1International Programs in the College of Agriculture and Life Sciences, and Plant Breeding and Genetics Section in the School of Integrative Plant Science, Cornell University, USA, and CIMMYT, Mexico
Stem rust is a globally important wheat disease that can cause severe yield loss. Breeding for quantitative stem rust resistance (QSRR) is important for developing cultivars with durable resistance. Genomic selection (GS) could increase rates of genetic gain for quantitative traits, but few experiments comparing GS and phenotypic selection (PS) have been conducted. Our objectives were to compare realized gain from GS based on markers only with that of PS for QSRR in spring wheat using equal selection intensities; determine if gains agree with theoretical expectations; and compare the impact of GS and PS on inbreeding, genetic variance, and correlated response for pseudo-black chaff (PBC), a correlated and likely pleiotropic trait. Over two years, two cycles of GS were performed in parallel with one cycle of PS, with each method replicated twice. For GS, markers were generated using genotyping-by-sequencing, the prediction model was initially trained using historical data, and the model was updated before the second GS cycle. Overall, GS and PS led to a 31±11 and 42±12% increase in QSRR and a 138±22 and 180±70% increase in PBC, respectively. Genetic gains were not significantly different, but were in agreement with expectations. Per year, gains from GS and PS were equal, but GS led to significantly lower genetic variance. This shows that while GS and PS can lead to equal rates of short-term gains, GS can reduce genetic variance more rapidly. Further work to develop efficient GS implementation strategies in spring wheat is warranted.
Department of Animal, Plant and Soil Sciences, La Trobe University, Australia
Climatic changes permit the spread of plant diseases to new areas. To ensure grain production meets the needs of the growing world population, wheat breeding must combine multiple disease resistances in single cultivars in order to maintain current yield potential. Over the last three decades, classical mapping and association studies have identified disease resistance loci for individual diseases, but few studies have investigated loci that confer resistance to multiple diseases. To address this limitation, we extensively surveyed the literature to identify wheat genomic regions harboring resistance to multiple diseases. We identified 174 trait-linked markers distributed across all wheat chromosomes, except chromosome 4A, and the numbers of disease resistance loci in each region ranged from two to ten. Our survey suggests that some regions of the genome contain multiple disease resistance genes, or genes with pleiotropic effects. We are using the Chinese Spring flow sorted chromosome survey contigs to investigate the genic contents of genomic regions containing multiple disease trait loci to address this question.
The University of Sydney Plant Breeding Institute, Australia
Stripe rust of wheat was estimated to cause losses of A$127 m annually in Australia. Although stripe rust can be controlled through the use of chemicals, breeding for resistance is considered to be the best means of control. Identification and characterization of diverse sources of resistance is essential to achieve durable stripe rust control. A common wheat landrace AWCC618 showed resistance (IT 1CN) to Australian Puccinia striiformis f. sp. tritici (Pst) pathotypes. AWCC618 was crossed with the susceptible genotype Avocet S (AvS) to determine the genetic basis of resistance. Seedling tests on 123 AWCC618/AvS F3 families using Australian Pst pathotype 134 E16 A+ 17+ 27+ indicated monogenic inheritance of resistance (22HR:68SEG:33HS; χ21:2:1=3.34, non-significant at P=0.05 and 2 d.f.). The resistance locus was temporarily named YrAW3. Selective genotyping of eight homozygous resistant (HR) and eight homozygous susceptible (HS) F3 families using the 90K SNP Infinium assay tentatively located YrAW3 on chromosome 6A. The AWCC618/AvS population was advanced to F6 for detailed mapping of the target region. YrAW3 appears to be a new locus. AWCC618 was crossed with three current Australian cultivars to transfer YrAW3 to modern wheat backgrounds. Backcross-derivatives will also be useful for validation of linked markers.
Department of Plant Sciences, University of the Free State, South Africa
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Leaf rust is a common wheat disease in South Africa. Annual surveys conducted by the Agricultural Research Council - Small Grain Institute (ARC-SGI) during the last 35 years used infection type (IT) data on a defined differential set to identify individual field isolates. Results from these surveys confirmed that the South African Pt population is affected by both local evolution and foreign introductions. A good correlation was found between avirulence/virulence phenotypes and simple sequence repeat (SSR) genotypes in the South African Pt population. We therefore evaluated whether identification of field isolates by SSR analysis would complement the traditional IT analysis using 47 field isolates collected during the 2013 growing season. Of the 39 phenotyped isolates, 35 were correctly genotyped while three were incorrectly genotyped only because the corresponding race was not included as a control. Five isolates that could not be phenotyped due to non-viable spores were successfully genotyped. The dominant race 3SA145 (North American race annotation CCPS) was represented by nine different genotypes sharing 82% genetic similarity. The SSR data further showed that the field isolates formed part of two distinct lineages with little admixture between them. This study confirmed the supporting value of SSR genotyping to traditional race analysis in monitoring the South African Pt population.
Kulumsa Agricutural Research Center, Ethiopian Institute of Agricultural Research, Ethiopia
Pgt race TKTTF, virulent for the SrTmp gene present in Ethiopian cv. Digalu and first detected in 2012, caused significant yield losses in Digalu during the 2013 and 2014 seasons. No suitable replacement varieties with significant seed volume were available, and alternate solutions were sought. EIAR, with the support of the DRRW project through CIMMYT-Ethiopia, introduced 5 tonnes of adult plant, rust resistant wheat cv. Kingbird from Kenya. Kingbird was evaluated for agronomic performance at seven locations vs. three checks in 2014, and was also evaluated for stem rust reaction in single-race nurseries (TKTTF, TTKSK, TRTTF and JRCQC). With support from USAID/CIMMYT, seed was concurrently multiplied on 37 ha producing 80 tonnes of seed that was distributed to farmers in 2015. Mean grain yield over locations was 2.76 t ha-1. Mean performance of Kingbird was 3.00 t ha-1 compared to 2.79 t ha-1 for Ogolcho, 2.83 t ha-1 for Biqa and 2.42 t ha-1 for Kakaba. Thus Kingbird gave yield advantages of 5 to 22% over the check varieties. Stem rust severities on Kingbird in the single race nurseries ranged from Tr to 15% and reactions ranged from TMR to SMS. The check varieties rated up to 45% severity with S type reactions. Thus Kingbird was superior in terms of yield potential and stem rust resistance as measured in these trials vs. the check varieties. Stem rust resistance of Kingbird is based on Sr2 and Sr57 and is hypothesized to have at least three additional APR loci. Seedling reactions of Kingbird to races TKTTF and Ug99 are characterized as susceptible. Sr57 is pleiotropic and confers partial resistance to all three rusts, powdery mildew, spot blotch, and BYDV. Based on early maturity, yield performance, and stem rust resistance, Kingbird is recommended for low- to mid-altitude wheat-growing areas of Ethiopia.
The University of Sydney, Plant Breeding Institute, Australia
Landraces and wild relatives of wheat are rich repositories of new rust resistance genes. Landraces are preferred over wild relatives for the absence of deleterious effects associated with large alien segments. A common wheat landrace, AUS 27969 (ex Portugal), from the Watkins Collection was resistant under field conditions and produced seedling infection type (IT) 2C against the widely virulent Australian Puccinia striiformis f. sp. tritici (Pst) pathotype 134 E16 A+ Yr17+ Yr27+. AUS 27969 was crossed with the susceptible genotype Avocet S (AvS) and the distribution of F3 lines conformed to monogenic segregation [40 non-segregating resistant (NSR), 93 segregating (Seg), and 37 non-segregating susceptible (NSS); ?2 = 1.61, P2d.f. >0.05] when tested with the same pathotype at the seedling stage. The population is currently being selfed to F6. DNA from NSR and NSS lines will be sent for high throughput analysis to identify the genomic region carrying the resistance gene. Resistance-linked SNPs will be mapped on the F6 RIL population. The resistance gene will be backcrossed into modern Australian wheat backgrounds.