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Germplasm Screening Using DNA Markers and Genome-Wide Association Study for the Identification of Powdery Mildew Resistance Loci in Tomato. Int J Mol Sci 2022; 23:ijms232113610. [DOI: 10.3390/ijms232113610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Powdery mildew (PM), caused by Oidium spp. in tomato, is a global concern that leads to diminished yield. We aimed to evaluate previously reported DNA markers linked to powdery mildew resistance (PMR) and identify novel quantitative trait loci (QTLs) for PMR through a genome-wide association study in tomato. Sequencing analysis of the internal transcribed spacer (ITS) of a PM strain (PNU_PM) isolated from Miryang, Gyeongnam, led to its identification as Oidium neolycopersici. Thereafter, a PM bioassay was conducted for a total of 295 tomato accessions, among which 24 accessions (4 S. lycopersicum accessions and 20 accessions of seven wild species) showed high levels of resistance to PNU_PM. Subsequently, we genotyped 11 markers previously linked to PMR in 56 accessions. PMR-specific banding patterns were detected in 15/22 PMR accessions, while no such bands were observed in the powdery mildew-susceptible accessions. The genome-wide association study was performed using TASSEL and GAPIT, based on the phenotypic data of 290 accessions and 11,912 single nucleotide polymorphisms (SNPs) obtained from the Axiom® Tomato SNP Chip Array. Nine significant SNPs in chromosomes 1, 4, 6, 8, and 12, were selected and five novel QTL regions distinct from previously known PMR-QTL regions were identified. Of these QTL regions, three putative candidate genes for PMR were selected from chromosomes 4 and 8, including two nucleotide binding site-leucine rich repeat class genes and a receptor-like kinase gene, all of which have been identified previously as causative genes for PMR in several crop species. The SNPs discovered in these genes provide useful information for understanding the molecular basis of PMR and developing DNA markers for marker-assisted selection of PMR in tomato.
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Sowa S, Sozoniuk M, Toporowska J, Kowalczyk K, Paczos-Grzęda E. Reference genes expression stability in Avena sativa L. during compatible and incompatible interactions with Puccinia graminis. Sci Rep 2022; 12:18369. [PMID: 36319744 PMCID: PMC9626582 DOI: 10.1038/s41598-022-22993-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
A reliable qPCR experiment requires the selection of reference genes with a stable level of expression in a given experimental system. This study attempts to determine the reference genes (RGs) for the A. sativa-P. graminis experimental setup. We evaluated nine candidate reference genes in A. sativa (oat line Pg4 and the cultivar Kasztan) during compatible and incompatible interactions with different pathotypes of Puccinia graminis f. sp. avenae in six time points post-inoculation. The identification of genes with high expression stability was performed by four algorithms (geNorm, NormFinder, BestKeeper and ΔCt method). We found that the most appropriate combination of RGs for RT-qPCR data normalization were HNR (heterogeneous nuclear ribonucleoprotein 27C) + EF1A (elongation factor 1-alpha) + EIF4A (eukaryotic initiation factor 4A-3). The worst candidates for normalization in this dataset were CYP (cyclophilin) and TUA (alpha tubulin). Identified reference genes are suitable candidates for the standardization of gene expression studies in the A. sativa-P. graminis interaction system and potentially other related pathogens. To date, this is the first report of RGs selection in this pathosystem.
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Affiliation(s)
- Sylwia Sowa
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Magdalena Sozoniuk
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Joanna Toporowska
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Krzysztof Kowalczyk
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Edyta Paczos-Grzęda
- grid.411201.70000 0000 8816 7059Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
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Park RF, Boshoff WHP, Cabral AL, Chong J, Martinelli JA, McMullen MS, Fetch JWM, Paczos-Grzęda E, Prats E, Roake J, Sowa S, Ziems L, Singh D. Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3709-3734. [PMID: 35665827 PMCID: PMC9729147 DOI: 10.1007/s00122-022-04121-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/01/2022] [Indexed: 05/05/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae (Pca), is a significant impediment to global oat production. Some 98 alleles at 92 loci conferring resistance to Pca in Avena have been designated; however, allelic relationships and chromosomal locations of many of these are unknown. Long-term monitoring of Pca in Australia, North America and elsewhere has shown that it is highly variable even in the absence of sexual recombination, likely due to large pathogen populations that cycle between wild oat communities and oat crops. Efforts to develop cultivars with genetic resistance to Pca began in the 1950s. Based almost solely on all all-stage resistance, this has had temporary benefits but very limited success. The inability to eradicate wild oats, and their common occurrence in many oat growing regions, means that future strategies to control Pca must be based on the assumption of a large and variable prevailing pathogen population with high evolutionary potential, even if cultivars with durable resistance are deployed and grown widely. The presence of minor gene, additive APR to Pca in hexaploid oat germplasm opens the possibility of pyramiding several such genes to give high levels of resistance. The recent availability of reference genomes for diploid and hexaploid oat will undoubtedly accelerate efforts to discover, characterise and develop high throughput diagnostic markers to introgress and pyramid resistance to Pca in high yielding adapted oat germplasm.
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Affiliation(s)
- R F Park
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia.
| | - W H P Boshoff
- Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - A L Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - J Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - J A Martinelli
- Department of Crop Science, Agronomy School, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves, 7712, Porto Alegre, RS, 91501-970, Brazil
| | - M S McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105-5051, USA
| | - J W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Canada
| | - E Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - E Prats
- CSIC-Institute for Sustainable Agriculture, Avda. Menéndez Pidal s/n. , 14004, Córdoba, Spain
| | - J Roake
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - S Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - L Ziems
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - D Singh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
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Admassu-Yimer B, Klos KE, Griffiths I, Cowan A, Howarth C. Mapping of Crown Rust ( Puccinia coronata f. sp. avenae) Resistance Gene Pc54 and a Novel Quantitative Trait Locus Effective Against Powdery Mildew ( Blumeria graminis f. sp. avenae) in the Oat ( Avena sativa) Line Pc54. PHYTOPATHOLOGY 2022; 112:1316-1322. [PMID: 34982574 DOI: 10.1094/phyto-10-21-0445-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The Pc54 oat line carries the crown rust resistance gene Pc54 and an unknown gene effective against powdery mildew. In this study, two recombinant inbred line (RIL) populations were developed to identify the genomic locations of the two genes and produce lists of molecular markers with a potential for marker-assisted selection. The RILs and parents were phenotyped for crown rust and powdery mildew in a controlled environment. They were also genotyped using the 6K Illumina Infinium iSelect oat single nucleotide polymorphism (SNP) chip. Multiple interval mapping placed Pc54 on the linkage group Mrg02 (chromosome 7D) and the novel powdery mildew quantitative trait locus (QTL) QPm.18 on Mrg18 (chromosome 1A) both in mapping and in the validating populations. A total of 9 and 31 significant molecular markers were identified linked with the Pc54 gene and QPm.18, respectively. Reactions to crown rust inoculations have justified separate identities of Pc54 from other genes and QTLs that have previously been reported on Mrg02 except for qPCRFd. Pm3 is the only powdery mildew resistance gene previously mapped on Mrg18. However, the pm3 differential line, Mostyn, was susceptible to the powdery mildew race used in this study, suggesting that Pm3 and QPm.18 are different genes. Determining the chromosomal locations of Pc54 and QPm.18 is helpful for better understanding of the molecular mechanism of resistance to crown rust and powdery mildew in oats. Furthermore, SNPs and single sequence repeats that are closely linked with the genes could be valuable for developing PCR-based molecular markers and facilitating the utilization of these genes in oat breeding programs.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Belayneh Admassu-Yimer
- Oak Ridge Institute for Science and Education Research Participant, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - Kathy Esvelt Klos
- United States Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - Irene Griffiths
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, United Kingdom
| | - Alexander Cowan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, United Kingdom
| | - Catherine Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, United Kingdom
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Yao E, Blake VC, Cooper L, Wight CP, Michel S, Cagirici HB, Lazo GR, Birkett CL, Waring DJ, Jannink JL, Holmes I, Waters AJ, Eickholt DP, Sen TZ. GrainGenes: a data-rich repository for small grains genetics and genomics. Database (Oxford) 2022; 2022:6591224. [PMID: 35616118 PMCID: PMC9216595 DOI: 10.1093/database/baac034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/01/2022] [Accepted: 04/26/2022] [Indexed: 05/16/2023]
Abstract
As one of the US Department of Agriculture-Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System (WheatIS). Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue (WGC). There are >4.8 million gene models in 51 genome browser assemblies, 6273 quantitative trait loci and >1.4 million genetic loci on 4756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley PanGenome projects have been created. We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository. Database URL:https://wheat.pw.usda.gov.
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Affiliation(s)
- Eric Yao
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
- Department of Bioengineering, University of California, Stanley Hall, Berkeley, CA 94720-1762, USA
| | - Victoria C Blake
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
- Department of Plant Sciences and Plant Pathology, Montana State University, 119 Plant Biosciences Building, Bozeman, MT 59717, USA
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, 1500 SW Jefferson Way, Corvallis, OR 97331, USA
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Steve Michel
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - H Busra Cagirici
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Gerard R Lazo
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Clay L Birkett
- United States Department of Agriculture—Agricultural Research Service, Robert Holley Center, 538 Tower Rd., Ithaca, NY 14853, USA
| | - David J Waring
- Section of Plant Breeding and Genetics, Cornell University, Bradfield Hall, 306 Tower Rd, Ithaca, NY 14853, USA
| | - Jean-Luc Jannink
- United States Department of Agriculture—Agricultural Research Service, Robert Holley Center, 538 Tower Rd., Ithaca, NY 14853, USA
- Section of Plant Breeding and Genetics, Cornell University, Bradfield Hall, 306 Tower Rd, Ithaca, NY 14853, USA
| | - Ian Holmes
- Department of Bioengineering, University of California, Stanley Hall, Berkeley, CA 94720-1762, USA
| | - Amanda J Waters
- PepsiCo R&D, 1991 Upper Buford Circle, 210 Borlaug Hall, St. Paul, MN 55108, USA
| | - David P Eickholt
- PepsiCo R&D, 1991 Upper Buford Circle, 210 Borlaug Hall, St. Paul, MN 55108, USA
| | - Taner Z Sen
- *Corresponding author: Tel: +1 (510) 559-5982; Fax: + 1 (510) 559-5963;
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You FM, Rashid KY, Zheng C, Khan N, Li P, Xiao J, He L, Yao Z, Cloutier S. Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax ( Linum usitatissimum L.). Int J Mol Sci 2022; 23:ijms23094960. [PMID: 35563347 PMCID: PMC9104541 DOI: 10.3390/ijms23094960] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/29/2022] Open
Abstract
Powdery mildew (PM), caused by the fungus Oidium lini in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (Pm1) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010–2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (R2 = 10–30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (r = 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (r = 0.93) than those constructed using the 247,160 genome-wide random SNP (r = 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4–5.6 Mb and 9.4–16.9 Mb) and 13 (4.7–5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.
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Affiliation(s)
- Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Nadeem Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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Genome-Wide Association Mapping of Crown and Brown Rust Resistance in Perennial Ryegrass. Genes (Basel) 2021; 13:genes13010020. [PMID: 35052360 PMCID: PMC8774571 DOI: 10.3390/genes13010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
A population of 239 perennial ryegrass (Lolium perenne L.) genotypes was analyzed to identify marker-trait associations for crown rust (Puccinia coronata f. sp. lolii) and brown rust (Puccinia graminis f. sp. loliina) resistance. Phenotypic data from field trials showed a low correlation (r = 0.17) between the two traits. Genotypes were resequenced, and a total of 14,538,978 SNPs were used to analyze population structure, linkage disequilibrium (LD), and for genome-wide association study. The SNP heritability (h2SNP) was 0.4 and 0.8 for crown and brown rust resistance, respectively. The high-density SNP dataset allowed us to estimate LD decay with the highest possible precision to date for perennial ryegrass. Results showed a low LD extension with a rapid decay of r2 value below 0.2 after 520 bp on average. Additionally, QTL regions for both traits were detected, as well as candidate genes by applying Genome Complex Trait Analysis and Multi-marker Analysis of GenoMic Annotation. Moreover, two significant genes, LpPc6 and LpPl6, were identified for crown and brown rust resistance, respectively, when SNPs were aggregated to the gene level. The two candidate genes encode proteins with phosphatase activity, which putatively can be induced by the host to perceive, amplify and transfer signals to downstream components, thus activating a plant defense response.
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Rio S, Gallego-Sánchez L, Montilla-Bascón G, Canales FJ, Isidro Y Sánchez J, Prats E. Genomic prediction and training set optimization in a structured Mediterranean oat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3595-3609. [PMID: 34341832 DOI: 10.1007/s00122-021-03916-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/13/2021] [Indexed: 05/22/2023]
Abstract
The strong genetic structure observed in Mediterranean oats affects the predictive ability of genomic prediction as well as the performance of training set optimization methods. In this study, we investigated the efficiency of genomic prediction and training set optimization in a highly structured population of cultivars and landraces of cultivated oat (Avena sativa) from the Mediterranean basin, including white (subsp. sativa) and red (subsp. byzantina) oats, genotyped using genotype-by-sequencing markers and evaluated for agronomic traits in Southern Spain. For most traits, the predictive abilities were moderate to high with little differences between models, except for biomass for which Bayes-B showed a substantial gain compared to other models. The consistency between the structure of the training population and the population to be predicted was key to the predictive ability of genomic predictions. The predictive ability of inter-subspecies predictions was indeed much lower than that of intra-subspecies predictions for all traits. Regarding training set optimization, the linear mixed model optimization criteria (prediction error variance (PEVmean) and coefficient of determination (CDmean)) performed better than the heuristic approach "partitioning around medoids," even under high population structure. The superiority of CDmean and PEVmean could be explained by their ability to adapt the representation of each genetic group according to those represented in the population to be predicted. These results represent an important step towards the implementation of genomic prediction in oat breeding programs and address important issues faced by the genomic prediction community regarding population structure and training set optimization.
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Affiliation(s)
- Simon Rio
- Centro de Biotecnologia y Genómica de Plantas (CBGP, UPM-INIA), Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
| | - Luis Gallego-Sánchez
- Institute for Sustainable Agriculture, Spanish Research Council (CSIC), Córdoba, Spain
| | | | - Francisco J Canales
- Institute for Sustainable Agriculture, Spanish Research Council (CSIC), Córdoba, Spain
| | - Julio Isidro Y Sánchez
- Centro de Biotecnologia y Genómica de Plantas (CBGP, UPM-INIA), Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Elena Prats
- Institute for Sustainable Agriculture, Spanish Research Council (CSIC), Córdoba, Spain
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Canales FJ, Montilla-Bascón G, Bekele WA, Howarth CJ, Langdon T, Rispail N, Tinker NA, Prats E. Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2063-2077. [PMID: 33770189 PMCID: PMC8263550 DOI: 10.1007/s00122-021-03805-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 05/03/2023]
Abstract
Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.
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Affiliation(s)
- F J Canales
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - G Montilla-Bascón
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - W A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - C J Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - T Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - N Rispail
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - N A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - E Prats
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain.
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10
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Canales FJ, Montilla-Bascón G, Bekele WA, Howarth CJ, Langdon T, Rispail N, Tinker NA, Prats E. Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2063-2077. [PMID: 33770189 DOI: 10.5061/dryad.0gb5mkm0g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 05/19/2023]
Abstract
Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.
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Affiliation(s)
- F J Canales
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - G Montilla-Bascón
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - W A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - C J Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - T Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - N Rispail
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - N A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - E Prats
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain.
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11
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Importance of Landraces in Cereal Breeding for Stress Tolerance. PLANTS 2021; 10:plants10071267. [PMID: 34206299 PMCID: PMC8309184 DOI: 10.3390/plants10071267] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022]
Abstract
The renewed focus on cereal landraces is a response to some negative consequences of modern agriculture and conventional breeding which led to a reduction of genetic diversity. Cereal landraces are still cultivated on marginal lands due to their adaptability to unfavourable conditions, constituting an important source of genetic diversity usable in modern plant breeding to improve the adaptation to abiotic or biotic stresses, yield performance and quality traits in limiting environments. Traditional agricultural production systems have played an important role in the evolution and conservation of wide variability in gene pools within species. Today, on-farm and ex situ conservation in gene bank collections, together with data sharing among researchers and breeders, will greatly benefit cereal improvement. Many efforts are usually made to collect, organize and phenotypically and genotypically analyse cereal landrace collections, which also utilize genomic approaches. Their use in breeding programs based on genomic selection, and the discovery of beneficial untapped QTL/genes/alleles which could be introgressed into modern varieties by MAS, pyramiding or biotechnological tools, increase the potential for their better deployment and exploitation in breeding for a more sustainable agricultural production, particularly enhancing adaptation and productivity in stress-prone environments to cope with current climate changes.
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12
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Huang CT, Klos KE, Huang YF. Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats. G3 (BETHESDA, MD.) 2020; 10:4489-4503. [PMID: 33028627 PMCID: PMC7718755 DOI: 10.1534/g3.120.401602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/02/2020] [Indexed: 12/29/2022]
Abstract
Seed vigor is crucial for crop early establishment in the field and is particularly important for forage crop production. Oat (Avena sativa L.) is a nutritious food crop and also a valuable forage crop. However, little is known about the genetics of seed vigor in oats. To investigate seed vigor-related traits and their genetic architecture in oats, we developed an easy-to-implement image-based phenotyping pipeline and applied it to 650 elite oat lines from the Collaborative Oat Research Enterprise (CORE). Root number, root surface area, and shoot length were measured in two replicates. Variables such as growth rate were derived. Using a genome-wide association (GWA) approach, we identified 34 and 16 unique loci associated with root traits and shoot traits, respectively, which corresponded to 41 and 16 unique SNPs at a false discovery rate < 0.1. Nine root-associated loci were organized into four sets of homeologous regions, while nine shoot-associated loci were organized into three sets of homeologous regions. The context sequences of five trait-associated markers matched to the sequences of rice, Brachypodium and maize (E-value < 10-10), including three markers matched to known gene models with potential involvement in seed vigor. These were a glucuronosyltransferase, a mitochondrial carrier protein domain containing protein, and an iron-sulfur cluster protein. This study presents the first GWA study on oat seed vigor and data of this study can provide guidelines and foundation for further investigations.
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Affiliation(s)
- Ching-Ting Huang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Kathy Esvelt Klos
- Small Grains and Potato Germplasm Research, USDA, ARS, Aberdeen, ID 83210
| | - Yung-Fen Huang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
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13
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Isidro-Sánchez J, D'Arcy Cusack K, Verheecke-Vaessen C, Kahla A, Bekele W, Doohan F, Magan N, Medina A. Genome-wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.). THE PLANT GENOME 2020; 13:e20023. [PMID: 33016604 DOI: 10.1002/tpg2.20023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
Fusarium langsethiae is a symptomless pathogen of oat panicles that produces T-2 and HT-2 mycotoxins, two of the most potent trichothecenes produced by Fusarium fungi in cereals. In the last few years, the levels of these mycotoxin in oat grain has increased and the European commission have already recommended a maximum level for of 1000 μg kg-1 for unprocessed oat for human consumption. The optimal and most sustainable way of combating infection and mycotoxin contamination is by releasing resistant oat varieties. Here the objective was to determine if we could identify any genomic loci associated with either the accumulation of F. langsethiae DNA or mycotoxins in the grain. In each of two years, field trials were conducted wherein 190 spring oat varieties were inoculated with a mixture of three isolate of the pathogen. Mycotoxins were quantified using liquid chromatography-tandem mass spectrometry. Varieties were genotyped using 16,863 genotyping by sequencing markers. Genome-wide association studies associated 5 SNPs in the linkage group Mr06 with T-2 + HT-2 mycotoxin accumulation. Markers were highly correlated, and a single QTL was identified. The marker avgbs_6K_95238.1 mapped within genes showing similarity to lipase, lipase-like or lipase precursor mRNA sequences and zinc-finger proteins. These regions have previously been shown to confer a significant increase in resistance to Fusarium species.
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Affiliation(s)
- Julio Isidro-Sánchez
- UCD Agriculture & Food Science, College of Health and Agriculture Science, University College Dublin, Belfield, Dublin, 4, Ireland
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Kane D'Arcy Cusack
- UCD Agriculture & Food Science, College of Health and Agriculture Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Carol Verheecke-Vaessen
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Amal Kahla
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Wubishet Bekele
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Fiona Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Naresh Magan
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Angel Medina
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
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14
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McNish IG, Zimmer CM, Susko AQ, Heuschele DJ, Tiede T, Case AJ, Smith KP. Mapping crown rust resistance at multiple time points in elite oat germplasm. THE PLANT GENOME 2020; 13:e20007. [PMID: 33016637 DOI: 10.1002/tpg2.20007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/22/2019] [Indexed: 06/11/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae Erikss., is the most important disease impacting cultivated oat (Avena sativa L.). Genetic resistance is the most desirable management strategy. The genetic architecture of crown rust resistance is not fully understood, and previous mapping investigations have mostly ignored temporal variation. A collection of elite oat lines sourced from oat breeding programs in the American Upper Midwest and Canada was genotyped using a high-density genotyping-by-sequencing system and evaluated for crown rust disease severity at multiple time points throughout the growing season in three disease nursery environments. Genome-wide association mapping was conducted for disease severity on each observation date of each trial, area under the disease progress curve for each trial, heading date for each trial, and area under the disease progress curve in a multi-environment model. Crown rust resistance quantitative trait loci (QTL) were detected on linkage groups Mrg05, Mrg12, Mrg15, Mrg18, Mrg20, and Mrg33. None of these QTL were coincident with a days-to-heading QTL detected on Mrg02. Only the QTL detected on Mrg15 was detected in multiple mapping models. The QTL on Mrg05, Mrg12, Mrg18, Mrg20, and Mrg33 were detected on only a single observation date and were not detected on observations just days before and after. This result uncovers the importance of temporal variation in mapping experiments which is usually ignored. It is possible that high density temporal data could be used to more precisely characterize the nature of plant resistance in other systems.
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Affiliation(s)
- Ian G McNish
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
| | - Cristiano M Zimmer
- Dep. of Crop Science, Federal Univ. of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alexander Q Susko
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
| | - D Jo Heuschele
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
| | | | | | - Kevin P Smith
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN, 55108
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15
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Yabe S, Iwata H. Genomics-assisted breeding in minor and pseudo-cereals. BREEDING SCIENCE 2020; 70:19-31. [PMID: 32351301 PMCID: PMC7180141 DOI: 10.1270/jsbbs.19100] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/22/2019] [Indexed: 05/20/2023]
Abstract
Minor and pseudo-cereals, which can grow with lower input and often produce specific nutrients compared to major cereal crops, are attracting worldwide attention. Since these crops generally have a large genetic diversity in a breeding population, rapid genetic improvement can be possible by the application of genomics-assisted breeding methods. In this review, we discuss studies related to biparental quantitative trait locus (QTL) mapping, genome-wide association study, and genomic selection for minor and pseudo-cereals. Especially, we focus on the current progress in a pseudo-cereal, buckwheat. Prospects for the practical utilization of genomics-assisted breeding in minor and pseudo-cereals are discussed including the issues to overcome especially for these crops.
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Affiliation(s)
- Shiori Yabe
- Institute of Crop Science, NARO, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657 Japan
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16
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Roy A, van Staden J. Insights into the riddles of codon usage patterns and codon context signatures in fungal genus
Puccinia
, a persistent threat to global agriculture. J Cell Biochem 2019; 120:19555-19566. [DOI: 10.1002/jcb.29263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Ayan Roy
- Research Centre for Plant Growth and Development School of Life Sciences, University of KwaZulu‐Natal Pietermaritzburg South Africa
| | - Johannes van Staden
- Research Centre for Plant Growth and Development School of Life Sciences, University of KwaZulu‐Natal Pietermaritzburg South Africa
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17
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Paczos-Grzęda E, Sowa S, Boczkowska M, Langdon T. Detached Leaf Assays for Resistance to Crown Rust Reveal Diversity Within Populations of Avena sterilis. PLANT DISEASE 2019; 103:832-840. [PMID: 30806576 DOI: 10.1094/pdis-06-18-1045-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Crown rust is the most widespread and damaging disease of oat (Avena species). Genetic resistance to the pathogen is the preferred method for crop protection but widespread deployment of limited numbers of major effect genes has promoted the rapid emergence and spread of pathogen races that are able to overcome these genes. Combining genes with even partial resistance may help develop durable cultivars that are less vulnerable to changes in pathogen virulence. Partial resistance is expected to be relatively common in populations of wild species where constant pathogen pressure encourages diversity in host resistance mechanisms, but it may be discarded in conventional screens for major gene resistance. Here, we used a detached leaf assay to detect resistance to the crown rust pathogen, Puccinia coronata Cda. f. sp. avenae, in previously uncharacterized collections of the hexaploid wild oat relative A. sterilis made by the Polish National Centre for Plant Genetic Resources. Many of the accessions were collected in Morocco, the center of diversity for the Avena genus. The detached leaf assessment allowed individual plants to be challenged with multiple pathotypes and their responses compared with 34 known differentials. Broad-spectrum resistance was identified within accession PL 51855, which behaved as a single major locus on crossing to three cultivars. The locus provided resistance to over 50 rust pathotypes, a greater range than seen for any of the known host resistance (Pc) genes. Strong resistance was identified in other accessions, and heterogeneity in response within accessions was common. Several accessions show multiple partial resistance responses that may be of value for developing durable resistance in cultivars. Because the sources of resistance in all but two differential lines were collected outside of Morocco, resistance in all accessions tested here are potentially novel. This study demonstrates that diversity within A. sterilis accessions collected in Morocco could be a very valuable source of resistance to crown rust, and it provides new germplasm for use in resistance breeding programs. Detached leaf assessment provides a valuable first step in the identification of promising candidates in complex gene bank accessions.
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Affiliation(s)
- Edyta Paczos-Grzęda
- 1 Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Sylwia Sowa
- 1 Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Maja Boczkowska
- 2 Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, 02-973 Warsaw, Poland
- 3 Plant Breeding and Acclimatization Institute, National Research Institute 05-870 Radzikow, Poland; and
| | - Tim Langdon
- 4 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3EE Aberystwyth, U.K
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18
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Nazareno ES, Li F, Smith M, Park RF, Kianian SF, Figueroa M. Puccinia coronata f. sp. avenae: a threat to global oat production. MOLECULAR PLANT PATHOLOGY 2018; 19:1047-1060. [PMID: 28846186 PMCID: PMC6638059 DOI: 10.1111/mpp.12608] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 05/20/2023]
Abstract
UNLABELLED Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. CONTROL Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/.
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Affiliation(s)
- Eric S. Nazareno
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Feng Li
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Madeleine Smith
- Department of Plant PathologyUniversity of Minnesota‐Northwest Research and Outreach CenterCrookstonMN 56716USA
| | - Robert F. Park
- Plant Breeding InstituteThe University of SydneyNarellanNSW2567Australia
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, US Department of Agriculture‐Agricultural Research ServiceSt. PaulMN 55108USA
| | - Melania Figueroa
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
- Stakman‐Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMN 55108USA
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19
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Rispail N, Montilla-Bascón G, Sánchez-Martín J, Flores F, Howarth C, Langdon T, Rubiales D, Prats E. Multi-Environmental Trials Reveal Genetic Plasticity of Oat Agronomic Traits Associated With Climate Variable Changes. FRONTIERS IN PLANT SCIENCE 2018; 9:1358. [PMID: 30283476 PMCID: PMC6156136 DOI: 10.3389/fpls.2018.01358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/28/2018] [Indexed: 05/06/2023]
Abstract
Although oat cultivation around the Mediterranean basin is steadily increasing, its yield in these regions lags far behind those of Northern Europe. This results mainly from the poor adaptation of current oat cultivars to Mediterranean environments. Local landraces may act as reservoirs of favorable traits that could contribute to increase oat resilience in this region. To aid selection of suitable agro-climate adapted genotypes we integrated genome-wide association approaches with analysis of field assessed phenotypes of genetic variants and of the weight of associated markers across different environmental variables. Association models accounting for oat population structure were applied on either arithmetic means or best linear unbiased prediction (BLUPs) to ensure robust identification of associations with the agronomic traits evaluated. The meta-analysis of the six joint environments (mega-environment) identified several markers associated with several agronomic traits and crown rust severity. Five of these associated markers were located within expressed genes. These associations were only mildly influenced by climatic variables indicating that these markers are good candidates to improve the genetic potential of oat under Mediterranean conditions. The models also highlighted several marker-trait associations, strongly affected by particular climatic variables including high rain pre- or post-heading dates and high temperatures, revealing strong potential for oat adaptation to specific agro-climatic conditions. These results will contribute to increase oat resilience for particular climatic conditions and facilitate breeding for plant adaptation to a wider range of climatic conditions in the current scenario of climate change.
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Affiliation(s)
| | | | | | - Fernando Flores
- ETSI La Rábida, University of Huelva, Palos de la Frontera, Spain
| | - Catherine Howarth
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | - Elena Prats
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
- *Correspondence: Elena Prats,
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20
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Klos KE, Yimer BA, Babiker EM, Beattie AD, Bonman JM, Carson ML, Chong J, Harrison SA, Ibrahim AMH, Kolb FL, McCartney CA, McMullen M, Fetch JM, Mohammadi M, Murphy JP, Tinker NA. Genome-Wide Association Mapping of Crown Rust Resistance in Oat Elite Germplasm. THE PLANT GENOME 2017; 10. [PMID: 28724060 DOI: 10.3835/plantgenome2016.10.0107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale. Overall, 29 SNPs on 12 linkage groups were predictive of crown rust reaction in at least one experiment at a genome-wide level of statistical significance. The QTL identified here include those in regions previously shown to be linked with seedling resistance genes , , , , , and and also with adult-plant resistance and adaptation-related QTL. In addition, QTL on linkage groups Mrg03, Mrg08, and Mrg23 were identified in regions not previously associated with crown rust resistance. Evaluation of marker genotypes in a set of crown rust differential lines supported as the identity of . The SNPs with rare alleles associated with lower disease scores may be suitable for use in marker-assisted selection of oat lines for crown rust resistance.
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21
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Zeng B, Yan H, Liu X, Zang W, Zhang A, Zhou S, Huang L, Liu J. Genome-wide association study of rust traits in orchardgrass using SLAF-seq technology. Hereditas 2017; 154:5. [PMID: 28250720 PMCID: PMC5322626 DOI: 10.1186/s41065-017-0027-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 01/24/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND While orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass. RESULTS In this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs. ADMIXTURE analysis revealed unstructured subpopulations for 33 accessions, indicating that this orchardgrass population could be used for association analysis. Linkage disequilibrium (LD) analysis revealed an average r2 of 0.4 across all SNP pairs, indicating a high extent of LD in these samples. Through GWAS, a total of 4,604 SNPs were found to be significantly (P < 0.01) associated with the rust trait. The bulk analysis discovered a number of 5,211 SNPs related to rust trait. Two candidate genes, including cytochrome P450, and prolamin were implicated in disease resistance through prediction of functional genes surrounding each high-quality SNP (P < 0.01) associated with rust traits based on GWAS analysis and bulk analysis. CONCLUSIONS The large number of SNPs associated with rust traits and these two candidate genes may provide the basis for further research on rust resistance mechanisms and marker-assisted selection (MAS) for rust-resistant lineages.
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Affiliation(s)
- Bing Zeng
- Department of Animal Science, Southwest University, Rongchang, Chongqing, 402460 China
| | - Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xinchun Liu
- Agricultural College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wenjing Zang
- College of Life Science, China West Normal University, Nanchong, 637009 China
| | - Ailing Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Sifan Zhou
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jinping Liu
- College of Life Science, China West Normal University, Nanchong, 637009 China
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22
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Abstract
Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for sampling genome-wide genetic variation, performing genome-wide association mapping, and conducting genomic selection. It is a combined one-step process of SNP marker discovery and genotyping through genome reduction with restriction enzymes and SNP calling with or without a sequenced genome. This approach has the advantage of being rapid, high throughput, cost effective, and applicable to organisms without sequenced genomes. It has been increasingly applied to generate SNP genotype data for plant genetic and genomic studies. To facilitate a wider GBS application, particularly in oat genetic and genomic research, we describe the GBS approach, review the current applications of GBS in plant species, and highlight some applications of GBS to oat research. We also discuss issues in various applications of GBS and provide some perspectives in GBS research. Recent developments of bioinformatics pipelines in high-quality SNP discovery for polyploid crops will enhance the application of GBS to oat genetic and genomic research.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
| | - Mo-Hua Yang
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
- College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
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23
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Sánchez-Martín J, Montilla-Bascón G, Mur LAJ, Rubiales D, Prats E. Compromised Photosynthetic Electron Flow and H 2O 2 Generation Correlate with Genotype-Specific Stomatal Dysfunctions during Resistance against Powdery Mildew in Oats. FRONTIERS IN PLANT SCIENCE 2016; 7:1660. [PMID: 27877184 PMCID: PMC5099169 DOI: 10.3389/fpls.2016.01660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/21/2016] [Indexed: 06/06/2023]
Abstract
Stomatal dysfunction known as "locking" has been linked to the elicitation of a hypersensitive response (HR) following attack of fungal pathogens in cereals. We here assess how spatial and temporal patterns of different resistance mechanisms, such as HR and penetration resistance influence stomatal and photosynthetic parameters in oat (Avena sativa) and the possible involvement of hydrogen peroxide (H2O2) in the dysfunctions observed. Four oat cultivars with differential resistance responses (i.e., penetration resistance, early and late HR) to powdery mildew (Blumeria graminis f. sp. avenae, Bga) were used. Results demonstrated that stomatal dysfunctions were genotype but not response-type dependent since genotypes with similar resistance responses when assessed histologically showed very different locking patterns. Maximum quantum yield (Fv/Fm) of photosystem II were compromised in most Bga-oat interactions and photoinhibition increased. However, the extent of the photosynthetic alterations was not directly related to the extent of HR. H2O2 generation is triggered during the execution of resistance responses and can influence stomatal function. Artificially increasing H2O2 by exposing plants to increased light intensity further reduced Fv/Fm ratios and augmented the patterns of stomatal dysfunctions previously observed. The latter results suggest that the observed dysfunctions and hence a cost of resistance may be linked with oxidative stress occurring during defense induced photosynthetic disruption.
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Affiliation(s)
- Javier Sánchez-Martín
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC)Córdoba, Spain
| | - Gracia Montilla-Bascón
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC)Córdoba, Spain
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC)Córdoba, Spain
| | - Elena Prats
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC)Córdoba, Spain
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24
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A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus. Sci Rep 2016; 6:36452. [PMID: 27811979 PMCID: PMC5095561 DOI: 10.1038/srep36452] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/14/2016] [Indexed: 01/02/2023] Open
Abstract
Harvest index (HI), the ratio of seed mass to total biomass of the aboveground plant parts, is an important trait for harvestable yield of crops. Unfortunately, HI of Brassica napus is lower than that of other economically important crops. To identify candidate genes associated with high HI, a genome-wide association study of HI and four HI-related traits was conducted with 520 B. napus accessions cultivated in both Yunnan and Chongqing. We detected 294 single nucleotide polymorphisms significantly associated with the abovementioned traits, including 79 SNPs that affected two or more traits. Differentially expressed genes between extremely high- and low-HI accessions were identified in 8 tissues at two cultivated regions. Combination of linkage disequilibrium and transcriptome analyses revealed 33 functional candidate genes located within the confidence intervals of significant SNPs associated with more than one trait, such as SHOOT GRAVITROPISM 5 (Bna.SGR5), ATP-CITRATE LYASE A-3 (Bna.ACLA-3) and CAROTENOID CLEAVAGE DIOXYGENASE 1 (Bna.CCD1), their orthologs in the Arabidopsis thaliana have been shown to play key roles in photosynthesis, inflorescence, and silique development. Our results provide insight into the molecular mechanisms underlying establishment of high-HI B. napus and lay a foundation for characterization of candidate genes aimed at developing high-HI B. napus varieties.
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25
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Tumino G, Voorrips RE, Rizza F, Badeck FW, Morcia C, Ghizzoni R, Germeier CU, Paulo MJ, Terzi V, Smulders MJM. Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1711-24. [PMID: 27318699 PMCID: PMC4983288 DOI: 10.1007/s00122-016-2734-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/21/2016] [Indexed: 05/19/2023]
Abstract
Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option. Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward's clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits.
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Affiliation(s)
- Giorgio Tumino
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
| | - Roeland E Voorrips
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Fulvia Rizza
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Franz W Badeck
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Caterina Morcia
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Roberta Ghizzoni
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Christoph U Germeier
- Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, 06484, Quedlinburg, Germany
| | - Maria-João Paulo
- Biometris, Wageningen UR, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Valeria Terzi
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Marinus J M Smulders
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
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26
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Association Mapping in Turkish Olive Cultivars Revealed Significant Markers Related to Some Important Agronomic Traits. Biochem Genet 2016; 54:506-533. [PMID: 27209034 DOI: 10.1007/s10528-016-9738-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
Olive (Olea europaea L.) is one of the most important fruit trees especially in the Mediterranean countries due to high consumption of table olive and olive oil. In olive breeding, the phenotypic traits associated to fruit are the key factors that determine productivity. Association mapping has been used in some tree species and a lot of crop plant species, and here, we perform an initial effort to detect marker-trait associations in olive tree. In the current study, a total of 96 olive genotypes, including both oil and table olive genotypes from Turkish Olive GenBank Resources, were used to examine marker-trait associations. For olive genotyping, SNP, AFLP, and SSR marker data were selected from previously published study and association analysis was performed between these markers and 5 yield-related traits. Three different approaches were used to check for false-positive results in association tests, and association results obtained from these models were compared. Using the model utilizing both population structure and relative kinship, eleven associations were significant with FDR ≤ 0.05. The largest number of significant associations was detected for fruit weight and stone weight. Our results suggested that association mapping could be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations. This study shows for the first time the use of association mapping for identifying molecular markers linked to important traits in olive tree.
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27
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Zhang J, Mason AS, Wu J, Liu S, Zhang X, Luo T, Redden R, Batley J, Hu L, Yan G. Identification of Putative Candidate Genes for Water Stress Tolerance in Canola (Brassica napus). FRONTIERS IN PLANT SCIENCE 2015; 6:1058. [PMID: 26640475 PMCID: PMC4661274 DOI: 10.3389/fpls.2015.01058] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/13/2015] [Indexed: 05/20/2023]
Abstract
Drought stress can directly inhibit seedling establishment in canola (Brassica napus), resulting in lower plant densities and reduced yields. To dissect this complex trait, 140 B. napus accessions were phenotyped under normal (0.0 MPa, S0) and water-stressed conditions simulated by polyethylene glycol (PEG) 6000 (-0.5 MPa, S5) in a hydroponic system. Phenotypic variation and heritability indicated that the root to shoot length ratio was a reliable indicator for water stress tolerance. Thereafter, 66 accessions (16 water stress tolerant, 34 moderate and 16 sensitive lines) were genotyped using 25,495 Brassica single nucleotide polymorphisms (SNPs). Genome-wide association studies (GWAS) identified 16 loci significantly associated with water stress response. Two B. napus accessions were used for RNA sequencing, with differentially-expressed genes under normal and water-stressed conditions examined. By combining differentially-expressed genes detected by RNA sequencing with significantly associated loci from GWAS, 79 candidate genes were identified, of which eight were putatively associated with drought tolerance based on gene ontology of Arabidopsis. Functional validation of these genes may confirm key drought-related genes for selection and breeding in B. napus. Our results provide insight into the genetic basis of water stress tolerance in canola.
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Affiliation(s)
- Jing Zhang
- Ministry of Agriculture (MOA) Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Annaliese S. Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of QueenslandBrisbane, QLD, Australia
| | - Jian Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Sheng Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xuechen Zhang
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Tao Luo
- Ministry of Agriculture (MOA) Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Robert Redden
- Australian Grains Genebank, Department of Economic Development Jobs Transport and ResourcesHorsham, VIC, Australia
| | - Jacqueline Batley
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of QueenslandBrisbane, QLD, Australia
| | - Liyong Hu
- Ministry of Agriculture (MOA) Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Liyong Hu
| | - Guijun Yan
- Centre for Plant Genetics and Breeding, School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
- Guijun Yan
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