Identification of Putative SNP Markers Associated with Resistance to Egyptian Loose Smut Race(s) in Spring Barley

Abstract

Loose smut (LS) disease is a serious problem that affects barley yield. Breeding of resistant cultivars and identifying new genes controlling LS has received very little attention. Therefore, it is important to understand the genetic basis of LS control in order to genetically improve LS resistance. To address this challenge, a set of 57 highly diverse barley genotypes were inoculated with Egyptian loose smut race(s) and the infected seeds/plants were evaluated in two growing seasons. Loose smut resistance (%) was scored on each genotype. High genetic variation was found among all tested genotypes indicating considerable differences in LS resistance that can be used for breeding. The broad-sense heritability (H²) of LS (0.95) was found. Moreover, genotyping-by-sequencing (GBS) was performed on all genotypes and generated in 16,966 SNP markers which were used for genetic association analysis using single-marker analysis. The analysis identified 27 significant SNPs distributed across all seven chromosomes that were associated with LS resistance. One SNP (S6_17854595) was located within the HORVU6Hr1G010050 gene model that encodes a protein kinase domain-containing protein (similar to the Un8 LS resistance gene, which contains two kinase domains). A TaqMan marker (0751D06 F6/R6) for the Un8 gene was tested in the diverse collection. The results indicated that none of the Egyptian genotypes had the Un8 gene. The result of this study provided new information on the genetic control of LS resistance. Moreover, good resistance genotypes were identified and can be used for breeding cultivars with improved resistance to Egyptian LS.

Keywords: Hordeum vulgare L.; Ustilago nuda; candidate genes; genetic analysis; single-nucleotide polymorphism.

Figure 1

(a) Distribution of loose smut reaction among the 60 genotypes comprising the Egyptian spring barley collection, (b) Venn diagram illustrating the identification of immune genotypes in 2019 and 2020, (c) Correlation of loose smut reactions measured in 2019 and 2020 among the genotypes demonstrating an immune reaction in at least one year. ** p < 0.01.

Figure 2

The effect of the Egyptian loose smut race on barley spikes (a) health spikes (b) susceptible spikes, (c,d) different degrees from few partially infected spikes found in some resistant genotypes.

Figure 3

(a) Manhattan plot showing the significant SNPs (red circles) associated with LS resistance and their locations on barley chromosomes. The red line indicated the significant threshold at 0.001, (b) LD (r²) among significant SNPs located on chr 3H.

Figure 4

Position and candidate gene with its annotation for S6_17854595 SNP associated with loose smut resistance.

Figure 5

(a) number of resistant alleles in the most resistant genotypes and (b) genetic distance and dendrogram analyses among the most resistant genotypes based on the presence of resistance alleles.