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Zhang X, Wang T. Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years. Plant Cell Physiol 2021; 62:1648-1661. [PMID: 34486654 PMCID: PMC8664644 DOI: 10.1093/pcp/pcab134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 05/05/2023]
Abstract
Over the past few decades, eukaryotic linear genomes and epigenomes have been widely and extensively studied for understanding gene expression regulation. More recently, the three-dimensional (3D) chromatin organization was found to be important for determining genome functionality, finely tuning physiological processes for appropriate cellular responses. With the development of visualization techniques and chromatin conformation capture (3C)-based techniques, increasing evidence indicates that chromosomal architecture characteristics and chromatin domains with different epigenetic modifications in the nucleus are correlated with transcriptional activities. Subsequent studies have further explored the intricate interplay between 3D genome organization and the function of interacting regions. In this review, we summarize spatial distribution patterns of chromatin, including chromatin positioning, configurations and domains, with a particular focus on the effect of a unique form of interaction between varieties of factors that shape the 3D genome conformation in plants. We further discuss the methods, advantages and limitations of various 3C-based techniques, highlighting the applications of these technologies in plants to identify chromatin domains, and address their dynamic changes and functional implications in evolution, and adaptation to development and changing environmental conditions. Moreover, the future implications and emerging research directions of 3D genome organization are discussed.
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Affiliation(s)
- Xinxin Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P. R. China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Tianzuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, P. R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100093, P. R. China
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2
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Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble‐Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu YQ, Mascher M, Dvorak J, Luo M. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant J 2021; 107:303-314. [PMID: 33893684 PMCID: PMC8360199 DOI: 10.1111/tpj.15289] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 05/09/2023]
Abstract
Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.
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Affiliation(s)
- Tingting Zhu
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Le Wang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Hélène Rimbert
- GDECUniversité Clermont AuvergneINRAEClermont‐Ferrand63000France
| | | | - Karin R. Deal
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | | | - Frédéric Choulet
- GDECUniversité Clermont AuvergneINRAEClermont‐Ferrand63000France
| | | | - Josquin Tibbits
- Centre for AgriBioscienceAgriculture VictoriaAgriBioBundooraVIC3083Australia
| | - Jane Rogers
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Kellye Eversole
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Rudi Appels
- Centre for AgriBioscienceAgriculture VictoriaAgriBioBundooraVIC3083Australia
- International Wheat Genome Sequencing ConsortiumEau ClaireWI54701USA
| | - Yong Q. Gu
- Crop Improvement and Genetics Research UnitUSDA‐ARSAlbanyCA94710USA
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jan Dvorak
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
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3
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Kudryavtseva N, Ermolaev A, Karlov G, Kirov I, Shigyo M, Sato S, Khrustaleva L. A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps. Int J Mol Sci 2021; 22:5860. [PMID: 34070753 PMCID: PMC8215642 DOI: 10.3390/ijms22115860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps.
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Affiliation(s)
- Natalya Kudryavtseva
- Laboratory of Plant Cell Engineering, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia;
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
| | - Aleksey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Kurchatov Genomics Center of ARRIAB, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Masayoshi Shigyo
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan;
| | - Shusei Sato
- Graduate School of Life Science, Tohoku University, Miyagi 980-8577, Japan;
| | - Ludmila Khrustaleva
- Laboratory of Plant Cell Engineering, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia;
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
- Department of Botany, Breeding and Seed Production of Garden Plants, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
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4
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Melonek J, Duarte J, Martin J, Beuf L, Murigneux A, Varenne P, Comadran J, Specel S, Levadoux S, Bernath-Levin K, Torney F, Pichon JP, Perez P, Small I. The genetic basis of cytoplasmic male sterility and fertility restoration in wheat. Nat Commun 2021; 12:1036. [PMID: 33589621 PMCID: PMC7884431 DOI: 10.1038/s41467-021-21225-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/15/2021] [Indexed: 01/31/2023] Open
Abstract
Hybrid wheat varieties give higher yields than conventional lines but are difficult to produce due to a lack of effective control of male fertility in breeding lines. One promising system involves the Rf1 and Rf3 genes that restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility (T-CMS). Here, by genetic mapping and comparative sequence analyses, we identify Rf1 and Rf3 candidates that can restore normal pollen production in transgenic wheat plants carrying T-CMS. We show that Rf1 and Rf3 bind to the mitochondrial orf279 transcript and induce cleavage, preventing expression of the CMS trait. The identification of restorer genes in wheat is an important step towards the development of hybrid wheat varieties based on a CMS-Rf system. The characterisation of their mode of action brings insights into the molecular basis of CMS and fertility restoration in plants.
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Affiliation(s)
- Joanna Melonek
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Jorge Duarte
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Jerome Martin
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Laurent Beuf
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Alain Murigneux
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Pierrick Varenne
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Jordi Comadran
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Sebastien Specel
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Sylvain Levadoux
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Kalia Bernath-Levin
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - François Torney
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | | | - Pascual Perez
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.
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5
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Kubalová I, Němečková A, Weisshart K, Hřibová E, Schubert V. Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes. Int J Mol Sci 2021; 22:ijms22041903. [PMID: 33672992 PMCID: PMC7917581 DOI: 10.3390/ijms22041903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
| | - Alžběta Němečková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | | | - Eva Hřibová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
- Correspondence: ; Tel.: +49-394-825-212
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6
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Yu L, Ma X, Deng B, Yue J, Ming R. Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol Genet Genomics 2021; 296:41-53. [PMID: 32955620 DOI: 10.1007/s00438-020-01723-1724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/04/2020] [Indexed: 05/18/2023]
Abstract
Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990 Mb, which is challenging for de-novo genome assembly. In our study, a segregating F1 (double pseudo-testcross) population from 'Viroflay' × 'Cornell-NO. 9' was used for genetic mapping by resequencing genotyping. In the paternal 'Cornell-NO. 9' map, 212,414 SNPs were mapped, and the total linkage distance was 476.83 cM; the maternal 'Viroflay' map included 29,282 SNPs with 401.28 cM total genetic distance. Both paternal and maternal maps have the expected number of six linkage groups (LGs). A non-recombining region with 5678 SNPs (39 bin markers) co-segregates with sex type which located at 45.2 cM of LG1 in the 'Cornell-NO. 9' map while indicates the sex determination region (SDR). Integration of two maps into a consensus map guided us to anchor additional 1242 contigs to six pseudomolecules from the published reference genome, which improved additional 233 Mb (23.4%) assembly based on spinach estimated genome size. Particularly, the X counterpart of SDR in our assembly is estimated around 18.4 Mb which locates at the largest chromosome, as consensus with sex-biased FISH signals from previous cytogenetics studies. The region is featured by reduced gene density, higher percentage of repetitive sequences, and no recombination. Our linkage maps provide the resource for improving spinach genome de-novo assembly and identification of sex-determining genes in spinach.
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Affiliation(s)
- Li'ang Yu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ban Deng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingjing Yue
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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7
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Gratias A, Geffroy V. Deciphering the Impact of a Bacterial Infection on Meiotic Recombination in Arabidopsis with Fluorescence Tagged Lines. Genes (Basel) 2020; 11:genes11070832. [PMID: 32708324 PMCID: PMC7397157 DOI: 10.3390/genes11070832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
Plants are under strong evolutionary pressure to maintain surveillance against pathogens. One major disease resistance mechanism is based on NB-LRR (NLR) proteins that specifically recognize pathogen effectors. The cluster organization of the NLR gene family could favor sequence exchange between NLR genes via recombination, favoring their evolutionary dynamics. Increasing data, based on progeny analysis, suggest the existence of a link between the perception of biotic stress and the production of genetic diversity in the offspring. This could be driven by an increased rate of meiotic recombination in infected plants, but this has never been strictly demonstrated. In order to test if pathogen infection can increase DNA recombination in pollen meiotic cells, we infected Arabidopsis Fluorescent Tagged Lines (FTL) with the virulent bacteria Pseudomonas syringae. We measured the meiotic recombination rate in two regions of chromosome 5, containing or not an NLR gene cluster. In all tested intervals, no significant difference in genetic recombination frequency between infected and control plants was observed. Although it has been reported that pathogen exposure can sometimes increase the frequency of recombinant progeny in plants, our findings suggest that meiotic recombination rate in Arabidopsis may be resilient to at least some pathogen attack. Alternative mechanisms are discussed.
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Affiliation(s)
- Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
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8
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Lo S, Fatokun C, Boukar O, Gepts P, Close TJ, Muñoz-Amatriaín M. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). PLoS One 2020; 15:e0229167. [PMID: 32343700 PMCID: PMC7188242 DOI: 10.1371/journal.pone.0229167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/28/2020] [Indexed: 12/16/2022] Open
Abstract
Perennial habit and floral scent are major traits that distinguish domesticated cowpeas from their wild relatives. However, the genetic basis of these two important traits remains largely unknown in cowpea. Plant longevity, a perenniality-related trait, and floral scent, an outcrossing trait, were investigated using a RIL population derived from a cross between a domesticated and a wild cowpea. QTL analysis revealed three significant loci, one on chromosome 8 associated with plant longevity and two, on chromosomes 1 and 11, for floral scent. Genes within the QTL regions were identified. Genes encoding an F-box protein (Vigun08g215300) and two kinases (Vigun08g217000, Vigun08g217800), and involved in physiological processes including regulation of flowering time and plant longevity, were identified within the perenniality QTL region. A cluster of O-methyltransferase genes (Vigun11g096800, Vigun11g096900, Vigun11g097000, Vigun11g097600, and Vigun11g097800) was identified within the floral scent QTL region. These O-methyltransferase cowpea genes are orthologs of the Arabidopsis N-acetylserotonin O-methyltransferase (ASMT) gene, which is involved in the biosynthesis of melatonin. Melatonin is an indole derivative, which is an essential molecule for plant interactions with pollinators. These findings lay the foundation for further exploration of the genetic mechanisms of perenniality and floral scent in cowpea. Knowledge from this study can help in the development of new extended-growth cycle lines with increased yield or lines with increased outcrossing for population breeding.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States of America
- * E-mail: (MMA); (SL)
| | | | - Ousmane Boukar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Paul Gepts
- Department of Plant Sciences, University of California Davis, Davis, CA, United States of America
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States of America
| | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States of America
- * E-mail: (MMA); (SL)
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9
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Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H. The genome of broomcorn millet. Nat Commun 2019; 10:436. [PMID: 30683860 PMCID: PMC6347628 DOI: 10.1038/s41467-019-08409-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.
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Affiliation(s)
- Changsong Zou
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, 475001, Kaifeng, Henan, China
| | - Leiting Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Delin Li
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
| | - Qiming Tang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Lihong Xiao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | | | - Ping Deng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Wei Jia
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Ru Huang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Meiling Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Yidan Sun
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Jiamin Hu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Patrick S Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3650, USA
| | - Yuxiao Chang
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Feng Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Hui Zhang
- Key Laboratory of Plant Stress Research, Shandong Normal University, No. 88 Wenhua East Rd, Jinan, 250014, Shandong, China
| | - Baili Feng
- School of Agronomy, Northwest Agriculture & Forestry University, 3 Weihui Rd, 712100, Yangling, China
| | - Xinguang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, 200032, Shanghai, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - James C Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
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10
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Pernickova K, Linc G, Gaal E, Kopecky D, Samajova O, Lukaszewski AJ. Out-of-position telomeres in meiotic leptotene appear responsible for chiasmate pairing in an inversion heterozygote in wheat (Triticum aestivum L.). Chromosoma 2018; 128:31-39. [PMID: 30483879 DOI: 10.1007/s00412-018-0686-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 11/26/2022]
Abstract
Chromosome pairing in meiosis usually starts in the vicinity of the telomere attachment to the nuclear membrane and congregation of telomeres in the leptotene bouquet is believed responsible for bringing homologue pairs together. In a heterozygote for an inversion of a rye (Secale cereale L.) chromosome arm in wheat, a distal segment of the normal homologue is capable of chiasmate pairing with its counterpart in the inverted arm, located near the centromere. Using 3D imaging confocal microscopy, we observed that some telomeres failed to be incorporated into the bouquet and occupied various positions throughout the entire volume of the nucleus, including the centromere pole. Rye telomeres appeared ca. 21 times more likely to fail to be included in the telomere bouquet than wheat telomeres. The frequency of the out-of-bouquet rye telomere position in leptotene was virtually identical to the frequency of telomeres deviating from Rabl's orientation in the nuclei of somatic cells, and was similar to the frequency of synapsis of the normal and inverted chromosome arms, but lower than the MI pairing frequency of segments of these two arms normally positioned across the volume of the nucleus. Out-of-position placement of the rye telomeres may be responsible for reduced MI pairing of rye chromosomes in hybrids with wheat and their disproportionate contribution to aneuploidy, but appears responsible for initiating chiasmate pairing of distantly positioned segments of homology in an inversion heterozygote.
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Affiliation(s)
- Katerina Pernickova
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, Olomouc, Czech Republic
| | - Gabriella Linc
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Martonvasar, 2462, Hungary
- National Food Chain Safety Office, Budaörsi Str. 141-145, Budapest, 1118, Hungary
| | - Eszter Gaal
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Martonvasar, 2462, Hungary
- National Food Chain Safety Office, Budaörsi Str. 141-145, Budapest, 1118, Hungary
| | - David Kopecky
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, Olomouc, Czech Republic
| | - Olga Samajova
- Faculty of Science, Centre of the Region Hana for Biotechnological and Agricultural Research, Department of Cell Biology, Palacky University Olomouc, Slechtitelu 27, Olomouc, Czech Republic
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
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11
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Hiraga SI, Monerawela C, Katou Y, Shaw S, Clark KR, Shirahige K, Donaldson AD. Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks. EMBO Rep 2018; 19:e46222. [PMID: 30104203 PMCID: PMC6123642 DOI: 10.15252/embr.201846222] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/17/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022] Open
Abstract
Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome-wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with replication progressing normally or blocked by hydroxyurea. Rif1 associates strongly with telomeres through interaction with Rap1. By comparing genomic binding of wild-type Rif1 and truncated Rif1 lacking the Rap1-interaction domain, we identify hundreds of Rap1-dependent and Rap1-independent chromosome interaction sites. Rif1 binds to centromeres, highly transcribed genes and replication origins in a Rap1-independent manner, associating with both early and late-initiating origins. Interestingly, Rif1 also binds around activated origins when replication progression is blocked by hydroxyurea, suggesting association with blocked forks. Using nascent DNA labelling and DNA combing techniques, we find that in cells treated with hydroxyurea, yeast Rif1 stabilises recently synthesised DNA Our results indicate that, in addition to controlling DNA replication initiation, budding yeast Rif1 plays an ongoing role after initiation and controls events at blocked replication forks.
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Affiliation(s)
| | | | - Yuki Katou
- Institute for Quantitative Biosciences, University of Tokyo, Tokyo, Japan
| | - Sophie Shaw
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Kate Rm Clark
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
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12
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Yau S, Caravello G, Fonvieille N, Desgranges É, Moreau H, Grimsley N. Rapidity of Genomic Adaptations to Prasinovirus Infection in a Marine Microalga. Viruses 2018; 10:v10080441. [PMID: 30126244 PMCID: PMC6116238 DOI: 10.3390/v10080441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/19/2022] Open
Abstract
Prasinoviruses are large dsDNA viruses commonly found in aquatic systems worldwide, where they can infect and lyse unicellular prasinophyte algae such as Ostreococcus. Host susceptibility is virus strain-specific, but resistance of susceptible Ostreococcus tauri strains to a virulent virus arises frequently. In clonal resistant lines that re-grow, viruses are usually present for many generations, and genes clustered on chromosome 19 show physical rearrangements and differential expression. Here, we investigated changes occurring during the first two weeks after inoculation of the prasinovirus OtV5. By serial dilutions of cultures at the time of inoculation, we estimated the frequency of resistant cells arising in virus-challenged O. tauri cultures to be 10-3⁻10-4 of the inoculated population. Re-growing resistant cells were detectable by flow cytometry 3 days post-inoculation (dpi), visible re-greening of cultures occurred by 6 dpi, and karyotypic changes were visually detectable at 8 dpi. Resistant cell lines showed a modified spectrum of host-virus specificities and much lower levels of OtV5 adsorption.
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Affiliation(s)
- Sheree Yau
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Gaëtan Caravello
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Nadège Fonvieille
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Élodie Desgranges
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Hervé Moreau
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
| | - Nigel Grimsley
- Integrative Biology of Marine Organisms Laboratory (BIOM), CNRS UMR7232, 66650 Banuyls-sur-Mer, France.
- Sorbonne University, OOB, Avenue de Pierre Fabre, 66650 Banyuls-sur-Mer, France.
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13
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Lee CY, Lin HJ, Viswanath KK, Lin CP, Chang BCH, Chiu PH, Chiu CT, Wang RH, Chin SW, Chen FC. The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L. PLoS One 2018; 13:e0194605. [PMID: 29566053 PMCID: PMC5864051 DOI: 10.1371/journal.pone.0194605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/06/2018] [Indexed: 11/19/2022] Open
Abstract
Carica papaya L. is an important economic crop worldwide and is used as a model plant for sex-determination research. To study the different flower sex types, we screened sex-related genes using alternative splicing sequences (AS-seqs) from a transcriptome database of the three flower sex types, i.e., males, females, and hermaphrodites, established at 28 days before flowering using 15 bacterial artificial chromosomes (BACs) of C. papaya L. After screening, the cDNA regions of the three sex-related loci, including short vegetative phase-like (CpSVPL), the chromatin assembly factor 1 subunit A-like (CpCAF1AL), and the somatic embryogenesis receptor kinase (CpSERK), which contained eight sex-related single-nucleotide polymorphisms (SNPs) from the different sex types of C. papaya L., were genotyped using high-resolution melting (HRM). The three loci were examined regarding the profiles of the third whorl, as described below. CpSVPL, which had one SNP associated with the three sex genotypes, was highly expressed in the male and female sterile flowers (abnormal hermaphrodite flowers) that lacked the fourth whorl structure. CpCAF1AL, which had three SNPs associated with the male genotype, was highly expressed in male and normal hermaphrodite flowers, and had no AS-seqs, whereas it exhibited low expression and an AS-seqs in intron 11 in abnormal hermaphrodite flowers. Conversely, carpellate flowers (abnormal hermaphrodite flowers) showed low expression of CpSVPL and AS-seqs in introns 5, 6, and 7 of CpSERK, which contained four SNPs associated with the female genotype. Specifically, the CpSERK and CpCAF1AL loci exhibited no AS-seq expression in the third whorl of the male and normal hermaphrodite flowers, respectively, and variance in the AS-seq expression of all other types of flowers. Functional mapping of the third whorl of normal hermaphrodites indicated no AS-seq expression in CpSERK, low CpSVPL expression, and, for CpCAF1AL, high expression and no AS-seq expression on XYh-type chromosomes.
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Affiliation(s)
- Chen-Yu Lee
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
- * E-mail: (CYL); (FCC)
| | - Hui-Jun Lin
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kotapati Kasi Viswanath
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chih-Peng Lin
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | | | - Pei-Hsun Chiu
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | - Chan-Tai Chiu
- Pingtung Seed & Seedling Research Center, Taiwan Seed Improvement and Propagation Station, Pingtung, Taiwan
| | - Ren-Huang Wang
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, Pingtung, Taiwan
| | - Shih-Wen Chin
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Fure-Chyi Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
- * E-mail: (CYL); (FCC)
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14
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Shi X, Yan L, Yang C, Yan W, Moseley DO, Wang T, Liu B, Di R, Chen P, Zhang M. Identification of a major quantitative trait locus underlying salt tolerance in 'Jidou 12' soybean cultivar. BMC Res Notes 2018; 11:95. [PMID: 29402302 PMCID: PMC5800283 DOI: 10.1186/s13104-018-3202-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/23/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of the quantitative trait locus (QTL) underlying salt tolerance is a prerequisite for marker-assisted selection in the salt-tolerant breeding process. METHODS In this study, the recombinant inbred lines derived from the salt-tolerant elite soybean cultivar 'Jidou 12' and the salt-sensitive elite cultivar 'Ji NF 58' were used to identify the QTL associated with salt tolerance, using both salt tolerance rating (STR) and leaf chlorophyll content (SPAD) as indicators. RESULTS A major salt-tolerant QTL, which was flanked by SSR markers GMABAB and Barcsoyssr_03_1421 on chromosome 3, was identified based on single-marker regression, single trait composite interval mapping, and multiple interval mapping analysis. For STR, the LOD ranged from 19.8 to 20.1; R2 ranged from 44.3 to 44.7%; and the additive effect ranged from 0.876 to 0.885 among the three mapping methods. For SPAD, the LOD ranged from 10.6 to 11.0; R2 ranged from 27.0 to 27.6%; and the additive effect ranged from 1.634 to 1.679 among the three mapping methods. CONCLUSIONS In this study, a major QTL conditioning salt tolerance on chromosome 3 was identified. The DNA markers closely associated with the QTLs might be useful in marker-assisted selection for soybean salt tolerance improvement in Huanghuaihai, China.
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Affiliation(s)
- XiaoLei Shi
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
| | - Long Yan
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
- Department of Crop, Soil and Environment Sciences, University of Arkansas, Fayetteville, AR 72701 USA
| | - ChunYan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
| | - WeiWen Yan
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
| | - David Octor Moseley
- Department of Crop, Soil and Environment Sciences, University of Arkansas, Fayetteville, AR 72701 USA
| | - Tao Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
| | - BingQiang Liu
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
| | - Rui Di
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
| | - PengYin Chen
- Department of Crop, Soil and Environment Sciences, University of Arkansas, Fayetteville, AR 72701 USA
| | - MengChen Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Shijiazhuang Branch Center of National Center for Soybean Improvement/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture/Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050035 China
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15
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Abstract
With Chromosome Conformation Capture (3C), the relative interaction frequency of one chromosomal fragment with another can be determined. The technique is especially suited for unraveling the 3D organization of specific loci when focusing on aspects such as enhancer-promoter interactions or other topological conformations of the genome. 3C has been extensively used in animal systems, among others providing insight into gene regulation by distant cis-regulatory elements. In recent years, the 3C technique has been applied in plant research. However, the complexity of plant tissues prevents direct application of existing protocols from animals. Here, we describe an adapted protocol suitable for plant tissues, especially Arabidopsis thaliana and Zea mays.
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Affiliation(s)
- Blaise Weber
- Laboratory of Plant Development and Epigenetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Maike Stam
- Laboratory of Plant Development and Epigenetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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16
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Adhikari P, Oh Y, Panthee DR. Current Status of Early Blight Resistance in Tomato: An Update. Int J Mol Sci 2017; 18:E2019. [PMID: 28934121 PMCID: PMC5666701 DOI: 10.3390/ijms18102019] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 12/01/2022] Open
Abstract
Early blight (EB) is one of the dreadful diseases of tomato caused by several species of Alternaria including Alternaria linariae (which includes A. solani and A. tomatophila), as well as A. alternata. In some instances, annual economic yield losses due to EB have been estimated at 79%. Alternaria are known only to reproduce asexually, but a highly-virulent isolate has the potential to overcome existing resistance genes. Currently, cultural practices and fungicide applications are employed for the management of EB due to the lack of strong resistant cultivars. Resistance sources have been identified in wild species of tomato; some breeding lines and cultivars with moderate resistance have been developed through conventional breeding methods. Polygenic inheritance of EB resistance, insufficient resistance in cultivated species and the association of EB resistance with undesirable horticultural traits have thwarted the effective breeding of EB resistance in tomato. Several quantitative trait loci (QTL) conferring EB resistance have been detected in the populations derived from different wild species including Solanum habrochaites, Solanum arcanum and S. pimpinellifolium, but none of them could be used in EB resistance breeding due to low individual QTL effects. Pyramiding of those QTLs would provide strong resistance. More research is needed to identify additional sources of useful resistance, to incorporate resistant QTLs into breeding lines through marker-assisted selection (MAS) and to develop resistant cultivars with desirable horticultural traits including high yielding potential and early maturity. This paper will review the current understanding of causal agents of EB of tomato, resistance genetics and breeding, problems associated with breeding and future prospects.
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Affiliation(s)
- Pragya Adhikari
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, 455 Research Dr., Mills River, NC 28759, USA.
| | - Yeonyee Oh
- Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA.
| | - Dilip R Panthee
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, 455 Research Dr., Mills River, NC 28759, USA.
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17
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Wonneberger R, Ficke A, Lillemo M. Mapping of quantitative trait loci associated with resistance to net form net blotch (Pyrenophora teres f. teres) in a doubled haploid Norwegian barley population. PLoS One 2017; 12:e0175773. [PMID: 28448537 PMCID: PMC5407769 DOI: 10.1371/journal.pone.0175773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/31/2017] [Indexed: 12/01/2022] Open
Abstract
Barley net blotch caused by the necrotrophic fungus Pyrenophora teres is a major barley disease in Norway. It can cause grain shriveling and yield losses, and resistance in currently grown cultivars is insufficient. In this study, a set of 589 polymorphic SNP markers was used to map resistance loci in a population of 109 doubled haploid lines from a cross between the closely related Norwegian cultivars Arve (moderately susceptible) and Lavrans (moderately resistant). Resistance to three net form net blotch (P. teres f. teres) single spore isolates was evaluated at the seedling stage in the greenhouse and at the adult plant stage under field conditions during three years. Days to heading and plant height were scored to assess their influence on disease severity. At the seedling stage, three to four quantitative trait loci (QTL) associated with resistance were found per isolate used. A major, putatively novel QTL was identified on chromosome 5H, accounting for 23-48% of the genetic variation. Additional QTL explaining between 12 and 16.5% were found on chromosomes 4H, 5H, 6H and 7H, with the one on 6H being race-specific. The major QTL on 5H was also found in adult plants under field conditions in three years (explaining up to 55%) and the 7H QTL was found in field trials in one year. Additional adult plant resistance QTL on 3H, 6H and 7H were significant in single years. The resistance on chromosomes 3H, 5H, 6H and 7H originates from the more resistant parent Lavrans, while the resistance on 4H is conferred by Arve. The genetic markers associated with the QTL found in this study will benefit marker-assisted selection for resistance against net blotch.
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Affiliation(s)
- Ronja Wonneberger
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Andrea Ficke
- Division for Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
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18
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Sun Z, Yin X, Ding J, Yu D, Hu M, Sun X, Tan Y, Sheng X, Liu L, Mo Y, Ouyang N, Jiang B, Yuan G, Duan M, Yuan D, Fang J. QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and 'Nipponbare'. PLoS One 2017; 12:e0175692. [PMID: 28422981 PMCID: PMC5396889 DOI: 10.1371/journal.pone.0175692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/29/2017] [Indexed: 02/04/2023] Open
Abstract
Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar ‘Nipponbare’ as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.
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Affiliation(s)
- Zhizhong Sun
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Xiaoling Yin
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Jia Ding
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Dong Yu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Miao Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
| | - Xuewu Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Yanning Tan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Xiabing Sheng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Ling Liu
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Yi Mo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Ning Ouyang
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Beibei Jiang
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Guilong Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Meijuan Duan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
| | - Dingyang Yuan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
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Zhu H, Wu J, Jiang Y, Jin J, Zhou W, Wang Y, Han G, Zhao Y, Cheng B. Genomewide analysis of MATE-type gene family in maize reveals microsynteny and their expression patterns under aluminum treatment. J Genet 2017; 95:691-704. [PMID: 27659341 DOI: 10.1007/s12041-016-0686-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro-exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The Ka/Ks ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize.
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Affiliation(s)
- Huasheng Zhu
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, People's Republic of
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Shakiba E, Edwards JD, Jodari F, Duke SE, Baldo AM, Korniliev P, McCouch SR, Eizenga GC. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PLoS One 2017; 12:e0172133. [PMID: 28282385 PMCID: PMC5345765 DOI: 10.1371/journal.pone.0172133] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/31/2017] [Indexed: 01/11/2023] Open
Abstract
Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.
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Affiliation(s)
- Ehsan Shakiba
- University of Arkansas, Rice Research and Extension Center, Stuttgart, Arkansas, United States of America
| | - Jeremy D. Edwards
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Farman Jodari
- Rice Experiment Station (RES), Biggs, California, United States of America
| | - Sara E. Duke
- USDA/ARS Plains Area, College Station, Texas, United States of America
| | - Angela M. Baldo
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Pavel Korniliev
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Susan R. McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, United States of America
| | - Georgia C. Eizenga
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
- * E-mail:
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21
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Fedak G, Cao W, Wolfe D, Chi D, Xue A. [Not Available]. Tsitol Genet 2017; 51:74-78. [PMID: 30484620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A cross was made of Elymus repens onto the wheat cultivar Crocus and BC1 progeny advanced to BC1F7 by single seed descent. Sixteen lines were selected based on agronomic performance and evaluated in an FHB epiphytotic nursery. Eight lines with FHB resistance were selected. Based on GISH analysis, line P1142-3-1-5 had 42 chromosomes with one pair of chromosomes showing telomeric translocations on both arms. This chromosome was identified as 3D by using SSR markers. An evaluation of lines with single translocations revealed that FHB resistance was contributed by the translocation on the long arm of chromosome 3D. That line has minimal linkage drag and should be amenable to applications in breeding for disease resistance.
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22
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Vuong TD, Walker DR, Nguyen BT, Nguyen TT, Dinh HX, Hyten DL, Cregan PB, Sleper DA, Lee JD, Shannon JG, Nguyen HT. Molecular Characterization of Resistance to Soybean Rust (Phakopsora pachyrhizi Syd. & Syd.) in Soybean Cultivar DT 2000 (PI 635999). PLoS One 2016; 11:e0164493. [PMID: 27935940 PMCID: PMC5147787 DOI: 10.1371/journal.pone.0164493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/26/2016] [Indexed: 11/18/2022] Open
Abstract
Resistance to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd. & Syd., has been identified in many soybean germplasm accessions and is conferred by either dominant or recessive genes that have been mapped to six independent loci (Rpp1 -Rpp6), but No U.S. cultivars are resistant to SBR. The cultivar DT 2000 (PI 635999) has resistance to P. pachyrhizi isolates and field populations from the United States as well as Vietnam. A F6:7 recombinant inbred line (RIL) population derived from Williams 82 × DT 2000 was used to identify genomic regions associated with resistance to SBR in the field in Ha Noi, Vietnam, and in Quincy, Florida, in 2008. Bulked segregant analysis (BSA) was conducted using the soybean single nucleotide polymorphism (SNP) USLP 1.0 panel along with simple sequence repeat (SSR) markers to detect regions of the genome associated with resistance. BSA identified four BARC_SNP markers near the Rpp3 locus on chromosome (Chr.) 6. Genetic analysis identified an additional genomic region around the Rpp4 locus on Chr. 18 that was significantly associated with variation in the area under disease progress curve (AUDPC) values and sporulation in Vietnam. Molecular markers tightly linked to the DT 2000 resistance alleles on Chrs. 6 and 18 will be useful for marker-assisted selection and backcrossing in order to pyramid these genes with other available SBR resistance genes to develop new varieties with enhanced and durable resistance to SBR.
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Affiliation(s)
- Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - David R. Walker
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, USDA-ARS, and Department of Crop Sciences, University of Illinois, Urbana, Illinois,United States of America
| | - Binh T. Nguyen
- Plant Protection Research Institute (PPRI), Ha Noi, Vietnam
| | | | - Hoan X. Dinh
- Plant Protection Research Institute (PPRI), Ha Noi, Vietnam
| | - David L. Hyten
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - Perry B. Cregan
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, United States of America
| | - David A. Sleper
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jeong D. Lee
- Division of Plant Sciences, University of Missouri, Portageville, Missouri, United States of America
| | - James G. Shannon
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
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Wendell DL, Vaziri A, Shergill G. The Gene Encoding Dihydroflavonol 4-Reductase Is a Candidate for the anthocyaninless Locus of Rapid Cycling Brassica rapa (Fast Plants Type). PLoS One 2016; 11:e0161394. [PMID: 27548675 PMCID: PMC4993499 DOI: 10.1371/journal.pone.0161394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/06/2016] [Indexed: 11/18/2022] Open
Abstract
Rapid cycling Brassica rapa, also known as Wisconsin Fast Plants, are a widely used organism in both K-12 and college science education. They are an excellent system for genetics laboratory instruction because it is very easy to conduct genetic crosses with this organism, there are numerous seed stocks with variation in both Mendelian and quantitative traits, they have a short generation time, and there is a wealth of educational materials for instructors using them. Their main deficiency for genetics education is that none of the genetic variation in RCBr has yet been characterized at the molecular level. Here we present the first molecular characterization of a gene responsible for a trait in Fast Plants. The trait under study is purple/nonpurple variation due to the anthocyaninless locus, which is one of the Mendelian traits most frequently used for genetics education with this organism. We present evidence that the DFR gene, which encodes dihyroflavonol 4-reductase, is the candidate gene for the anthocyaninless (ANL) locus in RCBr. DFR shows complete linkage with ANL in genetic crosses with a total of 948 informative chromosomes, and strains with the recessive nonpurple phenotype have a transposon-related insertion in the DFR which is predicted to disrupt gene function.
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Affiliation(s)
- Douglas L. Wendell
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
- * E-mail:
| | - Anoumid Vaziri
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
| | - Gurbaksh Shergill
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
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Saeed I, Bachir DG, Chen L, Hu YG. The Expression of TaRca2-α Gene Associated with Net Photosynthesis Rate, Biomass and Grain Yield in Bread Wheat (Triticum aestivum L.) under Field Conditions. PLoS One 2016; 11:e0161308. [PMID: 27548477 PMCID: PMC4993480 DOI: 10.1371/journal.pone.0161308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/03/2016] [Indexed: 11/19/2022] Open
Abstract
Improvement in activation of Rubisco by Rubisco activase can potentially enhance CO2 assimilation and photosynthetic efficiency in plants. The three homoeologous copies of TaRca2-α were identified on chromosomes 4AL, 4BS and 4DS (TaRca2-α-4AL, TaRca2-α-4BS, and TaRca2-α-4DS) in bread wheat. Expression patterns of the three copies at heading (Z55), anthesis (Z67) and grain-filling (Z73) stages were investigated through qRT-PCR analyses in a panel of 59 bread wheat genotypes and their effects on net photosynthesis rate (Pn), biomass plant-1 (BMPP) and grain yield plant-1 (GYPP) were further explored. Different but similar expression patterns were observed for the three copies of TaRca2-α at the three growth stages with highest expression at grain-filling stage. TaRca2-α-4BS expressed higher at the three stages than TaRca2-α-4AL and TaRca2-α-4DS. The 59 genotypes could be clustered into three groups as high (7 genotypes), intermediate (41 genotypes) and low (11 genotypes) expression based on the expression of the three copies of TaRca2-α at three growth stages. Significant variations (P<0.01) were observed among the three groups of bread wheat genotypes for Pn, BMPP and GYPP. Generally, the genotypes with higher TaRca2-α expression also showed higher values for Pn, BMPP and GYPP. The expressions of the three copies of TaRca2-α at heading, anthesis and grain-filling stages were positively correlated with Pn, BMPP and GYPP (P<0.01) with stronger association for TaRca2-α-4BS at grain-filling stage. These results revealed that the expression of TaRca2-α contribute substantially to Pn, BMPP and GYPP, and suggested that manipulating TaRca-α expression may efficiently improve Pn, BMPP and GYPP in bread wheat and detecting TaRca-α expression levels with emphasis on TaRca2-α-4BS may be a positive strategy for selection in improving photosynthetic efficiency and grain yield of bread wheat.
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Affiliation(s)
- Iqbal Saeed
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P.R. China
- NIFA, PO Box 446, Tarnab, Peshawar, KP, Pakistan
| | - Daoura Goudia Bachir
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Institute of Water Saving Agriculture in Arid Regions of China, Yangling, Shaanxi, 712100, China
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25
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Schneider R, Rolling W, Song Q, Cregan P, Dorrance AE, McHale LK. Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea. BMC Genomics 2016; 17:607. [PMID: 27515508 PMCID: PMC4982113 DOI: 10.1186/s12864-016-2918-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 07/07/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae. RESULTS Resistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes. CONCLUSIONS QTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial resistance to P. sojae.
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Affiliation(s)
- Rhiannon Schneider
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Present Address: Pioneer Hi-Bred International Inc., Napoleon, OH, 43545, USA
| | - William Rolling
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Qijian Song
- US Department of Agriculture, Soybean Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Perry Cregan
- US Department of Agriculture, Soybean Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Anne E Dorrance
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
- Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Leah K McHale
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA.
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Revathi S, Sakthivel K, Manonmani S, Umadevi M, Ushakumari R, Robin S. Genetics of wide compatible gene and variability studies in rice (Oryza sativa L.). J Genet 2016; 95:463-7. [PMID: 27350693 DOI: 10.1007/s12041-016-0640-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- S Revathi
- 1Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641 003, India.
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Liang H, Xu L, Yu Y, Yang H, Dong W, Zhang H. Identification of QTLs with main, epistatic and QTL by environment interaction effects for seed shape and hundred-seed weight in soybean across multiple years. J Genet 2016; 95:475-7. [PMID: 27350695 DOI: 10.1007/s12041-016-0648-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Huizhen Liang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, People's Republic of China.
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Hao Y, Wang X, Wang K, Li H, Duan X, Tang C, Kang Z. TaMCA1, a regulator of cell death, is important for the interaction between wheat and Puccinia striiformis. Sci Rep 2016; 6:26946. [PMID: 27230563 PMCID: PMC4882554 DOI: 10.1038/srep26946] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/06/2016] [Indexed: 11/08/2022] Open
Abstract
Metacaspase orthologs are conserved in fungi, protozoa and plants, however, their roles in plant disease resistance are largely unknown. In this study, we identified a Triticum aestivum metacaspase gene, TaMCA1, with three copies located on chromosomes 1A, 1B and 1D. The TaMCA1 protein contained typical structural features of type I metacaspases domains, including an N-terminal pro-domain. Transient expression analyses indicated that TaMCA1 was localized in cytosol and mitochondria. TaMCA1 exhibited no caspase-1 activity in vitro, but was able to inhibit cell death in tobacco and wheat leaves induced by the mouse Bax gene. In addition, the expression level of TaMCA1 was up-regulated following challenge with the Puccinia striiformis f. sp. tritici (Pst). Knockdown of TaMCA1 via virus-induced gene silencing (VIGS) enhanced plant disease resistance to Pst, and the accumulation of hydrogen peroxide (H2O2). Further study showed that TaMCA1 decreased yeast cell resistance similar to the function of yeast metacaspase, and there was no interaction between TaMCA1 and TaLSD1. Based on these combined results, we speculate that TaMCA1, a regulator of cell death, is important during the compatible interaction of wheat and Pst.
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Affiliation(s)
- Yingbin Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Kang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Huayi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xiaoyuan Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
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Bolsheva NL, Zelenin AV, Nosova IV, Amosova AV, Samatadze TE, Yurkevich OY, Melnikova NV, Zelenina DA, Volkov AA, Muravenko OV. The diversity of karyotypes and genomes within section Syllinum of the Genus Linum (Linaceae) revealed by molecular cytogenetic markers and RAPD analysis. PLoS One 2015; 10:e0122015. [PMID: 25835524 PMCID: PMC4383504 DOI: 10.1371/journal.pone.0122015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/05/2015] [Indexed: 11/18/2022] Open
Abstract
The wide variation in chromosome number found in species of the genus Linum (2n = 16, 18, 20, 26, 28, 30, 32, 36, 42, 72, 84) indicates that chromosomal mutations have played an important role in the speciation of this taxon. To contribute to a better understanding of the genetic diversity and species relationships in this genus, comparative studies of karyotypes and genomes of species within section Syllinum Griseb. (2n = 26, 28) were carried out. Elongated with 9-aminoacridine chromosomes of 10 species of section Syllinum were investigated by C- and DAPI/С-banding, CMA and Ag-NOR-staining, FISH with probes of rDNA and of telomere repeats. RAPD analysis was also performed. All the chromosome pairs in karyotypes of the studied species were identified. Chromosome DAPI/C-banding patterns of 28-chromosomal species were highly similar. Two of the species differed from the others in chromosomal location of rDNA sites. B chromosomes were revealed in all the 28-chromosomal species. Chromosomes of Linum nodiflorum L. (2n = 26) and the 28-chromosomal species were similar in DAPI/C-banding pattern and localization of several rDNA sites, but they differed in chromosomal size and number. The karyotype of L. nodiflorum was characterized by an intercalary site of telomere repeat, one additional 26S rDNA site and also by the absence of B chromosomes. Structural similarities between different chromosome pairs in karyotypes of the studied species were found indicating their tetraploid origin. RAPD analysis did not distinguish the species except L. nodiflorum. The species of section Syllinum probably originated from a common tetraploid ancestor. The 28-chromosomal species were closely related, but L. nodiflorum diverged significantly from the rest of the species probably due to chromosomal rearrangements occurring during evolution.
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Affiliation(s)
- Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V. Zelenin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Inna V. Nosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daria A. Zelenina
- Russian Federal Research Institute for Fisheries and Oceanography, Moscow, Russia
| | - Alexander A. Volkov
- Russian Federal Research Institute for Fisheries and Oceanography, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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30
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Zhou L, Wang SB, Jian J, Geng QC, Wen J, Song Q, Wu Z, Li GJ, Liu YQ, Dunwell JM, Zhang J, Feng JY, Niu Y, Zhang L, Ren WL, Zhang YM. Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Sci Rep 2015; 5:9350. [PMID: 25797785 PMCID: PMC4369735 DOI: 10.1038/srep09350] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/02/2015] [Indexed: 12/02/2022] Open
Abstract
Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes.
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Affiliation(s)
- Ling Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Shi-Bo Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Qing-Chun Geng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, USA
| | | | - Guang-Jun Li
- College of Life Science, Linyi University, Linyi 276005, China
| | - Yu-Qin Liu
- Crop Research Institute, Linyi Academy of Agricultural Sciences, Linyi 276012, China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, United Kingdom
| | - Jin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Ying Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Long Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Begum H, Spindel JE, Lalusin A, Borromeo T, Gregorio G, Hernandez J, Virk P, Collard B, McCouch SR. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa). PLoS One 2015; 10:e0119873. [PMID: 25785447 PMCID: PMC4364887 DOI: 10.1371/journal.pone.0119873] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 02/02/2015] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.
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Affiliation(s)
- Hasina Begum
- International Rice Research Institute, Los Baños, Philippines
| | - Jennifer E. Spindel
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Antonio Lalusin
- Crop Science Cluster, University of the Philippines Los Baños, Los Baños, Philippines
| | - Teresita Borromeo
- Crop Science Cluster, University of the Philippines Los Baños, Los Baños, Philippines
| | - Glenn Gregorio
- International Rice Research Institute, Los Baños, Philippines
| | - Jose Hernandez
- Crop Science Cluster, University of the Philippines Los Baños, Los Baños, Philippines
| | - Parminder Virk
- International Center for Tropical Agriculture, Cali, Colombia
| | | | - Susan R. McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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Ederveen A, Lai Y, van Driel MA, Gerats T, Peters JL. Modulating crossover positioning by introducing large structural changes in chromosomes. BMC Genomics 2015; 16:89. [PMID: 25879408 PMCID: PMC4359564 DOI: 10.1186/s12864-015-1276-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Crossing over assures the correct segregation of the homologous chromosomes to both poles of the dividing meiocyte. This exchange of DNA creates new allelic combinations thus increasing the genetic variation present in offspring. Crossovers are not uniformly distributed along chromosomes; rather there are preferred locations where they may take place. The positioning of crossovers is known to be influenced by both exogenous and endogenous factors as well as structural features inherent to the chromosome itself. We have introduced large structural changes into Arabidopsis chromosomes and report their effects on crossover positioning. RESULTS The introduction of large deletions and putative inversions silenced recombination over the length of the structural change. In the majority of cases analyzed, the total recombination frequency over the chromosomes was unchanged. The loss of crossovers at the sites of structural change was compensated for by increases in recombination frequencies elsewhere on the chromosomes, mostly in single intervals of one to three megabases in size. Interestingly, two independent cases of induced structural changes in the same chromosomal interval were found on both chromosomes 1 and 2. In both cases, compensatory increases in recombination frequencies were of similar strength and took place in the same chromosome region. In contrast, deletions in chromosome arms carrying the nucleolar organizing region did not change recombination frequencies in the remainder of those chromosomes. CONCLUSIONS When taken together, these observations show that changes in the physical structure of the chromosome can have large effects on the positioning of COs within that chromosome. Moreover, different reactions to induced structural changes are observed between and within chromosomes. However, the similarity in reaction observed when looking at chromosomes carrying similar changes suggests a direct causal relation between induced change and observed reaction.
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Affiliation(s)
- Antoine Ederveen
- Department of Molecular Plant Physiology, Radboud University Nijmegen, Institute for Water and Wetland Research (IWWR), Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Yuching Lai
- Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands.
| | - Marc A van Driel
- Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Current affiliation: Philips Research, High Tech Campus 11, 5656 AE, Eindhoven, The Netherlands.
| | - Tom Gerats
- Department of Molecular Plant Physiology, Radboud University Nijmegen, Institute for Water and Wetland Research (IWWR), Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Janny L Peters
- Department of Molecular Plant Physiology, Radboud University Nijmegen, Institute for Water and Wetland Research (IWWR), Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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Sharma R, Rawat V, Suresh CG. Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome. PLoS One 2014; 9:e109715. [PMID: 25290312 PMCID: PMC4188811 DOI: 10.1371/journal.pone.0109715] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 09/12/2014] [Indexed: 12/20/2022] Open
Abstract
UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes coded by an important gene family of higher plants. They are involved in the modification of secondary metabolites, phytohormones, and xenobiotics by transfer of sugar moieties from an activated nucleotide molecule to a wide range of acceptors. This modification regulates various functions like detoxification of xenobiotics, hormone homeostasis, and biosynthesis of secondary metabolites. Here, we describe the identification of 96 UGT genes in Cicer arietinum (CaUGT) and report their tissue-specific differential expression based on publically available RNA-seq and expressed sequence tag data. This analysis has established medium to high expression of 84 CaUGTs and low expression of 12 CaUGTs. We identified several closely related orthologs of CaUGTs in other genomes and compared their exon-intron arrangement. An attempt was made to assign functional specificity to chickpea UGTs by comparing substrate binding sites with experimentally determined specificity. These findings will assist in precise selection of candidate genes for various applications and understanding functional genomics of chickpea.
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Affiliation(s)
- Ranu Sharma
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Vimal Rawat
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - C. G. Suresh
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- * E-mail:
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34
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Zhou T, Gao C, Du L, Feng H, Wang L, Lan Y, Sun F, Wei L, Fan Y, Shen W, Zhou Y. Genetic analysis and QTL detection for resistance to white tip disease in rice. PLoS One 2014; 9:e106099. [PMID: 25162680 PMCID: PMC4146579 DOI: 10.1371/journal.pone.0106099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/01/2014] [Indexed: 11/18/2022] Open
Abstract
The inheritance of resistance to white tip disease (WTDR) in rice (Oryza sativa L.) was analyzed with an artificial inoculation test in a segregating population derived from the cross between Tetep, a highly resistant variety that was identified in a previous study, and a susceptible cultivar. Three resistance-associated traits, including the number of Aphelenchoides besseyi (A. besseyi) individuals in 100 grains (NA), the loss rate of panicle weight (LRPW) and the loss rate of the total grains per panicle (LRGPP) were analyzed for the detection of the quantitative trait locus (QTL) in the population after construction of a genetic map. Six QTLs distributed on chromosomes 3, 5 and 9 were mapped. qNA3 and qNA9, conferring reproduction number of A. besseyi in the panicle, accounted for 16.91% and 12.54% of the total phenotypic variance, respectively. qDRPW5a and qDRPW5b, associated with yield loss, were located at two adjacent marker intervals on chromosome 5 and explained 14.15% and 14.59% of the total phenotypic variation and possessed LOD values of 3.40 and 3.39, respectively. qDRPW9 was considered as a minor QTL and only explained 1.02% of the phenotypic variation. qLRGPP5 contributed to the loss in the number of grains and explained 10.91% of the phenotypic variation. This study provides useful information for the breeding of resistant cultivars against white tip disease in rice.
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Affiliation(s)
- Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Cunyi Gao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hui Feng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lijiao Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Feng Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lihui Wei
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yongjian Fan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenbiao Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, China
- * E-mail: (YZ); (WS)
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail: (YZ); (WS)
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35
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Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE. Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell 2014; 55:694-707. [PMID: 25132175 DOI: 10.1016/j.molcel.2014.07.008] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 06/02/2014] [Accepted: 07/10/2014] [Indexed: 11/18/2022]
Abstract
Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered long-range interactions such as those among small heterochromatic regions embedded in euchromatic arms. We also found that interactions are correlated with various epigenetic marks that are localized in active or silenced chromatin. Arabidopsis chromosomes do not contain large local interactive domains that resemble the topological domains described in animals but, instead, contain relatively small interactive regions scattered around the genome that contain H3K27me3 or H3K9me2. We generated interaction maps in mutants that are defective in specific epigenetic pathways and found altered interaction patterns that correlate with changes in the epigenome. These analyses provide further insights into molecular mechanisms of epigenetic regulation of the genome.
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Affiliation(s)
- Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn J Cokus
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Jixian Zhai
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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36
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Grob S, Schmid MW, Grossniklaus U. Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila. Mol Cell 2014; 55:678-93. [PMID: 25132176 DOI: 10.1016/j.molcel.2014.07.009] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/15/2014] [Accepted: 07/10/2014] [Indexed: 12/17/2022]
Abstract
Chromosomes are folded, spatially organized, and regulated by epigenetic marks. How chromosomal architecture is connected to the epigenome is not well understood. We show that chromosomal architecture of Arabidopsis is tightly linked to the epigenetic state. Furthermore, we show how physical constraints, such as nuclear size, correlate with the folding principles of chromatin. We also describe a nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes interact. These KNOT ENGAGED ELEMENT (KEE) regions represent heterochromatic islands within euchromatin. Similar to PIWI-interacting RNA clusters, such as flamenco in Drosophila, KEEs represent preferred landing sites for transposable elements, which may be part of a transposon defense mechanism in the Arabidopsis nucleus.
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Affiliation(s)
- Stefan Grob
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Marc W Schmid
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland.
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37
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Adiredjo AL, Navaud O, Muños S, Langlade NB, Lamaze T, Grieu P. Genetic control of water use efficiency and leaf carbon isotope discrimination in sunflower (Helianthus annuus L.) subjected to two drought scenarios. PLoS One 2014; 9:e101218. [PMID: 24992022 PMCID: PMC4081578 DOI: 10.1371/journal.pone.0101218] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/04/2014] [Indexed: 01/22/2023] Open
Abstract
High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production.
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Affiliation(s)
- Afifuddin Latif Adiredjo
- Université de Toulouse, INP-ENSAT, UMR 1248 AGIR (INPT-INRA), Castanet-Tolosan, France
- Brawijaya University, Faculty of Agriculture, Department of Agronomy, Plant Breeding Laboratory, Malang, Indonesia
| | - Olivier Navaud
- Université de Toulouse, UPS-Toulouse III, UMR 5126 CESBIO, Toulouse, France
| | - Stephane Muños
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes(LIPM), UMR 2594, Castanet-Tolosan, France
| | - Nicolas B. Langlade
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes(LIPM), UMR 2594, Castanet-Tolosan, France
| | - Thierry Lamaze
- Université de Toulouse, UPS-Toulouse III, UMR 5126 CESBIO, Toulouse, France
| | - Philippe Grieu
- Université de Toulouse, INP-ENSAT, UMR 1248 AGIR (INPT-INRA), Castanet-Tolosan, France
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38
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Escudero M, Martín-Bravo S, Mayrose I, Fernández-Mazuecos M, Fiz-Palacios O, Hipp AL, Pimentel M, Jiménez-Mejías P, Valcárcel V, Vargas P, Luceño M. Karyotypic changes through dysploidy persist longer over evolutionary time than polyploid changes. PLoS One 2014; 9:e85266. [PMID: 24416374 PMCID: PMC3887030 DOI: 10.1371/journal.pone.0085266] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 11/25/2013] [Indexed: 01/08/2023] Open
Abstract
Chromosome evolution has been demonstrated to have profound effects on diversification rates and speciation in angiosperms. While polyploidy has predated some major radiations in plants, it has also been related to decreased diversification rates. There has been comparatively little attention to the evolutionary role of gains and losses of single chromosomes, which may or not entail changes in the DNA content (then called aneuploidy or dysploidy, respectively). In this study we investigate the role of chromosome number transitions and of possible associated genome size changes in angiosperm evolution. We model the tempo and mode of chromosome number evolution and its possible correlation with patterns of cladogenesis in 15 angiosperm clades. Inferred polyploid transitions are distributed more frequently towards recent times than single chromosome gains and losses. This is likely because the latter events do not entail changes in DNA content and are probably due to fission or fusion events (dysploidy), as revealed by an analysis of the relationship between genome size and chromosome number. Our results support the general pattern that recently originated polyploids fail to persist, and suggest that dysploidy may have comparatively longer-term persistence than polyploidy. Changes in chromosome number associated with dysploidy were typically observed across the phylogenies based on a chi-square analysis, consistent with these changes being neutral with respect to diversification.
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Affiliation(s)
- Marcial Escudero
- Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
- Herbarium, The Morton Arboretum, Lisle, Illinois, United States of America
- Botany, The Field Museum, Chicago, Illinois, United States of America
| | - Santiago Martín-Bravo
- Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
- * E-mail:
| | - Itay Mayrose
- Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Andrew L. Hipp
- Herbarium, The Morton Arboretum, Lisle, Illinois, United States of America
- Botany, The Field Museum, Chicago, Illinois, United States of America
| | - Manuel Pimentel
- Plant and Animal Biology and Ecology, University of A Coruña, A Coruña, Spain
| | - Pedro Jiménez-Mejías
- Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
- Biodiversity and Conservation, Real Jardín Botánico CSIC, Madrid, Spain
| | | | - Pablo Vargas
- Biodiversity and Conservation, Real Jardín Botánico CSIC, Madrid, Spain
| | - Modesto Luceño
- Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
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Mascher M, Wu S, Amand PS, Stein N, Poland J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 2013; 8:e76925. [PMID: 24098570 PMCID: PMC3789676 DOI: 10.1371/journal.pone.0076925] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/04/2013] [Indexed: 12/17/2022] Open
Abstract
The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Shuangye Wu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Paul St. Amand
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jesse Poland
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
- * E-mail:
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40
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Mascher M, Wu S, Amand PS, Stein N, Poland J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 2013; 8:e76925. [PMID: 24098570 DOI: 10.1371/journal.pone.076925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/04/2013] [Indexed: 05/27/2023] Open
Abstract
The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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41
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Thurber CS, Ma JM, Higgins RH, Brown PJ. Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production. Genome Biol 2013; 14:R68. [PMID: 23803286 PMCID: PMC3706989 DOI: 10.1186/gb-2013-14-6-r68] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/11/2013] [Accepted: 06/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sorghum is a tropical C4 cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation. RESULTS We apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time. CONCLUSIONS Generating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.
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Affiliation(s)
- Carrie S Thurber
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
| | - Justin M Ma
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
| | - Race H Higgins
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Brown
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Šimková H, Šafář J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KFX, Korol A, Bergès H, Doležel J, Feuillet C. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol 2013; 14:R64. [PMID: 23800011 PMCID: PMC4054855 DOI: 10.1186/gb-2013-14-6-r64] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/24/2013] [Accepted: 06/25/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. RESULTS Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. CONCLUSIONS Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
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Affiliation(s)
- Romain Philippe
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Etienne Paux
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Isabelle Bertin
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Fréderic Choulet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Christel Laugier
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Sonia Vautrin
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Federica Magni
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Simone Scalabrin
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | | | - Klaus FX Mayer
- MIPS/IBIS; Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Abraham Korol
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Catherine Feuillet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
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Ning S, Wang N, Sakuma S, Pourkheirandish M, Wu J, Matsumoto T, Koba T, Komatsuda T. Structure, transcription and post-transcriptional regulation of the bread wheat orthologs of the barley cleistogamy gene Cly1. Theor Appl Genet 2013. [PMID: 23381807 DOI: 10.1007/s00122-013-20526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The majority of genes present in the hexaploid bread wheat genome are present as three homoeologs. Here, we describe the three homoeologous orthologs of the barley cleistogamy gene Cly1, a member of the AP2 gene family. As in barley, the wheat genes (designated TaAP2-A, -B and -D) map to the sub-telomeric region of the long arms of the group 2 chromosomes. The structure and pattern of transcription of the TaAP2 homoeologs were similar to those of Cly1. Transcript abundance was high in the florets, and particularly in the lodicule. The TaAP2 message was cleaved at its miR172 target sites. The set of homoeolog-specific PCR assays developed will be informative for identifying either naturally occurring or induced cleistogamous alleles at each of the three wheat homoeologs. By combining such alleles via conventional crossing, it should be possible to generate a cleistogamous form of bread wheat, which would be advantageous both with respect to improving the level of the crop's resistance against the causative pathogen of fusarium head blight, and for controlling pollen-mediated gene flow to and from genetically modified cultivars.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Base Sequence
- Biomarkers/metabolism
- Chromosomes, Artificial, Bacterial
- Chromosomes, Plant/chemistry
- Chromosomes, Plant/genetics
- Flowers/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Genome, Plant
- Hordeum/genetics
- Hordeum/growth & development
- Hordeum/metabolism
- MicroRNAs/genetics
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis
- Phylogeny
- Plant Proteins/genetics
- Plant Proteins/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Plant/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Triticum/genetics
- Triticum/growth & development
- Triticum/metabolism
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Affiliation(s)
- Shunzong Ning
- Plant Genome Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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44
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Ning S, Wang N, Sakuma S, Pourkheirandish M, Wu J, Matsumoto T, Koba T, Komatsuda T. Structure, transcription and post-transcriptional regulation of the bread wheat orthologs of the barley cleistogamy gene Cly1. Theor Appl Genet 2013; 126:1273-83. [PMID: 23381807 DOI: 10.1007/s00122-013-2052-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/19/2013] [Indexed: 05/22/2023]
Abstract
The majority of genes present in the hexaploid bread wheat genome are present as three homoeologs. Here, we describe the three homoeologous orthologs of the barley cleistogamy gene Cly1, a member of the AP2 gene family. As in barley, the wheat genes (designated TaAP2-A, -B and -D) map to the sub-telomeric region of the long arms of the group 2 chromosomes. The structure and pattern of transcription of the TaAP2 homoeologs were similar to those of Cly1. Transcript abundance was high in the florets, and particularly in the lodicule. The TaAP2 message was cleaved at its miR172 target sites. The set of homoeolog-specific PCR assays developed will be informative for identifying either naturally occurring or induced cleistogamous alleles at each of the three wheat homoeologs. By combining such alleles via conventional crossing, it should be possible to generate a cleistogamous form of bread wheat, which would be advantageous both with respect to improving the level of the crop's resistance against the causative pathogen of fusarium head blight, and for controlling pollen-mediated gene flow to and from genetically modified cultivars.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Base Sequence
- Biomarkers/metabolism
- Chromosomes, Artificial, Bacterial
- Chromosomes, Plant/chemistry
- Chromosomes, Plant/genetics
- Flowers/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Genome, Plant
- Hordeum/genetics
- Hordeum/growth & development
- Hordeum/metabolism
- MicroRNAs/genetics
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis
- Phylogeny
- Plant Proteins/genetics
- Plant Proteins/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Plant/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Triticum/genetics
- Triticum/growth & development
- Triticum/metabolism
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Affiliation(s)
- Shunzong Ning
- Plant Genome Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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45
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Kumar S, Jeelani SM, Rani S, Gupta RC, Kumari S. Cytology of five species of subfamily Papaveroideae from the Western Himalayas. Protoplasma 2013; 250:307-16. [PMID: 22643839 DOI: 10.1007/s00709-012-0413-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 04/23/2012] [Indexed: 05/12/2023]
Abstract
During the present course, population-based meiotic studies were carried out on five species of subfamily Papaveroideae from selected localities of Kashmir and Himachal Pradesh in the Western Himalayas (India). Varied intraspecific chromosome counts were reported for the first time in Argemone mexicana and Meconopsis latifolia, both existing on 2n = 2x = 14. The x = 7, confirmed for the first time from the newly found diploid cytotype, is suggested to be the primary chromosomal basic number for the Meconopsis. Furthermore, meiotic course was noted to be normal in Argemone ochroleuca, it varied from normal to abnormal in the populations of A. mexicana and Papaver dubium whereas it was invariably found to be abnormal in all the populations of Meconopsis aculeata and M. latifolia. These anomalous taxa were marked with meiotic abnormalities in the form of cytomixis, chromosomal stickiness, unoriented bivalents, formation of laggards and bridges resulting in abnormal microsporogenesis, and production of heterogeneous-sized fertile pollen grains along with reduced pollen fertility.
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Affiliation(s)
- Sanjeev Kumar
- Department of Botany, Punjabi University, Patiala, Punjab, India 147002
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46
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Bauer E, Falque M, Walter H, Bauland C, Camisan C, Campo L, Meyer N, Ranc N, Rincent R, Schipprack W, Altmann T, Flament P, Melchinger AE, Menz M, Moreno-González J, Ouzunova M, Revilla P, Charcosset A, Martin OC, Schön CC. Intraspecific variation of recombination rate in maize. Genome Biol 2013; 14:R103. [PMID: 24050704 PMCID: PMC4053771 DOI: 10.1186/gb-2013-14-9-r103] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 09/10/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation. RESULTS Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework reveals a negative association between re combination rate and interference strength. CONCLUSIONS To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.
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Affiliation(s)
- Eva Bauer
- Plant Breeding, Technische Universität München, 85354 Freising, Germany
| | - Matthieu Falque
- INRA, UMR de Génétique Végétale/Université Paris-Sud - CNRS, 91190 Gif-sur-Yvette, France
| | - Hildrun Walter
- Plant Breeding, Technische Universität München, 85354 Freising, Germany
| | - Cyril Bauland
- INRA, UMR de Génétique Végétale/Université Paris-Sud - CNRS, 91190 Gif-sur-Yvette, France
| | | | - Laura Campo
- Centro Investigacións Agrarias Mabegondo (CIAM), 15080 La Coruña, Spain
| | | | | | - Renaud Rincent
- INRA, UMR de Génétique Végétale/Université Paris-Sud - CNRS, 91190 Gif-sur-Yvette, France
- Limagrain Europe, 63720 Chappes, France
- KWS SAAT AG, 37574 Einbeck, Germany
- BIOGEMMA, Genetics and Genomics in Cereals, 63720 Chappes, France
| | | | - Thomas Altmann
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | | | | | | | | | | | - Pedro Revilla
- Misión Biológica de Galicia (CSIC), 36080 Pontevedra, Spain
| | - Alain Charcosset
- INRA, UMR de Génétique Végétale/Université Paris-Sud - CNRS, 91190 Gif-sur-Yvette, France
| | - Olivier C Martin
- INRA, UMR de Génétique Végétale/Université Paris-Sud - CNRS, 91190 Gif-sur-Yvette, France
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47
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Grosso V, Farina A, Gennaro A, Giorgi D, Lucretti S. Flow sorting and molecular cytogenetic identification of individual chromosomes of Dasypyrum villosum L. (H. villosa) by a single DNA probe. PLoS One 2012; 7:e50151. [PMID: 23185561 PMCID: PMC3502404 DOI: 10.1371/journal.pone.0050151] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/19/2012] [Indexed: 11/19/2022] Open
Abstract
Dasypyrum villosum (L.) Candargy (sin. Haynaldia villosa) is an annual wild diploid grass species (2n = 2x = 14; genome VV) belonging to the Poaceae family, which is considered to be an important source of biotic and abiotic stress resistance genes for wheat breeding. Enhanced characterization of D. villosum chromosomes can facilitate exploitation of its gene pool and its use in wheat breeding programs. Here we present the cytogenetic identification of D. villosum chromosomes on slide by fluorescent in situ hybridization (FISH), with the GAA simple sequence repeat (SSR) as a probe. We also describe the isolation and the flow cytometric analysis of D. villosum chromosomes in suspension, resulting in a distinguished flow karyotype. Chromosomes were flow sorted into three fractions, according their DNA content, one of which was composed of a single type of chromosome, namely 6 V, sorted with over 85% purity. Chromosome 6 V is known to carry genes to code for important resistance and seed storage characteristics, and its isolation represents a new source of genetic traits and specific markers useful for wheat improvement.
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Affiliation(s)
| | | | - Andrea Gennaro
- Department of Agriculture, Forestry, Nature and Energy - DAFNE, University of Tuscia, Viterbo, Italy
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48
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Tiwari VK, Riera-Lizarazu O, Gunn HL, Lopez K, Iqbal MJ, Kianian SF, Leonard JM. Endosperm tolerance of paternal aneuploidy allows radiation hybrid mapping of the wheat D-genome and a measure of γ ray-induced chromosome breaks. PLoS One 2012; 7:e48815. [PMID: 23144983 PMCID: PMC3492231 DOI: 10.1371/journal.pone.0048815] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 10/01/2012] [Indexed: 11/21/2022] Open
Abstract
Physical mapping and genome sequencing are underway for the ≈17 Gb wheat genome. Physical mapping methods independent of meiotic recombination, such as radiation hybrid (RH) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination in Triticeae genomes. Reports of endosperm development following pollination with irradiated pollen at dosages that cause embryo abortion prompted us to investigate endosperm as a potential source of RH mapping germplasm. Here, we report a novel approach to construct RH based physical maps of all seven D-genome chromosomes of the hexaploid wheat ‘Chinese Spring’, simultaneously. An 81-member subset of endosperm samples derived from 20-Gy irradiated pollen was genotyped for deletions, and 737 markers were mapped on seven D-genome chromosomes. Analysis of well-defined regions of six chromosomes suggested a map resolution of ∼830 kb could be achieved; this estimate was validated with assays of markers from a sequenced contig. We estimate that the panel contains ∼6,000 deletion bins for D-genome chromosomes and will require ∼18,000 markers for high resolution mapping. Map-based deletion estimates revealed a majority of 1–20 Mb interstitial deletions suggesting mutagenic repair of double-strand breaks in pollen provides a useful resource for RH mapping and map based cloning studies.
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Affiliation(s)
- Vijay K. Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Oscar Riera-Lizarazu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | - Hilary L. Gunn
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - KaSandra Lopez
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - M. Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Shahryar F. Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jeffrey M. Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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Yelina NE, Choi K, Chelysheva L, Macaulay M, de Snoo B, Wijnker E, Miller N, Drouaud J, Grelon M, Copenhaver GP, Mezard C, Kelly KA, Henderson IR. Epigenetic remodeling of meiotic crossover frequency in Arabidopsis thaliana DNA methyltransferase mutants. PLoS Genet 2012; 8:e1002844. [PMID: 22876192 PMCID: PMC3410864 DOI: 10.1371/journal.pgen.1002844] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 06/07/2012] [Indexed: 12/25/2022] Open
Abstract
Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including epigenetic organization, for example methylation of the DNA and histones. Here we investigate the role of DNA methylation in determining patterns of CO frequency along Arabidopsis thaliana chromosomes. In A. thaliana the pericentromeric regions are repetitive, densely DNA methylated, and suppressed for both RNA polymerase-II transcription and CO frequency. DNA hypomethylated methyltransferase1 (met1) mutants show transcriptional reactivation of repetitive sequences in the pericentromeres, which we demonstrate is coupled to extensive remodeling of CO frequency. We observe elevated centromere-proximal COs in met1, coincident with pericentromeric decreases and distal increases. Importantly, total numbers of CO events are similar between wild type and met1, suggesting a role for interference and homeostasis in CO remodeling. To understand recombination distributions at a finer scale we generated CO frequency maps close to the telomere of chromosome 3 in wild type and demonstrate an elevated recombination topology in met1. Using a pollen-typing strategy we have identified an intergenic nucleosome-free CO hotspot 3a, and we demonstrate that it undergoes increased recombination activity in met1. We hypothesize that modulation of 3a activity is caused by CO remodeling driven by elevated centromeric COs. These data demonstrate how regional epigenetic organization can pattern recombination frequency along eukaryotic chromosomes.
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Affiliation(s)
- Nataliya E. Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Liudmila Chelysheva
- Institut Jean-Pierre Bourgin, INRA Centre de Versailles-Grignon, Versailles, France
| | | | | | - Erik Wijnker
- Wageningen University, Wageningen, The Netherlands
| | - Nigel Miller
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jan Drouaud
- Institut Jean-Pierre Bourgin, INRA Centre de Versailles-Grignon, Versailles, France
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, INRA Centre de Versailles-Grignon, Versailles, France
| | - Gregory P. Copenhaver
- Department of Biology and The Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Christine Mezard
- Institut Jean-Pierre Bourgin, INRA Centre de Versailles-Grignon, Versailles, France
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Matsuda O, Tanaka A, Fujita T, Iba K. Hyperspectral imaging techniques for rapid identification of Arabidopsis mutants with altered leaf pigment status. Plant Cell Physiol 2012; 53:1154-70. [PMID: 22470059 PMCID: PMC3367163 DOI: 10.1093/pcp/pcs043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 03/22/2012] [Indexed: 05/18/2023]
Abstract
The spectral reflectance signature of living organisms provides information that closely reflects their physiological status. Because of its high potential for the estimation of geomorphic biological parameters, particularly of gross photosynthesis of plants, two-dimensional spectroscopy, via the use of hyperspectral instruments, has been widely used in remote sensing applications. In genetics research, in contrast, the reflectance phenotype has rarely been the subject of quantitative analysis; its potential for illuminating the pathway leading from the gene to phenotype remains largely unexplored. In this study, we employed hyperspectral imaging techniques to identify Arabidopsis mutants with altered leaf pigment status. The techniques are comprised of two modes; the first is referred to as the 'targeted mode' and the second as the 'non-targeted mode'. The 'targeted' mode is aimed at visualizing individual concentrations and compositional parameters of leaf pigments based on reflectance indices (RIs) developed for Chls a and b, carotenoids and anthocyanins. The 'non-targeted' mode highlights differences in reflectance spectra of leaf samples relative to reference spectra from the wild-type leaves. Through the latter approach, three mutant lines with weak irregular reflectance phenotypes, that are hardly identifiable by simple observation, were isolated. Analysis of these and other mutants revealed that the RI-based targeted pigment estimation was robust at least against changes in trichome density, but was confounded by genetic defects in chloroplast photorelocation movement. Notwithstanding such a limitation, the techniques presented here provide rapid and high-sensitive means to identify genetic mechanisms that coordinate leaf pigment status with developmental stages and/or environmental stress conditions.
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Affiliation(s)
- Osamu Matsuda
- Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan.
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