المؤلفون: Michael Abrouk, Yajun Wang, Emile Cavalet-Giorsa, Maxim Troukhan, Maksym Kravchuk, Simon G. Krattinger

المصدر: Scientific Data, Vol 10, Iss 1, Pp 1-7 (2023)

مصطلحات موضوعية: Science

الوصف: Abstract Wild wheat relatives have been explored in plant breeding to increase the genetic diversity of bread wheat, one of the most important food crops. Aegilops umbellulata is a diploid U genome-containing grass species that serves as a genetic reservoir for wheat improvement. In this study, we report the construction of a chromosome-scale reference assembly of Ae. umbellulata accession TA1851 based on corrected PacBio HiFi reads and chromosome conformation capture. The total assembly size was 4.25 Gb with a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We benchmarked the performance of hifiasm and LJA, two of the most widely used assemblers using standard and corrected HiFi reads, revealing a positive effect of corrected input reads. Comparative genome analysis confirmed substantial chromosome rearrangements in Ae. umbellulata compared to bread wheat. In summary, the Ae. umbellulata assembly provides a resource for comparative genomics in Triticeae and for the discovery of agriculturally important genes.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2052-4463Test

الوصول الحر: https://doaj.org/article/64edbbd163d24524a9dab97e0d4c6155Test

المؤلفون: Gautam Saripalli, Laxman Adhikari, Cameron Amos, Ashraf Kibriya, Hanin Ibrahim Ahmed, Matthias Heuberger, John Raupp, Naveenkumar Athiyannan, Thomas Wicker, Michael Abrouk, Sydney Wallace, Seyedali Hosseinirad, Parveen Chhuneja, Janelle Livesay, Nidhi Rawat, Simon G. Krattinger, Jesse Poland, Vijay Tiwari

المصدر: Communications Biology, Vol 6, Iss 1, Pp 1-14 (2023)

مصطلحات موضوعية: Biology (General), QH301-705.5

الوصف: Abstract Einkorn wheat (Triticum monococcum) is an ancient grain crop and a close relative of the diploid progenitor (T. urartu) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2399-3642Test

الوصول الحر: https://doaj.org/article/8e946778e9aa4a7a97fba14614674c61Test

المؤلفون: Michael Abrouk, Naveenkumar Athiyannan, Thomas Müller, Yveline Pailles, Christoph Stritt, Anne C. Roulin, Chenggen Chu, Shuyu Liu, Takumi Morita, Hirokazu Handa, Jesse Poland, Beat Keller, Simon G. Krattinger

المصدر: Communications Biology, Vol 4, Iss 1, Pp 1-11 (2021)

مصطلحات موضوعية: Biology (General), QH301-705.5

الوصف: Krattinger, Abrouk et al. use genome wide association study and haplotype analyses to investigate the genetics of glume colour in ten reference grade wheat genomes. Haplotype comparison identifies a MYB transcription factor as a candidate gene for red glume colour.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2399-3642Test

الوصول الحر: https://doaj.org/article/badc5c24b31646fd94b95acf706411c2Test

المؤلفون: Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, Denisa Šimoníková, Stéphane Cauet, Yveline Pailles, Jan Bettgenhaeuser, Liubov Gapa, Nora Scarcelli, Marie Couderc, Leila Zekraoui, Nagarajan Kathiresan, Jana Čížková, Eva Hřibová, Jaroslav Doležel, Sandrine Arribat, Hélène Bergès, Jan J. Wieringa, Mathieu Gueye, Ndjido A. Kane, Christian Leclerc, Sandrine Causse, Sylvie Vancoppenolle, Claire Billot, Thomas Wicker, Yves Vigouroux, Adeline Barnaud, Simon G. Krattinger

المصدر: Nature Communications, Vol 11, Iss 1, Pp 1-13 (2020)

مصطلحات موضوعية: Science

الوصف: Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2041-1723Test

الوصول الحر: https://doaj.org/article/520d2fa477e24ce3aeed2f598edff68cTest

المؤلفون: Mahmoud Said, Katerina Holušová, András Farkas, László Ivanizs, Eszter Gaál, Petr Cápal, Michael Abrouk, Mihaela M. Martis-Thiele, Balázs Kalapos, Jan Bartoš, Bernd Friebe, Jaroslav Doležel, István Molnár

المصدر: Frontiers in Plant Science, Vol 12 (2021)

مصطلحات موضوعية: goat grasses, Aegilops comosa, Aegilops umbellulata, single-gene FISH, chromosome flow sorting and sequencing, chromosome rearrangements, Plant culture, SB1-1110

الوصف: Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fpls.2021.689031/fullTest; https://doaj.org/toc/1664-462XTest

الوصول الحر: https://doaj.org/article/988442f3c509482cafabf9fe267c18b7Test

المؤلفون: Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Raj Pasam, Matthew Hayden, Kerrie Forrest, Zeev Frenkel, Abraham Korol, B. Emma Huang, Colin Cavanagh, Jen Taylor, Michael Abrouk, Andrew Sharpe, David Konkin, Pierre Sourdille, Benoît Darrier, Frédéric Choulet, Aurélien Bernard, Simone Rochfort, Adam Dimech, Nathan Watson-Haigh, Ute Baumann, Paul Eckermann, Delphine Fleury, Angela Juhasz, Sébastien Boisvert, Marc-Alexandre Nolin, Jaroslav Doležel, Hana Šimková, Helena Toegelová, Jan Šafář, Ming-Cheng Luo, Francisco Câmara, Matthias Pfeifer, Don Isdale, Johan Nyström-Persson, IWGSC, Dal-Hoe Koo, Matthew Tinning, Dangqun Cui, Zhengang Ru, Rudi Appels

المصدر: Genome Biology, Vol 19, Iss 1, Pp 1-18 (2018)

مصطلحات موضوعية: Wheat sequence finishing, Megabase-scale integration, Optical/physical maps Grain quality, Yield, Biology (General), QH301-705.5, Genetics, QH426-470

الوصف: Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

وصف الملف: electronic resource

العلاقة: http://link.springer.com/article/10.1186/s13059-018-1475-4Test; https://doaj.org/toc/1474-760XTest

الوصول الحر: https://doaj.org/article/0c850329a2e2415bae69d4ee3f8e54dfTest

المؤلفون: Mahmoud Said, Kateřina Holušová, András Farkas, László Ivanizs, Eszter Gaál, Petr Cápal, Michaël Abrouk, Mihaela M. Martis, Balázs Kalapos, Jan Bartoš, Bernd Friebe, Jaroslav Doležel, István Molnár

مصطلحات موضوعية: Genetic Diversity and Breeding of Wheat, Plant Science, Agricultural and Biological Sciences, Life Sciences, Genome Evolution and Polyploidy in Plants, Genetics and Epidemiology of Plant Pathogens, Breeding, Genetic Mapping, Aegilops, Biology, Genetics, FOS Biological sciences, Genome, Triticeae, Chromosome, Gene

الوصف: Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat ( Triticum aestivum ), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops . The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed ... : يعيق تكاثر المحاصيل الزراعية المتكيفة مع تغير المناخ والمقاومة للأمراض والآفات تجمع الجينات المحدود بسبب التدجين وآلاف السنين من الانتقاء البشري. تتمثل إحدى طرق زيادة التنوع الجيني في نقل الجينات بوساطة الكروموسومات من الأقارب البرية عن طريق التهجين المتقاطع. في حالة القمح ( Triticum aestivum )، تعد أنواع جنس Aegilops مصدرًا جذابًا بشكل خاص للجينات والأليلات الجديدة. ومع ذلك، خلال تطور أجناس Aegilops و Triticum، أدى تنويع سلالة الجينوم D إلى تكوين جينوم ثنائي الصيغة الصبغية C و M و U من Aegilops . إن مدى التغيرات الهيكلية في الجينوم، التي رافقت تطورها وانتواعها، ونقص الأدوات الجزيئية للكشف عن Aegilops chromatin يعيق نقل الجينات إلى القمح. للتحقيق في بنية الكروموسوم والمساعدة في تطوير علامات جزيئية ذات موضع مادي معروف يمكن أن يحسن كفاءة اختيار الاندفاعات المرغوبة، قمنا بتطوير خرائط تهجين في الموقع أحادية الجين (FISH) لأسلاف الجينوم M و U، Aegilops comosa و Aegilops umbellulata، على التوالي. تم العثور على ثلاثة وأربعين جينًا عظميًا في 47 موقعًا في Ae. comosa وفي 52 موقعًا في Ae. umbellulata باستخدام مسابير ...

العلاقة: https://dx.doi.org/10.60692/pae8a-s4y58Test

الإتاحة: https://doi.org/10.60692/set53-mh71310.60692/pae8a-s4y58Test

المؤلفون: Yajun Wang, Michael Abrouk, Spyridon Gourdoupis, Dal-Hoe Koo, Miroslava Karafiátová, István Molnár, Kateřina Holušová, Jaroslav Doležel, Naveenkumar Athiyannan, Emile Cavalet-Giorsa, Łukasz Jaremko, Jesse Poland, Simon G. Krattinger

المصدر: Nature Genetics.

مصطلحات موضوعية: Genetics

الوصف: The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata2. We established that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Aegilopstriuncialis3, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::71bf2252744a6429d8ffdd5d422f23a3Test
https://doi.org/10.1038/s41588-023-01401-2Test

المؤلفون: Michael Abrouk, MD, Yasmine Noussari, BS, Jill S. Waibel, MD

المصدر: JAAD Case Reports, Vol 6, Iss 9, Pp 852-853 (2020)

مصطلحات موضوعية: calcifications, calcinosis cutis, carbon dioxide, dermatomyositis, laser, picosecond, Dermatology, RL1-803

العلاقة: http://www.sciencedirect.com/science/article/pii/S2352512620304495Test; https://doaj.org/toc/2352-5126Test; https://doaj.org/article/edb63d31a9924fda897a02e4ee75d08aTest

الإتاحة: https://doi.org/10.1016/j.jdcr.2020.06.022Test
https://doaj.org/article/edb63d31a9924fda897a02e4ee75d08aTest

المؤلفون: Jin Xiao, Keli Dai, Lian Fu, Jan Vrána, Marie Kubaláková, Wentao Wan, Haojie Sun, Jing Zhao, Chunyan Yu, Yufeng Wu, Michael Abrouk, Haiyan Wang, Jaroslav Doležel, Xiue Wang

المصدر: BMC Genomics, Vol 18, Iss 1, Pp 1-11 (2017)

مصطلحات موضوعية: Haynaldia villosa, Flow sorting, Chromosome arm 4VS, Scaffold, Genome zipper, Biotechnology, TP248.13-248.65, Genetics, QH426-470

الوصف: Abstract Background Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. Results In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1.5% of the arm. The syntenic regions of the 4VS were searched and identified on wheat group 4 chromosomes 4AL, 4BS, 4DS, Brachypodium chromosomes 1 and 4, rice chromosomes 3 and 11, and sorghum chromosomes 1, 5 and 8. Based on genome-zipper analysis, a virtual gene order comprising 735 gene loci on 4VS genome was built by referring to the Brachypodium genome, which was relatively consistent with the scaffold order determined for Ae. tauschii chromosome 4D. The homologous alleles of several cloned genes on wheat group 4 chromosomes including Rht-1 gene were identified. Conclusions The sequences provided valuable information for mapping and positional-cloning genes located on 4VS, such as the wheat yellow mosaic virus resistance gene Wss1. The work on 4VS provided detailed insights into the genome of H. villosa, and may also serve as a model for sequencing the remaining parts of H. villosa genome.

وصف الملف: electronic resource

العلاقة: http://link.springer.com/article/10.1186/s12864-017-4211-7Test; https://doaj.org/toc/1471-2164Test

الوصول الحر: https://doaj.org/article/21d839dee48544889052f4cd49dd5907Test