Unveiling yellow rust resistance in the near-Himalayan region: insights from a nested association mapping study

Abstract

This study identified two potentially novel yellow rust resistance loci in traditional Asian wheat varieties and gives insights into the distribution of resistances in high disease-pressure regions near the Himalayas. The global spread of yellow rust has posed a significant threat to wheat production, making the identification of novel resistance-conferring genetic loci crucial. The near-Himalayan region has been proposed as the pathogen's origin and is characterized by strong and diverse disease pressure. Even though this makes wheat varieties from this region likely to harbor resistance, Asian germplasm has been highly underrepresented in modern breeding. To explore this potential, we screened an Asian nested association mapping (NAM) population comprising traditional and modern wheat varieties under artificial epidemics in multiple field trials. Combined quantitative trait locus (QTL) mapping revealed the two resistance genes Lr67/Yr46/Sr55 and Lr34/Yr18/Sr57, as well as two potentially novel yellow rust resistance loci. The resistant allele of the first one, located on chromosome 3D, is unique to a traditional variety from Nepal, while the second one, found on chromosome 5B, is present in several NAM families. The broad geographic distribution of this QTL across regions with high disease pressure suggests it may serve as a durable source of resistance. Strong observed resistances were conferred by a combination of several resistance loci, suggesting the stacking of resistances as a successful strategy in yellow rust hotspot areas.

Fig. 1

a Disease severity (% of infected leaf area) under artificial YR infection was assessed in NAM parents across two locations, Toluca and Zurich, over two years. In Toluca, Mugami (sus) and Quaiu (res) served as checks, while in Zurich, Eridano (sus) and Nara (res) were used. Labels above the plot indicate the origin of genotypes (JP = Japan, CN = China, PK = Pakistan, NP = Nepal) and whether they are categorized as modern or traditional varieties. b Disease severity (% of infected leaf area) of NAM parents under artificial YR infection averaged over the four environments is indicated by the color gradient and plotted at the geographic origin of each NAM parent. A more robust red indicates a highly resistant genotype, while the white ones are entirely susceptible. The shapes define if the genotype is considered a modern or traditional variety. The gray color gradient represents the elevation. In both plots, the genotypes selected for further trials are underlined

Fig. 2

Disease severity (% of infected leaf/stem area) scored in NAM families for YR, LR, and SR over three years. Environments are visualized in different colors. The dotted lines represent the mean disease severity of the NAM parents for YR: the line that is the same in all plots represents Norin 61. In contrast, the line that varies between families represents the corresponding alternative parent

Fig. 3

Significant QTL peaks from consensus mapping for YR, LR, and SR infection scores (% of infected leaf/stem area) collected in seven environments, which are represented by color. The horizontal dashed line indicates the mean significance threshold over all locations (based on permutation tests), and the numbers close to the peaks indicate the amount of phenotypic variation (PVE %) explained by the corresponding QTLs

Fig. 4

Positions of a QLrYrSr.uzh-7D, b QLrYrSr.uzh-4D, c QYr.uzh-5B, and d QYr.uzh-3D.1 are shown as colored bars on the consensus map (centimorgans (cM), upper box) and the physical map of the common parent Norin 61 (megabases (Mb), lower box). QTL intervals are defined as the full width of each significant peak, from the sharp LOD score rise at the start to the peak’s end. The colors of QTLs correspond to the environments in which they were identified. Vertical black lines on both maps present observed markers, while the long vertical black line (marked with c in panel d) indicates the centromere position. Black crosses mark the known resistance genes at their respective physical position

Fig. 5

The plots represent the QTL effects of NAM families at a QLrYrSr.uzh-7D, b QLrYrSr.uzh-4D, c QYr.uzh-5B, and d QYr.uzh-3D.1, detected by combined family mapping. The color gradient of each QTL indicates the direction and strength of the effect (different color scale for each QTL), and each section of the pie chart represents one environment. Only environments with significant QTLs are represented