84 results on '"Steuernagel B"'
Search Results
2. A complex receptor locus confers responsiveness to necrosis and ethylene-inducing like peptides in Brassica napus
- Author
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Universidad de Sevilla. Departamento de Microbiología, UK Research & Innovation (UKRI), Biotechnology and Biological Sciences Research Council (BBSRC), Yalcin, HA., Jacott, Catherine N., Ramírez-González, R, Steuernagel, B, Sidhu, GS, Kirby, R., Verbeek, E., Schoonbeek, HJ., Ridout, CJ., Wells, R., Universidad de Sevilla. Departamento de Microbiología, UK Research & Innovation (UKRI), Biotechnology and Biological Sciences Research Council (BBSRC), Yalcin, HA., Jacott, Catherine N., Ramírez-González, R, Steuernagel, B, Sidhu, GS, Kirby, R., Verbeek, E., Schoonbeek, HJ., Ridout, CJ., and Wells, R.
- Abstract
Brassica crops are susceptible to diseases which can be mitigated by breeding for resistance. MAMPs (microbe-associated molecular patterns) are conserved molecules of pathogens that elicit host defences known as pattern-triggered immunity (PTI). Necrosis and Ethylene-inducing peptide 1-like proteins (NLPs) are MAMPs found in a wide range of phytopathogens. We studied the response to BcNEP2, a representative NLP from Botrytis cinerea, and showed that it contributes to disease resistance in Brassica napus. To map regions conferring NLP response, we used the production of reactive oxygen species (ROS) induced during PTI across a population of diverse B. napus accessions for associative transcriptomics (AT), and bulk segregant analysis (BSA) on DNA pools created from a cross of NLP-responsive and non-responsive lines. In silico mapping with AT identified two peaks for NLP responsiveness on chromosomes A04 and C05 whereas the BSA identified one peak on A04. BSA delimited the region for NLP-responsiveness to 3 Mbp, containing 245 genes on the Darmor-bzh reference genome and four co-segregating KASP markers were identified. The same pipeline with the ZS11 genome confirmed the highest-associated region on chromosome A04. Comparative BLAST analysis revealed unannotated clusters of receptor-like protein (RLP) homologues on ZS11 chromosome A04. However, no specific RLP homologue conferring NLP response could be identified. Our results also suggest that BR-SIGNALLING KINASE1 may be involved with modulating the NLP response. Overall, we demonstrate that responsiveness to NLP contributes to disease resistance in B. napus and define the associated genomic location. These results can have practical application in crop improvement.
- Published
- 2024
3. Shifting the limits in wheat research and breeding using a fully annotated reference genome
- Author
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Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., Pozniak, C.J., Choulet, F., Distelfeld, A., Poland, J., Ronen, G., Barad, O., Baruch, K., Keeble-Gagnère, G., Mascher, M., Sharpe, A.G., Ben-Zvi, G., Josselin, A-A, Himmelbach, A., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Koh, C., Muehlbauer, G., Pasam, R.K., Paux, E., Rigault, P., Tibbits, J., Tiwari, V., Spannagl, M., Lang, D., Gundlach, H., Haberer, G., Mayer, K.F.X., Ormanbekova, D., Prade, V., Šimková, H., Wicker, T., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Kaithakottil, G., Keilwagen, J., Leroy, P., Lux, T., Twardziok, S., Venturini, L., Juhász, A., Abrouk, M., Fischer, I., Uauy, C., Borrill, P., Ramirez-Gonzalez, R.H., Arnaud, D., Chalabi, S., Chalhoub, B., Cory, A., Datla, R., Davey, M.W., Jacobs, J., Robinson, S.J., Steuernagel, B., van Ex, F., Wulff, B.B.H., Benhamed, M., Bendahmane, A., Concia, L., Latrasse, D., Alaux, M., Bartoš, J., Bellec, A., Berges, H., Doležel, J., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O-A, Singh, K., Valárik, M., van der Vossen, E., Vautrin, S., Weining, S., Fahima, T., Glikson, V., Raats, D., Číhalíková, J., Toegelová, H., Vrána, J., Sourdille, P., Darrier, B., Barabaschi, D., Cattivelli, L., Hernandez, P., Galvez, S., Budak, H., Jones, J.D.G., Witek, K., Yu, G., Small, I., Melonek, J., Zhou, R., Belova, T., Kanyuka, K., King, R., Nilsen, K., Walkowiak, S., Cuthbert, R., Knox, R., Wiebe, K., Xiang, D., Rohde, A., Gold, T., Čížková, J., Akpinar, B.A., Biyiklioglu, S., Gao, L., N’Daiye, A., Kubaláková, M., Šafář, J., Alfama, F., Adam-Blondon, A-F, Flores, R., Guerche, C., Loaec, M., Quesneville, H., Condie, J., Ens, J., Koh, C.S., Maclachlan, R., Tan, Y., Alberti, A., Aury, J-M, Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., Kaur, G., Luo, M., Sehgal, S., Chhuneja, P., Gupta, O.P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., Singh, N.K., Khurana, J.P., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R.S., Holušová, K., Plíhal, O., Clark, M.D., Heavens, D., Kettleborough, G., Wright, J., Balcárková, B., Hu, Y., Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., Cattonaro, F., Jiumeng, M., Kugler, K.G., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., Batley, J., Bayer, P.E., Edwards, D., Hayashi, S., Tulpová, Z., Visendi, P., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., Pozniak, C.J., Choulet, F., Distelfeld, A., Poland, J., Ronen, G., Barad, O., Baruch, K., Keeble-Gagnère, G., Mascher, M., Sharpe, A.G., Ben-Zvi, G., Josselin, A-A, Himmelbach, A., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Koh, C., Muehlbauer, G., Pasam, R.K., Paux, E., Rigault, P., Tibbits, J., Tiwari, V., Spannagl, M., Lang, D., Gundlach, H., Haberer, G., Mayer, K.F.X., Ormanbekova, D., Prade, V., Šimková, H., Wicker, T., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Kaithakottil, G., Keilwagen, J., Leroy, P., Lux, T., Twardziok, S., Venturini, L., Juhász, A., Abrouk, M., Fischer, I., Uauy, C., Borrill, P., Ramirez-Gonzalez, R.H., Arnaud, D., Chalabi, S., Chalhoub, B., Cory, A., Datla, R., Davey, M.W., Jacobs, J., Robinson, S.J., Steuernagel, B., van Ex, F., Wulff, B.B.H., Benhamed, M., Bendahmane, A., Concia, L., Latrasse, D., Alaux, M., Bartoš, J., Bellec, A., Berges, H., Doležel, J., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O-A, Singh, K., Valárik, M., van der Vossen, E., Vautrin, S., Weining, S., Fahima, T., Glikson, V., Raats, D., Číhalíková, J., Toegelová, H., Vrána, J., Sourdille, P., Darrier, B., Barabaschi, D., Cattivelli, L., Hernandez, P., Galvez, S., Budak, H., Jones, J.D.G., Witek, K., Yu, G., Small, I., Melonek, J., Zhou, R., Belova, T., Kanyuka, K., King, R., Nilsen, K., Walkowiak, S., Cuthbert, R., Knox, R., Wiebe, K., Xiang, D., Rohde, A., Gold, T., Čížková, J., Akpinar, B.A., Biyiklioglu, S., Gao, L., N’Daiye, A., Kubaláková, M., Šafář, J., Alfama, F., Adam-Blondon, A-F, Flores, R., Guerche, C., Loaec, M., Quesneville, H., Condie, J., Ens, J., Koh, C.S., Maclachlan, R., Tan, Y., Alberti, A., Aury, J-M, Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., Kaur, G., Luo, M., Sehgal, S., Chhuneja, P., Gupta, O.P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., Singh, N.K., Khurana, J.P., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R.S., Holušová, K., Plíhal, O., Clark, M.D., Heavens, D., Kettleborough, G., Wright, J., Balcárková, B., Hu, Y., Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., Cattonaro, F., Jiumeng, M., Kugler, K.G., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., Batley, J., Bayer, P.E., Edwards, D., Hayashi, S., Tulpová, Z., Visendi, P., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., and Wang, L.
- Abstract
Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.
- Published
- 2018
4. The transcriptional landscape of polyploid wheat
- Author
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Ramirez-Gonzalez, R.H., Borrill, P., Lang, D., Harrington, S.A., Brinton, J., Venturini, L., Davey, M., Jacobs, J., van Ex, F., Pasha, A., Khedikar, Y., Robinson, S.J., Cory, A.T., Florio, T., Concia, L., Juery, C., Schoonbeek, H., Steuernagel, B., Xiang, D., Ridout, C.J., Chalhoub, B., Mayer, K.F.X., Benhamed, M., Latrasse, D., Bendahmane, A., Wulff, B.B.H., Appels, R., Tiwari, V., Datla, R., Choulet, F., Pozniak, C.J., Provart, N.J., Sharpe, A.G., Paux, E., Spannagl, M., Bräutigam, A., Uauy, C., Ramirez-Gonzalez, R.H., Borrill, P., Lang, D., Harrington, S.A., Brinton, J., Venturini, L., Davey, M., Jacobs, J., van Ex, F., Pasha, A., Khedikar, Y., Robinson, S.J., Cory, A.T., Florio, T., Concia, L., Juery, C., Schoonbeek, H., Steuernagel, B., Xiang, D., Ridout, C.J., Chalhoub, B., Mayer, K.F.X., Benhamed, M., Latrasse, D., Bendahmane, A., Wulff, B.B.H., Appels, R., Tiwari, V., Datla, R., Choulet, F., Pozniak, C.J., Provart, N.J., Sharpe, A.G., Paux, E., Spannagl, M., Bräutigam, A., and Uauy, C.
- Abstract
Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.
- Published
- 2018
5. A physical, genetic and functional sequence assembly of the barley genome
- Author
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Mayer, Kf, Waugh, R, Langridge, P, Close, Tj, Wise, Rp, Graner, A, Matsumoto, T, Sato, K, Schulman, A, Muehlbauer, Gj, Stein, N, Ariyadasa, R, Schulte, D, Poursarebani, N, Zhou, R, Steuernagel, B, Mascher, M, Scholz, U, Shi, B, Madishetty, K, Svensson, Jt, Bhat, P, Moscou, M, Resnik, J, Hedley, P, Liu, H, Morris, J, Frenkel, Z, Korol, A, Bergès, H, Taudien, S, Felder, M, Groth, M, Platzer, M, Himmelbach, A, Lonardi, S, Duma, D, Alpert, M, Cordero, Francesca, Beccuti, Marco, Ciardo, G, Ma, Y, Wanamaker, S, Cattonaro, F, Vendramin, V, Scalabrin, S, Radovic, S, Wing, R, Morgante, M, Nussbaumer, T, Gundlach, H, Martis, M, Poland, J, Spannagl, M, Pfeifer, M, Moisy, C, Tanskanen, J, Zuccolo, A, Russell, J, Druka, A, Marshall, D, Bayer, M, Swarbreck, D, Sampath, D, Ayling, S, Febrer, M, Caccamo, M, Tanaka, T, Wannamaker, S, Schmutzer, T, Brown, Jw, Fincher, Gb, Stein, N., MIPS/IBIS, Helmholtz-Zentrum München (HZM), The James Hutton Institute, University of Adelaide, Iowa State University (ISU), Leibniz Institute of Plant Genetics and Crop Plant Research, Natl Inst Agrobiol Sci, Partenaires INRAE, Okayama University, University of Helsinki, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Inst Evolut, University of Haifa [Haifa], German Ministry of Education and Research (BMBF) [0314000], Leibniz Association, European project of the 7th framework programme 'TriticeaeGenome', Austrian Wissenschaftsfond (FWF) [SFB F3705], ERA-NET PG project 'BARCODE', Scottish Government/BBSRC [BB/100663X/1], National Science Foundation [DBI 0321756, DBI-1062301], USDA-CSREES-NRI [2006-55606-16722], Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA-CSREES-NIFA [2009-65300-05645], BRAIN and NBRP-Japan, and Japanese MAFF [TRG1008]
- Subjects
0106 biological sciences ,[SDV]Life Sciences [q-bio] ,Sequence assembly ,01 natural sciences ,Genome ,Gene Expression Regulation, Plant ,2. Zero hunger ,Genetics ,0303 health sciences ,MESSENGER-RNA DECAY ,Multidisciplinary ,food and beverages ,Genomics ,ARABIDOPSIS ,Physical Chromosome Mapping ,Molecular Sequence Annotation ,Codon, Nonsense ,MAP ,HORDEUM-VULGARE L ,Genome, Plant ,EXPRESSION ,Crops, Agricultural ,Sequence analysis ,Computational biology ,Biology ,MILDEW RESISTANCE LOCUS ,Genes, Plant ,Polymorphism, Single Nucleotide ,Plant sciences ,Evolution, Molecular ,03 medical and health sciences ,REVEALS ,RICE ,Gene ,030304 developmental biology ,Repetitive Sequences, Nucleic Acid ,Comparative genomics ,Hordeum ,Sequence Analysis, DNA ,15. Life on land ,EVOLUTION ,Alternative Splicing ,NONCODING RNAS ,Hordeum vulgare ,Transcriptome ,010606 plant biology & botany - Abstract
International audience; Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
- Published
- 2012
6. PHYSICAL MAP AND DE NOVO SEQUENCING OF BARLEY FR-H2 FROST RESISTANCE LOCUS
- Author
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Pasquariello, Marianna, Barabaschi, Delfina, Himmelbach, A, Ariyadasa, R, Knox, A. K., Stockinger, E. J., Steuernagel, B, Stein, N, Pecchioni, Nicola, and Francia, Enrico
- Subjects
physical mapping ,Fr-H2 locus ,Frost resistance ,DE NOVO sequencing - Published
- 2012
7. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
- Author
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Mayer, K.F.X., Rogers, J., Dole el, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A.J., Sourdille, P., Endo, T.R., Kubalakova, M., Ihalikova, J., Dubska, Z., Vrana, J., Perkova, R., Imkova, H., Febrer, M., Clissold, L., McLay, K., Singh, K., Chuneja, P., Singh, N.K., Khurana, J., Akhunov, E., Choulet, F., Alberti, A., Barbe, V., Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J., Ogihara, Y., Handa, H., Maclachlan, P.R., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Olsen, O-A, Sandve, S.R., Lien, S., Steuernagel, B., Wulff, B., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R.H., Clavijo, B.J., Wright, J., Pfeifer, M., Spannagl, M., Martis, M.M., Mascher, M., Chapman, J., Poland, J.A., Scholz, U., Barry, K., Waugh, R., Rokhsar, D.S., Muehlbauer, G.J., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Faccioli, P., Colaiacovo, M., Stanca, A.M., Budak, H., Cattivelli, L., Glover, N., Pingault, L., Paux, E., Sharma, S., Appels, R., Bellgard, M., Chapman, B., Nussbaumer, T., Bader, K.C., Rimbert, H., Wang, S., Knox, R., Kilian, A., Alaux, M., Alfama, F., Couderc, L., Guilhot, N., Viseux, C., Loaec, M., Keller, B., Praud, S., Mayer, K.F.X., Rogers, J., Dole el, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A.J., Sourdille, P., Endo, T.R., Kubalakova, M., Ihalikova, J., Dubska, Z., Vrana, J., Perkova, R., Imkova, H., Febrer, M., Clissold, L., McLay, K., Singh, K., Chuneja, P., Singh, N.K., Khurana, J., Akhunov, E., Choulet, F., Alberti, A., Barbe, V., Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J., Ogihara, Y., Handa, H., Maclachlan, P.R., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Olsen, O-A, Sandve, S.R., Lien, S., Steuernagel, B., Wulff, B., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R.H., Clavijo, B.J., Wright, J., Pfeifer, M., Spannagl, M., Martis, M.M., Mascher, M., Chapman, J., Poland, J.A., Scholz, U., Barry, K., Waugh, R., Rokhsar, D.S., Muehlbauer, G.J., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Faccioli, P., Colaiacovo, M., Stanca, A.M., Budak, H., Cattivelli, L., Glover, N., Pingault, L., Paux, E., Sharma, S., Appels, R., Bellgard, M., Chapman, B., Nussbaumer, T., Bader, K.C., Rimbert, H., Wang, S., Knox, R., Kilian, A., Alaux, M., Alfama, F., Couderc, L., Guilhot, N., Viseux, C., Loaec, M., Keller, B., and Praud, S.
- Abstract
An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
- Published
- 2014
8. Schulung von Hausärzten/-Innen und Arzthelferinnen in partnerschaftlicher Arzt - Patienten - Konsultation nach dem Prinzip des 'Shared decision making' (SDM)
- Author
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Vahlbruch, S, Doering, TJ, Steuernagel, B, Hübner, MS, Broll, A, Buttler, K, Rohlfing, H, and Kehl, U
- Subjects
ddc: 610 - Published
- 2004
9. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives
- Author
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Wicker, Thomas, Mayer, K F X, Gundlach, H, Martis, M, Steuernagel, B, Scholz, Uwe, Simková, H, Kubaláková, M, Choulet, F, Taudien, S, Platzer, M, Feuillet, C, Fahima, T, Budak, H, Dolezel, J, Keller, B, Stein, N, Wicker, Thomas, Mayer, K F X, Gundlach, H, Martis, M, Steuernagel, B, Scholz, Uwe, Simková, H, Kubaláková, M, Choulet, F, Taudien, S, Platzer, M, Feuillet, C, Fahima, T, Budak, H, Dolezel, J, Keller, B, and Stein, N
- Abstract
All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were sampled per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely diverse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.
- Published
- 2011
10. Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array
- Author
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Kloosterman, B.A., de Koeyer, D., Griffiths, R., Flinn, B., Steuernagel, B., Scholz, U., Sonnewald, S., Sonnewald, U., Bryan, G.J., Prat, S., Banfalvi, Z., Hammond, J.P., Geigenberger, P., Nielsen, K.L., Visser, R.G.F., Bachem, C.W.B., Kloosterman, B.A., de Koeyer, D., Griffiths, R., Flinn, B., Steuernagel, B., Scholz, U., Sonnewald, S., Sonnewald, U., Bryan, G.J., Prat, S., Banfalvi, Z., Hammond, J.P., Geigenberger, P., Nielsen, K.L., Visser, R.G.F., and Bachem, C.W.B.
- Abstract
The increasing amount of available expressed gene sequence data makes whole-transcriptome analysis of certain crop species possible. Potato currently has the second largest number of publicly available expressed sequence tag (EST) sequences among the Solanaceae. Most of these ESTs, plus other proprietary sequences, were combined and used to generate a unigene assembly. The set of 246,182 sequences produced 46,345 unigenes, which were used to design a 44K 60-mer oligo array (Potato Oligo Chip Initiative: POCI). In this study, we attempt to identify genes controlling and driving the process of tuber initiation and growth by implementing large-scale transcriptional changes using the newly developed POCI array. Major gene expression profiles could be identified exhibiting differential expression at key developmental stages. These profiles were associated with functional roles in cell division and growth. A subset of genes involved in the regulation of the cell cycle, based on their Gene Ontology classification, exhibit a clear transient upregulation at tuber onset indicating increased cell division during these stages. The POCI array allows the study of potato gene expression on a much broader level than previously possible and will greatly enhance analysis of transcriptional control mechanisms in a wide range of potato research areas. POCI sequence and annotation data are publicly available through the POCI database
- Published
- 2008
11. Using Data Warehouse Technology in Crop Plant Bioinformatics
- Author
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Kuenne Christian, Grosse Ivo, Matthies Inge, Scholz Uwe, Sretenovic-Rajicic Tatjana, Stein Nils, Stephanik Andreas, Steuernagel Burkhard, and Weise Stephan
- Subjects
Biotechnology ,TP248.13-248.65 - Abstract
Plant-specific data is managed in heterogeneous formats and is dispersed geographically. Based on this data, efficient analyses require a materialised integration, often realised with data warehouse technology today. We describe the requirements, problems and solution strategies for domain-crossing integration as the fundament for analysing plant biological data based on three current case studies. First, we introduce a system for retrieval of markers and mapping positions based on clustering of ESTs. The second case study illustrates the steps for diversity studies after genotyping a collection of about 3,000 ryegrass accessions (Lolium spp.), whereas in the third example data of approximately 250 barley cultivars (Hordeum vulgare) were used for associating haplotype- and SNP-patterns with malting parameters. For all case studies, we integrate data from different domains - sequence and marker data as well as IPK Genebank data including passport and phenotypic information. Specific problems associated with plant biological data and possible solution strategies are shown.
- Published
- 2007
- Full Text
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12. Rapid gene isolation in barley and wheat by mutant chromosome sequencing
- Author
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Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Sg, Krattinger, Wicker T, Doležel J, Keller B, and Brande Wulff
13. A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq
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Kohl Stefan, Hollmann Julien, Blattner Frank R, Radchuk Volodymyr, Andersch Franka, Steuernagel Burkhard, Schmutzer Thomas, Scholz Uwe, Krupinska Karin, Weber Hans, and Weschke Winfriede
- Subjects
Barley ,Vegetative organs ,Developing grains ,N remobilisation ,N accumulation ,RNA-seq ,Cysteine peptidases ,N transporter genes ,Source-sink communication ,Botany ,QK1-989 - Abstract
Abstract Background The majority of nitrogen accumulating in cereal grains originates from proteins remobilised from vegetative organs. However, interactions between grain filling and remobilisation are poorly understood. We used transcriptome large-scale pyrosequencing of flag leaves, glumes and developing grains to identify cysteine peptidase and N transporter genes playing a role in remobilisation and accumulation of nitrogen in barley. Results Combination of already known and newly derived sequence information reduced redundancy, increased contig length and identified new members of cysteine peptidase and N transporter gene families. The dataset for N transporter genes was aligned with N transporter amino acid sequences of rice and Arabidopsis derived from Aramemnon database. 57 AAT, 45 NRT1/PTR and 22 OPT unigenes identified by this approach cluster to defined subgroups in the respective phylogenetic trees, among them 25 AAT, 8 NRT1/PTR and 5 OPT full-length sequences. Besides, 59 unigenes encoding cysteine peptidases were identified and subdivided into different families of the papain cysteine peptidase clade. Expression profiling of full-length AAT genes highlighted amino acid permeases as the group showing highest transcriptional activity. HvAAP2 and HvAAP6 are highly expressed in vegetative organs whereas HvAAP3 is grain-specific. Sequence similarities cluster HvAAP2 and the putative transporter HvAAP6 together with Arabidopsis transporters, which are involved in long-distance transfer of amino acids. HvAAP3 is closely related to AtAAP1 and AtAAP8 playing a role in supplying N to developing seeds. An important role in amino acid re-translocation can be considered for HvLHT1 and HvLHT2 which are specifically expressed in glumes and flag leaves, respectively. PCA and K-means clustering of AAT transcript data revealed coordinate developmental stages in flag leaves, glumes and grains. Phloem-specific metabolic compounds are proposed that might signal high grain demands for N to distantly located plant organs. Conclusions The approach identified cysteine peptidases and specific N transporters of the AAT family as obviously relevant for grain filling and thus, grain yield and quality in barley. Up to now, information is based only on transcript data. To make it relevant for application, the role of identified candidates in sink-source communication has to be analysed in more detail.
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- 2012
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14. Sequencing of BAC pools by different next generation sequencing platforms and strategies
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Scholz Uwe, Petzold Andreas, Felder Marius, Groth Marco, Schmutzer Thomas, Schulte Daniela, Ariyadasa Ruvini, Steuernagel Burkhard, Taudien Stefan, Mayer Klaus FX, Stein Nils, and Platzer Matthias
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BAC pools ,next generation sequencing ,454 ,Illumina ,barcoding ,mate pairs ,scaffolding ,barley ,Medicine ,Biology (General) ,QH301-705.5 ,Science (General) ,Q1-390 - Abstract
Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.
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- 2011
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15. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley
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Scholz Uwe, Graner Andreas, Felder Marius, Petzold Andreas, Schulte Daniela, Ariyadasa Ruvini, Seidel Michael, Gundlach Heidrun, Taudien Stefan, Steuernagel Burkhard, Mayer Klaus FX, Platzer Matthias, and Stein Nils
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L.) is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable. Results To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb) and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes. By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies. Conclusion The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.
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- 2009
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16. A chromosome-scale reference genome of grasspea (Lathyrus sativus).
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Vigouroux M, Novák P, Oliveira LC, Santos C, Cheema J, Wouters RHM, Paajanen P, Vickers M, Koblížková A, Vaz Patto MC, Macas J, Steuernagel B, Martin C, and Emmrich PMF
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- Lathyrus genetics, Genome, Plant, Chromosomes, Plant genetics
- Abstract
Grasspea (Lathyrus sativus L.) is an underutilised but promising legume crop with tolerance to a wide range of abiotic and biotic stress factors, and potential for climate-resilient agriculture. Despite a long history and wide geographical distribution of cultivation, only limited breeding resources are available. This paper reports a 5.96 Gbp genome assembly of grasspea genotype LS007, of which 5.03 Gbp is scaffolded into 7 pseudo-chromosomes. The assembly has a BUSCO completeness score of 99.1% and is annotated with 31719 gene models and repeat elements. This represents the most contiguous and accurate assembly of the grasspea genome to date., (© 2024. The Author(s).)
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- 2024
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17. An optimised CRISPR Cas9 and Cas12a mutagenesis toolkit for Barley and Wheat.
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Lawrenson T, Clarke M, Kirby R, Forner M, Steuernagel B, Brown JKM, and Harwood W
- Abstract
Background: CRISPR Cas9 and Cas12a are the two most frequently used programmable nucleases reported in plant systems. There is now a wide range of component parts for both which likely have varying degrees of effectiveness and potentially applicability to different species. Our aim was to develop and optimise Cas9 and Cas12a based systems for highly efficient genome editing in the monocotyledons barley and wheat and produce a user-friendly toolbox facilitating simplex and multiplex editing in the cereal community., Results: We identified a Zea mays codon optimised Cas9 with 13 introns in conjunction with arrayed guides driven by U6 and U3 promoters as the best performer in barley where 100% of T0 plants were simultaneously edited in all three target genes. When this system was used in wheat > 90% of T0 plants were edited in all three subgenome targets. For Cas12a, an Arabidopsis codon optimised sequence with 8 introns gave the best editing efficiency in barley when combined with a tRNA based multiguide array, resulting in 90% mutant alleles in three simultaneously targeted genes. When we applied this Cas12a system in wheat 86% & 93% of T0 plants were mutated in two genes simultaneously targeted. We show that not all introns contribute equally to enhanced mutagenesis when inserted into a Cas12a coding sequence and that there is rationale for including multiple introns. We also show that the combined effect of two features which boost Cas12a mutagenesis efficiency (D156R mutation and introns) is more than the sum of the features applied separately., Conclusion: Based on the results of our testing, we describe and provide a GoldenGate modular cloning system for Cas9 and Cas12a use in barley and wheat. Proven Cas nuclease and guide expression cassette options found in the toolkit will facilitate highly efficient simplex and multiplex mutagenesis in both species. We incorporate GRF-GIF transformation boosting cassettes in wheat options to maximise workflow efficiency., (© 2024. Crown.)
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- 2024
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18. Harnessing landrace diversity empowers wheat breeding.
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Cheng S, Feng C, Wingen LU, Cheng H, Riche AB, Jiang M, Leverington-Waite M, Huang Z, Collier S, Orford S, Wang X, Awal R, Barker G, O'Hara T, Lister C, Siluveru A, Quiroz-Chávez J, Ramírez-González RH, Bryant R, Berry S, Bansal U, Bariana HS, Bennett MJ, Bicego B, Bilham L, Brown JKM, Burridge A, Burt C, Buurman M, Castle M, Chartrain L, Chen B, Denbel W, Elkot AF, Fenwick P, Feuerhelm D, Foulkes J, Gaju O, Gauley A, Gaurav K, Hafeez AN, Han R, Horler R, Hou J, Iqbal MS, Kerton M, Kondic-Spica A, Kowalski A, Lage J, Li X, Liu H, Liu S, Lovegrove A, Ma L, Mumford C, Parmar S, Philp C, Playford D, Przewieslik-Allen AM, Sarfraz Z, Schafer D, Shewry PR, Shi Y, Slafer GA, Song B, Song B, Steele D, Steuernagel B, Tailby P, Tyrrell S, Waheed A, Wamalwa MN, Wang X, Wei Y, Winfield M, Wu S, Wu Y, Wulff BBH, Xian W, Xu Y, Xu Y, Yuan Q, Zhang X, Edwards KJ, Dixon L, Nicholson P, Chayut N, Hawkesford MJ, Uauy C, Sanders D, Huang S, and Griffiths S
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- Alleles, Genetic Introgression, Genome, Plant genetics, Haplotypes genetics, Linkage Disequilibrium genetics, Quantitative Trait Loci genetics, Whole Genome Sequencing, Phylogeny, Genetic Association Studies, Food Security, Crops, Agricultural genetics, Genetic Variation genetics, Phenotype, Plant Breeding methods, Triticum classification, Triticum genetics, Biodiversity
- Abstract
Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security
1 . Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker-trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security., (© 2024. The Author(s).)- Published
- 2024
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19. Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9.
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Zhang J, Nirmala J, Chen S, Jost M, Steuernagel B, Karafiatova M, Hewitt T, Li H, Edae E, Sharma K, Hoxha S, Bhatt D, Antoniou-Kourounioti R, Dodds P, Wulff BBH, Dolezel J, Ayliffe M, Hiebert C, McIntosh R, Dubcovsky J, Zhang P, Rouse MN, and Lagudah E
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- Chromosome Mapping, Alleles, Haplotypes, Amino Acid Sequence, Plant Diseases genetics, Disease Resistance genetics, Basidiomycota genetics
- Abstract
Most rust resistance genes thus far isolated from wheat have a very limited number of functional alleles. Here, we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) are characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation are used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1 and Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differs from SR9B by a single amino acid. SR9B and SR9G resistance proteins are also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences. Together, our results show that functional diversification of allelic variants at the SR9 locus involves single and multiple amino acid changes that recognize isolates of wheat stem rust., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
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- 2023
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20. Author Correction: Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus.
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Edwards A, Njaci I, Sarkar A, Jiang Z, Kaithakottil GG, Moore C, Cheema J, Stevenson CEM, Rejzek M, Novák P, Vigouroux M, Vickers M, Wouters RHM, Paajanen P, Steuernagel B, Moore JD, Higgins J, Swarbreck D, Martens S, Kim CY, Weng JK, Mundree S, Kilian B, Kumar S, Loose M, Yant L, Macas J, Wang TL, Martin C, and Emmrich PMF
- Published
- 2023
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21. Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus.
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Edwards A, Njaci I, Sarkar A, Jiang Z, Kaithakottil GG, Moore C, Cheema J, Stevenson CEM, Rejzek M, Novák P, Vigouroux M, Vickers M, Wouters RHM, Paajanen P, Steuernagel B, Moore JD, Higgins J, Swarbreck D, Martens S, Kim CY, Weng JK, Mundree S, Kilian B, Kumar S, Loose M, Yant L, Macas J, Wang TL, Martin C, and Emmrich PMF
- Subjects
- Neurotoxins metabolism, Genomics, Lathyrus genetics, Lathyrus metabolism, Amino Acids, Diamino metabolism
- Abstract
Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop's association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce β-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin., (© 2023. The Author(s).)
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- 2023
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22. A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat.
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Kale SM, Schulthess AW, Padmarasu S, Boeven PHG, Schacht J, Himmelbach A, Steuernagel B, Wulff BBH, Reif JC, Stein N, and Mascher M
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- Chromosome Mapping, Chromosomes, Disease Resistance genetics, Plant Diseases genetics, Plant Diseases microbiology, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Basidiomycota genetics, Triticum genetics, Triticum microbiology
- Abstract
A resistance gene atlas is an integral component of the breeder's arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ genebank accessions and current elite cultivars. In addition, we use accurate long-read sequencing and chromosome conformation capture sequencing to construct a chromosome-scale genome sequence assembly of cv. Attraktion, an elite variety representative of European winter wheat. We illustrate the value of our resource for breeders and geneticists by (i) comparing the resistance gene complements in plant genetic resources and elite varieties and (ii) conducting genome-wide associations scans (GWAS) for the fungal diseases yellow rust and leaf rust using reference-based and reference-free GWAS approaches. The gene content under GWAS peaks was scrutinized in the assembly of cv. Attraktion., (© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)
- Published
- 2022
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23. MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat.
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Dixon LE, Pasquariello M, Badgami R, Levin KA, Poschet G, Ng PQ, Orford S, Chayut N, Adamski NM, Brinton J, Simmonds J, Steuernagel B, Searle IR, Uauy C, and Boden SA
- Subjects
- Alleles, Edible Grain genetics, Edible Grain metabolism, Gene Expression Regulation, Plant, Genes, Homeobox, Inflorescence genetics, Plant Proteins genetics, Plant Proteins metabolism, Triticum, Grain Proteins metabolism, MicroRNAs genetics, MicroRNAs metabolism
- Abstract
Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 ( HB-2 ), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.
- Published
- 2022
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24. Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics.
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Vendelbo NM, Mahmood K, Steuernagel B, Wulff BBH, Sarup P, Hovmøller MS, Justesen AF, Kristensen PS, Orabi J, and Jahoor A
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- Disease Resistance genetics, Genes, Plant, Genome-Wide Association Study, Plant Diseases genetics, Puccinia, Basidiomycota genetics, Secale genetics
- Abstract
The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita ( Pr ) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio
® long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.- Published
- 2022
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25. Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement.
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Avni R, Lux T, Minz-Dub A, Millet E, Sela H, Distelfeld A, Deek J, Yu G, Steuernagel B, Pozniak C, Ens J, Gundlach H, Mayer KFX, Himmelbach A, Stein N, Mascher M, Spannagl M, Wulff BBH, and Sharon A
- Subjects
- Genome, Plant genetics, Phylogeny, Poaceae genetics, Triticum genetics, Aegilops genetics
- Abstract
Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement., (© 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)
- Published
- 2022
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26. Characterisation of the Introgression of Brassica villosa Genome Into Broccoli to Enhance Methionine-Derived Glucosinolates and Associated Health Benefits.
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Neequaye M, Steuernagel B, Saha S, Trick M, Troncoso-Rey P, van den Bosch F, Traka MH, Østergaard L, and Mithen R
- Abstract
Broccoli cultivars that have enhanced accumulation of methionine-derived glucosinolates have been developed through the introgression of a novel allele of the MYB28 transcription factor from the wild species Brassica villosa . Through a novel k-mer approach, we characterised the extent of the introgression of unique B. villosa genome sequences into high glucosinolate broccoli genotypes. RNAseq analyses indicated that the introgression of the B. villosa MYB28 C2 allele resulted in the enhanced expression of the MYB28 transcription factor, and modified expression of genes associated with sulphate absorption and reduction, and methionine and glucosinolate biosynthesis when compared to standard broccoli. A adenine-thymine (AT) short tandem repeat (STR) was identified within the 5' untranslated region (UTR) B. villosa MYB28 allele that was absent from two divergent cultivated forms of Brassica oleracea , which may underpin the enhanced expression of B. villosa MYB28 ., Competing Interests: The broccoli with elevated glucoraphanin is the subject of patents filed by Plant Bioscience Limited (PBL), the technology transfer company of the John Innes Centre. RM and MHT are inventors named on these patents. FB was employed by Bayer. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Neequaye, Steuernagel, Saha, Trick, Troncoso-Rey, van den Bosch, Traka, Østergaard and Mithen.)
- Published
- 2022
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27. Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62.
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Yu G, Matny O, Champouret N, Steuernagel B, Moscou MJ, Hernández-Pinzón I, Green P, Hayta S, Smedley M, Harwood W, Kangara N, Yue Y, Gardener C, Banfield MJ, Olivera PD, Welchin C, Simmons J, Millet E, Minz-Dub A, Ronen M, Avni R, Sharon A, Patpour M, Justesen AF, Jayakodi M, Himmelbach A, Stein N, Wu S, Poland J, Ens J, Pozniak C, Karafiátová M, Molnár I, Doležel J, Ward ER, Reuber TL, Jones JDG, Mascher M, Steffenson BJ, and Wulff BBH
- Subjects
- Disease Resistance genetics, Genes, Plant genetics, Plant Breeding, Plant Diseases genetics, Triticum genetics, Aegilops genetics, Basidiomycota genetics
- Abstract
The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance., (© 2022. The Author(s).)
- Published
- 2022
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28. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement.
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Gaurav K, Arora S, Silva P, Sánchez-Martín J, Horsnell R, Gao L, Brar GS, Widrig V, John Raupp W, Singh N, Wu S, Kale SM, Chinoy C, Nicholson P, Quiroz-Chávez J, Simmonds J, Hayta S, Smedley MA, Harwood W, Pearce S, Gilbert D, Kangara N, Gardener C, Forner-Martínez M, Liu J, Yu G, Boden SA, Pascucci A, Ghosh S, Hafeez AN, O'Hara T, Waites J, Cheema J, Steuernagel B, Patpour M, Justesen AF, Liu S, Rudd JC, Avni R, Sharon A, Steiner B, Kirana RP, Buerstmayr H, Mehrabi AA, Nasyrova FY, Chayut N, Matny O, Steffenson BJ, Sandhu N, Chhuneja P, Lagudah E, Elkot AF, Tyrrell S, Bian X, Davey RP, Simonsen M, Schauser L, Tiwari VK, Randy Kutcher H, Hucl P, Li A, Liu DC, Mao L, Xu S, Brown-Guedira G, Faris J, Dvorak J, Luo MC, Krasileva K, Lux T, Artmeier S, Mayer KFX, Uauy C, Mascher M, Bentley AR, Keller B, Poland J, and Wulff BBH
- Subjects
- Bread, Genomics, Metagenomics, Plant Breeding, Triticum genetics, Aegilops genetics
- Abstract
Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding., (© 2021. The Author(s).)
- Published
- 2022
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29. An Integrated Linkage Map of Three Recombinant Inbred Populations of Pea ( Pisum sativum L.).
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Sawada C, Moreau C, Robinson GHJ, Steuernagel B, Wingen LU, Cheema J, Sizer-Coverdale E, Lloyd D, Domoney C, and Ellis N
- Subjects
- Chromosome Mapping, Genetic Linkage, Phenotype, Pisum sativum genetics, Quantitative Trait Loci
- Abstract
Biparental recombinant inbred line (RIL) populations are sets of genetically stable lines and have a simple population structure that facilitates the dissection of the genetics of interesting traits. On the other hand, populations derived from multiparent intercrosses combine both greater diversity and higher numbers of recombination events than RILs. Here, we describe a simple population structure: a three-way recombinant inbred population combination. This structure was easy to produce and was a compromise between biparental and multiparent populations. We show that this structure had advantages when analyzing cultivar crosses, and could achieve a mapping resolution of a few genes.
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- 2022
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30. Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response.
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Woodhouse S, He Z, Woolfenden H, Steuernagel B, Haerty W, Bancroft I, Irwin JA, Morris RJ, and Wells R
- Subjects
- Genome-Wide Association Study, Plant Breeding, Transcriptome, Brassica genetics, Brassica napus genetics
- Abstract
Background: Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood., Results: Here, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC.C2 as a further candidate for vernalisation response., Conclusions: This study describes a new pipeline for performing associative transcriptomics studies in B. oleracea. Using flowering time as an example trait, it provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2. These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields., (© 2021. The Author(s).)
- Published
- 2021
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31. A recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes.
- Author
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Zhang J, Hewitt TC, Boshoff WHP, Dundas I, Upadhyaya N, Li J, Patpour M, Chandramohan S, Pretorius ZA, Hovmøller M, Schnippenkoetter W, Park RF, Mago R, Periyannan S, Bhatt D, Hoxha S, Chakraborty S, Luo M, Dodds P, Steuernagel B, Wulff BBH, Ayliffe M, McIntosh RA, Zhang P, and Lagudah ES
- Subjects
- Chromosomes, Plant genetics, Genes, Plant, Genetic Engineering, Genetic Markers, Plant Breeding methods, Plant Diseases genetics, Plant Diseases microbiology, Plant Proteins genetics, Plant Stems microbiology, Plants, Genetically Modified genetics, Puccinia isolation & purification, Triticum genetics, Disease Resistance genetics, NLR Proteins genetics, Plants, Genetically Modified microbiology, Puccinia pathogenicity, Triticum microbiology
- Abstract
The re-emergence of stem rust on wheat in Europe and Africa is reinforcing the ongoing need for durable resistance gene deployment. Here, we isolate from wheat, Sr26 and Sr61, with both genes independently introduced as alien chromosome introgressions from tall wheat grass (Thinopyrum ponticum). Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. Using gene-specific markers, we validate the presence of both genes on a single recombinant alien segment developed in wheat. The co-location of these genes on a small non-recombinogenic segment simplifies their deployment as a gene stack and potentially enhances their resistance durability.
- Published
- 2021
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32. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals.
- Author
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Li Y, Leveau A, Zhao Q, Feng Q, Lu H, Miao J, Xue Z, Martin AC, Wegel E, Wang J, Orme A, Rey MD, Karafiátová M, Vrána J, Steuernagel B, Joynson R, Owen C, Reed J, Louveau T, Stephenson MJ, Zhang L, Huang X, Huang T, Fan D, Zhou C, Tian Q, Li W, Lu Y, Chen J, Zhao Y, Lu Y, Zhu C, Liu Z, Polturak G, Casson R, Hill L, Moore G, Melton R, Hall N, Wulff BBH, Doležel J, Langdon T, Han B, and Osbourn A
- Subjects
- Avena metabolism, Edible Grain genetics, Evolution, Molecular, High-Throughput Nucleotide Sequencing, In Situ Hybridization, Fluorescence, Multigene Family, RNA-Seq, Repetitive Sequences, Nucleic Acid, Saponins biosynthesis, Saponins chemistry, Saponins genetics, Synteny genetics, Nicotiana metabolism, Whole Genome Sequencing, Avena genetics, Disease Resistance genetics, Metabolic Networks and Pathways genetics, Telomere genetics
- Abstract
Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat-the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a 'self-poisoning' scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.
- Published
- 2021
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33. A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat.
- Author
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Luo M, Xie L, Chakraborty S, Wang A, Matny O, Jugovich M, Kolmer JA, Richardson T, Bhatt D, Hoque M, Patpour M, Sørensen C, Ortiz D, Dodds P, Steuernagel B, Wulff BBH, Upadhyaya NM, Mago R, Periyannan S, Lagudah E, Freedman R, Lynne Reuber T, Steffenson BJ, and Ayliffe M
- Subjects
- Basidiomycota pathogenicity, Chromosome Mapping, Plant Breeding, Plant Diseases microbiology, Transgenes genetics, Triticum microbiology, Virulence genetics, Basidiomycota genetics, Disease Resistance genetics, Plant Diseases genetics, Triticum genetics
- Abstract
Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness.
- Published
- 2021
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34. Identification of specificity-defining amino acids of the wheat immune receptor Pm2 and powdery mildew effector AvrPm2.
- Author
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Manser B, Koller T, Praz CR, Roulin AC, Zbinden H, Arora S, Steuernagel B, Wulff BBH, Keller B, and Sánchez-Martín J
- Subjects
- Alleles, Amino Acids metabolism, Ascomycota physiology, Disease Resistance, Fungal Proteins genetics, Genetic Variation, Host-Pathogen Interactions, Mutation, NLR Proteins genetics, Plant Diseases microbiology, Plant Immunity, Plant Proteins genetics, Nicotiana genetics, Nicotiana physiology, Triticum immunology, Triticum microbiology, Aegilops genetics, Ascomycota genetics, Fungal Proteins metabolism, NLR Proteins metabolism, Plant Diseases immunology, Plant Proteins metabolism, Triticum genetics
- Abstract
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) act as intracellular sensors for pathogen-derived effector proteins and trigger an immune response, frequently resulting in the hypersensitive cell death response (HR) of the infected host cell. The wheat (Triticum aestivum) NLR Pm2 confers resistance against the fungal pathogen Blumeria graminis f. sp. tritici (Bgt) if the isolate contains the specific RNase-like effector AvrPm2. We identified and isolated seven new Pm2 alleles (Pm2e-i) in the wheat D-genome ancestor Aegilops tauschii and two new natural AvrPm2 haplotypes from Bgt. Upon transient co-expression in Nicotiana benthamiana, we observed a variant-specific HR of the Pm2 variants Pm2a and Pm2i towards AvrPm2 or its homolog from the AvrPm2 effector family, BgtE-5843, respectively. Through the introduction of naturally occurring non-synonymous single nucleotide polymorphisms and structure-guided mutations, we identified single amino acids in both the wheat NLR Pm2 and the fungal effector proteins AvrPm2 and BgtE-5843 responsible for the variant-specific HR of the Pm2 variants. Exchanging these amino acids led to a modified HR of the Pm2-AvrPm2 interaction and allowed the identification of the effector head epitope, a 20-amino-acid long unit of AvrPm2 involved in the HR. Swapping of the AvrPm2 head epitope to the non-HR-triggering AvrPm2 family member BgtE-5846 led to gain of a HR by Pm2a. Our study presents a molecular approach to identify crucial effector surface structures involved in the HR and demonstrates that natural and induced diversity in an immune receptor and its corresponding effectors can provide the basis for understanding and modifying NLR-effector specificity., (© 2021 Society for Experimental Biology and John Wiley & Sons Ltd.)
- Published
- 2021
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35. A highly differentiated region of wheat chromosome 7AL encodes a Pm1a immune receptor that recognizes its corresponding AvrPm1a effector from Blumeria graminis.
- Author
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Hewitt T, Müller MC, Molnár I, Mascher M, Holušová K, Šimková H, Kunz L, Zhang J, Li J, Bhatt D, Sharma R, Schudel S, Yu G, Steuernagel B, Periyannan S, Wulff B, Ayliffe M, McIntosh R, Keller B, Lagudah E, and Zhang P
- Subjects
- Chromosomes, Disease Resistance genetics, Plant Diseases genetics, Ascomycota genetics, Triticum genetics
- Abstract
Pm1a, the first powdery mildew resistance gene described in wheat, is part of a complex resistance (R) gene cluster located in a distal region of chromosome 7AL that has suppressed genetic recombination. A nucleotide-binding, leucine-rich repeat (NLR) immune receptor gene was isolated using mutagenesis and R gene enrichment sequencing (MutRenSeq). Stable transformation confirmed Pm1a identity which induced a strong resistance phenotype in transgenic plants upon challenge with avirulent Blumeria graminis (wheat powdery mildew) pathogens. A high-density genetic map of a B. graminis family segregating for Pm1a avirulence combined with pathogen genome resequencing and RNA sequencing (RNAseq) identified AvrPm1a effector gene candidates. In planta expression identified an effector, with an N terminal Y/FxC motif, that induced a strong hypersensitive response when co-expressed with Pm1a in Nicotiana benthamiana. Single chromosome enrichment sequencing (ChromSeq) and assembly of chromosome 7A suggested that suppressed recombination around the Pm1a region was due to a rearrangement involving chromosomes 7A, 7B and 7D. The cloning of Pm1a and its identification in a highly rearranged region of chromosome 7A provides insight into the role of chromosomal rearrangements in the evolution of this complex resistance cluster., (© 2020 The Authors New Phytologist © 2020 New Phytologist Foundation.)
- Published
- 2021
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36. The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley.
- Author
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Hatta MAM, Arora S, Ghosh S, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Steuernagel B, Richardson T, Mago R, Lagudah ES, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan S, Steffenson BJ, and Wulff BBH
- Subjects
- Plant Diseases microbiology, Basidiomycota, Disease Resistance genetics, Hordeum genetics, Plant Diseases genetics
- Abstract
In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley., (© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)
- Published
- 2021
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37. Multiple wheat genomes reveal global variation in modern breeding.
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Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri JN, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo DH, Ens J, Wiebe K, N'Diaye A, Fritz AK, Gutwin C, Fiebig A, Fosker C, Fu BX, Accinelli GG, Gardner KA, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh CS, Deek J, Costamagna AC, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnère G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl PJ, Sharpe AG, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger SG, Handa H, Shimizu KK, Distelfeld A, Chalmers K, Keller B, Mayer KFX, Poland J, Stein N, McCartney CA, Spannagl M, Wicker T, and Pozniak CJ
- Subjects
- Acclimatization genetics, Animals, Centromere genetics, Centromere metabolism, Chromosome Mapping, Cloning, Molecular, DNA Copy Number Variations genetics, DNA Transposable Elements genetics, Edible Grain genetics, Edible Grain growth & development, Genes, Plant genetics, Genetic Introgression, Haplotypes, Insecta pathogenicity, NLR Proteins genetics, Plant Diseases genetics, Plant Proteins genetics, Polymorphism, Single Nucleotide genetics, Polyploidy, Triticum classification, Triticum growth & development, Genetic Variation, Genome, Plant genetics, Genomics, Internationality, Plant Breeding methods, Triticum genetics
- Abstract
Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome
1 , and the lack of genome-assembly data for multiple wheat lines2,3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.- Published
- 2020
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38. Extensive Genetic Variation at the Sr22 Wheat Stem Rust Resistance Gene Locus in the Grasses Revealed Through Evolutionary Genomics and Functional Analyses.
- Author
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Md Hatta MA, Ghosh S, Athiyannan N, Richardson T, Steuernagel B, Yu G, Rouse MN, Ayliffe M, Lagudah ES, Radhakrishnan GV, Periyannan SK, and Wulff BBH
- Subjects
- Australia, Chromosome Mapping, Evolution, Molecular, Genetic Variation, Genomics, Plant Diseases microbiology, Poaceae microbiology, Basidiomycota pathogenicity, Disease Resistance genetics, Plant Diseases genetics, Poaceae genetics
- Abstract
In the last 20 years, severe wheat stem rust outbreaks have been recorded in Africa, Europe, and Central Asia. This previously well controlled disease, caused by the fungus Puccinia graminis f. sp. tritici , has reemerged as a major threat to wheat cultivation. The stem rust ( Sr ) resistance gene Sr22 encodes a nucleotide-binding and leucine-rich repeat receptor which confers resistance to the highly virulent African stem rust isolate Ug99. Here, we show that the Sr22 gene is conserved among grasses in the Triticeae and Poeae lineages. Triticeae species contain syntenic loci with single-copy orthologs of Sr22 on chromosome 7, except Hordeum vulgare , which has experienced major expansions and rearrangements at the locus. We also describe 14 Sr22 sequence variants obtained from both Triticum boeoticum and the domesticated form of this species, T. monococcum , which have been postulated to encode both functional and nonfunctional Sr22 alleles. The nucleotide sequence analysis of these alleles identified historical sequence exchange resulting from recombination or gene conversion, including breakpoints within codons, which expanded the coding potential at these positions by introduction of nonsynonymous substitutions. Three Sr22 alleles were transformed into wheat cultivar Fielder and two postulated resistant alleles from Schomburgk (hexaploid wheat introgressed with T. boeoticum segment carrying Sr22 ) and T. monococcum accession PI190945, respectively, conferred resistance to P. graminis f. sp. tritici race TTKSK, thereby unequivocally confirming Sr22 effectiveness against Ug99. The third allele from accession PI573523, previously believed to confer susceptibility, was confirmed as nonfunctional against Australian P. graminis f. sp. tritici race 98-1,2,3,5,6.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
- Published
- 2020
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39. The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire.
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Steuernagel B, Witek K, Krattinger SG, Ramirez-Gonzalez RH, Schoonbeek HJ, Yu G, Baggs E, Witek AI, Yadav I, Krasileva KV, Jones JDG, Uauy C, Keller B, Ridout CJ, and Wulff BBH
- Subjects
- Disease Resistance, Genome, Plant genetics, Phylogeny, Plant Diseases microbiology, Plant Proteins genetics, Triticum metabolism, Triticum microbiology, Software
- Abstract
Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat ( Triticum aestivum ) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny, and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress, we found up-regulation of 266 of the NLRs To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties., (© 2020 American Society of Plant Biologists. All Rights Reserved.)
- Published
- 2020
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40. Discovery and characterisation of a new leaf rust resistance gene introgressed in wheat from wild wheat Aegilops peregrina.
- Author
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Narang D, Kaur S, Steuernagel B, Ghosh S, Bansal U, Li J, Zhang P, Bhardwaj S, Uauy C, Wulff BBH, and Chhuneja P
- Subjects
- Chromosome Mapping, Genes, Plant, In Situ Hybridization, Fluorescence, Disease Resistance genetics, Plant Diseases genetics, Plant Diseases microbiology, Triticum genetics, Triticum microbiology
- Abstract
Wild wheat species Aegilops peregrina (U
p Up Sp Sp ), harbours resistance to various diseases including leaf rust and stripe rust. Inheritance studies in a recombinant inbred line population of wheat-Ae. peregrina introgression line IL pau16061 revealed the transfer of a single major dominant gene conditioning all stage resistance, herein temporarily designated as LrAp. Genomic in situ hybridisation of IL pau16061, resistant and susceptible RILs with U- and S-genome DNA probes confirmed that the introgression with leaf rust resistance is from the Up genome of Ae. peregrina. Fluorescence in situ hybridisation using chromosome specific probes identified Up genome introgression to be on the long arm of wheat chromosome 6B. To genetically map LrAp, bulked segregant analysis was combined with resistance gene enrichment sequencing (MapRenSeq). Five nucleotide binding leucine-rich repeat contigs distinguished resistant and susceptible bulks and single nucleotide polymorphism (SNP) markers from these contigs co-segregated with LrAp. All five RenSeq NB_ARC contigs showed identity with the long arm of wheat chromosome 6B confirming the introgression on 6BL which we propose is a compensating translocation from Ae. peregrina chromosome 6Up L due to homoeology between the alien and wheat chromosomes. The SNP markers developed in this study will aid in cloning and marker assisted gene pyramiding of LrAp.- Published
- 2020
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41. Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.
- Author
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Hiebert CW, Moscou MJ, Hewitt T, Steuernagel B, Hernández-Pinzón I, Green P, Pujol V, Zhang P, Rouse MN, Jin Y, McIntosh RA, Upadhyaya N, Zhang J, Bhavani S, Vrána J, Karafiátová M, Huang L, Fetch T, Doležel J, Wulff BBH, Lagudah E, and Spielmeyer W
- Subjects
- Basidiomycota pathogenicity, Chromosome Mapping, Chromosomes, Plant genetics, Gene Duplication, Gene Expression, Gene Expression Regulation, Plant, Genes, Plant genetics, Mutation, Phenotype, Plant Diseases immunology, Plant Diseases microbiology, Plant Immunity genetics, Poaceae classification, Poaceae genetics, Triticum immunology, Triticum microbiology, Disease Resistance genetics, Mediator Complex genetics, Plant Diseases genetics, Triticum genetics
- Abstract
Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar 'Canthatch' suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat.
- Published
- 2020
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42. Natural Polymorphisms in Arabidopsis Result in Wide Variation or Loss of the Amylose Component of Starch.
- Author
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Seung D, Echevarría-Poza A, Steuernagel B, and Smith AM
- Subjects
- Amylopectin analysis, Amylopectin genetics, Amylopectin metabolism, Amylose analysis, Amylose genetics, Amylose metabolism, Arabidopsis enzymology, Arabidopsis genetics, Arabidopsis Proteins genetics, Cytoplasmic Granules enzymology, Cytoplasmic Granules genetics, Cytoplasmic Granules metabolism, Gene Expression Regulation, Plant genetics, Genetic Variation, Genotype, Phenotype, Plant Leaves genetics, Plant Leaves metabolism, Plant Roots enzymology, Plant Roots genetics, Plant Roots metabolism, Polymorphism, Single Nucleotide, Recombinant Proteins genetics, Recombinant Proteins isolation & purification, Recombinant Proteins metabolism, Sequence Analysis, DNA, Starch metabolism, Amylose biosynthesis, Arabidopsis metabolism, Arabidopsis Proteins metabolism, Starch analysis, Starch Synthase genetics, Starch Synthase metabolism
- Abstract
Starch granules contain two Glc polymers, amylopectin and amylose. Amylose makes up approximately 10% to 30% (w/w) of all natural starches thus far examined, but mutants of crop and model plants that produce amylose-free starch are generally indistinguishable from their wild-type counterparts with respect to growth, starch content, and granule morphology. Since the function and adaptive significance of amylose are unknown, we asked whether there is natural genetic variation in amylose synthesis within a wild, uncultivated species. We examined polymorphisms among the 1,135 sequenced accessions of Arabidopsis ( Arabidopsis thaliana ) in GRANULE-BOUND STARCH SYNTHASE ( GBSS ), encoding the enzyme responsible for amylose synthesis. We identified 18 accessions that are predicted to have polymorphisms in GBSS that affect protein function, and five of these accessions produced starch with no or extremely low amylose (< 0.5% [w/w]). Eight further accessions had amylose contents that were significantly lower or higher than that of Col-0 (9% [w/w]), ranging from 5% to 12% (w/w). We examined the effect of the polymorphisms on GBSS function and uncovered three mechanisms by which GBSS sequence variation led to different amylose contents: (1) altered GBSS abundance, (2) altered GBSS activity, and (3) altered affinity of GBSS for binding PROTEIN TARGETING TO STARCH1-a protein that targets GBSS to starch granules. These findings demonstrate that amylose in leaves is not essential for the viability of some naturally occurring Arabidopsis genotypes, at least over short timescales and under some environmental conditions and open an opportunity to explore the adaptive significance of amylose., (© 2020 American Society of Plant Biologists. All Rights Reserved.)
- Published
- 2020
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43. The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.
- Author
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Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, and Martin C
- Subjects
- Flavonoids metabolism, Genome, Plant, Medicine, Chinese Traditional, Plant Extracts, Plant Roots metabolism, Plants, Medicinal genetics, Plants, Medicinal metabolism, Scutellaria baicalensis metabolism, Whole Genome Sequencing, Biosynthetic Pathways genetics, Flavanones genetics, Flavanones metabolism, Flavonoids genetics, Scutellaria baicalensis genetics
- Abstract
Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionalizations were involved in the evolution of 4'-deoxyflavone synthesis in the genus Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2019
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44. The Coiled-Coil NLR Rph1 , Confers Leaf Rust Resistance in Barley Cultivar Sudan.
- Author
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Dracatos PM, Bartoš J, Elmansour H, Singh D, Karafiátová M, Zhang P, Steuernagel B, Svačina R, Cobbin JCA, Clark B, Hoxha S, Khatkar MS, Doležel J, Wulff BB, and Park RF
- Subjects
- Chromosome Mapping, Genes, Plant, Plant Proteins physiology, Sequence Analysis, DNA, Hordeum physiology, Host-Pathogen Interactions, NLR Proteins physiology
- Abstract
Unraveling and exploiting mechanisms of disease resistance in cereal crops is currently limited by their large repeat-rich genomes and the lack of genetic recombination or cultivar (cv)-specific sequence information. We cloned the first leaf rust resistance gene Rph1 ( Rph1 a ) from cultivated barley ( Hordeum vulgare ) using "MutChromSeq," a recently developed molecular genomics tool for the rapid cloning of genes in plants. Marker-trait association in the CI 9214/Stirling doubled haploid population mapped Rph1 to the short arm of chromosome 2H in a physical region of 1.3 megabases relative to the barley cv Morex reference assembly. A sodium azide mutant population in cv Sudan was generated and 10 mutants were confirmed by progeny-testing. Flow-sorted 2H chromosomes from Sudan (wild type) and six of the mutants were sequenced and compared to identify candidate genes for the Rph1 locus. MutChromSeq identified a single gene candidate encoding a coiled-coil nucleotide binding site Leucine-rich repeat (NLR) receptor protein that was altered in three different mutants. Further Sanger sequencing confirmed all three mutations and identified an additional two independent mutations within the same candidate gene. Phylogenetic analysis determined that Rph1 clustered separately from all previously cloned NLRs from the Triticeae and displayed highest sequence similarity (89%) with a homolog of the Arabidopsis ( Arabidopsis thaliana ) disease resistance protein 1 protein in Triticum urartu In this study we determined the molecular basis for Rph1 -mediated resistance in cultivated barley enabling varietal improvement through diagnostic marker design, gene editing, and gene stacking technologies., (© 2019 American Society of Plant Biologists. All Rights Reserved.)
- Published
- 2019
- Full Text
- View/download PDF
45. Resistance gene cloning from a wild crop relative by sequence capture and association genetics.
- Author
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Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, Johnson R, Enk J, Periyannan S, Singh N, Asyraf Md Hatta M, Athiyannan N, Cheema J, Yu G, Kangara N, Ghosh S, Szabo LJ, Poland J, Bariana H, Jones JDG, Bentley AR, Ayliffe M, Olson E, Xu SS, Steffenson BJ, Lagudah E, and Wulff BBH
- Subjects
- Chromosome Mapping, Genetic Association Studies, Genetic Variation, Genomics, Genotype, Models, Genetic, Phenotype, Phylogeny, Polymorphism, Single Nucleotide, Seedlings, Triticum genetics, Cloning, Molecular, Crops, Agricultural genetics, Disease Resistance genetics, Genes, Plant, Plant Diseases genetics
- Abstract
Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.
- Published
- 2019
- Full Text
- View/download PDF
46. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars.
- Author
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Thind AK, Wicker T, Müller T, Ackermann PM, Steuernagel B, Wulff BBH, Spannagl M, Twardziok SO, Felder M, Lux T, Mayer KFX, Keller B, and Krattinger SG
- Subjects
- Base Pairing genetics, Crossing Over, Genetic, DNA Breaks, Double-Stranded, DNA Copy Number Variations genetics, DNA Repair genetics, Gene Flow, Genes, Plant, Haplotypes genetics, Multigene Family, Polymorphism, Single Nucleotide genetics, Sequence Deletion genetics, Synteny genetics, Chromosomes, Plant genetics, Genome, Plant, Sequence Analysis, DNA, Triticum genetics
- Abstract
Background: Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale., Results: Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes-the old landrace Chinese Spring and the elite Swiss spring wheat line 'CH Campala Lr22a'. Both chromosomes were assembled into megabase-sized scaffolds. There is a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations reveals four large indels of more than 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Analysis of SNP density reveals four haploblocks of 4, 8, 9 and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.4 to 0.7%., Conclusions: This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.
- Published
- 2018
- Full Text
- View/download PDF
47. Rht18 Semidwarfism in Wheat Is Due to Increased GA 2-oxidaseA9 Expression and Reduced GA Content.
- Author
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Ford BA, Foo E, Sharwood R, Karafiatova M, Vrána J, MacMillan C, Nichols DS, Steuernagel B, Uauy C, Doležel J, Chandler PM, and Spielmeyer W
- Subjects
- Centromere genetics, Chromosome Mapping, Chromosomes, Plant, Gene Expression Regulation, Plant, Gibberellins genetics, Mixed Function Oxygenases genetics, Mixed Function Oxygenases metabolism, Mutagenesis, Plant Proteins metabolism, Polyploidy, Promoter Regions, Genetic, Triticum metabolism, Gibberellins metabolism, Plant Proteins genetics, Triticum genetics, Triticum growth & development
- Abstract
Semidwarfing genes have improved crop yield by reducing height, improving lodging resistance, and allowing plants to allocate more assimilates to grain growth. In wheat ( Triticum aestivum ), the Rht18 semidwarfing gene was identified and deployed in durum wheat before it was transferred into bread wheat, where it was shown to have agronomic potential. Rht18 , a dominant and gibberellin (GA) responsive mutant, is genetically and functionally distinct from the widely used GA-insensitive semidwarfing genes Rht-B1b and Rht-D1b In this study, the Rht18 gene was identified by mutagenizing the semidwarf durum cultivar Icaro ( Rht18 ) and generating mutants with a range of tall phenotypes. Isolating and sequencing chromosome 6A of these "overgrowth" mutants showed that they contained independent mutations in the coding region of GA2oxA9 GA2oxA9 is predicted to encode a GA 2-oxidase that metabolizes GA biosynthetic intermediates into inactive products, effectively reducing the amount of bioactive GA (GA
1 ). Functional analysis of the GA2oxA9 protein demonstrated that GA2oxA9 converts the intermediate GA12 to the inactive metabolite GA110 Furthermore, Rht18 showed higher expression of GA2oxA9 and lower GA content compared with its tall parent. These data indicate that the increased expression of GA2oxA9 in Rht18 results in a reduction of both bioactive GA content and plant height. This study describes a height-reducing mechanism that can generate new genetic diversity for semidwarfism in wheat by combining increased expression with mutations of specific amino acid residues in GA2oxA9 ., (© 2018 American Society of Plant Biologists. All Rights Reserved.)- Published
- 2018
- Full Text
- View/download PDF
48. A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.
- Author
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Olohan L, Gardiner LJ, Lucaci A, Steuernagel B, Wulff B, Kenny J, Hall N, and Hall A
- Subjects
- Genome, Chloroplast, Polymorphism, Single Nucleotide, Sequence Analysis, DNA standards, DNA Methylation, Genome, Plant, Sequence Analysis, DNA methods, Triticum genetics
- Abstract
Background: Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq., Results: Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat., Conclusions: We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses.
- Published
- 2018
- Full Text
- View/download PDF
49. Rapid gene isolation in barley and wheat by mutant chromosome sequencing.
- Author
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Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, and Wulff BB
- Subjects
- Phenotype, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Chromosomes, Plant, Cloning, Molecular, Genes, Plant, Hordeum genetics, Mutation, Triticum genetics
- Abstract
Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes. We apply MutChromSeq to six mutants each of the barley Eceriferum-q gene and the wheat Pm2 genes. This approach unambiguously identified single candidate genes that were verified by Sanger sequencing of additional mutants. MutChromSeq enables reference-free forward genetics in barley and wheat, thus opening up their pan-genomes to functional genomics.
- Published
- 2016
- Full Text
- View/download PDF
50. A Homolog of Blade-On-Petiole 1 and 2 (BOP1/2) Controls Internode Length and Homeotic Changes of the Barley Inflorescence.
- Author
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Jost M, Taketa S, Mascher M, Himmelbach A, Yuo T, Shahinnia F, Rutten T, Druka A, Schmutzer T, Steuernagel B, Beier S, Taudien S, Scholz U, Morgante M, Waugh R, and Stein N
- Subjects
- Arabidopsis Proteins metabolism, Base Pairing genetics, Chromosome Mapping, Cloning, Molecular, Ecotype, Genetic Variation, Molecular Sequence Annotation, Mutation, Phenotype, Phylogeny, Plants, Genetically Modified, Recombination, Genetic genetics, Sequence Analysis, DNA, Sequence Deletion, Arabidopsis Proteins chemistry, Genes, Homeobox, Genes, Plant, Hordeum anatomy & histology, Hordeum genetics, Inflorescence anatomy & histology, Sequence Homology, Amino Acid
- Abstract
Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement. We analyzed the recessive mutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected., (© 2016 American Society of Plant Biologists. All Rights Reserved.)
- Published
- 2016
- Full Text
- View/download PDF
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