Function and evolution of allelic variations of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.).

The resistance gene Sr13 is one of the most important genes in durum wheat for controlling stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The Sr13 functional gene CNL13 has haplotypes R1, R2 and R3. The R1/R3 and R2 haplotypes were originally designated as alleles Sr13a and Sr13b, respectively. To detect additional Sr13 alleles, we developed Kompetitive allele specific PCR (KASP™) marker KASPSr13 and four semi-thermal asymmetric reverse PCR markers, rwgsnp37-rwgsnp40, based on the CNL13 sequence. These markers were shown to detect R1, R2 and R3 haplotypes in a panel of diverse tetraploid wheat accessions. We also observed the presence of Sr13 in durum line CAT-A1, although it lacked any of the known haplotypes. Sequence analysis revealed that CNL13 of CAT-A1 differed from the susceptible haplotype S1 by a single nucleotide (C2200T) in the leucine-rich repeat region and differed from the other three R haplotypes by one or two additional nucleotides, confirming that CAT-A1 carries a new (R4) haplotype. Stem rust tests on the monogenic, transgenic and mutant lines showed that R1 differed from R3 in its susceptibility to races TCMJC and THTSC, whereas R4 differed from all other haplotypes for susceptibility to TTKSK, TPPKC and TCCJC. Based on these differences, we designate the R1, R3 and R4 haplotypes as alleles Sr13a, Sr13c and Sr13d, respectively. This study indicates that Sr13d may be the primitive functional allele originating from the S1 haplotype via a point mutation, with the other three R alleles probably being derived from Sr13d through one or two additional point mutations.

Mapping and characterization of two stem rust resistance genes derived from cultivated emmer wheat accession PI 193883.

KEY MESSAGE: Two stem rust resistance genes identified on chromosome arms 2BL and 6AL of the cultivated emmer wheat accession PI 193883 can be used for protecting modern varieties against Ug99 strains. The wheat research community consistently strives to identify new genes that confer resistance to stem rust caused by the fungal pathogen Puccinia graminis f. sp. tritici Eriks & E. Henn (Pgt). In the current study, our objective was to identify and genetically characterize the stem rust resistance derived from the cultivated emmer accession PI 193883. A recombinant inbred line population developed from a cross between the susceptible durum wheat line Rusty and PI 193883 was genotyped and evaluated for reaction to Pgt races TTKSK, TRTTF, and TMLKC. Two QTLs conferring resistance were identified on chromosome arms 2BL (QSr.fcu-2B) and 6AL (QSr.fcu-6A). The stem rust resistance gene (Sr883-2B) underlying QSr.fcu-2B was recessive, and based on its physical location it is located proximal to the Sr9 region. QSr.fcu-6A was located in the Sr13 region, but PI 193883 is known to carry the susceptible haplotype S4 for Sr13, indicating that the gene underlying QSr.fcu-6A (Sr883-6A) is likely a new allele of Sr13 or a gene residing close to Sr13. Three IWGSC scaffold-based simple sequence repeat (SSR) and two SNP-based semi-thermal asymmetric reverse PCR (STARP) markers were developed for the Sr883-2B region, and one STARP marker was developed for Sr883-6A. Sr883-2B was epistatic to Sr883-6A for reaction to TTKSK and TRTTF, and the two genes had additive effects for TMLKC. These two genes and the markers developed in this research provide additional resources and tools for the improvement in stem rust resistance in durum and common wheat breeding programs.

Genetic analysis of threshability and other spike traits in the evolution of cultivated emmer to fully domesticated durum wheat.

Genetic mutations in genes governing wheat threshability were critical for domestication. Knowing when these genes mutated during wheat evolution will provide more insight into the domestication process and lead to further exploitation of primitive alleles for wheat improvement. We evaluated a population of recombinant inbred lines derived from a cross between the durum variety Rusty and the cultivated emmer accession PI 193883 for threshability, rachis fragility, and other spike-related traits. Quantitative trait loci (QTL) associated with spike length, spikelets per spike, and spike compactness were primarily associated with known genes such as the pleiotropic domestication gene Q. Interestingly, rachis fragility was not associated with the Q locus, suggesting that this trait, usually a pleiotropic effect of the q allele, can be influenced by the genetic background. Threshability QTL were identified on chromosome arms 2AS, 2BS, and 5AL corresponding to the tenacious glume genes Tg2A and Tg2B as well as the Q gene, respectively, further demonstrating that cultivated emmer harbors the primitive non-free-threshing alleles at all three loci. Genetic analysis indicated that the effects of the three genes are mostly additive, with Q having the most profound effects on threshability, and that free-threshing alleles are necessary at all three loci to attain a completely free-threshing phenotype. These findings provide further insight into the timeline and possible pathways of wheat domestication and evolution that led to the formation of modern day domesticated wheats.