Unravelling the Complex Genetics of Karnal Bunt (Tilletia indica) Resistance in Common Wheat (Triticum aestivum) by Genetic Linkage and Genome-Wide Association Analyses

Abstract

Karnal bunt caused by Tilletia indica Mitra [syn. Neovossia indica (Mitra) Mundkur] is a significant biosecurity concern for wheat-exporting countries that are free of the disease. It is a seed-, soil-and air-borne disease with no effective chemical control measures. The current study used data from multi-year field experiments of two bi-parental populations and a genome-wide association (GWA) mapping panel to unravel the genetic basis for resistance in common wheat. Broad-sense heritability for Karnal bunt resistance in the populations varied from 0.52 in the WH542×HD29 population, to 0.61 in the WH542×W485 cross and 0.71 in a GWAS panel. Quantitative trait locus (QTL) analysis with seven years of phenotypic data identified a major locus on chromosome 3B (R 2 = 27.8%) and a minor locus on chromosome 1A (R 2 = 12.2%), in the WH542×HD29 population, with both parents contributing the high-value alleles. A major locus (R 2 = 27.8%) and seven minor loci (R 2 = 4.4–15.8%) were detected in the WH542×W485 population. GWA mapping validated QTL regions in the bi-parent populations, but also identified novel loci not previously associated with Karnal bunt resistance. Meta-QTL analysis aligned the results from this study with those reported in wheat over the last two decades. Two major clusters were detected, the first on chromosome 4B, which clustered with Qkb.ksu-4B , QKb.cimmyt-4BL , Qkb.cim-4BL , and the second on chromosome 3B, which clustered with Qkb.cnl-3B , QKb.cimmyt-3BS and Qkb.cim-3BS1 . The results provide definitive chromosomal assignments for QTL/genes controlling Karnal bunt resistance in common wheat, and will be useful in pre-emptive breeding against the pathogen in wheat-producing areas that are free of the disease.

GWAS revealed a novel resistance locus on chromosome 4D for the quarantine disease Karnal bunt in diverse wheat pre-breeding germplasm

“…The results of the current study validated the consensus region on chromosome 3B reported in previous studies 2,15 (Fig. 4).…”

“…Similar results were recorded during QTL mapping for KB resistance in two different studies 2,8 . The heritability of trait was high in both years (91% and 87% in E-1 and E-2, respectively) (Supplementary Table S3), suggesting that KB resistance can be mapped through QTL mapping and GWAS 2,15 . The phenotyping protocols established at CENEB, Cd.…”

“…Previous studies reported the presence of KB resistance loci scattered on many chromosomes in all three genomes of wheat 15,16 . Hence, cultivar pyramiding/stacking of favourable alleles from multiple loci is a prerequisite to develop KB resistance 22 .…”

“…This mapping population-independent method relies on a population consisting of a set of unrelated accessions and has been successfully used to identify numerous traits in many crops, such as Arabidopsis thaliana 11 , rice 12 , barley 13 and wheat 14 . However, only two GWAS studies have been reported to date with the aim of determining marker-trait associations (MTAs) for KB resistance in elite wheat lines 15,16 . Both these studies were carried out with wheat germplasm collection.…”

Accuracy of Single and Multi-Trait Genomic Prediction Models for Grain Yield in US Pacific Northwest Winter Wheat

“…The wealth of genomic information available for important crops has enabled the use of marker data for molecular breeding and DNA-based selection for plant improvement. In recent years, genomic approaches such as genome-wide association studies (GWAS) have been used to understand the genetic basis of important traits such as grain yield, disease resistance, and adaptation traits in wheat [1][2][3][4]. However, association mapping could not identify small effect loci and with such, the power of GWAS for the dissection of complex traits is limited [5,6].…”