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

Abstract

This study was initiated to identify genomic regions conferring resistance to Karnal Bunt (KB) disease in wheat through a genome-wide association study (GWAS) on a set of 179 pre-breeding lines (PBLs). A GWAS of 6,382 high-quality DArTseq SNPs revealed 15 significant SNPs (P-value <10 −3) on chromosomes 2D, 3B, 4D and 7B that were associated with KB resistance in individual years. In particular, two SNPs (chromosome 4D) had the maximum R 2 values: SNP 1114200 | F | 0-63:T > c at 1.571 cM and R 2 of 12.49% and SNP 1103052 | F | 0-61:C > A at 1.574 cM and R 2 of 9.02%. These two SNPs displayed strong linkage disequilibrium (LD). An in silico analysis of SNPs on chromosome 4D identified two candidate gene hits, TraesCS4D02G352200 (TaNox8; an NADPH oxidase) and TraesCS4D02G350300 (a rhomboid-like protein belonging to family S54), with SNPs 1103052 | F | 0-61:C > A and 1101835 | F | 0-5:C > A, respectively, both of which function in biotic stress tolerance. The epistatic interaction analysis revealed significant interactions among 4D and 7B loci. A pedigree analysis of confirmed resistant PBLs revealed that Aegilops species is one of the parents and contributed the D genome in these resistant PBLs. These identified lines can be crossed with any elite cultivar across the globe to incorporate novel KB resistance identified on 4B.

Karnal Bunt: A Re-Emerging Old Foe of Wheat

“…This data warrants a thorough scan of the D-genome by including the T. aestivum lines originating from diverse geographies in the panel to have an idea about the diversity and evolution of KB resistance. Recently, Singh S. et al (2020) reported two candidate gene hits on chromosome 4D that substantiate the hypothesis that the wheat genome and particularly the D-genome has a high potentiality of harboring KB resistance genes. It can be assumed that the non-pleiotropic KB resistance genes had not been favored by natural selection, in the global genotypes, because of the absence of the pathogen.…”

“…This agronomically minor but quarantine major disease is a major hindrance to wheat cultivation, production, and movement from the areas of its endemism. Therefore, it is of paramount importance that wheat breeding programs in the affected and vulnerable countries augment the efforts toward the identification and development of resistant sources ( Singh S. et al, 2020 ). In spite of the high economic importance of KB, unfortunately, resistance breeding targeting KB has never been given much priority compared to other fungal diseases of wheat like rusts and Fusarium head blight possibly owing to geographical confinement of the disease to a few countries or low direct yield loss that mostly stands between 1% and only in rare cases up to 20% to 40% ( Vocke et al, 2002 ).…”

“…In spite of the high economic importance of KB, unfortunately, resistance breeding targeting KB has never been given much priority compared to other fungal diseases of wheat like rusts and Fusarium head blight possibly owing to geographical confinement of the disease to a few countries or low direct yield loss that mostly stands between 1% and only in rare cases up to 20% to 40% ( Vocke et al, 2002 ). Compared to rusts and mildews, the identification, characterization, and cloning of the KB resistance genes have lagged much behind ( Singh S. et al, 2020 ). The neglect of this disease is not justified given the quarantine consequences and its widespread occurrence in different countries spread across the continents of Asia, Africa, and North and South America.…”

“…We also analyze the challenges leading to poor identification, quantification, and introgression of KB resistance into agronomically superior cultivars. We also explore how to circumvent these KB breeding pipeline stumbling blocks through application of next-generation sequencing tools, associated gene discovery, annotation, and the use of pathogen effectors based breeding in the absence of this overtly regulated pathogen ( Singh S. et al, 2020 ).…”

Genetic basis of some physiological traits and their association with yield in pre-breeding germplasm of bread wheat (Triticum aestivm L.)

“…In this regard, Seeds of Discovery (SeeD) project at CIMMYT has resulted in the creation of new pre-breeding germplasm with a view to enhance the use of genetic resources in breeding programs (Singh et al 2018). The same germplasm has been used to track loci linked to yield-related traits (Akram et al 2020), nematode resistance (Dababat et al 2021), karnal bunt (Singh et al 2020) and terminal drought stress (Shokat et al 2020a). However, determining the genetic basis of physiological traits has not been attempted so far.…”