Marker-trait association and epistasis for brown rust resistance in sugarcane

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Association mapping of stem rust resistance in durum wheat at the seedling and adult plant stages

In wheat, stem rust is known to rapidly evolve new virulence to resistance genes. While more than 50 stem rust resistance (Sr) loci have been identified in wheat, only a few remain effective, particularly against the highly virulent race Ug99 (TTKSK race) and a mixture of durum-specific races. An association mapping (AM) study based on 183 durum wheat accessions was utilized to identify resistance loci for stem rust response in Ethiopia over four seasons and artificial inoculation with Ug99 (TTKSK race) and a mixture of durum-specific races under field conditions as well as in greenhouse test at seedling stage under controlled conditions for resistance to four highly virulent stem rust races: TRTTF, TTTTF, (TTKSK (Ug99) and JRCQC. The panel was profiled with 1,253 SSR and DArT markers. Twelve QTL-tagging markers were significant (P < 0.05) across three to four seasons. The role of Sr13, Sr9, Sr14, Sr17, and Sr28 was confirmed. Thirteen significant markers were in regions with no Sr genes/QTLs. The results under controlled conditions showed that 15, 20, 19 and 19 chromosome regions harbored markers that showed significant effects for races TRTTF, TTTTF, TTKSK and JRCQC, respectively. These genomic regions showed marker R2 values ranging from 1.13 to 8.34, 1.92 to 17.64, 1.75 to 23.12 and 1.51 to 15.33% for races TRTTF, TTTTF, TTKSK and JRCQC, respectively. The study demonstrates that stem rust resistance in durum wheat is governed in part by shared loci and in part by race-specific ones. The QTLs identified in this study through AM will be useful in the marker-assisted development of durum wheat cultivars with durable stem rust resistance.

Contrasting complexity of two rust resistance loci in flax.

DNA probes from the L6 rust resistance gene of flax (Linum usitatissimum) hybridize to resistance genes at the unlinked M locus, indicating sequence similarities between genes at the two loci. Genetic and molecular data indicate that the L locus is simple and contains a single gene with 13 alleles and that the M locus is complex and contains a tandem array of genes of similar sequence. Thus the evolution of these two related loci has been different. The consequence of the contrasting structures of the L and M loci on the evolution of different rust resistance specificities can now be investigated at the molecular level

Biology of rust resistance in forest trees: proceedings of a NATO-IUFRO advanced study institute.

The institute was held at the University of Idaho, Moscow, Id., August 17-24, 1969; it was supported by the North Atlantic Treaty Organization ... [et al.].

Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum

As part of a comparative mapping study between sugarcane and sorghum, a sugarcane cDNA clone with homology to the maize Rp1-D rust resistance gene was mapped in sorghum. The cDNA probe hybridised to multiple loci, including one on sorghum linkage group (LG) E in a region where a major rust resistance QTL had been previously mapped. Partial sorghum Rp1-D homologues were isolated from genomic DNA of rust-resistant and -susceptible progeny selected from a sorghum mapping population. Sequencing of the Rp1-D homologues revealed five discrete sequence classes: three from resistant progeny and two from susceptible progeny. PCR primers specific to each sequence class were used to amplify products from the progeny and confirmed that the five sequence classes mapped to the same locus on LG E. Cluster analysis of these sorghum sequences and available sugarcane, maize and sorghum Rp1-D homologue sequences showed that the maize Rp1-D sequence and the partial sugarcane Rp1-D homologue were clustered with one of the sorghum resistant progeny sequence classes, while previously published sorghum Rp1-D homologue sequences clustered with the susceptible progeny sequence classes. Full-length sequence information was obtained for one member of a resistant progeny sequence class (Rp1-SO) and compared with the maize Rp1-D sequence and a previously identified sorghum Rp1 homologue (Rph1-2). There was considerable similarity between the two sorghum sequences and less similarity between the sorghum and maize sequences. These results suggest a conservation of function and gene sequence homology at the Rp1 loci of maize and sorghum and provide a basis for convenient PCR-based screening tools for putative rust resistance alleles in sorghum.

Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Selecting for rust (Puccinia psidii) resistance in Eucalyptus grandis in São Paulo State, Brazil

In Brazil, Eucalyptus grandis is a key species for wood production. However, some genotypes are susceptible to rust (Puccinia psidii), mainly in São Paulo State, where climatic conditions are favorable for its development. Rust represents a high economic risk to forest companies because of the high potential of damage to commercial eucalypt plantations. The aims of the present study were (i) to select progenies of E. grandis for stability and adaptability regarding resistance to rust at different locations; (ii) compare the selections under these different climatic conditions; and (iii) compare rust severity in the field with the theoretical model. We observed that climatic conditions were extremely influential factors for rust development, but even under favorable conditions for disease development, we found rust-resistant progenies. In sites unfavorable for rust development, we detected highly susceptible progenies. We found significant correlation among the genetic material, environmental conditions and disease symptoms, however, we observed a simple genotype-environmental interaction and significant genetic variability among the progenies. The average heritability was high among the progenies in all sites, indicating substantial genetic control for rust resistance. We also observed a good relationship between rust severity in the field and the theoretical model that considered annual average temperature and leaf wetness. © 2013 Elsevier B.V.

RESPONSE OF LOCALLY ADAPTED PEARL MILLET POPULATIONS TO S1 PROGENY RECURRENT SELECTION FOR GRAIN YIELD AND RESISTANCE TO RUST

In the semi-arid zones of Uganda, pearl millet ( Pennisetum glaucum (L.) R. Br.) is mainly grown for food and income; but rust (Puccinia substriata var indica (L.) R. Br.) is the main foliar constraint lowering yield. The objective of the study was to genetically improve grain yield and rust resistance of two locally adapted populations (Lam and Omoda), through two cycles of modified phenotypic S1 progeny recurrent selection. Treatments included three cycles of two locally adapted pearl millet populations, evaluated at three locations. Significant net genetic gain for grain yield (72 and 36%) were achieved in Lam and Omoda populations, respectively. This led to grain yield of 1,047 from 611 kg ha-1 in Lam population and 943 from 693 kg ha-1 in Omoda population. Significant improvement in rust resistance was achieved in the two populations, with a net genetic gain of -55 and -71% in Lam and Omoda populations, respectively. Rust severity reduced from 30 to 14% in Lam population and from 57 to 17% in Omoda population. Net positive genetic gains of 68 and 8% were also achieved for 1000-grain weight in Lam and Omoda, respectively. Traits with a net negative genetic gain in both populations were days to 50% flowering, days to 50% anthesis, days to 50% physiological maturity, flower-anthesis interval, plant height and leaf area.

Genetic variability in progenies of Eucalyptus dunnii Maiden for resistance to Puccinia psidii

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Increased atmospheric carbon dioxide concentration: effects on eucalypt rust (Puccinia psidii), C:N ratio and essential oils in eucalypt clonal plantlets

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Selecting for rust (Puccinia psidii) reistance in Euclyptus grandis in São Paulo state, Brazil

In Brazil, Eucalyptus grandis is a key species for wood production. However, some genotypes are susceptible to rust (Puccinia psidii), mainly in São Paulo State, where climatic conditions are favorable for its development. Rust represents a high economic risk to forest companies because of the high potential of damage to commercial eucalypt plantations. The aims of the present study were (i) to select progenies of E. grandis for stability and adaptability regarding resistance to rust at different locations; (ii) compare the selections under these different climatic conditions; and (iii) compare rust severity in the field with the theoretical model. We observed that climatic conditions were extremely influential factors for rust development, but even under favorable conditions for disease development, we found rust-resistant progenies. In sites unfavorable for rust development, we detected highly susceptible progenies. We found significant correlation among the genetic material, environmental conditions and disease symptoms, however, we observed a simple genotype-environmental interaction and significant genetic variability among the progenies. The average heritability was high among the progenies in all sites, indicating substantial genetic control for rust resistance. We also observed a good relationship between rust severity in the field and the theoretical model that considered annual average temperature and leaf wetness.

Analysing diversity in sugarcane resistance gene analogues

As resistance genes have been shown to contain conserved motifs and cluster in many plant genomes, the identification of resistance gene analogues can be used as a strategy for both the discovery of DNA markers linked to disease resistance loci and the map-based cloning of disease resistance genes. Sugarcane suffers from many important diseases and an analysis of resistance gene analogues offers a means to identify DNA markers linked to resistance loci. However, sugarcane has the most complex genome of any crop plant and initially it is important to understand the extent of resistance gene analogue diversity in the sugarcane genome before genetic analysis. We review herein how more than 100 expressed sequence tags with homology to different resistance genes have been identified in sugarcane with many mapped as single-dose restriction fragment length polymorphism markers. Importantly, some of these resistance gene analogues have been shown to be linked to disease resistance genes or disease quantitative trait loci. In an attempt to more efficiently analyse additional resistance gene analogues in sugarcane, we report on experiments aimed at investigating the molecular diversity of several resistance gene analogue families using a modified form of a technique termed Ecotilling. Using Ecotilling, we were able to rapidly detect single nucleotide polymorphisms in fragments amplified by PCR from four different resistance gene analogue families, SoRP1D, SoPTO, SoXa21 and SoHs1pro-1. An analysis of a diverse set of sugarcane varieties, including modern sugarcane cultivars and several S. officinarum and S. spontaneum clones, indicated that all amplicons, apart from SoHs1pro-1, contained significant polymorphism within the gene region studied. However, a comparison among these sugarcane clones, including between the parents of two sugarcane mapping populations, indicated that most polymorphisms were multi-dose, not single-dose, preventing their genetic map location or association with disease susceptibility or resistance from being determined.

Evidence for different QTL underlying the immune and hypersensitive responses of Eucalyptus globulus to the rust pathogen Puccinia psidii

The rust Puccinia psidii infects many species in the family Myrtaceae. Native to South America, the pathogen has recently entered Australia which has a rich Myrtaceous flora, including trees of the ecologically and economically important genus Eucalyptus. We studied the genetic basis of variation in rust resistance in Eucalyptus globulus, the main plantation eucalypt in Australia. Quantitative trait loci (QTL) analysis was undertaken using 218 genotypes of an outcross F2 mapping family, phenotyped by controlled inoculation of their open pollinated progeny with the strain of P. psidii found in Australia. QTL analyses were conducted using a binary classification of individuals with no symptoms (immune) versus those with disease symptoms, and in a separate analysis dividing plants with disease symptoms into those exhibiting the hypersensitive response versus those with more severe symptoms. Four QTL were identified, two influencing whether a plant exhibited symptoms (Ppr2 and Ppr3), and two influencing the presence or absence of a hypersensitive reaction (Ppr4 and Ppr5). These QTL mapped to four different linkage groups, none of which overlap with Ppr1, the major QTL previously identified for rust resistance in Eucalyptus grandis. Candidate genes within the QTL regions are presented and possible mechanisms discussed. Together with past findings, our results suggest that P. psidii resistance in eucalypts is quantitative in nature and influenced by the complex interaction of multiple loci of variable effect.