Person: Yue Jin
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- Genetic loci conditioning adult plant resistance to the Ug99 Race group and seedling resistance to races TRTTF and TTTTF of the stem rust pathogen in wheat landrace CItr 15026(American Phytopathological Society (APS), 2017) Babiker, E.M.; Gordon, T.; Bonman, J.M.; Shiaoman Chao; Rouse, M.N.; Yue Jin; Newcomb, M.; Wanyera, R.; Bhavani, S.Wheat landrace CItr 15026 previously showed adult plant resistance (APR) to the Ug99 stem rust race group in Kenya and seedling resistance to Puccinia graminis f. sp. tritici races QFCSC, TTTTF, and TRTTF. CItr 15026 was crossed to susceptible accessions LMPG-6 and Red Bobs, and 180 double haploid (DH) lines and 140 recombinant inbred lines (RIL), respectively, were developed. The 90K wheat iSelect single-nucleotide polymorphism platform was used to genotype the parents and populations. Parents and 180 DH lines were evaluated in the field in Kenya for three seasons. A major quantitative trait locus (QTL) for APR was consistently detected on chromosome arm 6AS. This QTL was further detected in the RIL population screened in Kenya for one season. Parents, F1, and the two populations were tested as seedlings against races TRTTF and TTTTF. In addition, the DH population was tested against race QFCSC. Goodness-of-fit tests indicated that the TRTTF resistance in CItr 15026 was controlled by two complementary genes whereas the TTTTF and QFCSC resistance was conditioned by one dominant gene. The TRTTF resistance loci mapped to chromosome arms 6AS and 6DS, whereas the TTTTF and QFCSC resistance locus mapped to the same region on 6DS as the TRTTF resistance. The APR identified in CItr 15026 should be useful in developing cultivars with durable stem rust resistance.
Publication - Nested association mapping of stem rust resistance in wheat using genotyping by sequencing(Public Library of Science, 2016) Bajgain, P.; Rouse, M.N.; Tsilo, T.J.; Macharia, G.; Bhavani, S.; Yue Jin; Anderson, J.We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% – 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar markertrait association studies in other plant species.
Publication - Kenyan Isolates of Puccinia graminis f. sp. tritici from 2008 to 2014: virulence to SrTmp in the Ug99 race group and implications for breeding programs(American Phytopathological Society (APS), 2016) Newcomb, M.; Olivera Firpo, P.D.; Rouse, M.N.; Szabo, L.J.; Johnson, J.W.; Gale, S.; Luster, D.G.; Wanyera, R.; Macharia, G.; Bhavani, S.; Hodson, D.P.; Patpour, M.; Hovmoller, M.S.; Fetch, T.; Yue JinFrequent emergence of new variants in the Puccinia graminis f. sp. tritici Ug99 race group in Kenya has made pathogen survey a priority. We analyzed 140 isolates from 78 P. graminis f. sp. tritici samples collected in Kenya between 2008 and 2014 and identified six races, including three not detected prior to 2013. Genotypic analysis of 20 isolates from 2013 and 2014 collections showed that the new races TTHST, TTKTK, and TTKTT belong to the Ug99 race group. International advanced breeding lines were evaluated against an isolate of TTKTT (Sr31, Sr24, and SrTmp virulence) at the seedling stage. From 169 advanced lines from Kenya, 23% of lines with resistance to races TTKSK and TTKST were susceptible to TTKTT and, from two North American regional nurseries, 44 and 91% of resistant lines were susceptible. Three lines with combined resistance genes were developed to facilitate pathogen monitoring and race identification. These results indicate the increasing virulence and variability in the Kenyan P. graminis f. sp. tritici population and reveal vulnerabilities of elite germplasm to new races.
Publication - Specificity of a rust resistance suppressor on 7DL in the spring wheat cultivar Canthatch(American Phytopathological Society (APS), 2015) Talajoor, M.; Yue Jin; Anmin Wan; Xianming Chen; Bhavani, S.; Tabe, L.; Lagudah, E.; Li HuangThe spring wheat ‘Canthatch’ has been shown to suppress stem rust resistance genes in the background due to the presence of a suppressor gene located on the long arm of chromosome 7D. However, it is unclear whether the suppressor also suppresses resistance genes against leaf rust and stripe rust. In this study, we investigated the specificity of the resistance suppression. To determine whether the suppression is genome origin specific, chromosome location specific, or rust species or race specific, we introduced 11 known rust resistance genes into the Canthatch background, including resistance to leaf, stripe, or stem rusts, originating from A, B, or D genomes and located on different chromosome homologous groups. F1 plants of each cross were tested with the corresponding rust race, and the infection types were scored and compared with the parents. Our results show that the Canthatch 7DL suppressor only suppressed stem rust resistance genes derived from either the A or B genome, and the pattern of the suppression is gene specific and independent of chromosomal location.
Publication - Molecular mapping and validation of SrND643: a new wheat gene for resistance to the stem rust pathogen Ug99 race group(American Phytopathological Society (APS), 2015) Basnet, B.R.; Singh, S.; Lopez-Vera, E.E.; Huerta-Espino, J.; Bhavani, S.; Yue Jin; Rouse, M.N.; Singh, R.P.This study reports the identification of a new gene conferring resistance to the Ug99 lineage of races of Puccinia graminis f. sp. tritici in wheat (Triticum aestivum L.). Because the virulent races of stem rust pathogen continue to pose a serious threat in global wheat production, identification and molecular characterization of new resistance genes remains of utmost important to enhance resistance diversity and durability in wheat germplasm. Advanced wheat breeding line ‘ND643/2*Weebill1’ carries a stem rust resistance gene, temporarily designated as SrND643, effective against the Ug99 group of P. graminis f. sp. tritici races at both seedling and adult growth stages. This study was conducted to map the chromosomal location of SrND643 and identify closely linked molecular markers to allow its selection in breeding populations. In total, 123 recombinant inbred lines, developed by crossing ND643/2*Weebill1 with susceptible line ‘Cacuke’, were evaluated for stem rust response in field nurseries at Njoro, Kenya, during two growing seasons in 2010, and were genotyped with DNA markers, including Diversity Arrays Technology, simple sequence repeats (SSR), and single-nucleotide polymorphisms. Linkage mapping tagged SrND643 at the distal end of chromosome 4AL, showing close association with SSR markers Xgwm350 (0.5 centimorgans [cM]), Xwmc219 (4.1 cM), and Xwmc776 (2.9 cM). The race specificity of SrND643 is different from that of Sr7a and Sr7b, indicating that the resistance is conferred by a gene at a new locus or by a new allele of Sr7. The flanking markers Xgwm350 and Xwmc219 were predictive of the presence of SrND643 in advanced germplasm, thus validating the map location and their use in marker-assisted selection.
Publication - Emergence and spread of new races of wheat stem rust fungus: continued threat to food security and prospects of genetic control(American Phytopathological Society (APS), 2015) Singh, R.P.; Hodson, D.P.; Yue Jin; Lagudah, E.; Ayliffe, M.A.; Bhavani, S.; Rouse, M.N.; Pretorius, Z.; Szabo, L.J.; Huerta-Espino, J.; Basnet, B.R.; Lan, C.; Hovmoller, M.S.Race Ug99 (TTKSK) of Puccinia graminis f. sp. tritici, detected in Uganda in 1998, has been recognized as a serious threat to food security because it possesses combined virulence to a large number of resistance genes found in current widely grown wheat (Triticum aestivum) varieties and germplasm, leading to its potential for rapid spread and evolution. Since its initial detection, variants of the Ug99 lineage of stem rust have been discovered in Eastern and Southern African countries, Yemen, Iran, and Egypt. To date, eight races belonging to the Ug99 lineage are known. Increased pathogen monitoring activities have led to the identification of other races in Africa and Asia with additional virulence to commercially important resistance genes. This has led to localized but severe stem rust epidemics becoming common once again in East Africa due to the breakdown of race-specific resistance gene SrTmp, which was deployed recently in the ‘Digalu’ and ‘Robin’ varieties in Ethiopia and Kenya, respectively. Enhanced research in the last decade under the umbrella of the Borlaug Global Rust Initiative has identified various race-specific resistance genes that can be utilized, preferably in combinations, to develop resistant varieties. Research and development of improved wheat germplasm with complex adult plant resistance (APR) based on multiple slow-rusting genes has also progressed. Once only the Sr2 gene was known to confer slow rusting APR; now, four more genes—Sr55, Sr56, Sr57, and Sr58—have been characterized and additional quantitative trait loci identified. Cloning of some rust resistance genes opens new perspectives on rust control in the future through the development of multiple resistance gene cassettes. However, at present, disease-surveillance-based chemical control, large-scale deployment of new varieties with multiple race-specific genes or adequate levels of APR, and reducing the cultivation of susceptible varieties in rust hot-spot areas remains the best stem rust management strategy.
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