Genome Wide Association Study of Karnal Bunt Resistance in a Wheat Germplasm Collection from Afghanistan

Abstract

Karnal bunt disease of wheat, caused by the fungus Neovossia indica, is one of the most important challenges to the grain industry as it affects the grain quality and also restricts the international movement of infected grain. It is a seed-, soil- and airborne disease with limited effect of chemical control. Currently, this disease is contained through the deployment of host resistance but further improvement is limited as only a few genotypes have been found to carry partial resistance. To identify genomic regions responsible for resistance in a set of 339 wheat accessions, genome-wide association study (GWAS) was undertaken using the DArTSeq® technology, in which 18 genomic regions for Karnal bunt resistance were identified, explaining 5–20% of the phenotypic variation. The identified quantitative trait loci (QTL) on chromosome 2BL showed consistently significant effects across all four experiments, whereas another QTL on 5BL was significant in three experiments. Additional QTLs were mapped on chromosomes 1DL, 2DL, 4AL, 5AS, 6BL, 6BS, 7BS and 7DL that have not been mapped previously, and on chromosomes 4B, 5AL, 5BL and 6BS, which have been reported in previous studies. Germplasm with less than 1% Karnal bunt infection have been identified and can be used for resistance breeding. The SNP markers linked to the genomic regions conferring resistance to Karnal bunt could be used to improve Karnal bunt resistance through marker-assisted selection.

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

“…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 .…”

“…Therefore, KB resistance is controlled by minor additive and epistatic loci. Previous studies using bi-parental populations and a GWAS panel have reported additive QTLs for KB resistance 2,15,16 , but information on epistatic QTL is lacking. This report is the first to identify additive and epistatic QTL for KB resistance in a GWAS panel.…”

“…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.…”

Chromosomal Distribution of Genes Conferring Tolerance to Abiotic Stresses Versus That of Genes Controlling Resistance to Biotic Stresses in Plants

“…Among the 11 articles in the Special Issue on plant genes conferring resistance to biotic stresses [3,[25][26][27][28][29][30][31][32][33][34], seven articles reported results from single resistant genes (or QTL) for crops and plant species, including soybean, rice, wheat, Dasypyrum villosum, Aegilops searsii, Capsicum annuum, and Vitis quinquangularis. The other four articles [27,29,30,32] analyzed multiple QTLs or genomic regions for one or more diseases.…”

“…In the Special Issue, "Mapping Abiotic Stress-Tolerance Genes in Plants" of International Journal of Molecular Sciences, 21 papers, including two reviews and 19 research articles, were published . Eleven research articles [3,[25][26][27][28][29][30][31][32][33][34] were published in the Special Issue "Mapping Plant Genes that Confer Resistance to Biotic Stress. "…”