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Hautsalo J, Novakazi F, Jalli M, Göransson M, Manninen O, Isolahti M, Reitan L, Bergersen S, Krusell L, Damsgård Robertsen C, Orabi J, Due Jensen J, Jahoor A, Bengtsson T. Pyramiding of scald resistance genes in four spring barley MAGIC populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3829-3843. [PMID: 34350474 PMCID: PMC8580920 DOI: 10.1007/s00122-021-03930-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Genome-Wide Association Studies (GWAS) of four Multi-parent Advanced Generation Inter-Cross (MAGIC) populations identified nine regions on chromosomes 1H, 3H, 4H, 5H, 6H and 7H associated with resistance against barley scald disease. Three of these regions are putatively novel resistance Quantitative Trait Loci (QTL). Barley scald is caused by Rhynchosporium commune, one of the most important barley leaf diseases that are prevalent in most barley-growing regions. Up to 40% yield losses can occur in susceptible barley cultivars. Four MAGIC populations were generated in a Nordic Public-Private Pre-breeding of spring barley project (PPP Barley) to introduce resistance to several important diseases. Here, these MAGIC populations consisting of six to eight founders each were tested for scald resistance in field trials in Finland and Iceland. Eight different model covariate combinations were compared for GWAS studies, and the models that deviated the least from the expected p-values were selected. For all QTL, candidate genes were identified that are predicted to be involved in pathogen defence. The MAGIC progenies contained new haplotypes of significant SNP-markers with high resistance levels. The lines with successfully pyramided resistance against scald and mildew and the significant markers are now distributed among Nordic plant breeders and will benefit development of disease-resistant cultivars.
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Affiliation(s)
- Juho Hautsalo
- Natural Resources Institute Finland (Luke), Survontie 9, 40500, Jyväskylä, Finland
| | - Fluturë Novakazi
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22, Lomma, Sweden
| | - Marja Jalli
- Natural Resources Institute Finland (Luke), Tietotie 4, 31600, Jokioinen, Finland
| | - Magnus Göransson
- Faculty of Land and Animal Resources, The Agricultural University of Iceland, Hvanneyri, 311, Borgarnes, Iceland
| | - Outi Manninen
- Boreal Plant Breeding Ltd., Myllytie 10, 31600, Jokioinen, Norway
| | - Mika Isolahti
- Boreal Plant Breeding Ltd., Myllytie 10, 31600, Jokioinen, Norway
| | - Lars Reitan
- Graminor Ltd. Hommelstadvegen 60, 2322, Ridabu, Norway
| | | | - Lene Krusell
- Sejet Plant Breeding, Nørremarksvej 67, 8700, Horsens, Norway
| | | | - Jihad Orabi
- Nordic Seed A/S, Kornmarken 1, 8464, Galten, Denmark
| | | | - Ahmed Jahoor
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22, Lomma, Sweden
- Nordic Seed A/S, Kornmarken 1, 8464, Galten, Denmark
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22, Lomma, Sweden.
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Kushwaha SK, Åhman I, Bengtsson T. ResCap: plant resistance gene prediction and probe generation pipeline for resistance gene sequence capture. BIOINFORMATICS ADVANCES 2021; 1:vbab033. [PMID: 36700100 PMCID: PMC9710708 DOI: 10.1093/bioadv/vbab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/15/2021] [Accepted: 11/07/2021] [Indexed: 01/28/2023]
Abstract
Summary The discovery of novel resistance genes (R-genes) is an important component in disease resistance breeding. Nevertheless, R-gene identification from wild species and close relatives of plants is not only a difficult but also a cumbersome process. In this study, ResCap, a support vector machine-based high-throughput R-gene prediction and probe generation pipeline has been developed to generate probes from genomic datasets. ResCap contains two integral modules. The first module identifies the R-genes and R-gene like sequences under four categories containing different domains such as TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), Receptor-like kinase (RLK) and Receptor-like proteins (RLPs). The second module generates probes from extracted nucleotide sequences of resistance genes to conduct sequence capture (SeqCap) experiments. For the validation of ResCap pipeline, ResCap generated probes were synthesized and a sequence capture experiment was performed to capture expressed resistance genes among six spring barley genotypes. The developed ResCap pipeline in combination with the performed sequence capture experiment has shown to increase precision of R-gene identification while simultaneously allowing rapid gene validation including non-sequenced plants. Availability and implementation The ResCap pipeline is available at http://rescap.ltj.slu.se/ResCap/. Contact sandeep.kushwaha@slu.se or sandeep@niab.org.in. Supplementary information Supplementary materials are available at Bioinformatics Advances online.
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Affiliation(s)
- Sandeep K Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden,Bioinformatics, National Institute of Animal Biotechnology, Hyderabad 500 032, India,To whom correspondence should be addressed.
| | - Inger Åhman
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden
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Tuvesson SD, Larsson CT, Ordon F. Use of Molecular Markers for Doubled Haploid Technology: From Academia to Plant Breeding Companies. Methods Mol Biol 2021; 2288:49-72. [PMID: 34270004 DOI: 10.1007/978-1-0716-1335-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) ( https://Lantmannen.com ) using large-scale genotyping for variety development based on SSRs and SNPs.
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Affiliation(s)
| | | | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
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Novakazi F, Krusell L, Jensen JD, Orabi J, Jahoor A, Bengtsson T. You Had Me at "MAGIC"!: Four Barley MAGIC Populations Reveal Novel Resistance QTL for Powdery Mildew. Genes (Basel) 2020; 11:genes11121512. [PMID: 33352820 PMCID: PMC7766815 DOI: 10.3390/genes11121512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 11/23/2022] Open
Abstract
Blumeria graminis f. sp. hordei (Bgh), the causal agent of barley powdery mildew (PM), is one of the most important barley leaf diseases and is prevalent in most barley growing regions. Infection decreases grain quality and yields on average by 30%. Multi-parent advanced generation inter-cross (MAGIC) populations combine the advantages of bi-parental and association panels and offer the opportunity to incorporate exotic alleles into adapted material. Here, four barley MAGIC populations consisting of six to eight founders were tested for PM resistance in field trials in Denmark. Principle component and STRUCTURE analysis showed the populations were unstructured and genome-wide linkage disequilibrium (LD) decay varied between 14 and 38 Mbp. Genome-wide association studies (GWAS) identified 11 regions associated with PM resistance located on chromosomes 1H, 2H, 3H, 4H, 5H and 7H, of which three regions are putatively novel resistance quantitative trait locus/loci (QTL). For all regions high-confidence candidate genes were identified that are predicted to be involved in pathogen defense. Haplotype analysis of the significant SNPs revealed new allele combinations not present in the founders and associated with high resistance levels.
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Affiliation(s)
- Fluturë Novakazi
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (F.N.); (A.J.)
| | - Lene Krusell
- Sejet Plant Breeding, Nørremarksvej 67, 8700 Horsens, Denmark;
| | - Jens Due Jensen
- Nordic Seed A/S, Kornmarken 1, 8464 Galten, Denmark; (J.D.J.); (J.O.)
| | - Jihad Orabi
- Nordic Seed A/S, Kornmarken 1, 8464 Galten, Denmark; (J.D.J.); (J.O.)
| | - Ahmed Jahoor
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (F.N.); (A.J.)
- Nordic Seed A/S, Kornmarken 1, 8464 Galten, Denmark; (J.D.J.); (J.O.)
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053 Alnarp, Sweden; (F.N.); (A.J.)
- Correspondence:
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Kim SY, Bengtsson T, Olsson N, Hot V, Zhu LH, Åhman I. Mutations in Two Aphid-Regulated β-1,3-Glucanase Genes by CRISPR/Cas9 Do Not Increase Barley Resistance to Rhopalosiphum padi L. FRONTIERS IN PLANT SCIENCE 2020; 11:1043. [PMID: 32754185 PMCID: PMC7381296 DOI: 10.3389/fpls.2020.01043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/24/2020] [Indexed: 05/08/2023]
Abstract
Callose deposition is induced in plants by various stress factors such as when plants are attacked by herbivores and pathogens. In the case of aphids, callose plugging of aphid-damaged phloem sieve tubes is expected to reduce aphid access to the phloem sap, while aphid-induced upregulation of callose-degrading β-1,3-glucanase genes in the host plant might counteract this negative effect on aphid performance. We have tested this hypothesis with barley mutants in which one or both of two β-1,3-glucanase genes (1636 and 1639) have been mutated by CRISPR/Cas9 technique in cv. Golden Promise. These two genes were previously found to be upregulated by the cereal pest Rhopalosiphum padi L. in susceptible barley genotypes. Four 1636/1639 double mutant, three 1636 single mutant and two 1639 single mutant lines were tested for aphid resistance along with control lines. All mutant lines had single base insertions, causing frame shifts and premature stop codons. Three of the four double mutant lines showed significantly reduced β-1,3-glucanase activity, and bacterial flagellin-induction resulted in significantly more callose formation in the leaves of double mutant compared to control and single mutant lines. However, we found no effect of these modified plant traits on barley resistance to R. padi. Both genes were confirmed to be upregulated by R. padi in Golden Promise. The gene 1637 is another β-1,3-glucanase gene known to be upregulated by R. padi in barley and was here found to be higher expressed in a double mutant line when compared with a control line. If this can compensate for the general reduction of β-1,3-glucanase activity in the double mutants is difficult to discern since phloem concentrations of these proteins are unknown.
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Affiliation(s)
| | | | | | | | - Li-Hua Zhu
- *Correspondence: Li-Hua Zhu, ; Inger Åhman,
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