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794 results on '"Kilian, Andrzej"'

1. A Mid-Density Single-Nucleotide Polymorphism Panel for Molecular Applications in Cowpea (Vigna unguiculata (L.) Walp).

Author

Close, Timothy, Boukar, Ousmane, Ongom, Patrick, Fatokun, Christian, Togola, Abou, Garcia-Oliveira, Ana, Ng, Eng, Kilian, Andrzej, and Lonardi, Stefano

Abstract

Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array. The panels usefulness was assessed using 376 genotypes from different populations of known genetic backgrounds. The panel was informative, with over 78% of SNPs exceeding a minor allele frequency of 0.20. The panel decoded three stratifications in the constituted population, as was expected. Linkage disequilibrium (LD) decay was correctly depicted as slower in a biparental subset than in other populations. A known flower and seed coat color gene region was located on chromosome Vu07, suggesting that the mid-density panel may be used to hypothesize genomic regions underlying target traits in cowpea. Unexpected heterozygosity was detected in some lines and highly among F1 progenies, divulging the panels potential application in germplasm purity and hybridity verification. The study unveils the potential of an excellent genomic resource that can be tapped to enhance the development of improved cowpea cultivars.

Published
2024

4. A mosaic monoploid reference sequence for the highly complex genome of sugarcane.

Author

Garsmeur, Olivier, Droc, Gaetan, Antonise, Rudie, Grimwood, Jane, Potier, Bernard, Aitken, Karen, Jenkins, Jerry, Martin, Guillaume, Charron, Carine, Hervouet, Catherine, Costet, Laurent, Yahiaoui, Nabila, Healey, Adam, Sims, David, Cherukuri, Yesesri, Sreedasyam, Avinash, Kilian, Andrzej, Chan, Agnes, Van Sluys, Marie-Anne, Swaminathan, Kankshita, Town, Christopher, Bergès, Hélène, Simmons, Blake, Glaszmann, Jean Christophe, van der Vossen, Edwin, Henry, Robert, Schmutz, Jeremy, and D'Hont, Angélique

Subjects
Chromosomes, Artificial, Bacterial, Chromosomes, Plant, Saccharum, Sorghum, DNA Transposable Elements, Sequence Analysis, DNA, Gene Amplification, Base Sequence, Ploidies, Mosaicism, Polymorphism, Single Nucleotide, Genome, Plant, Models, Genetic, Genomic Structural Variation, Chromosomes, Artificial, Bacterial, Plant, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genome, Models, Genetic, Biotechnology, Genetics, Human Genome
Abstract

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.

Published
2018

5. Targeted genotyping-by-sequencing of potato and software for imputation

Author

Endelman, Jeffrey B., primary, Kante, Moctar, additional, Lindqvist-Kreuze, Hannele, additional, Kilian, Andrzej, additional, Shannon, Laura M., additional, Caraza-Harter, Maria V., additional, Vaillancourt, Brieanne, additional, Mailloux, Kathrine, additional, Hamilton, John P., additional, and Buell, C. Robin, additional

Published
2024
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11. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Author

Consortium, The International Wheat Genome Sequencing, Mayer, Klaus FX, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J, Sourdille, Pierre, Endo, Takashi R, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, McLay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Sandve, Simen Rød, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Pfeifer, Matthias, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikaël, Keller, Beat, and Praud, Sebastien

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Human Genome, Bread, Chromosomes, Plant, Evolution, Molecular, Gene Order, Genetic Variation, Genome, Plant, Molecular Sequence Annotation, Phylogeny, Plant Proteins, Polyploidy, Sequence Analysis, DNA, Transcriptome, Triticum, International Wheat Genome Sequencing Consortium, General Science & Technology
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

12. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

Author

Goodwin, Stephen B, M'barek, Sarrah Ben, Dhillon, Braham, Wittenberg, Alexander HJ, Crane, Charles F, Hane, James K, Foster, Andrew J, Van der Lee, Theo AJ, Grimwood, Jane, Aerts, Andrea, Antoniw, John, Bailey, Andy, Bluhm, Burt, Bowler, Judith, Bristow, Jim, van der Burgt, Ate, Canto-Canché, Blondy, Churchill, Alice CL, Conde-Ferràez, Laura, Cools, Hans J, Coutinho, Pedro M, Csukai, Michael, Dehal, Paramvir, De Wit, Pierre, Donzelli, Bruno, van de Geest, Henri C, van Ham, Roeland CHJ, Hammond-Kosack, Kim E, Henrissat, Bernard, Kilian, Andrzej, Kobayashi, Adilson K, Koopmann, Edda, Kourmpetis, Yiannis, Kuzniar, Arnold, Lindquist, Erika, Lombard, Vincent, Maliepaard, Chris, Martins, Natalia, Mehrabi, Rahim, Nap, Jan PH, Ponomarenko, Alisa, Rudd, Jason J, Salamov, Asaf, Schmutz, Jeremy, Schouten, Henk J, Shapiro, Harris, Stergiopoulos, Ioannis, Torriani, Stefano FF, Tu, Hank, de Vries, Ronald P, Waalwijk, Cees, Ware, Sarah B, Wiebenga, Ad, Zwiers, Lute-Harm, Oliver, Richard P, Grigoriev, Igor V, and Kema, Gert HJ

Subjects
Chromosomes, Fungal, Ascomycota, Triticum, Plant Diseases, Gene Rearrangement, Synteny, Genome, Fungal, Genetics, Infectious Diseases, Biotechnology, 2.2 Factors relating to the physical environment, Infection, Developmental Biology
Abstract

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors.

Published
2011

14. Development and mapping of DArT markers within the Festuca - Lolium complex

Author

Kopecký, David, Bartoš, Jan, Lukaszewski, Adam J, Baird, James H, Černoch, Vladimír, Kölliker, Roland, Rognli, Odd, Blois, Helene, Caig, Vanessa, Lübberstedt, Thomas, Studer, Bruno, Shaw, Paul, Doležel, Jaroslav, and Kilian, Andrzej

Abstract

Abstract Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT) array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used), we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins. Conclusion The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca × Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions.

Published
2009

17. Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Author

Sansaloni, Carolina, Franco, Jorge, Santos, Bruno, Percival-Alwyn, Lawrence, Singh, Sukhwinder, Petroli, Cesar, Campos, Jaime, Dreher, Kate, Payne, Thomas, Marshall, David, Kilian, Benjamin, Milne, Iain, Raubach, Sebastian, Shaw, Paul, Stephen, Gordon, Carling, Jason, Pierre, Carolina Saint, Burgueño, Juan, Crosa, José, Li, HuiHui, Guzman, Carlos, Kehel, Zakaria, Amri, Ahmed, Kilian, Andrzej, Wenzl, Peter, Uauy, Cristobal, Banziger, Marianne, Caccamo, Mario, and Pixley, Kevin

Published
2020
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25. Genetic Map of Diploid Wheat, Triticum monococcum L., and Its Comparison With Maps of Hordeum vulgare L.

Author

Dubcovsky, Jorge, Luo, Ming-Cheng, Zhong, Gan-Yuan, Bransteitter, Ronda, Desai, Amrita, Kilian, Andrzej, Kleinhofs, Andris, and Dvořák, Jan

Subjects
Genetics, Human Genome, Chromosome Mapping, Genes, Plant, Genetic Linkage, Hordeum, Recombination, Genetic, Triticum, Developmental Biology
Abstract

A genetic map of diploid wheat, Triticum monococcum L., involving 335 markers, including RFLP DNA markers, isozymes, seed storage proteins, rRNA, and morphological loci, is reported. T. monococcum and barley linkage groups are remarkably conserved. They differ by a reciprocal translocation involving the long arms of chromosomes 4 and 5, and paracentric inversions in the long arm of chromosomes 1 and 4; the latter is in a segment of chromosome arm 4L translocated to 5L in T. monococcum. The order of the markers in the inverted segments in the T. monococcum genome is the same as in the B and D genomes of T. aestivum L. The T. monococcum map differs from the barley maps in the distribution of recombination within chromosomes. The major 5S rRNA loci were mapped on the short arms of T. monococcum chromosomes 1 and 5 and the long arms of barley chromosomes 2 and 3. Since these chromosome arms are colinear, the major 5S rRNA loci must be subjected to positional changes in the evolving Triticeae genome that do not perturb chromosome colinearity. The positional changes of the major 5S rRNA loci in Triticeae genomes are analogous to those of the 18S-5.8S-26S rRNA loci.

Published
1996

29. Identification of Single Nucleotide Polymorphisms Associated with Brown Rust Resistance, α-Amylase Activity and Pre-harvest Sprouting in Rye (Secale cereale L.)

Author

Rakoczy-Trojanowska, Monika, Krajewski, Paweł, Bocianowski, Jan, Schollenberger, Małgorzata, Wakuliński, Wojciech, Milczarski, Paweł, Masojć, Piotr, Targońska-Karasek, Małgorzata, Banaszak, Zofia, Banaszak, Katarzyna, Brukwiński, Waldemar, Orczyk, Wacław, and Kilian, Andrzej

Published
2017
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33. Construction of a genetic linkage map and QTL analysis in bambara groundnut

Author

Ahmad, Nariman Salih, Redjeki, Endah Sri, Ho, Wai Kuan, Aliyu, Siise, Mayes, Katie, Massawe, Festo, Kilian, Andrzej, and Mayes, Sean

Subjects
Nucleotide sequencing -- Methods, Mimosaceae -- Genetic aspects, Quantitative trait loci -- Observations, Legumes -- Genetic aspects, DNA sequencing -- Methods, Beans -- Genetic aspects, Biological sciences
Abstract

Abstract: Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of [...]

Published
2016

35. Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water‐use efficiency and seed yield in canola

Author

Raman, Harsh, primary, Raman, Rosy, additional, Pirathiban, Ramethaa, additional, McVittie, Brett, additional, Sharma, Niharika, additional, Liu, Shengyi, additional, Qiu, Yu, additional, Zhu, Anyu, additional, Kilian, Andrzej, additional, Cullis, Brian, additional, Farquhar, Graham D., additional, Stuart‐Williams, Hilary, additional, White, Rosemary, additional, Tabah, David, additional, Easton, Andrew, additional, and Zhang, Yuanyuan, additional

Published
2022
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39. A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

Author

Paux, Etienne, Sourdille, Pierre, Salse, Jérôme, Saintenac, Cyrille, Choulet, Frédéric, Leroy, Philippe, Korol, Abraham, Michalak, Monika, Kianian, Shahryar, Spielmeyer, Wolfgang, Lagudah, Evans, Somers, Daryl, Kilian, Andrzej, Alaux, Michael, Vautrin, Sonia, Bergès, Hélène, Eversole, Kellye, Appels, Rudi, Safar, Jan, Simkova, Hana, Dolezel, Jaroslav, Bernard, Michel, and Feuillet, Catherine

Published
2008
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48. HIPHOP: Improved paternity assignment among close relatives using a simple exclusion method for biallelic markers

Author

Cockburn, Andrew, Penalba, Joshua, V, Jaccoud, Damian, Kilian, Andrzej, Brouwer, Lyanne, Double, Michael C., Kruuk, Loeske E.B., Pol, Martijn van de, Cockburn, Andrew, Penalba, Joshua, V, Jaccoud, Damian, Kilian, Andrzej, Brouwer, Lyanne, Double, Michael C., Kruuk, Loeske E.B., and Pol, Martijn van de

Abstract

Contains fulltext : 235938.pdf (Publisher’s version ) (Closed access)

Published
2021

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