyne spp.) is one of the major factors limiting mungbean production in South and South-East Asia. Host-pest-environment interaction in mungbean and root-knot nematode (M. incognita) was investigated in multi-location field evaluation using 38 promising mungbean genotypes extracted from initial evaluation of 250 genotypes under sick plots considering second stage freshly hatched juvenile as inoculants. The extent of environmental and genotype-by-environment interactions (GGE) was assessed to comprehend the dynamism of resistance and identification of durable resistant mungbean genotypes. Among environmental factors, nematode activity was highly influenced by rainfall and minimum temperature. The GGE biplot and multiple comparison tests detected a higher proportion of genotype × environment (GE) interaction followed by genotype and environment on number of nematode galls, gall index and reproduction factor. The first two principal components (PCs) explained 64.33% and 66.99% of the total variation of the environment-centered gall scoring and reproduction factor data, respectively. The high GE variation indicated the presence of non-cross over interactions which justify the necessities of multi-location testing. Detection of non-redundant testing locations would expedite optimum resource utilization in future. The GGE biplot analysis identified genotypes such as PM-10-12, IPM-410-3 and NVL-641 as the outperforming and desirable genotypes with durable resistance against M. incognita which can be exploited in mungbean breeding programmes globally. On the contrary, the highest gall scoring and reproduction factor were recorded in genotype IPM-9901-8. Computation of confidence interval (CI) at 95% level through bootstrapping increased precision of GGE biplot towards genotype recommendation. Furthermore, total phenol content, ascorbic acid, phenlylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO) activities were also higher in identified resistant genotypes and this information would be useful for devising mungbean breeding strategies in future for resistance against root-knot nematodes.