The evolution of a new race of stem rust, generally referred to as Ug99, threatens global wheat production because it can overcome widely deployed resistance genes that had been effective for many years. To identify loci conferring resistance to Ug99 in wheat, a genome-wide association study was conducted using 232 winter wheat breeding lines from the International Winter Wheat Improvement Program. Breeding lines were genotyped with diversity array technology, simple sequence repeat and sequence-tagged site markers, and phenotyped at the adult plant stage for resistance to stem rust in the stem rust resistance screening nursery at Njoro, Kenya during 2009–2011. A mixed linear model was used for detecting marker-trait associations. Twelve loci associated with Ug99 resistance were identified including markers linked to known genes Sr2 and Lr34. Other markers were located in the chromosome regions where no Sr genes have been previously reported, including one each on chromosomes 1A, 2B, 4A and 7B, two on chromosome 5B and four on chromosome 6B. The same data were used for investigating epistatic interactions between markers with or without main effects. The marker csSr2 linked to Sr2 interacted with wPt4930 on 6BS and wPt729773 in an unknown location. Another marker, csLV34 linked to Lr34, also interacted with wPt4930 on 6BS and wPt4916 on 2BS. The frequent involvement of wPt4916 on 2BS and wPt4930 on 6BS in interactions with other significant loci on the same or different chromosomes suggested complex genetic control for adult plant resistance to Ug99 in winter wheat germplasm.
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The Sr2 gene has been used extensively in bread wheat improvement for durable stem rust resistance. Interestingly, the resistance of Sr2, associated with the pleotrophic gene Pbc expressed as pseudo-black chaff (PBC), is tightly linked with Yr30/Lr27/Pm genes conferring multiple disease resistance. The linkage map of chromosome 3BS revealed that Sr2 is 0.43cM away from lesion mimic (lm) locus. The RIL population (Yangmai#6 ? Sonalika) of 88 lines including parents where Sonalika carries Sr2 and lm while Yangmai#6 is deficient to both was evaluated for three years (2013-2016). The objective was to determine if this fragment is inherited as one unit and provides resistance to multiple diseases. Twenty four SSR markers distributed between 0.00 to 7.09cM on 3BS covering both Sr2 (5.57cM) and lm locus (6.0cM) were studied in the RIL population. Phenotyping was done for Sr2 associated PBC and lesion mimic along with disease severity for leaf rust, and spot blotch. Positive and significant correlations were observed between leaf stem rust resistance with Sr2 carrying PBC and lm. However, lines with lm either alone or with Sr2 (showing PBC) exhibited spot blotch susceptibility. The reverse situation does not hold not true where genotypes carrying Sr2 alone showed no correlation with spot blotch resistance. This indicates that the Sr2 complex is inherited as a single unit. Use of 24 SSR also suggest that Sr2 and lm loci are tightly linked and inherited together. The co-inheritance of Sr2 and lm ensures the stability and durability of rust resistance. However, the discouraging observation of spot blotch susceptibility due to lm gene suggests a limitation in achieving multiple disease resistance in environments where spot blotch is important. We identified two transgressive segregates in the population showing least expression of lm despite the presence of Sr2 and lm together.
The rapid appearance of new races of rust pathogens with virulence for the major seedling resistance genes in wheat has intensified the focus to discover adult plant resistance (APR) genes in wheat and utilize them in breeding programs for sustainable wheat production. The experimental breeding line 'Copio' developed by the International Maize and Wheat Improvement Centre (CIMMYT) in Mexico has exhibited high levels of APR to all three rusts including the African stem rust Ug99 race group. To dissect the mechanism of APR in Copio it was crossed with APAV#1, which is susceptible to all three rusts and a population of 176 F4:F5 recombinant inbred lines (RILs) was developed at CIMMYT. Both parental lines were found to be susceptible (IT >3) at the seedling stage to races TTKSK and TKTTF, which ensures the field data from Africa will be applicable for APR mapping. Seedling tests were also conducted on the RIL population using the predominant Pakistani race RRTTF, and Chi-squared tests indicated segregation of two stem rust seedling genes (?2 test P value of 0.00002). Both parents were also tested for the known APR genes Lr34/Yr18/Sr57, Lr46/Yr29/Sr58, Lr67/Yr46/Sr55 and Sr2/Yr30 using molecular markers and results indicate that APAV#1 does not carry any known APR genes, while Copio might have Lr46 and Sr2. This population was tested in four field environments (US, Pakistan, Mexico, and Kenya) for leaf, stem and yellow rusts during 2015-16 and 2016-17. Disease severity distributions of all three rusts for the RILs across all environments were continuous, suggestive of quantitative and polygenic resistance.
We are using genotyping by sequencing (GBS) as a genotyping platform and anticipate having preliminary mapping results available by spring 2018.
A key objective of BGRI is to breed high yielding, stem rust resistant spring wheat germplasm suitable for releases as successful varieties in wheat growing countries of Africa, Middle East, Asia and Latin America. High emphasis was given to select adult plant resistance (APR) to stem rust in achieving this goal that is especially important in East African highlands where various variants belonging to the Ug99 race group and other lineages of stem rust fungus are now known, disease is endemic and present throughout the year on wheat crops. Recent molecular mapping studies show that combinations of partially effective APR gene Sr2 with 3 to 4 additional APR genes such as Sr55, Sr56, Sr57, Sr58 and other undesignated quantitative trait loci confer adequate to high levels of resistance to stem rust. A ‘Mexico-Kenya shuttle breeding scheme’ was initiated in 2008 to select APR to stem rust under high disease pressures at Njoro, Kenya while selecting for resistance to other rusts, yield, agronomic and quality traits in Mexico. This selection scheme, combined with phenotyping of advanced lines for multiple seasons in Kenya has resulted in identifying a small frequency of high yielding lines that possess a high level of resistance with a stable and low stem rust severity performance over seasons/locations under high disease pressures. These near-immune wheat lines are the best candidates for release in East Africa to achieve durable disease control and simultaneously curtail, or reduce, further selection of new virulences. A significantly higher proportion of wheat lines were also developed with moderate levels of resistance that is considered suitable for deployment in wheat growing areas where rust builds up later in the season. The worldwide distribution of the wheat lines derived from Mexico-Kenya shuttle breeding initiated in 2012 through the international yield trials and nurseries from CIMMYT. Potential releases and cultivation of these lines in different countries together with a reduction in area sown to susceptible varieties are expected to reduce the threat from stem rust.
Stem rust is a potentially destructive fungal disease of wheat worldwide. In 1998 Pgt pathotype TTKSK virulent to Sr31 was detected in Uganda. The same pathotype was confirmed in Lorestan and Hamedan provinces of Iran in 2007. We used a derivative of race TTKSK to phenotype 62 Iranian wheat landraces (resistant to stripe rust in a previous study) at the seedling stage to this new pathotype (TTSSK). Twenty eight accessions were evaluated for the presence of resistance genes Sr2, Sr22, Sr24, Sr25, Sr26, Sr35, Sr36 and Srweb using SSR markers. None carried Sr2, Sr24 or Sr26, but the presence of Sr22, Sr25, Sr35 and Sr36 was indicated. Some susceptible landraces predicted to carry Sr2 by marker analysis require further investigation. To evaluate defense gene expression in compatible and incompatible stem rust interactions we sampled resistant and susceptible cultivars at 0, 12, 18, 24, 72 hours post-inoculation (hpi). ?-1,3 glucanase expression was studied using qGLU-S and qGLUU-AS primers and a real-time PCR step-one ABI machine, with ?-tubulin and EF1-? genes used as internal controls. In incompatible interactions defense gene expression was increased at 24 hpi, but in compatible interactions the highest level of expression occurred at 12 hpi and was significantly decreased at 18 hpi. The results revealed that expression of defense genes such as ?-1,3 glucanase was earlier in compatible than in incompatible interactions but the expression level was less in incompatible interactions. On the other hand, in susceptible genotypes the expression of defense genes increased immediately after inoculation and declined sharply after infection. In contrast defense gene expression in resistant genotypes began to increase after establishment of the pathogen.
Durable resistance to wheat stem rust fungus can Be achieved by developing and deploying varieties that have race-nonspecific, adult plant resistance (APR) conferred by multiple minor, slow rusting genes. Wheat lines ‘Kingbird, ‘Kiritati’, ‘Huirivis#1’, ‘Juchi’, ‘Muu’ and ‘Pavon 76’ showed high levels of APR to Ug99 races of stem rust fungus when tested in Kenya. The F5 and F6 generation recombinant inbred line (RIL) populations developed from the crosses of moderately susceptible ‘PBW343’ with five resistant parents were used in mapping. The non-Sr26 fraction of the ‘Avocet’ x Pavon 76 RIL population, developed earlier for leaf rust and stripe rust resistance studies, was also included. Field phenotyping of the parents and RILs were conducted at Njoro, Kenya for at least two years with Ug99+Sr24 (TTKST) race under high stem rust pressures. The continuous variation of APR in each RIL population and genetic analyses indicated quantitative nature of resistance that was likely governed by 3 or 4 minor genes. Single and joint year analyses by Inclusive Composite Interval Mapping (ICIM) using informative DArT and/or SSR markers identified consistent APR QTLs on chromosomes 1AL, 3BS, 5BL, 7A and 7DS in Kingbird; 2D, 3BS, 5BL and 7DS in Kiritati; 2B, 3BS, 4A, 5BL and 6B in Juchi; 2B, 3BS, 7B in Huirivis#1; 2B, 3BS and 5BL in Muu; and 1BL, 3BS, 5A and 6B in Pavon 76. QTLs on each genomic regions explained 10- 46% of the phenotypic variation for APR. Pseudo-black chaff phenotype associated with APR gene Sr2 on chromosome 3BS in all six resistant parents and identification of an APR QTL in the same region in all mapping populations confirmed the role of Sr2 in reducing stem rust severity. The 1BL QTL in Pavon 76 was in the same region where pleiotropic APR gene Lr46/Yr29/Pm39 is located. Similarly a 7DS QTL in Kingbird and Huirivis#1 was in the chromosomal region where pleiotropic APR gene Lr34/Yr18/Pm38 is located. These results indicate that the above two pleiotropic resistance genes confer APR to stem rust in addition to leaf rust, yellow rust and powdery mildew. Further studies are underway to saturate the genomic regions harboring new APR QTLs with additional molecular markers.
The inheritance of resistance to races 56 and 15B-1L was studied in back-crosses of Hope and H-44 to Marquis. The results indicated that both varieties carry the same three genes. Resistance to race 56 is controlled by two dominant genes, Sr 1 which conditions seedling or physiological resistance and Sr 2 which conditions adult plant resistance. At either the seedling or adult plant stage both genes must be present to provide full resistance to race 56. A single recessive gene, not yet named, provides resistance to race 15B-1L.The gene Sr 1 was transferred from Hope to Marquis by backcrossing and the line was crossed to the Chinese Spring monosomics. The gene proved to be on chromosome 2B (XIII).
The appearance and spread of races of Puccinia graminis f. sp. tritici with virulence for the Sr31 resistance gene has renewed interest in breeding for durable resistance to stem rust of wheat. Since the occurrence of stem rust has been low in South Africa until the detection of race TTKSF in 2000, breeding for resistance to this disease has not been a primary objective. The aim of this study was to test bread wheat cultivars and lines at the seedling stage for their infection response to stem rust, thus determining their level of resistance or vulnerability. A collection of 65 bread wheat entries was tested with one USA race, two Eastern African races, and three South African races of P. graminis f. sp. tritici. The Eastern African and South African races all belong to the Ug99 lineage. The cultivars Duzi, Caledon, Elands, PAN 3364, PAN 3191, SST 047, SST 399, and Steenbras produced resistant infection types (IT <3) to all races. The molecular marker Sr24#50 indicated the presence of Sr24 in 12 entries. In cultivars resistant to TTTTF, TTKSF, and TTKSP but susceptible to TTKSK and PTKST, the iag95 DNA marker indicated the presence of Sr31 in five wheat lines. Using the cleaved amplified polymorphic sequence marker csSr2, Sr2 was detected in PAN 3377, Inia, and Steenbras. Few South African wheat cultivars appear to have a broad-based resistance to stem rust, as 88% of the entries were susceptible as seedlings to at least one of the races tested. Diversification of resistance sources and more directed breeding for stem rust resistance are needed in South Africa.
Stem rust or black rust is one of the most important diseases of wheat worldwide. In India, central, peninsular and southern hill zones are particularly prone to stem rust where favourable environmental conditions exist. The recent emergence of wheat stem rust race Ug99 (TTKSK) and related strains threatens global wheat production as Ug99 overcome resistance gene Sr31 effective for many years. Resistance gene Sr2, derived from cultivar 'Hope' is responsible for slow rusting and providing partial but durable resistance against stem rust of wheat. In addition to other unknown minor genes ( Sr2 complex), this gene tends to be non-specific and is currently effective against all isolates of Puccinia graminis tritici throughout wheat-growing regions of the world. A set of 135 bread wheat varieties developed in the last forty years for prominent northern, central, peninsular and southern hill regions of India was screened with molecular markers, CsSr2 and GWM533, developed and identified for Sr2 gene. Out of 135 varieties screened, 92 confirmed the presence of Sr2 gene at molecular level. The molecular information of Sr2 gene was corroborated with the available morphological marker data for selected varieties to evaluate the efficacy of these molecular markers in Indian wheat germplasm. It was observed that these two molecular markers in combination provide accuracy in 92% lines for this gene at molecular level with presumed Sr2 status in Indian wheat varieties. It is proposed that the use of CsSr2 and GWM533 will help in gene pyramiding of Sr2 along with other stem rust resistance genes in future wheat varieties to accelerate Indian breeding program for rust resistance.
Recessively inherited gene Sr2 has provided the basis of durable resistance to stem rust (caused by Puccinia graminis tritici) in wheat (Triticum aestivum L.) worldwide. The associated earhead and stem melanism or 'pseudo-black chaff' is generally used as a marker for this gene. Sr2 has been postulated in many wheat cultivars of India including 'Lok 1', based on associated pseudo-black chaff in adult plants, and leaf chlorosis in seedlings. However, dominant inheritance of the resistance factor operating in 'Lok 1', and a 13 : 3 (resistant : susceptible) F-2 segregation in the 'Sr2-line' ('Chinese Spring'(6) x 'Hope' 3B) x 'Lok 1' cross confirmed that Sr2 was absent in 'Lok 1'. Susceptible plants with a pseudo-black chaff phenotype were observed in F-2 populations of 'Agra Local' (susceptible) x 'Lok 1', and the 'Sr2-line' x 'Lok 1' crosses. Most of the F-3 families derived from the susceptible F-2 segregants with pseudo-black chaff phenotypes were true breeding for the expression of pseudo-black chaff with susceptibility to stem rust. Thus, linkage of pseudo-black chaff with Sr2 in wheat can be broken, and hence, caution may be exercised in using pseudo-black chaff as a marker for selecting Sr2 in breeding programmes.