The potential of hybrid breeding to enhance leaf rust and stripe rust resistance in wheat

Abstract

Hybrid wheat breeding is a promising strategy to improve the level of leaf rust and stripe rust resistance in wheat. Leaf rust and stripe rust belong to the most important fungal diseases in wheat production. Due to a dynamic development of new virulent races, epidemics appear in high frequency and causes significant losses in grain yield and quality. Therefore, research is needed to develop strategies to breed wheat varieties carrying highly efficient resistances. Stacking of dominant resistance genes through hybrid breeding is such an approach. Within this study, we investigated the genetic architecture of leaf rust and stripe rust resistance of 1750 wheat hybrids and their 230 parental lines using a genome-wide association study. We observed on average a lower rust susceptibility for hybrids in comparison to their parental inbred lines and some hybrids outperformed their better parent with up to 56%. Marker-trait associations were identified on chromosome 3D and 4A for leaf rust and on chromosome 2A, 2B, and 6A for stripe rust resistance by using a genome-wide association study with a Bonferroni-corrected threshold of P < 0.10. Detected loci on chromosomes 4A and 2A were located within previously reported genomic regions affecting leaf rust and stripe rust resistance, respectively. The degree of dominance was for most associations favorable in the direction of improved resistance. Thus, resistance can be increased in hybrid wheat breeding by fixing complementary leaf rust and stripe rust resistance genes with desired dominance effects in opposite parental pools.

Fig. 1

Summary of phenotypic data for leaf rust (a) and stripe rust severity (b). Histograms showing genotype frequencies for scoring grades one to nine on the x-axis for leaf rust and stripe rust severity. In addition, violin plots showing the distribution for rust severity clustered for single parental pools and hybrids

Fig. 2

Manhattan plots from the genome-wide association scan for additive and dominance effects on leaf rust severity. The dashed horizontal line symbolizes the significant threshold of P < 0.10 applying Bonferroni correction. Unmapped markers were outlined under “UM”

Fig. 3

Manhattan plots of the genome-wide association scan for additive and dominance effects on stripe rust severity. The dashed horizontal line symbolizes the significant threshold of P < 0.10 applying Bonferroni correction

Fig. 4

SNPs with dominant effects for leaf rust severity. Table including minor allele frequency (MAF), significance value (−log 10(P)), and genetic map position of respective SNP markers that contribute significantly to the dominant genetic variation of leaf rust severity. The heat plot presents the linkage disequilibrium (LD) measured as squared Pearson’s correlation coefficients (r²) among SNP markers

Fig. 5

SNPs with dominance effects for stripe rust severity. Table including minor allele frequency (MAF), significance value (−log 10(P)), and genetic map position of respective SNP markers that contribute significantly to the dominant genetic variation of stripe rust severity. The heat plot presents the linkage disequilibrium (LD) measured as squared Pearson’s correlation coefficients (r²) among SNP markers

Fig. 6

Plot of BLUEs for each phenotyped genotype comprising parents and hybrids. The x-axis represents the score for leaf rust severity while on the y-axis the stripe rust severity is shown. Furthermore, the correlation between leaf rust and stripe rust severity for parental groups, hybrids, and the whole population is presented

Fig. 7

Leaf rust (a) and stripe rust resistance (b) in dependence on genotypes detected by associated SNP markers. Box-whisker plots showing leaf rust severity of adult plants for different allele combinations at two resistance gene loci explaining each ≥ 12% of the phenotypic variation. SNP6846 (r₁/R₁) and SNP6577 (r₂/R₂) as well as SNP7071 (r₁/R₁) and SNP8770 (r₂/R₂) were observed for leaf and stripe rust resistance, respectively. R refers to the allele supporting susceptibility, while r represents the allele increasing resistance. The numbers at the top of each box refer to the observed numbers of hybrids (left) and parental inbred lines (right). Only homozygous parental lines and hybrids derived from them were considered