The three rusts are the most damaging diseases of wheat worldwide and continue to pose a threat to global food security. In the recent decades, stem rust races belonging to the Ug99 (TTKSK) and Digalu (TKTTF) race group resurfaced as a major threat in Africa, the Middle East and Europe threatening global wheat production. In addition, the evolution and migration of new aggressive races of yellow rust adapted to warmer temperatures into Europe and Asia from Himalayan region are becoming a significant risk in several wheat production environments. Unique and complex virulence patterns, continuous evolution to overcome effective resistance genes in varieties, shifts in population dynamics, transboundary migration have resulted in localized/regional epidemics leading to food insecurity threats. This underscores the need to identify, characterize, and deploy effective rust resistant genes from diverse sources into pre-breeding lines and future wheat varieties. The use of genetic resistance and deployment of multiple race specific and pleiotropic adult plant resistance genes in wheat lines can enhance resistance durability. Recent advances in sequencing annotated wheat reference genome with a detailed analysis of gene content among sub-genomes will not only accelerate our understanding of the genetic basis of rust resistance bread wheat, at the same time wheat breeders can now use this information to identify genes conferring rust resistance. Progress in genetic mapping techniques, new cloning techniques and wheat transformation methods over the last two decades have not only resulted in characterizing new genes and loci but also facilitated rapid cloning and stacking multiple genes as gene cassettes which can be future solution for enhancing durable resistance.

Three rust diseases namely; stem rust caused by Puccinia graminis f. sp. tritici (Pgt), leaf rust caused by Puccinia triticina (Pt), and stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), are the most common fungal diseases of wheat (Triticum aestivum L.) and cause significant yield losses worldwide including Australia. Recently characterized stripe rust resistance genes Yr51 and Yr57 are effective against pre- and post-2002 Pst pathotypes in Australia. Similarly, stem rust resistance genes Sr22, Sr26, and Sr50 are effective against the Pgt pathotype TTKSK (Ug99) and its derivatives in addition to commercially important Australian pathotypes. Effectiveness of these genes make them good candidates for combining with known pleiotropic adult plant resistance (PAPR) genes to achieve durable resistance against three rust pathogens. This study was planned to transfer rust resistance genes Yr51, Yr57, Sr22, Sr26, and Sr50 into two Australian (Gladius and Livingston) and two Indian (PBW550 and DBW17) wheat cultivars through marker assisted selection (MAS). These cultivars also carry other rust resistance genes: Gladius carries Lr37/Yr17/Sr38 and Sr24/Lr24; Livingston carries Lr34/Yr18/Sr57, Lr37/Yr17/Sr38, and Sr2; PBW550 and DBW17 carry Lr34/Yr18/Sr57 and Lr26/Yr9/Sr31. Donor sources of Yr51 (AUS91456), Yr57 (AUS91463), Sr22 (Sr22/3*K441), Sr26 (Sr26 WA1), and Sr50 (Dra-1/Chinese Spring ph1b/2/3* Gabo) were crossed with each of the recurrent parents to produce backcross progenies. Markers linked to Yr51 (sun104), Yr57 (gwm389 and BS00062676), Sr22 (cssu22), Sr26 (Sr26#43), and Sr50 (Sr50-5p-F3, R2) were used for their MAS and markers csLV34 (Lr34/Yr18/Sr57), VENTRIUP-LN2 (Lr37/Yr17/Sr38), Sr24#12 (Sr24/Lr24), and csSr2 (Sr2) were used to select genes present in recurrent parents. Progenies of selected individuals were grown and selected under field conditions for plant type and adult plant rust responses. Final selections were genotyped with the relevant markers. Backcross derivatives of these genes were distributed to breeding companies for use as resistance donors.

Since 1984, the ‘Chilero’ spring wheat line developed by CIMMYT has proven to be highly resistant to leaf rust and stripe rust. Amid efforts to understand the basis of resistance of this line, a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero was studied. The parents and RILs were characterized in field trials for leaf rust and stripe rust in three locations in Mexico between 2012 and 2015 and genotyped with DArT-array, DArT-GBS, and SSR markers. A total of 6,168 polymorphic markers were used to construct genetic linkage maps. Inclusive composite interval mapping detected four colocated resistance loci to both rust diseases and two stripe rust resistant loci in the Avocet × Chilero population. Among these, the quantitative trait locus (QTL) on chromosome 1BL was identified as a pleotropic adult plant resistance gene Lr46/Yr29, whereas QLr.cim-5DS/QYr.cim-5DS was a newly discovered colocated resistance locus to both rust diseases in Chilero. Additionally, one new stripe rust resistance locus on chromosome 7BL was mapped in the current population. Avocet also contributed two minor colocated resistance QTLs situated on chromosomes 1DL and 4BS. The flanking SNP markers can be converted to breeder friendly Kompetitive Allele Specific PCR (KASP) markers for wheat breeding programs.

Stem rust of wheat caused by Puccinia graminis Pers. f.sp. trtici Eriks and E. Henn., is the most damaging fungal disease of both common (Triticum aestivum L.) and durum (Triticum turgidum L., ssp. Durum) wheat. Continuously emerging races virulent to many of the commercially deployed qualitative resistance genes have caused remarkable loss worldwide and threaten global wheat production. The objectives of this study were to evaluate the response of a panel of 283 durum wheat lines assembled by the International Maize and Wheat Improvement Center (CIMMYT) to multiple races of stem rust in East Africa at the adult plant stage and map loci associated with field resistance. The lines were evaluated in Debre Zeit, Ethiopia and Njoro, Kenya from 2018 to 2019 in five environments (year × season). The panel was genotyped using genotyping-by-sequencing. After filtering, 26,439 Single Nucleotide Polymorphism (SNP) markers and 280 lines and three checks were retained for analysis. Population structure was assessed using principal component analysis. Genome-wide association analysis (GWAS) was conducted using Genomic Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability of the phenotype data revealed that 64–83% of the variation in stem rust response explained by the genotypes and lines with multiple race resistance were identified. GWAS analysis detected a total of 160 significant marker trait associations representing 42 quantitative trait loci. Of those, 21 were potentially novel and 21 were mapped to the same regions as previously reported loci. Known stem rust resistance genes/alleles were postulated including Sr8a, Sr8155B1, SrWeb/Sr9h, Sr11, Sr12, Sr13/Sr13 alleles, Sr17, Sr28/Sr16, Sr22, and Sr49. Lines resistant to multiple races in East Africa can be utilized as parents in durum wheat breeding programs. Further studies are needed to determine if there are new alleles at the Sr13 locus and potential markers for the known Sr13 alleles.

Leaf (brown) rust (LR) and stripe (yellow) rust (YR), caused by Puccinia triticina and P. striiformis f. sp. tritici, respectively, significantly reduce wheat production worldwide. Disease-resistant wheat varieties offer farmers one of the most effective ways to manage these diseases. The common wheat (Triticum aestivum L.) Arableu#1, developed by the International Maize and Wheat Improvement Center and released as Deka in Ethiopia, shows susceptibility to both LR and YR at the seedling stage but a high level of adult plant resistance (APR) to the diseases in the field. We used 142 F₅ recombinant inbred lines (RILs) derived from Apav#1 × Arableu#1 to identify quantitative trait loci (QTLs) for APR to LR and YR. A total of 4,298 genotyping-by-sequencing markers were used to construct a genetic linkage map. The study identified four LR resistance QTLs and six YR resistance QTLs in the population. Among these, QLr.cim-1BL.1/QYr.cim-1BL.1 was located in the same location as Lr46/Yr29, a known pleiotropic resistance gene. QLr.cim-1BL.2 and QYr.cim-1BL.2 were also located on wheat chromosome 1BL at 37 cM from Lr46/Yr29 and may represent a new segment for pleiotropic resistance to both rusts. QLr.cim-7BL is likely Lr68 given its association with the tightly linked molecular marker cs7BLNLRR. In addition, QLr.cim-3DS, QYr.cim-2AL, QYr.cim-4BL, QYr.cim-5AL, and QYr.cim-7DS are probably new resistance loci based on comparisons with published QTLs for resistance to LR and YR. Our results showed the diversity of minor resistance QTLs in Arableu#1 and their role in conferring near-immune levels of APR to both LR and YR, when combined with the pleiotropic APR gene Lr46/Yr29.

Races belonging to Ug99 lineage of stem rust fungus Puccinia graminis f. sp. tritici (Pgt) continue to pose a threat to wheat (Triticum aestivum L.) production in various African countries. Growing resistant varieties is the most economical and environmentally friendly control measure. Recombinant inbred line (RIL) populations from the crosses of susceptible parent ‘Cacuke’ with the resistant parents ‘Huhwa’ and ‘Yaye’ were phenotyped for resistance at the seedling stage to Pgt race TTKSK (Ug99) and in adult plants in field trials at Njoro, Kenya for two seasons in 2016. Using the Affymetrix Axiom breeders SNP array, two stem rust resistance genes, temporarily designated as SrH and SrY, were identified and mapped on chromosome arm 2BL through selective genotyping and bulked segregant analysis (BSA), respectively. Kompetitive allele specific polymorphism (KASP) markers and simple sequence repeat (SSR) markers were used to saturate chromosome arm 2BL in both RIL populations. SrH mapped between markers cim109 and cim114 at a distance of 0.9 cM proximal, and cim117 at 2.9 cM distal. SrY was flanked by markers cim109 and cim116 at 0.8 cM proximal, and IWB45932 at 1.9 cM distal. Two Ug99-effective stem rust resistance genes derived from bread wheat, Sr9h and Sr28, have been reported on chromosome arm 2BL. Infection types and map position in Huhwa and Yaye indicated that Sr28 was absent in both the parents. However, susceptible reactions produced by resistant lines from both populations against Sr9h-virulent race TTKSF+ confirmed the presence of a common resistance locus Sr9h in both lines. Test of allelism is required to establish genetic relationships between genes identified in present study and Sr9h. Marker cim117 linked to SrH was genotyped on set of wheat lines with Huhwa in the pedigree and is advised to be used for marker assisted selection for this gene, however, a combination of phenotypic and genotypic assays is desirable for both genes especially for selection of Sr9h in breeding programs.