Genetic Mapping of Resistance in Hexaploid Wheat for a Quarantine Disease: Karnal Bunt

Abstract

Karnal bunt (KB) of wheat, caused by Tilletia indica, is one of the greatest challenges to grain industry, not because of yield loss, but quarantine regulations that restrict international movement and trade of affected stocks. Genetic resistance is the best way to manage this disease. Although several different sources of resistance have been identified to date, very few of those have been subjected to genetic analyses. Understanding the genetics of resistance, characterization and mapping of new resistance loci can help in development of improved germplasm. The objective of this study was to identify and characterize resistance loci (QTL) in two independent recombinant inbred lines (RILs) populations utilizing different wheat lines as resistance donors. Elite CIMMYT wheat lines Blouk#1 and Huirivis#1 were used as susceptible female parents and WHEAR/KUKUNA/3/C80.1/3∗BATAVIA//2∗WBLL1 (WKCBW) and Mutus as moderately resistant male parents in Pop1 and Pop2 populations, respectively. Populations were evaluated for KB resistance in 2015–16 and 2016–17 cropping seasons at two seeding dates (total four environments) in Cd. Obregon, Mexico. Two stable QTL from each population were identified in each environment: QKb.cim-2B and QKb.cim-3D (Pop1), QKb.cim-3B1 and QKb.cim-5B2 (Pop2). Other than those four QTL, other QTL were detected in each population which were specific to environments: QKb.cim-5B1, QKb.cim-6A, and QKb.cim-7A (Pop1), QKb.cim-3B2, QKb.cim-4A1, QKb.cim-4A2, QKb.cim-4B, QKb.cim-5A1, QKb.cim-5A2, and QKb.cim-7A2 (Pop2). Among the four stable QTL, all but QKb.cim-3B1 were derived from the resistant parent. QKb.cim-2B and QKb.cim-3D in Pop1 and QKb.cim-3B1 and QKb.cim-5B2 in Pop2 explained 5.0–11.4% and 3.3–7.1% phenotypic variance, respectively. A combination of two stable QTL in each population reduced KB infection by 24–33%, respectively. Transgressive resistant segregants lines derived with resistance alleles from both parents in each population were identified. Single nucleotide polymorphism (SNP) markers flanking these QTL regions may be amenable to marker-assisted selection. The best lines from both populations (in agronomy, end-use quality and KB resistance) carrying resistance alleles at all identified loci, may be used for inter-crossing and selection of improved germplasm in future. Markers flanking these QTL may assist in selection of such lines.

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

“…The analysis of variance suggested that both the genotype and year exerted a significant effect on KB ( Supplementary Table S2). 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 results of the current study validated the consensus region on chromosome 3B reported in previous studies 2,15 (Fig. 4).…”

“…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.…”

“…After the attack, the fungus forms black teliospores in sori and deteriorates the grain quality by generating an unpleasant, and foul smell attributed to trimethylamine produced by the fungus 1 . The infection of approximately 4% of kernels is sufficient for the grain to become unfit for human consumption due to a low palatability 2 . Internationally, approximately 70 countries have placed an embargo on the import of Karnal bunt-infected wheat 3 .…”

“…As a seed-, soil-and air-borne fungus, the control of the disease through cultural practices and/or seed treatment is not very effective 6 . The chemical control of KB by spraying fungicides at the anthesis stage is possible but not cost-effective for farmers; thus, conventional methods are not sufficient to cope with KB 2,7 .…”