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Sun C, Liang W, Yan K, Xu D, Qin T, Fiaz S, Kear P, Bi Z, Liu Y, Liu Z, Zhang J, Bai J. Expression of Potato StDRO1 in Arabidopsis Alters Root Architecture and Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:836063. [PMID: 35665176 PMCID: PMC9161210 DOI: 10.3389/fpls.2022.836063] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Potato (Solanum tuberosum L) is the third important crop for providing calories to a large human population, and is considered sensitive to moderately sensitive to drought stress conditions. The development of drought-tolerant, elite varieties of potato is a challenging task, which can be achieved through molecular breeding. Recently, the DEEPER ROOTING 1 (DRO1) gene has been identified in rice, which influences plant root system and regulates grain yield under drought stress conditions. The potato StDRO1 protein is mainly localized in the plasma membrane of tobacco leaf cells, and overexpression analysis of StDRO1 in Arabidopsis resulted in an increased lateral root number, but decreased lateral root angle, lateral branch angle, and silique angle. Additionally, the drought treatment analysis indicated that StDRO1 regulated drought tolerance and rescued the defective root architecture and drought-tolerant phenotypes of Atdro1, an Arabidopsis AtDRO1 null mutant. Furthermore, StDRO1 expression was significantly higher in the drought-tolerant potato cultivar "Unica" compared to the drought-sensitive cultivar "Atlantic." The transcriptional response of StDRO1 under drought stress occurred significantly earlier in Unica than in Atlantic. Collectively, the outcome of the present investigation elucidated the role of DRO1 function in the alternation of root architecture, which potentially acts as a key gene in the development of a drought stress-tolerant cultivar. Furthermore, these findings will provide the theoretical basis for molecular breeding of drought-tolerant potato cultivars for the farming community.
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Affiliation(s)
- Chao Sun
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wenjun Liang
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Derong Xu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Tianyuan Qin
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing, China
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhen Liu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Junlian Zhang
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
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Shoaib N, Liu L, Ali A, Mughal N, Yu G, Huang Y. Molecular Functions and Pathways of Plastidial Starch Phosphorylase (PHO1) in Starch Metabolism: Current and Future Perspectives. Int J Mol Sci 2021; 22:ijms221910450. [PMID: 34638789 PMCID: PMC8509025 DOI: 10.3390/ijms221910450] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
Starch phosphorylase is a member of the GT35-glycogen-phosphorylase superfamily. Glycogen phosphorylases have been researched in animals thoroughly when compared to plants. Genetic evidence signifies the integral role of plastidial starch phosphorylase (PHO1) in starch biosynthesis in model plants. The counterpart of PHO1 is PHO2, which specifically resides in cytosol and is reported to lack L80 peptide in the middle region of proteins as seen in animal and maltodextrin forms of phosphorylases. The function of this extra peptide varies among species and ranges from the substrate of proteasomes to modulate the degradation of PHO1 in Solanum tuberosum to a non-significant effect on biochemical activity in Oryza sativa and Hordeum vulgare. Various regulatory functions, e.g., phosphorylation, protein–protein interactions, and redox modulation, have been reported to affect the starch phosphorylase functions in higher plants. This review outlines the current findings on the regulation of starch phosphorylase genes and proteins with their possible role in the starch biosynthesis pathway. We highlight the gaps in present studies and elaborate on the molecular mechanisms of phosphorylase in starch metabolism. Moreover, we explore the possible role of PHO1 in crop improvement.
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Affiliation(s)
- Noman Shoaib
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
| | - Lun Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Nishbah Mughal
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
- Correspondence: (G.Y.); (Y.H.); Tel.: +86-180-0803-9351 (G.Y.); +86-028-8629-0868 (Y.H.)
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (N.S.); (L.L.); (N.M.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (G.Y.); (Y.H.); Tel.: +86-180-0803-9351 (G.Y.); +86-028-8629-0868 (Y.H.)
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Estimation of Genome Size in the Endemic Species Reseda pentagyna and the Locally Rare Species Reseda lutea Using comparative Analyses of Flow Cytometry and K-Mer Approaches. PLANTS 2021; 10:plants10071362. [PMID: 34371565 PMCID: PMC8309327 DOI: 10.3390/plants10071362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022]
Abstract
Genome size is one of the fundamental cytogenetic features of a species, which is critical for the design and initiation of any genome sequencing projects and can provide essential insights in studying taxonomy, cytogenetics, phylogenesis, and evolutionary studies. However, this key cytogenetic information is almost lacking in the endemic species Reseda pentagyna and the locally rare species Reseda lutea in Saudi Arabia. Therefore, genome size was analyzed by propidium iodide PI flow cytometry and compared to k-mer analysis methods. The standard method for genome size measures (flow cytometry) estimated the genome size of R. lutea and R. pentagyna with nuclei isolation MB01 buffer were found to be 1.91 ± 0.02 and 2.09 ± 0.03 pg/2 °C, respectively, which corresponded approximately to a haploid genome size of 934 and 1.022 Mbp, respectively. For validation, K-mer analysis was performed on both species' Illumina paired-end sequencing data from both species. Five k-mer analysis approaches were examined for biocomputational estimation of genome size: A general formula and four well-known programs (CovEST, Kmergenie, FindGSE, and GenomeScope). The parameter preferences had a significant impact on GenomeScope and Kmergenie estimates. While the general formula estimations did not differ considerably, with an average genome size of 867.7 and 896. Mbp. The differences across flow cytometry and biocomputational predictions may be due to the high repeat content, particularly long repetitive regions in both genomes, 71% and 57%, which interfered with k-mer analysis. GenomeScope allowed quantification of high heterozygosity levels (1.04 and 1.37%) of R. lutea and R. pentagyna genomes, respectively. Based on our observations, R. lutea may have a tetraploid genome or higher. Our results revealed fundamental cytogenetic information for R. lutea and R. pentagyna, which should be used in future taxonomic studies and whole-genome sequencing.
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Jayakodi M, Schreiber M, Stein N, Mascher M. Building pan-genome infrastructures for crop plants and their use in association genetics. DNA Res 2021; 28:6117190. [PMID: 33484244 PMCID: PMC7934568 DOI: 10.1093/dnares/dsaa030] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/20/2022] Open
Abstract
Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
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Affiliation(s)
- Murukarthick Jayakodi
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Mona Schreiber
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Saxony, Germany
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Gichuki DK, Ma L, Zhu Z, Du C, Li Q, Hu G, Zhong Z, Li H, Wang Q, Xin H. Genome size, chromosome number determination, and analysis of the repetitive elements in Cissus quadrangularis. PeerJ 2019; 7:e8201. [PMID: 31875149 PMCID: PMC6927348 DOI: 10.7717/peerj.8201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/13/2019] [Indexed: 02/03/2023] Open
Abstract
Cissus quadrangularis (Vitaceae) is a perennial climber endemic to Africa and is characterized by succulent angular stems. The plant grows in arid and semi-arid regions of Africa especially in the African savanna. The stem of C. quadrangularis has a wide range of applications in both human and animal medicine, but there is limited cytogenetic information available for this species. In this study, the chromosome number, genome size, and genome composition for C. quadrangularis were determined. Flow cytometry results indicated that the genome size of C. quadrangularis is approximately 2C = 1.410 pg. Fluorescence microscopy combined with DAPI stain showed the chromosome numbers to be 2n = 48. It is likely that C. quadrangularis has a tetraploid genome after considering the basic chromosome numbers in Cissus genus (n = 10, 11, or 12). A combination of low-throughput genome sequencing and bioinformatics analysis allowed identification and quantification of repetitive elements that make up about 52% of the C. quadrangularis genome, which was dominated by LTR-retrotransposons. Two LTR superfamilies were identified as Copia and Gypsy, with 24% and 15% of the annotated clusters, respectively. The comparison of repeat elements for C. quadrangularis, Vitis vinifera, and four other selected members in the Cissus genus revealed a high diversity in the repetitive element components, which could suggest recent amplification events in the Cissus genus. Our data provides a platform for further studies on the phylogeny and karyotype evolution in this genus and in the family Vitaceae.
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Affiliation(s)
- Duncan Kiragu Gichuki
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, Peoples Republic of China
| | - Lu Ma
- Shenzhen Tobeacon Technology Co. Ltd., Shenzhen, Peoples Republic of China
| | - Zhenfei Zhu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, Peoples Republic of China
| | - Chang Du
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Qingyun Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Zhixiang Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Honglin Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Qingfeng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Haiping Xin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan CKK, Staňková H, Batley J, Šimková H, Doležel J, Edwards D. An efficient approach to BAC based assembly of complex genomes. PLANT METHODS 2016; 12:2. [PMID: 26793268 PMCID: PMC4719536 DOI: 10.1186/s13007-016-0107-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/08/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. RESULTS We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. CONCLUSIONS We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.
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Affiliation(s)
- Paul Visendi
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, P. O. Box 30197, Nairobi, 00100 Kenya
| | | | - Satomi Hayashi
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Agnieszka A. Golicz
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Philipp E. Bayer
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Pradeep Ruperao
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Bhavna Hurgobin
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Juan Montenegro
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Chon-Kit Kenneth Chan
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Helena Staňková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jacqueline Batley
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Hana Šimková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jaroslav Doležel
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - David Edwards
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
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Musungu B, Bhatnagar D, Brown RL, Fakhoury AM, Geisler M. A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. Front Genet 2015; 6:201. [PMID: 26089837 PMCID: PMC4454876 DOI: 10.3389/fgene.2015.00201] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/21/2015] [Indexed: 12/30/2022] Open
Abstract
Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM) is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs) that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.
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Affiliation(s)
- Bryan Musungu
- Department of Plant Biology, Southern Illinois University Carbondale, IL, USA
| | - Deepak Bhatnagar
- Food and Feed Safety Research, Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service New Orleans, LA, USA
| | - Robert L Brown
- Food and Feed Safety Research, Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service New Orleans, LA, USA
| | - Ahmad M Fakhoury
- Department of Plant Soil and Agriculture Systems, Southern Illinois University Carbondale, IL, USA
| | - Matt Geisler
- Department of Plant Biology, Southern Illinois University Carbondale, IL, USA
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Opitz N, Paschold A, Marcon C, Malik WA, Lanz C, Piepho HP, Hochholdinger F. Transcriptomic complexity in young maize primary roots in response to low water potentials. BMC Genomics 2014; 15:741. [PMID: 25174417 PMCID: PMC4174653 DOI: 10.1186/1471-2164-15-741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Widespread and more frequently occurring drought conditions are a consequence of global warming and increase the demand for tolerant crop varieties to feed the growing world population. A better understanding of the molecular mechanisms underlying the water deficit response of crops will enable targeted breeding strategies to develop robust cultivars. RESULTS In the present study, the transcriptional response of maize (Zea mays L.) primary roots to low water potentials was monitored by RNA sequencing (RNA-Seq) experiments. After 6 h and 24 h of mild (-0.2 MPa) and severe (-0.8 MPa) water deficit conditions, the primary root transcriptomes of seedlings grown under water deficit and control conditions were compared. The number of responsive genes was dependent on and increased with intensification of water deficit treatment. After short-term mild and severe water deficit 249 and 3,000 genes were differentially expressed, respectively. After a 24 h treatment the number of affected genes increased to 7,267 and 12,838 for mild and severe water deficit, respectively, including more than 80% of the short-term responsive genes. About half of the differentially expressed genes were up-regulated and maximal fold-changes increased with treatment intensity to more than 300-fold. A consensus set of 53 genes was differentially regulated independently of the nature of deficit treatment. Characterization revealed an overrepresentation of the Gene Ontology (GO) categories "oxidoreductase activity" and "heme binding" among regulated genes connecting the water deficit response to ROS metabolism. CONCLUSION This study gives a comprehensive insight in water deficit responsive genes in young maize primary roots and provides a set of candidate genes that merit further genetic analyses in the future.
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Affiliation(s)
| | | | | | | | | | | | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany.
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Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KFX, Scholz U, Poland JA, Stein N, Waugh R. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:718-27. [PMID: 23998490 PMCID: PMC4298792 DOI: 10.1111/tpj.12319] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/07/2013] [Accepted: 08/29/2013] [Indexed: 05/18/2023]
Abstract
Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
- For correspondence (e-mails ; )
| | - Gary J Muehlbauer
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
- University of Minnesota, Department of Plant BiologySt Paul, MN 55108, USA
- For correspondence (e-mails ; )
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA, 94720, USA
| | - Jarrod Chapman
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, 35806, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - María Muñoz-Amatriaín
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
| | - Timothy J Close
- Department of Botany & Plant Sciences, University of CaliforniaRiverside, CA, 92521, USA
| | - Roger P Wise
- US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State UniversityAmes, IA, 50011–1020, USA
| | - Alan H Schulman
- Institute of Biotechnology, University of Helsinki/MTT Agrifood ResearchPO Box 65, 00014, Helsinki, Finland
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Klaus FX Mayer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum MünchenD–85764, Neuherberg, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Jesse A Poland
- US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State UniversityManhattan, KS, 65506, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
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Abstract
Monocot cereals develop a complex root system comprising embryonic roots at an early seedling stage and postembryonic roots which make up the fibrous root system of adult crops. In the model cereals maize, rice, and barley a number of mutants affecting root development have been identified in the past and a subset of the affected genes have been recently cloned and functionally characterized. The present review summarizes genetic and molecular data of cereal root mutants impaired in the elongation or initiation of embryonic and postembryonic roots and the elongation of root hairs for which the affected genes have been recently cloned.
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Affiliation(s)
- Caroline Marcon
- Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, University of Bonn, Bonn, Germany
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11
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Chang CH, Wang HI, Lu HC, Chen CE, Chen HH, Yeh HH, Tang CY. An efficient RNA interference screening strategy for gene functional analysis. BMC Genomics 2012; 13:491. [PMID: 22988976 PMCID: PMC3533828 DOI: 10.1186/1471-2164-13-491] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 09/11/2012] [Indexed: 01/14/2023] Open
Abstract
Background RNA interference (RNAi) is commonly applied in genome-scale gene functional screens. However, a one-on-one RNAi analysis that targets each gene is cost-ineffective and laborious. Previous studies have indicated that siRNAs can also affect RNAs that are near-perfectly complementary, and this phenomenon has been termed an off-target effect. This phenomenon implies that it is possible to silence several genes simultaneously with a carefully designed siRNA. Results We propose a strategy that is combined with a heuristic algorithm to design suitable siRNAs that can target multiple genes and a group testing method that would reduce the number of required RNAi experiments in a large-scale RNAi analysis. To verify the efficacy of our strategy, we used the Orchid expressed sequence tag data as a case study to screen the putative transcription factors that are involved in plant disease responses. According to our computation, 94 qualified siRNAs were sufficient to examine all of the predicated 229 transcription factors. In addition, among the 94 computer-designed siRNAs, an siRNA that targets both TF15 (a previously identified transcription factor that is involved in the plant disease-response pathway) and TF21 was introduced into orchids. The experimental results showed that this siRNA can simultaneously silence TF15 and TF21, and application of our strategy successfully confirmed that TF15 is involved in plant defense responses. Interestingly, our second-round analysis, which used an siRNA specific to TF21, indicated that TF21 is a previously unidentified transcription factor that is related to plant defense responses. Conclusions Our computational results showed that it is possible to screen all genes with fewer experiments than would be required for the traditional one-on-one RNAi screening. We also verified that our strategy is capable of identifying genes that are involved in a specific phenotype.
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Affiliation(s)
- Chih-Hung Chang
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
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12
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Smith S, De Smet I. Root system architecture: insights from Arabidopsis and cereal crops. Philos Trans R Soc Lond B Biol Sci 2012; 367:1441-52. [PMID: 22527386 DOI: 10.1098/rstb.2011.0234] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Understanding the development and architecture of roots holds potential for the exploitation and manipulation of root characteristics to both increase food plant yield and optimize agricultural land use. This theme issue highlights the importance of investigating specific aspects of root architecture in both the model plant Arabidopsis thaliana and (cereal) crops, presents novel insights into elements that are currently hardly addressed and provides new tools and technologies to study various aspects of root system architecture. This introduction gives a broad overview of the importance of the root system and provides a snapshot of the molecular control mechanisms associated with root branching and responses to the environment in A. thaliana and cereal crops.
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Affiliation(s)
- Stephanie Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
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13
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Figueroa DM, Bass HW. Development of pachytene FISH maps for six maize chromosomes and their integration with other maize maps for insights into genome structure variation. Chromosome Res 2012; 20:363-80. [PMID: 22588802 PMCID: PMC3391363 DOI: 10.1007/s10577-012-9281-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/27/2012] [Accepted: 03/28/2012] [Indexed: 12/18/2022]
Abstract
Integrated cytogenetic pachytene fluorescence in situ hybridization (FISH) maps were developed for chromosomes 1, 3, 4, 5, 6, and 8 of maize using restriction fragment length polymorphism marker-selected Sorghum propinquum bacterial artificial chromosomes (BACs) for 19 core bin markers and 4 additional genetic framework loci. Using transgenomic BAC FISH mapping on maize chromosome addition lines of oats, we found that the relative locus position along the pachytene chromosome did not change as a function of total arm length, indicative of uniform axial contraction along the fibers during mid-prophase for tested loci on chromosomes 4 and 5. Additionally, we cytogenetically FISH mapped six loci from chromosome 9 onto their duplicated syntenic regions on chromosomes 1 and 6, which have varying amounts of sequence divergence, using sorghum BACs homologous to the chromosome 9 loci. We found that successful FISH mapping was possible even when the chromosome 9 selective marker had no counterpart in the syntenic block. In total, these 29 FISH-mapped loci were used to create the most extensive pachytene FISH maps to date for these six maize chromosomes. The FISH-mapped loci were then merged into one composite karyotype for direct comparative analysis with the recombination nodule-predicted cytogenetic, genetic linkage, and genomic physical maps using the relative marker positions of the loci on all the maps. Marker colinearity was observed between all pair-wise map comparisons, although marker distribution patterns varied widely in some cases. As expected, we found that the recombination nodule-based predictions most closely resembled the cytogenetic map positions overall. Cytogenetic and linkage map comparisons agreed with previous studies showing a decrease in marker spacing in the peri-centromeric heterochromatin region on the genetic linkage maps. In fact, there was a general trend with most loci mapping closer towards the telomere on the linkage maps than on the cytogenetic maps, regardless of chromosome number or maize inbred line source, with just some of the telomeric loci exempted. Finally and somewhat surprisingly, we observed considerable variation between the relative arm positions of loci when comparing our cytogenetic FISH map to the B73 genomic physical maps, even where comparisons were to a B73-derived cytogenetic map. This variation is more evident between different chromosome arms, but less so within a given arm, ruling out any type of inbred-line dependent global features of linear deoxyribonucleic acid compared with the meiotic fiber organization. This study provides a means for analyzing the maize genome structure by producing new connections for integrating the cytogenetic, linkage, and physical maps of maize.
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Affiliation(s)
- Debbie M Figueroa
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295, USA.
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14
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Ma XF, Jensen E, Alexandrov N, Troukhan M, Zhang L, Thomas-Jones S, Farrar K, Clifton-Brown J, Donnison I, Swaller T, Flavell R. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis. PLoS One 2012; 7:e33821. [PMID: 22439001 PMCID: PMC3306302 DOI: 10.1371/journal.pone.0033821] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 02/17/2012] [Indexed: 11/19/2022] Open
Abstract
We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.
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Affiliation(s)
- Xue-Feng Ma
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Elaine Jensen
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | | | - Maxim Troukhan
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Liping Zhang
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Sian Thomas-Jones
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - John Clifton-Brown
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Iain Donnison
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Timothy Swaller
- Ceres, Inc., Thousand Oaks, California, United States of America
- * E-mail:
| | - Richard Flavell
- Ceres, Inc., Thousand Oaks, California, United States of America
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15
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Abstract
The science of genomes: only within the past few decades have scientists progressed from the analysis of a single or a small number of genes at once to the investigation of thousands of genes, going from the study of the units of inheritance to the investigation of the whole genome of an organism. The science of the genomes, or "genomics," initially dedicated to the determination of DNA sequences (the nucleotide order on a given fragment of DNA), has promptly expanded toward a more functional level--studying the expression profiles and the roles of both genes and proteins. The aim of the chapter is to review some basic assumptions and definitions that are the fabric of genomics, and to elucidate key concepts and approaches on which genomics rely.
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Affiliation(s)
- Luca Del Giacco
- Division of Functional and Reproductive Biology, Department of Biology, University of Milan, Milan-MI, Italy.
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16
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Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, Stein N, Waugh R. Patterns of polymorphism and linkage disequilibrium in cultivated barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:523-31. [PMID: 21076812 PMCID: PMC3026706 DOI: 10.1007/s00122-010-1466-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 09/30/2010] [Indexed: 05/18/2023]
Abstract
We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure, patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the 'genetic centromeres'. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10 by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable genome and genetic features.
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Affiliation(s)
- Jordi Comadran
- Genetics Programme, Scottish Crop Research Institute, Dundee, DD2 5DA Scotland, UK
| | - Luke Ramsay
- Genetics Programme, Scottish Crop Research Institute, Dundee, DD2 5DA Scotland, UK
| | | | - Patrick Hayes
- Oregon State University, Barley Project Crop Science Bldg. 30th and Campus Way, Corvallis, OR 97333 USA
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026 USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Robbie Waugh
- Genetics Programme, Scottish Crop Research Institute, Dundee, DD2 5DA Scotland, UK
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17
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Patterns of polymorphism and linkage disequilibrium in cultivated barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010. [PMID: 21076812 DOI: 10.1007/s00122‐010‐1466‐7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure, patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the 'genetic centromeres'. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10 by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable genome and genetic features.
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18
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Neilson KA, Gammulla CG, Mirzaei M, Imin N, Haynes PA. Proteomic analysis of temperature stress in plants. Proteomics 2010; 10:828-45. [PMID: 19953552 DOI: 10.1002/pmic.200900538] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this review we examine current approaches used for proteomic analysis of temperature stress in plants. Rapid advances in this field in recent years are discussed, including metabolic, chemical and isotopic labeling, and label-free quantitative techniques. These are compared and contrasted with well-established methods such as 2-DE approaches. Examples of applications of various methods are presented, and technical difficulties and limitations of each are also considered. Results of previous studies are examined in detail, and commonly occurring temperature stress response proteins are collated. We conclude that technical advances, and improvements in genome sequence availability, will have an ever increasing impact on our understanding of molecular mechanisms of stress response in plants.
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Affiliation(s)
- Karlie A Neilson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW, Australia
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19
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Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC. A single molecule scaffold for the maize genome. PLoS Genet 2009; 5:e1000711. [PMID: 19936062 PMCID: PMC2774507 DOI: 10.1371/journal.pgen.1000711] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. The maize genome contains abundant repeats interspersed by low-copy, gene-coding sequences that make it a challenge to sequence; consequently, current BAC sequence assemblies average 11 contigs per clone. The iMap deals with such complexity by the judicious integration of IBM genetic and B73 physical maps, but the B73 genome structure could differ from the IBM population because of genetic recombination and subsequent rearrangements. Accordingly, we report a genome-wide, high-resolution optical map of maize B73 genome that was constructed from the direct analysis of genomic DNA molecules without using genetic markers. The integration of optical and iMap resources with comparisons to FPC maps enabled a uniquely comprehensive and scalable assessment of a given BAC's sequence assembly, its placement within a FPC contig, and the location of this FPC contig within a chromosome-wide pseudomolecule. As such, the overall utility of the maize optical map for the validation of sequence assemblies has been significant and demonstrates the inherent advantages of single molecule platforms. Construction of the maize optical map represents the first physical map of a eukaryotic genome larger than 400 Mb that was created de novo from individual genomic DNA molecules.
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Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Fusheng Wei
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - John Nguyen
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Mike Bechner
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Konstantinos Potamousis
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Steve Goldstein
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Louise Pape
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael R. Mehan
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Chris Churas
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dan K. Forrest
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Roger Wise
- Corn Insects and Crop Genetics Research, United States Department of Agriculture–Agricultural Research Service and Department of Plant Pathology, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Plant, Soil, and Nutrition Research, United States Department of Agriculture–Agricultural Research Service, Ithaca, New York, United States of America
| | - Rod A. Wing
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Michael S. Waterman
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Miron Livny
- Computer Sciences Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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20
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Vallabhaneni R, Gallagher CE, Licciardello N, Cuttriss AJ, Quinlan RF, Wurtzel ET. Metabolite sorting of a germplasm collection reveals the hydroxylase3 locus as a new target for maize provitamin A biofortification. PLANT PHYSIOLOGY 2009; 151:1635-45. [PMID: 19767386 PMCID: PMC2773064 DOI: 10.1104/pp.109.145177] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 09/08/2009] [Indexed: 05/18/2023]
Abstract
Vitamin A deficiency, a global health burden, can be alleviated through provitamin A carotenoid biofortification of major crop staples such as maize (Zea mays) and other grasses in the Poaceae. If regulation of carotenoid biosynthesis was better understood, enhancement could be controlled by limiting beta-carotene hydroxylation to compounds with lower or no nonprovitamin A activity. Natural maize genetic diversity enabled identification of hydroxylation genes associated with reduced endosperm provitamin A content. A novel approach was used to capture the genetic and biochemical diversity of a large germplasm collection, representing 80% of maize genetic diversity, without having to sample the entire collection. Metabolite data sorting was applied to select a 10-line genetically diverse subset representing biochemical extremes for maize kernel carotenoids. Transcript profiling led to discovery of the Hydroxylase3 locus that coincidently mapped to a carotene quantitative trait locus, thereby prompting investigation of allelic variation in a broader collection. Three natural alleles in 51 maize lines explained 78% of variation and approximately 11-fold difference in beta-carotene relative to beta-cryptoxanthin and 36% of the variation and 4-fold difference in absolute levels of beta-carotene. A simple PCR assay to track and identify Hydroxylase3 alleles will be valuable for predicting nutritional content in genetically diverse cultivars found worldwide.
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21
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Kronmiller BA, Wise RP. Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. PLANT PHYSIOLOGY 2009; 151:483-495. [PMID: 19675151 PMCID: PMC2754626 DOI: 10.1104/pp.109.143370] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 08/03/2009] [Indexed: 05/26/2023]
Abstract
The architecture of grass genomes varies on multiple levels. Large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. To characterize the organization and distribution of repeat clusters and gene islands across large grass genomes, we present 961- and 594-kb contiguous sequence contigs associated with the rf1 (for restorer of fertility1) locus in the near-centromeric region of maize (Zea mays) chromosome 3. We present two methods for computational finishing of highly repetitive bacterial artificial chromosome clones that have proved successful to close all sequence gaps caused by transposable element insertions. Sixteen repeat clusters were observed, ranging in length from 23 to 155 kb. These repeat clusters are almost exclusively long terminal repeat retrotransposons, of which the paleontology of insertion varies throughout the cluster. Gene islands contain from one to four predicted genes, resulting in a gene density of one gene per 16 kb in gene islands and one gene per 111 kb over the entire sequenced region. The two sequence contigs, when compared with the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes, retain gene colinearity of 50% and 71%, respectively, and 70% and 100%, respectively, for high-confidence gene models. Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations.
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Affiliation(s)
- Brent A Kronmiller
- Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa 50011-1020, USA
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22
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Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. THE PLANT CELL 2009; 4:760-2. [PMID: 19376930 PMCID: PMC2685623 DOI: 10.1105/tpc.109.065714] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Revised: 03/04/2009] [Accepted: 04/01/2009] [Indexed: 05/17/2023]
Abstract
Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organ-specific distribution of canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), indicative of their tissue-specific biogenesis. Furthermore, we observed that a decreasing level of mop1 led to a concomitant decrease of 24-nucleotide siRNAs relative to 21-nucleotide miRNAs in a tissue-specific manner. A group of 22-nucleotide siRNAs may originate from long-hairpin double-stranded RNAs and preferentially target gene-coding regions. Additionally, a class of miRNA-like smRNAs, whose putative precursors can form short hairpins, potentially targets genes in trans. In summary, our data provide a critical analysis of the maize epigenome and its relationships to mRNA and smRNA transcriptomes.
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MESH Headings
- DNA Methylation
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Genome, Plant
- Histones/metabolism
- MicroRNAs/chemistry
- MicroRNAs/metabolism
- Nucleic Acid Conformation
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/metabolism
- Sequence Analysis, RNA
- Zea mays/genetics
- Zea mays/metabolism
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Affiliation(s)
- Xiangfeng Wang
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
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23
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Batrinou AM, Koraki D, Sinanoglou VJ, Karagouni AD, Sflomos K, Pletsa V. Effect of Ionizing Radiation on the Quantification of Genetically Modified Foods. FOOD BIOTECHNOL 2008. [DOI: 10.1080/08905430802458438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Sharpe RM, Dunn SN, Cahoon AB. A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae species. PLANT METHODS 2008; 4:14. [PMID: 18518993 PMCID: PMC2453112 DOI: 10.1186/1746-4811-4-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 06/02/2008] [Indexed: 05/26/2023]
Abstract
BACKGROUND Quantitative Real Time RT-PCR (q2(RT)PCR) is a maturing technique which gives researchers the ability to quantify and compare very small amounts of nucleic acids. Primer design and optimization is an essential yet time consuming aspect of using q2(RT)PCR. In this paper we describe the design and empirical optimization of primers to amplify and quantify plastid RNAs from Zea mays that are robust enough to use with other closely related species. RESULTS Primers were designed and successfully optimized for 57 of the 104 reported genes in the maize plastome plus two nuclear genes. All 59 primer pairs produced single amplicons after end-point reverse transcriptase polymerase chain reactions (RT-PCR) as visualized on agarose gels and subsequently verified by q2(RT)PCR. Primer pairs were divided into several categories based on the optimization requirements or the uniqueness of the target gene. An in silico test suggested the majority of the primer sets should work with other members of the Poaceae family. An in vitro test of the primer set on two unsequenced species (Panicum virgatum and Miscanthus sinensis) supported this assumption by successfully producing single amplicons for each primer pair. CONCLUSION Due to the highly conserved chloroplast genome in plant families it is possible to utilize primer pairs designed against one genomic sequence to detect the presence and abundance of plastid genes or transcripts from genomes that have yet to be sequenced. Analysis of steady state transcription of vital system genes is a necessary requirement to comprehensively elucidate gene expression in any organism. The primer pairs reported in this paper were designed for q2(RT)PCR of maize chloroplast genes but should be useful for other members of the Poaceae family. Both in silico and in vitro data are presented to support this assumption.
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Affiliation(s)
- Richard M Sharpe
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Sade N Dunn
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - A Bruce Cahoon
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
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A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zea mays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion. Genetics 2007; 177:1509-26. [PMID: 17947405 DOI: 10.1534/genetics.107.080846] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A cytogenetic FISH map of maize pachytene-stage chromosome 9 was produced with 32 maize marker-selected sorghum BACs as probes. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 cM. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole-chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC-FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between cdo17 (at 9L.03) and tda66 (at 9S.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum and creates additional tools and information for understanding the structure and evolution of the maize genome.
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Rösti S, Denyer K. Two paralogous genes encoding small subunits of ADP-glucose pyrophosphorylase in maize, Bt2 and L2, replace the single alternatively spliced gene found in other cereal species. J Mol Evol 2007; 65:316-27. [PMID: 17846820 DOI: 10.1007/s00239-007-9013-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Accepted: 07/06/2007] [Indexed: 10/22/2022]
Abstract
Two types of gene encoding small subunits (SSU) of ADP-glucose pyrophosphorylase, a starch-biosynthetic enzyme, have been found in cereals and other grasses. One of these genes encodes two SSU proteins. These are targeted to different subcellular compartments and expressed in different organs of the plant: the endosperm cytosol and the leaf plastids. The SSU gene encoding two proteins evolved from an ancestral gene encoding a single protein by the acquisition of an alternative first exon. Prior to the work reported here, this type of SSU gene had been found in all grasses examined except maize. In maize, two separate genes, Bt2 and L2, were known to have the same roles as the alternatively spliced gene found in other grasses. The evolutionary origin of these maize genes and their relationship to the SSU genes in other grasses were unclear. Here we show that Bt2 and L2 are paralogous genes that arose as a result of the tetraploidization of the maize genome. Both genes derive from an ancestral alternatively spliced SSU gene orthologous to that found in other grasses. Following duplication, the Bt2 and L2 genes diverged in function. Each took a different one of the two functions of the ancestral gene. Now Bt2 encodes the endosperm cytosolic SSU but does not contribute significantly to leaf AGPase activity. Similarly, L2 has lost the use of one of its two alternative first exons. It can no longer contribute to the endosperm cytosolic SSU but is probably responsible for the bulk of the leaf AGPase SSU.
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Lunn JE. Gene families and evolution of trehalose metabolism in plants. FUNCTIONAL PLANT BIOLOGY : FPB 2007; 34:550-563. [PMID: 32689383 DOI: 10.1071/fp06315] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Accepted: 01/11/2007] [Indexed: 05/25/2023]
Abstract
The genomes of Arabidopsis thaliana L., rice (Oryza sativa L.) and poplar (Populus trichocarpa Torr. & A.Gray) contain large families of genes encoding trehalose-phosphate synthase (TPS) and trehalose-phosphatase (TPP). The class I subfamily of TPS genes encodes catalytically active TPS enzymes, and is represented by only one or two genes in most species. A. thaliana is atypical in having four class I TPS genes, three of which (AtTPS2-4) encode unusual short isoforms of TPS that appear to be found only in members of the Brassicaceae family. The class II TPS genes encode TPS-like proteins with a C-terminal TPP-like domain, but there is no experimental evidence that they have any enzymatic activity and their function is unknown. Both classes of TPS gene are represented in the genomes of chlorophyte algae (Ostreococcus species) and non-flowering plants [Physcomitrella patens (Hedw.) Bruch & Schimp.(B.S.G.) and Selaginella moellendorffii (Hieron. in Engl. & Prantl.)]. This survey shows that the gene families encoding the enzymes of trehalose metabolism are very ancient, pre-dating the divergence of the streptophyte and chlorophyte lineages. It also provides a frame of reference for future studies to elucidate the function of trehalose metabolism in plants.
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Affiliation(s)
- John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14424 Potsdam, Germany. Email
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Sauer M, Jakob A, Nordheim A, Hochholdinger F. Proteomic analysis of shoot-borne root initiation in maize (Zea mays L.). Proteomics 2006; 6:2530-41. [PMID: 16521151 DOI: 10.1002/pmic.200500564] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Postembryonically formed shoot-borne roots make up the major backbone of the adult maize root stock. In this study the abundant soluble proteins of the first node (coleoptilar node) of wild-type and mutant rtcs seedlings, which do not initiate crown roots, were compared at two early stages of crown root formation. In Coomassie Bluestained 2-D gels, representing soluble proteins of coleoptilar nodes 5 and 10 days after germination, 146 and 203 proteins were detected, respectively. Five differentially accumulated proteins (> two-fold change; t-test: 95% significance) were identified in 5-day-old and 14 differentially accumulated proteins in 10-day-old coleoptilar nodes of wild-type versus rtcs. All 19 differentially accumulated proteins were identified via ESI MS/MS mass spectrometry. Five differentially accumulated proteins, including a regulatory G-protein and a putative auxin-binding protein, were further analyzed at the RNA expression level. These experiments confirmed differential gene expression and revealed subtle developmental regulation of these genes during early coleoptilar node development. This study represents the first proteomic analysis of shoot-borne root initiation in cereals and will contribute to a better understanding of the molecular basis of this developmental process unique to cereals.
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Affiliation(s)
- Michaela Sauer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, Tuebingen, Germany
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29
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McSteen P. Branching out: the ramosa pathway and the evolution of grass inflorescence morphology. THE PLANT CELL 2006; 18:518-22. [PMID: 16513602 PMCID: PMC1383629 DOI: 10.1105/tpc.105.040196] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Affiliation(s)
- Paula McSteen
- Department of Biology, The Pensylvania State University, University Park, PA 16802, USA.
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30
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Falque M, Décousset L, Dervins D, Jacob AM, Joets J, Martinant JP, Raffoux X, Ribière N, Ridel C, Samson D, Charcosset A, Murigneux A. Linkage mapping of 1454 new maize candidate gene Loci. Genetics 2005; 170:1957-66. [PMID: 15937132 PMCID: PMC1449757 DOI: 10.1534/genetics.104.040204] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 04/24/2005] [Indexed: 11/18/2022] Open
Abstract
Bioinformatic analyses of maize EST sequences have highlighted large numbers of candidate genes putatively involved in agriculturally important traits. To contribute to ongoing efforts toward mapping of these genes, we used two populations of intermated recombinant inbred lines (IRILs), which allow a higher map resolution than nonintermated RILs. The first panel (IBM), derived from B73 x Mo17, is publicly available from the Maize Genetics Cooperation Stock Center. The second panel (LHRF) was developed from F2 x F252 to map loci monomorphic on IBM. We built framework maps of 237 loci from the IBM panel and 271 loci from the LHRF panel. Both maps were used to place 1454 loci (1056 on map IBM_Gnp2004 and 398 on map LHRF_Gnp2004) that corresponded to 954 cDNA probes previously unmapped. RFLP was mostly used, but PCR-based methods were also performed for some cDNAs to map SNPs. Unlike in usual IRIL-based maps published so far, corrected meiotic centimorgan distances were calculated, taking into account the number of intermating generations undergone by the IRILs. The corrected sizes of our framework maps were 1825 cM for IBM_Gnp2004 and 1862 cM for LHRF_Gnp2004. All loci mapped on LHRF_Gnp2004 were also projected on a consensus map IBMconsensus_Gnp2004. cDNA loci formed clusters near the centromeres except for chromosomes 1 and 8.
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Affiliation(s)
- Matthieu Falque
- INRA-UPS-CNRS-INA.PG, UMR de Génétique Végétale, 91190 Gif-sur-Yvette, France.
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31
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Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 2004; 168:2169-85. [PMID: 15611184 PMCID: PMC1448716 DOI: 10.1534/genetics.104.032375] [Citation(s) in RCA: 215] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Accepted: 08/19/2004] [Indexed: 01/16/2023] Open
Abstract
Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation.
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Affiliation(s)
- Fabien Chardon
- INRA/INA-PG/UPS/CNRS, Station de Génétique Végétale, 91190 Gif-sur-Yvette, France
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Buchanan CD, Klein PE, Mullet JE. Phylogenetic analysis of 5'-noncoding regions from the ABA-responsive rab16/17 gene family of sorghum, maize and rice provides insight into the composition, organization and function of cis-regulatory modules. Genetics 2004; 168:1639-54. [PMID: 15579713 PMCID: PMC1448771 DOI: 10.1534/genetics.104.030346] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Accepted: 07/16/2004] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of sequences from gene families and homologous genes from species of varying divergence can be used to identify conserved noncoding regulatory elements. In this study, phylogenetic analysis of 5'-noncoding sequences was optimized using rab17, a well-characterized ABA-responsive gene from maize, and five additional rab16/17 homologs from sorghum and rice. Conserved 5'-noncoding sequences among the maize, sorghum, and rice rab16/17 homologs were identified with the aid of the software program FootPrinter and by screening for known transcription-factor-binding sites. Searches for 7 of 8 (7/8)bp sequence matches within aligned 5'-noncoding segments of the rab genes identified many of the cis-elements previously characterized by biochemical analysis in maize rab17 plus several additional putative regulatory elements. Differences in the composition of conserved noncoding sequences among rab16/17 genes were related to variation in rab gene mRNA levels in different tissues and to response to ABA treatment using qRT-PCR. Absence of a GRA-like element in the promoter of sorghum dhn2 relative to maize rab17 was correlated with an approximately 85-fold reduction of dhn2 RNA in sorghum shoots. Overall, we conclude that phylogenetic analysis of gene families among rice, sorghum, and maize will help identify regulatory sequences in the noncoding regions of genes and contribute to our understanding of grass gene regulatory networks.
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Affiliation(s)
- Christina D Buchanan
- Institute for Plant Genomics and Biotechnology, Texas A and M University, College Station, Texas 77843, USA
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33
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Castleden CK, Aoki N, Gillespie VJ, MacRae EA, Quick WP, Buchner P, Foyer CH, Furbank RT, Lunn JE. Evolution and function of the sucrose-phosphate synthase gene families in wheat and other grasses. PLANT PHYSIOLOGY 2004; 135:1753-64. [PMID: 15247374 PMCID: PMC519087 DOI: 10.1104/pp.104.042457] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Revised: 04/13/2004] [Accepted: 04/23/2004] [Indexed: 05/20/2023]
Abstract
Suc-phosphate synthase (SPS) is a key regulatory enzyme in the pathway of Suc biosynthesis and has been linked to quantitative trait loci controlling plant growth and yield. In dicotyledonous plants there are three SPS gene families: A, B, and C. Here we report the finding of five families of SPS genes in wheat (Triticum aestivum) and other monocotyledonous plants from the family Poaceae (grasses). Three of these form separate subfamilies within the previously described A, B, and C gene families, but the other two form a novel and distinctive D family, which on present evidence is only found in the Poaceae. The D-type SPS proteins lack the phosphorylation sites associated with 14-3-3 protein binding and osmotic stress activation, and the linker region between the N-terminal catalytic glucosyltransferase domain and the C-terminal Suc-phosphatase-like domain is 80 to 90 amino acid residues shorter than in the A, B, or C types. The D family appears to have arisen after the divergence of mono- and dicotyledonous plants, with a later duplication event resulting in the two D-type subfamilies. Each of the SPS gene families in wheat showed different, but overlapping, spatial and temporal expression patterns, and in most organs at least two different SPS genes are expressed. Analysis of expressed sequence tags indicated similar expression patterns to wheat for each SPS gene family in barley (Hordeum vulgare) but not in more distantly related grasses. We identified an expressed sequence tag from rice (Oryza sativa) that appears to be derived from an endogenous antisense SPS gene, and this might account for the apparently low level of expression of the related OsSPS11 sense gene, adding to the already extensive list of mechanisms for regulating the activity of SPS in plants.
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Affiliation(s)
- C Kate Castleden
- Crop Performance and Improvement Division, Rothamsted-Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
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Hochholdinger F, Woll K, Sauer M, Dembinsky D. Genetic dissection of root formation in maize (Zea mays) reveals root-type specific developmental programmes. ANNALS OF BOTANY 2004; 93:359-68. [PMID: 14980975 PMCID: PMC4242335 DOI: 10.1093/aob/mch056] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
BACKGROUND Maize (Zea mays) forms a complex root system comprising embryonic and post-embryonic roots. The embryonically formed root system is made up of the primary root and a variable number of seminal roots. Later in development the post-embryonic shoot-borne root system becomes dominant and is responsible together with its lateral roots for the major portion of water and nutrient uptake. Although the anatomical structure of the different root-types is very similar they are initiated from different tissues during embryonic and post-embryonic development. Recently, a number of mutants specifically affected in maize root development have been identified. These mutants indicate that various root-type specific developmental programmes are involved in the establishment of the maize root stock. SCOPE This review summarizes these genetic data in the context of the maize root morphology and anatomy and gives an outlook on possible perspectives of the molecular analysis of maize root formation.
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Affiliation(s)
- Frank Hochholdinger
- Center for Plant Molecular Biology (ZMBP), Eberhard Karls University Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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35
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Ouyang S, Buell CR. The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 2004; 32:D360-3. [PMID: 14681434 PMCID: PMC308833 DOI: 10.1093/nar/gkh099] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In a number of higher plants, a substantial portion of the genome is composed of repetitive sequences that can hinder genome annotation and sequencing efforts. To better understand the nature of repetitive sequences in plants and provide a resource for identifying such sequences, we constructed databases of repetitive sequences for 12 plant genera: Arabidopsis, Brassica, Glycine, Hordeum, Lotus, Lycopersicon, Medicago, Oryza, Solanum, Sorghum, Triticum and Zea (www.tigr.org/tdb/e2k1/plant. repeats/index.shtml). The repetitive sequences within each database have been coded into super-classes, classes and sub-classes based on sequence and structure similarity. These databases are available for sequence similarity searches as well as downloadable files either as entire databases or subsets of each database. To further the utility for comparative studies and to provide a resource for searching for repetitive sequences in other genera within these families, repetitive sequences have been combined into four databases to represent the Brassicaceae, Fabaceae, Gramineae and Solanaceae families. Collectively, these databases provide a resource for the identification, classification and analysis of repetitive sequences in plants.
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Affiliation(s)
- Shu Ouyang
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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36
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Dong Q, Schlueter SD, Brendel V. PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 2004; 32:D354-9. [PMID: 14681433 PMCID: PMC308780 DOI: 10.1093/nar/gkh046] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PlantGDB (http://www.plantgdb.org/) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that represent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome sequence fragments are assembled similarly. The goal of the PlantGDB web site is to establish the basis for identifying sets of genes common to all plants or specific to particular species by integrating a number of bioinformatics tools that facilitate gene prediction and cross- species comparisons. For species with large-scale genome sequencing efforts, PlantGDB provides genome browsing capabilities that integrate all available EST and cDNA evidence for current gene models (for Arabidopsis thaliana, see the AtGDB site at http://www.plantgdb.org/AtGDB/).
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Affiliation(s)
- Qunfeng Dong
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
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Hochholdinger F, Park WJ, Sauer M, Woll K. From weeds to crops: genetic analysis of root development in cereals. TRENDS IN PLANT SCIENCE 2004; 9:42-8. [PMID: 14729218 DOI: 10.1016/j.tplants.2003.11.003] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Root development of Arabidopsis, Zea mays (maize) and Oryza sativa (rice) differs in both overall architecture and the anatomy of individual roots. In maize and rice, the post-embryonic shoot-borne root system becomes the major backbone of the root stock; in Arabidopsis, the embryonic root system formed by a simple primary root and its lateral roots remains dominant. Recently, several specific root mutants and root-specific genes have been identified and characterized in maize and rice. Interestingly, some of these mutants indicate that the formation of primary-, seminal-, crown- and lateral roots is regulated by alternative root-type-specific pathways. Further analyses of these unique pathways will contribute to the understanding of the complex molecular networks involved in cereal root formation.
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Affiliation(s)
- Frank Hochholdinger
- Center for Plant Molecular Biology, Department of General Genetics, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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Tang W, Luo X, Nelson A, Collver H, Kinken K. Functional genomics of wood quality and properties. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:263-78. [PMID: 15629055 PMCID: PMC5172417 DOI: 10.1016/s1672-0229(03)01032-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide. In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus. The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.
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Affiliation(s)
- Wei Tang
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA.
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Engler FW, Hatfield J, Nelson W, Soderlund CA. Locating sequence on FPC maps and selecting a minimal tiling path. Genome Res 2003; 13:2152-63. [PMID: 12915486 PMCID: PMC403717 DOI: 10.1101/gr.1068603] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This study discusses three software tools, the first two aid in integrating sequence with an FPC physical map and the third automatically selects a minimal tiling path given genomic draft sequence and BAC end sequences. The first tool, FSD (FPC Simulated Digest), takes a sequenced clone and adds it back to the map based on a fingerprint generated by an in silico digest of the clone. This allows verification of sequenced clone positions and the integration of sequenced clones that were not originally part of the FPC map. The second tool, BSS (Blast Some Sequence), takes a query sequence and positions it on the map based on sequence associated with the clones in the map. BSS has multiple uses as follows: (1) When the query is a file of marker sequences, they can be added as electronic markers. (2) When the query is draft sequence, the results of BSS can be used to close gaps in a sequenced clone or the physical map. (3) When the query is a sequenced clone and the target is BAC end sequences, one may select the next clone for sequencing using both sequence comparison results and map location. (4) When the query is whole-genome draft sequence and the target is BAC end sequences, the results can be used to select many clones for a minimal tiling path at once. The third tool, pickMTP, automates the majority of this last usage of BSS. Results are presented using the rice FPC map, BAC end sequences, and whole-genome shotgun from Syngenta.
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Affiliation(s)
- Friedrich W Engler
- Arizona Genomics Computational Laboratory, University of Arizona, Tucson, Arizona 85721, USA
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Rudd S. Expressed sequence tags: alternative or complement to whole genome sequences? TRENDS IN PLANT SCIENCE 2003; 8:321-9. [PMID: 12878016 DOI: 10.1016/s1360-1385(03)00131-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Over three million sequences from approximately 200 plant species have been deposited in the publicly available plant expressed sequence tag (EST) sequence databases. Many of the ESTs have been sequenced as an alternative to complete genome sequencing or as a substrate for cDNA array-based expression analyses. This creates a formidable resource from both biodiversity and gene-discovery standpoints. Bioinformatics-based sequence analysis tools have extended the scope of EST analysis into the fields of proteomics, marker development and genome annotation. Although EST collections are certainly no substitute for a whole genome scaffold, this "poor man's genome" resource forms the core foundations for various genome-scale experiments within the as yet unsequenceable plant genomes.
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Affiliation(s)
- Stephen Rudd
- Institut für Bioinformatik, GSF Forschungszentrum für Umwelt und Gesundheit, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.
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Schlueter SD, Dong Q, Brendel V. GeneSeqer@PlantGDB: Gene structure prediction in plant genomes. Nucleic Acids Res 2003; 31:3597-600. [PMID: 12824374 PMCID: PMC168940 DOI: 10.1093/nar/gkg533] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The GeneSeqer@PlantGDB Web server (http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi) provides a gene structure prediction tool tailored for applications to plant genomic sequences. Predictions are based on spliced alignment with source-native ESTs and full-length cDNAs or non-native probes derived from putative homologous genes. The tool is illustrated with applications to refinement of current gene structure annotation and de novo annotation of draft genomic sequences. The service should facilitate expert annotation as a community effort by providing convenient access to all public plant sequences via the PlantGDB database, a simple four-step protocol for spliced alignment and visually appealing displays of the predicted gene structures in addition to detailed sequence alignments.
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Affiliation(s)
- Shannon D Schlueter
- Department of Zoology and Genetics, Iowa State University, Ames, IA 50011-3260, USA
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