Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, USA
The quest for durable rust resistance in wheat is burgeoning with the emergence of new virulent races. Breeders challenged with this unceasing plant-pathogen arms race have to devise strategies for effective evaluation and exploitation of the rust resistance genes. Considering the likely presence of useful variation for rust resistance in CIMMYT’s international bread wheat screening nurseries (IBWSN), we implemented genomic prediction in the 45th and 46th IBWSN entries to determine their genomic estimated breeding values (GEBV’s) for leaf, stem and stripe rust resistance. The 350 lines (45th IBWSN) and 329 lines (46th IBWSN) were phenotyped in replicated trials over two to three years in El Batan, Mexico (leaf rust); Njoro, Kenya (stem rust) and Toluca, Mexico (stripe rust). The filtered genotyping data for these two nurseries comprised of 6,786 and 11,218 genotyping by sequencing (GBS) markers. Our objective was to compare the GEBV’s estimated by four different models: multiple linear regression (MLR) with QTL-linked markers as fixed effects; Genomic-best linear unbiased prediction (G-BLUP); G-BLUP mixed model which includes QTL linked markers as fixed effects and Bayesian least absolute shrinkage and selection operator (LASSO). We observed that the prediction accuracies (calculated using 10-fold cross validation) were the highest for stripe rust (0.52 to 0.61), followed by stem rust (0.42 to 0.65) and leaf rust (0.15 to 0.45). Among the models, the MLR gave the lowest prediction accuracies (0.15,0.42 and 0.52), while G-BLUP (0.45,0.59 and 0.59), mixed G-BLUP (0.38,0.65 and 0.62) and the Bayesian LASSO (0.45,0.58 and 0.61) yielded relatively higher and almost similar accuracies. Overall, our results are promising and indicate that using genome-wide markers is advantageous than including only significant QTL-linked markers. We hope that implementing genomic prediction in breeding programs, would help to achieve rapid gains from selection and revolutionize our efforts in combating the rust pathogen.
National Institute of Agricultural Botany, UK
Emerging and re-emerging diseases of humans, animals and plants pose a significant hazard to public health and food security. With recent advances in sequencing technology, bacteriologists and virologists are now integrating high-resolution genotypic data into pathogen surveillance activities. However, the application of genomics to emerging filamentous plant pathogens has lagged. To address this, we developed a robust and rapid “field pathogenomics” strategy. We applied this method in 2013 to the wheat yellow rust pathogen Puccinia striiformis f. sp. tritici (Pst), using gene sequencing of Pst-infected wheat leaves taken directly from the field to gain insight into the population structure of a re-emerging pathogen. Our analysis uncovered a dramatic shift in the Pst population in the UK and supports the hypothesis that recent introduction of a diverse set of exotic Pst lineages may have displaced the previous population. Gene sequencing of infected host tissue can also be leveraged to assess the genotype of the host, rapidly confirming whether previously resistant wheat varieties have indeed been overcome. We have now expanded this study to analyze Pst-infected plant samples from across Europe and beyond and will provide an update on the insights we have gained regarding Pst population dynamics. Working with cross-institutional and industrial partners we are now developing this technique further to reduce cost so it can be applied routinely within the U.K. cereal disease surveillance program.
The University of Sydney, Plant Breeding Institute, Australia
Stem rust is considered one of the most important threats to world cereal production. The appearance and spread of the wheat stem rust pathogen [Puccinia graminis f. sp. tritici (Pgt)] race Ug99 has caused great concern for global wheat production. Barley is a host to different specialized pathogen species such as Pgt, but is characteristically a near nonhost to most non-adapted (heterologous) rust pathogens such as the wheat leaf rust pathogen [P. triticina] and oat stem rust pathogen [P. graminis f. sp. avenae (Pga)]. The barley research line SusPtrit, developed for susceptibility to heterologous rust pathogens, is a useful resource to study the genetics of nonhost resistance and to clone the genes involved, particularly due to the recent availability of the genome sequence. Studies in wheat suggest that resistance genes that are effective against multiple rust pathogens (pleiotropic) such as Lr34/Yr18/Sr55, confer durable disease control. We intercrossed the sequenced barley genotype Morex with SusPtrit to determine the inheritance of resistance to the wheat leaf rust and oat stem rust pathogens. The F2 population segregated for a single dominant resistance gene in response to both heterologous pathogens Pga and Pt. Subsequent progeny testing and genetic analysis of the segregating F3 population will be performed to map and determine the relationship between the resistance genes. Large F2 populations were developed to fine map and clone the genes, and ultimately to transfer them into related crop species as an alternative approach for crop protection.
The University of Sydney, Plant Breeding Institute, Australia
Plants are generally non-hosts to most diseases. Barley is a host to Puccinia striiformis f. sp. hordei, but is a near non-host to P. striiformis f. sp. tritici (Pst) and to P. striiformis f. sp. pseudohordei (Psp), which cause stripe rust on wheat and barley grass (Hordeum murinum, H. leporinum), respectively. This study was carried out to determine the inheritance of resistance in barley line 81882/BS1 using the mapping population: 81882/BS1/Biosaline-19. 81882/BS1 is a H. vulgare derivative of cv. Vada
, carrying an introgression from H. bulbosum on chromosome 2HS, and Biosaline-19 is susceptible to both Pst and Psp. Phenotyping of F3 lines with Psp culture 981549 and Pst pathotype 134 E16 A+ showed that 81882/BS1 carried two genes for resistance to Psp, and three genes for resistance to Pst. Cytogenetic analysis and molecular mapping were performed to further characterize the resistance of 81882/BS1 to Psp. Joint phenotypic and cytogenetic analysis indicated that at least one of the genes for resistance to Psp was associated with the H. bulbosum introgression previously located on chromosome 2H (Zhang unpublished). Preliminary molecular mapping of 15 non-segregating resistant and 15 non-segregating susceptible lines using >10K DArTseq molecular markers located the second gene on chromosome 1H. This gene was probably contributed by Vada. Further studies are underway to confirm the locations of these two loci by fine mapping.
State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, P.R. China
Pst is highly variable, and new races that overcome newly released resistant cultivars are regular events. The widely virulent race V26 (virulent to Yr26) has a significant potential to cause epidemics in China. In this study teliospores from a single urediniospore isolate of V26 (No. Pinglan 17-7) produced on the Nanjing wheat line 92R137 (Yr26) were induced to germinate and infect Berberis shensiana as a sexual host. One hundred and eighteen single aeciospore (SA) selfed progeny and the V26 parent were typed for pathogenicity on a set of differentials comprising 22 Yrnear-isogenic wheat lines (NILs). Virulence phenotyping was conducted twice for all isolates, and similar results were obtained each time. The V26 isolate (No. Pinglan 17-7) was avirulent on differentials with Yr5, Yr6, Yr8, Yr15, Yr43, YrSp, YrTr1 and virulent on those with Yr1, Yr2, Yr4, Yr7, Yr9, Yr10, Yr17, Yr25, Yr26, Yr27, Yr28, Yr32, Yr44, YrV23, and YrExp2. The progeny were all virulent to Yr1, Yr2 (Kalyansona), Yr7, Yr9, Yr10, Yr17, Yr25, Yr26, YrV23 (Vilmorin 23) and YrExp2, and all avirulent to Yr5, Yr8, Yr15, and YrTr1, suggesting that V26 is homozygous at the corresponding pathogenicity loci. Various segregation ratios were apparent for other Yrgenes (P values ranging from 0.6to 0.09).These included3 avirulent: 1 virulent with respect to Yr6 and Yr43, 1 avirulent : 3 virulent forYr27 and Yr28, 1 avirulent : 15 virulent forYr4, Yr32, and Yr44,and 13 avirulent : 3 virulent for YrSp. Among the 118 progeny，27 of new pathotypes were identified as compared with the avirulence/virulence loci of the parent isolate. A study of the population based on markers and development of a molecular map is in progress.