Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing

Abstract

Durable crop disease resistance is an essential component of global food security. Continuous pathogen evolution leads to a breakdown of resistance and there is a pressing need to characterize new resistance genes for use in plant breeding. Here we identified an accession of wild emmer wheat (Triticum turgidum ssp. dicoccoides), PI 487260, that is highly resistant to multiple stripe rust isolates. Genetic analysis revealed resistance was conferred by a single, incompletely dominant gene designated as Yr84. Through bulked segregant analysis sequencing (BSA-Seq) we identified a 52.7 Mb resistance-associated interval on chromosome 1BS. Detected variants were used to design genetic markers for recombinant screening, further refining the interval of Yr84 to a 2.3-3.3 Mb in tetraploid wheat genomes. This interval contains 34 candidate genes encoding for protein domains involved in disease resistance responses. Furthermore, KASP markers closely-linked to Yr84 were developed to facilitate marker-assisted selection for rust resistance breeding.

Fig. 1. Phenotypic responses of Yr84 at wild emmer wheat donor line PI 487260 and at different stages of its introgression into cultivated wheat backgrounds to inoculation with stripe rust.

a PI 487260 response to inoculation with ten Pst isolates from Israel, Canada and the USA. b Reactions to Pst race W001 observed at multiple filial generations of Yr84 introgression into hexaploid bread wheat cv. Ruta. Full resistance is expressed only after Yr84 is fixed in homozygous state at BC₂F₂ and following generations.

Fig. 2. Graphical representation of the results of BSA-Seq analysis for chromosome 1B with enrichment in the 0-52.7 Mb region.

Each blue dot corresponds to a SNP between the DNA bulks. The red line indicates the mean ΔSNP-index. Orange and green lines represent coverage-adjusted confidence interval of the simulated ΔSNP-index at 99% and 95%, respectively. The physical position of the cloned stripe rust resistance gene Yr15 is indicated.

Fig. 3. Genetic position of Yr84 on chromosome arm 1BS.

a Recombinant haplotypes in chromosome 1B region of Yr84. Marker alleles are as following: green = identical to allele of the Yr84 carrier PI 487260; yellow = identical to allele of the non-carrier Kronos. Phenotyping reaction to Pst W001 is based on the 0-9 IT scale: resistance is marked in green; susceptibility is marked in yellow. b The genetic map (cM) is based on 92 F₂ plants from the KSY_10 population (PI 487260 × Kronos).

Fig. 4. Boxplots of IT score and results of multiple means comparison using the Tukey–Kramer post hoc test between genotypes A, H and B.

a Analysis for three Yr84 populations and b for three treatments of KSY population with low, medium, and high Pst spore concentrations. Population codes are as following: KSY – PI 487260 × Kronos; PSY – KSY_10-64(Yr84 carrier) × CDC Precision; LSY – RSY_2-2-1-2(Yr84 carrier) × CDC Landmark. Boxplot shows the median (middle quartile), interquartile range (IQR) from 25th to the 75th percentile, “minimum” whisker as Q1 – 1.5*IQR and “maximum” whisker as Q3 + 1.5*IQR. Letters under each boxplot represent significantly different groups of IT score (two tailed; p < 0.05). Significance codes: **** < 0.0001; 0.0001 < *** < 0.001; 0.001 < ** < 0.01; 0.01 < * < 0.05; ns > 0.05.