S. A. Herrera-Foessel

The Emergence of Ug99 Races of the Stem Rust Fungus is a Threat to World Wheat Production

Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat.

Will stem rust destroy the world's wheat crop?

Race Ug99, or TTKSK, of fungus Puccinia graminis tritici , causing stem or black rust disease on wheat ( Triticum aestivum ), first identified in Uganda in 1998 has been recognized as a major threat to wheat production. Its spread in 2006 to Yemen and Sudan and further spread towards North Africa, Middle East and West-South Asia is predicted -aided by predominant wind currents and large areas of wheat varieties that are susceptible and grown under environments favorable for survival and multiplication of the pathogen. This has raised serious concerns of major epidemics that could destroy the wheat crop in these primary risk areas. Detection in Kenya of a new variant TTKST in 2006 with virulence to gene Sr24 , which caused severe epidemics in 2007 in some regions of Kenya and rendered about half of the previously known Ug99-resistant global wheat materials susceptible, has further increased the vulnerability globally. Rigorous screening since 2005 in Kenya and Ethiopia of wheat materials from 22 countries and International Centers has identified low frequency of resistant materials that have potential to replace susceptible cultivars. Diverse sources of resistance, both race-specific and adult-plant type, are now available in high-yielding wheat backgrounds and are being used in breeding. The proposed strategy is to deploy spring wheat varieties possessing durable, adult plant resistance in East Africa and other primary risk areas to reduce inoculum and selection of new virulences capable of overcoming undefeated race-specific resistance genes. Race-specific resistance genes can then be deployed in secondary risk areas preferably in combinations. We believe that Ug99 threat in most countries can be reduced to low levels by urgently identifying, releasing and providing seed of new high yielding, resistant varieties.

Race non-specific resistance to rust diseases in CIMMYT spring wheats

Rust diseases continue to cause significant losses to wheat production worldwide. Although the life of effective race-specific resistance genes can be prolonged by using gene combinations, an alternative approach is to deploy varieties that posses adult plant resistance (APR) based on combinations of minor, slow rusting genes. When present alone, APR genes do not confer adequate resistance especially under high disease pressure; however, combinations of 4–5 such genes usually result in “near-immunity” or a high level of resistance. Although high diversity for APR occurs for all three rusts in improved germplasm, relatively few genes are characterized in detail. Breeding for APR to leaf rust and stripe rust in CIMMYT spring wheats was initiated in the early 1970s by crossing slow rusting parents that lacked effective race-specific resistance genes to prevalent pathogen populations and selecting plants in segregating populations under high disease pressure in field nurseries. Consequently most of the wheat germplasm distributed worldwide now possesses near-immunity or adequate levels of resistance. Some semidwarf wheats such as Kingbird, Pavon 76, Kiritati and Parula show high levels of APR to stem rust race Ug99 and its derivatives based on the Sr2-complex, or a combination of Sr2 with other uncharacterized slow rusting genes. These parents are being utilized in our crossing program and a Mexico-Kenya shuttle breeding scheme is used for selecting resistance to Ug99. High frequencies of lines with near-immunity to moderate levels of resistance are now emerging from these activities. After further yield trials and quality assessments these lines will be distributed internationally through the CIMMYT nursery system.

Analysis of leaf and stripe rust severities reveals pathotype changes and multiple minor QTLs associated with resistance in an Avocet × Pastor wheat population

Leaf rust and stripe rust are important diseases of wheat world-wide and deployment of cultivars with genetic resistance is an effective and environmentally sound control method. The use of minor, additive genes conferring adult plant resistance (APR) has been shown to provide resistance that is durable. The wheat cultivar ‘Pastor’ originated from the CIMMYT breeding program that focuses on minor gene-based APR to both diseases by selecting and advancing generations alternately under leaf rust and stripe rust pressures. As a consequence, Pastor has good resistance to both rusts and was used as the resistant parent to develop a mapping population by crossing with the susceptible ‘Avocet’. All 148 F5 recombinant inbred lines were evaluated under artificially inoculated epidemic environments for leaf rust (3 environments) and stripe rust (4 environments, 2 of which represent two evaluation dates in final year due to the late build-up of a new race virulent to Yr31) in Mexico. Map construction and QTL analysis were completed with 223 polymorphic markers on 84 randomly selected lines in the population. Pastor contributed Yr31, a moderately effective race-specific gene for stripe rust resistance, which was overcome during this study, and this was clearly shown in the statistical analysis. Linked or pleiotropic chromosomal regions contributing to resistance against both pathogens included Lr46/Yr29 on 1BL, the Yr31 region on 2BS, and additional minor genes on 5A, 6B and 7BL. Other minor genes for leaf rust resistance were located on 1B, 2A and 2D and for stripe rust on 1AL, 1B, 3A, 3B, 4D, 6A, 7AS and 7AL. The 1AL, 1BS and 7AL QTLs are in regions that were not identified previously as having QTLs for stripe rust resistance. The development of uniform and severe epidemics facilitated excellent phenotyping, and when combined with multi-environment analysis, resulted in the relatively large number of QTLs identified in this study.

QTL characterization of resistance to leaf rust and stripe rust in the spring wheat line Francolin#1

Abstract Growing resistant wheat varieties is a key method of controlling two important wheat diseases, leaf rust and stripe rust. We analyzed quantitative trait loci (QTL) to investigate adult plant resistance (APR) to these rusts, using 141 F5 RILs derived from the cross ‘Avocet-YrA/Francolin#1’. Phenotyping of leaf rust resistance was conducted during two seasons at Ciudad Obregon, Mexico, whereas stripe rust was evaluated for two seasons in Toluca, Mexico, and one season in Chengdu, China. The genetic map was constructed with 581 markers, including diversity arrays technology and simple sequence repeat. Significant loci for reducing leaf rust severity were designated QLr.cim-1BL, QLr.cim-3BS.1, QLr.cim-3DC, and QLr.cim-7DS. The six QTL that reduced stripe rust severity were designated QYr.cim-1BL, QYr.cim-2BS, QYr.cim-2DS, QYr.cim-3BS.2, QYr.cim-5AL, and QYr.cim-6AL. All loci were conferred by Francolin#1, with the exception of QYr.cim-2DS, QYr.cim-5AL, and QYr.cim-6AL, which were derived from Avocet-YrA. Closely linked markers indicated that the 1BL locus was the pleiotropic APR gene Lr46/Yr29. QYr.cim-2BS was a seedling resistance gene designated as YrF that conferred intermediate seedling reactions and moderate resistance at the adult plant stage in both Mexican and Chinese environments. Significant additive interactions were detected between the six QTL for stripe rust, but not between the four QTL for leaf rust. Furthermore, we detected two new APR loci for leaf rust in common wheat: QLr.cim-3BS.1 and QLr.cim-7DS.

Progress Towards Genetics and Breeding for Minor Genes Based Resistance to Ug99 and Other Rusts in CIMMYT High-Yielding Spring Wheat

Wheat rusts continue to cause significant losses worldwide despite major efforts given to their genetic control. This is due to frequent evolution and selection of virulence in pathogen overcoming the deployed race-specific resistance genes. Although the life of effective race-specific resistance genes can be prolonged by using gene combinations, an alternative approach being implemented at CIMMYT is to deploy varieties that posses adult plant resistance (APR) based on combinations of minor, slow rusting genes. When present alone, the APR genes do not confer adequate resistance especially under high disease pressure; however, combinations of 4 or 5 minor genes usually result in “near-immunity” or a high level of resistance. Although only a few APR genes are catalogued, various APR QTLs are now known and could lead to further characterization of additional genes. Four characterized genes have pleiotropic effects in conferring partial APR to all 3 rusts and powdery mildew, thus simplifying the task of breeding wheat varieties that are resistant to multiple diseases. Significant progress was made recently in developing high-yielding wheat germplasm that possesses high levels of APR to all three rusts by implementing a Mexico-Kenya shuttle breeding scheme. Parents with APR to Ug99 were hybridized with high-yielding parents that had adequate to high levels of APR to leaf rust and yellow rust. Segregating populations and advanced lines from these crosses were selected under high rust pressures in Mexico (leaf rust and yellow rust) and Kenya (Ug99 stem rust and yellow rust) to identify high-yielding progenies that possess high to adequate APR to all three rusts. International distribution of these high-yielding wheats is underway through CIMMYT international yield trials and screening nurseries. It is expected that several wheat varieties with APR to three rusts will be released and grown in various countries in the near-future that will allow determining the durability of resistance.

Molecular Mapping of a Leaf Rust Resistance Gene on the Short Arm of Chromosome 6B of Durum Wheat

Leaf rust, caused by Puccinia triticina, is an important disease of durum wheat (Triticum turgidum subsp. durum) worldwide, and the most effective way to control it is through the use of resistant cultivars. A partially dominant leaf rust resistance gene present in the International Maize and Wheat Improvement Center-derived Chilean cv. Guayacan INIA and its sister line Guayacan 2 was mapped to chromosome arm 6BS by identifying linked amplified fragment length polymorphisms (AFLPs) and mapping two of the molecular markers in common wheat (T. aestivum) linkage maps of the International Triticeae Mapping Initiative and Oligoculm × Fukuho-komugi populations. Comparison of infection type responses of the two resistant durums with common wheat testers carrying the previously mapped resistance genes Lr36 and Lr53 on 6BS, and their chromosomal positions, indicated that the resistance gene in durum wheat Guayacan INIA is a new leaf rust resistance gene, which was designated as Lr61. Gene Lr61 is effective against the P. triticina race BBG/BN predominant in northwestern Mexico and other races infecting durum wheat in various countries.

Lr72 Confers Resistance to Leaf Rust in Durum Wheat Cultivar Atil C2000

Leaf rust, caused by Puccinia triticina (Pt), has become a globally important disease for durum wheat (Triticum turgidum subsp. durum) since the detection of race group BBG/BN, which renders ineffective a widely deployed seedling resistance gene present in several popular cultivars including Mexican cultivars Altar C84 and Atil C2000. The resistance gene continues to play a key role in protecting durum wheat against bread wheat-predominant races since virulence among this race group has not been found. We developed F3 and F5 mapping populations from a cross between Atil C2000 and the susceptible line Atred #1. Resistance was characterized by greenhouse seedling tests using three Pt races. Segregation tests indicated the presence of a single gene, which was mapped to the distal end of 7BS by bulk segregant analysis. The closest marker, wmc606, was located 5.5 cM proximal to the gene. No known leaf rust resistance genes are reported in this region; this gene was therefore designated as Lr72. The presence of Lr72 was further investigated in greenhouse tests in a collection of durum wheat using 13 Pt races. It was concluded that at least one additional gene protects durum wheat from bread wheat-predominant Pt races.

Different QTLs are associated with leaf rust resistance in wheat between China and Mexico

The wheat line ‘Chapio’ is resistant to leaf rust, caused by Puccinia triticinia, and was derived from a breeding programme that focuses on multi-genic resistance to provide durability. This line was crossed with the susceptible ‘Avocet’ to develop an F6 recombinant inbred line population. The population was phenotyped for leaf rust severity in two environments each in Mexico and China. There were significant differences in the loci providing resistance between the two intercontinental regions. The Lr34 locus had large effects in both Mexico and China, highlighting its importance in providing a basis for broad-spectrum resistance. The Lr46 locus on chromosome 1BL and a 3D locus had effects in Mexico but not in China. Presence of Sr2 was determined by the phenotypic marker of pseudo-black chaff and was mapped to chromosome 3BS. This region was associated with a QTL that had strong effects in China but no significant effect in Mexico, as did a locus on chromosome 4B. Seedling tests on the parents indicated that the 3B locus was not the complimentary gene Lr27, but the 4B locus was in the same position as Lr31 (or Lr12). Further investigations showed that these loci worked independently and additively in adult plants. Chapio was bred for quantitative, non-race-specific resistance under strong phenotypic selection for leaf rust in Mexico. It is interesting that different QTLs contribute to this resistance in another country, and these results suggest that environmental effects, as well as race specificity, can play a role in expression of resistance.

Characterization and Mapping of Leaf Rust and Stripe Rust Resistance Loci in Hexaploid Wheat Lines UC1110 and PI610750 under Mexican Environments

Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by the globally important wheat leaf rust (LR) and stripe rust (YR) diseases. In this study, a population of 186 F8 recombinant inbred lines (RILs) derived from a cross between a synthetic wheat derivative (PI610750) and an adapted common wheat line (cv. “UC1110”) were phenotyped for LR and YR response at both seedling and adult plant stages over multiple seasons. Using a genetic linkage map consisting of single sequence repeats and diversity arrays technology markers, in combination with inclusive composite interval mapping analysis, we detected a new LR adult plant resistance (APR) locus, QLr.cim-2DS, contributed by UC1110. One co-located resistance locus to both rusts, QLr.cim-3DC/QYr.cim-3DC, and the known seedling resistance gene Lr26 were also mapped. QLr.cim-2DS and QLr.cim-3DC showed a marginally significant interaction for LR resistance in the adult plant stage. In addition, two previously reported YR APR loci, QYr.ucw-3BS and Yr48, were found to exhibit stable performances in rust environments in both Mexico and the United States and showed a highly significant interaction in the field. Yr48 was also observed to confer intermediate seedling resistance against Mexican YR races, thus suggesting it should be re-classified as an all-stage resistance gene. We also identified 5 and 2 RILs that possessed all detected YR and LR resistance loci, respectively. With the closely linked molecular markers reported here, these RILs could be used as donors for multiple resistance loci to both rusts in wheat breeding programs.