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Wang Y, Chen G, Zeng F, Han Z, Qiu CW, Zeng M, Yang Z, Xu F, Wu D, Deng F, Xu S, Chater C, Korol A, Shabala S, Wu F, Franks P, Nevo E, Chen ZH. Molecular evidence for adaptive evolution of drought tolerance in wild cereals. THE NEW PHYTOLOGIST 2023; 237:497-514. [PMID: 36266957 DOI: 10.1111/nph.18560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight. Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium species collected from dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. We present the genomic and transcriptomic evidence accounting for differences, including co-expression gene modules, correlated with physiological traits, and selective sweeps, driven by the xeric site conditions on the African Slope (AS) at ECI. Co-expression gene module 'circadian rhythm' was linked to significant drought-induced delay in flowering time in Brachypodium stacei genotypes. African Slope-specific differentially expressed genes are important in barley drought tolerance, verified by silencing Disease-Related Nonspecific Lipid Transfer 1 (DRN1), Nonphotochemical Quenching 4 (NPQ4), and Brassinosteroid-Responsive Ring-H1 (BRH1). Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate with increasingly frequent drought events.
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Affiliation(s)
- Yuanyuan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fanrong Zeng
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Zhigang Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Cheng-Wei Qiu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zeng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, China
| | - Fei Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Dezhi Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fenglin Deng
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shengchun Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Caspar Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, 7004, Australia
- School of Biological Science, University of Western Australia, Crawley, WA, 6009, Australia
| | - Feibo Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Peter Franks
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
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2
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Mohanta TK, Bashir T, Hashem A, Abd Allah EF. Systems biology approach in plant abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 121:58-73. [PMID: 29096174 DOI: 10.1016/j.plaphy.2017.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 05/05/2023]
Abstract
Plant abiotic stresses are the major constraint on plant growth and development, causing enormous crop losses across the world. Plants have unique features to defend themselves against these challenging adverse stress conditions. They modulate their phenotypes upon changes in physiological, biochemical, molecular and genetic information, thus making them tolerant against abiotic stresses. It is of paramount importance to determine the stress-tolerant traits of a diverse range of genotypes of plant species and integrate those traits for crop improvement. Stress-tolerant traits can be identified by conducting genome-wide analysis of stress-tolerant genotypes through the highly advanced structural and functional genomics approach. Specifically, whole-genome sequencing, development of molecular markers, genome-wide association studies and comparative analysis of interaction networks between tolerant and susceptible crop varieties grown under stress conditions can greatly facilitate discovery of novel agronomic traits that protect plants against abiotic stresses.
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Affiliation(s)
- Tapan Kumar Mohanta
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Tufail Bashir
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Science, King Saud University, P.O. Box 24160, Riyadh, 11451, Saudi Arabia
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3
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Sood S, Kuraparthy V, Bai G, Gill BS. The major threshability genes soft glume (sog) and tenacious glume (Tg), of diploid and polyploid wheat, trace their origin to independent mutations at non-orthologous loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:341-51. [PMID: 19421730 DOI: 10.1007/s00122-009-1043-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 04/09/2009] [Indexed: 05/23/2023]
Abstract
Threshability is an important crop domestication trait. The wild wheat progenitors have tough glumes enveloping the floret that make spikes difficult to thresh, whereas cultivated wheats have soft glumes and are free-threshing. In hexaploid wheat, the glume tenacity gene Tg along with the major domestication locus Q control threshability. The Q gene was isolated recently and found to be a member of the AP2 class of transcription factors. However, only a few studies have reported on the tough glume trait. Here, we report comparative mapping of the soft glume (sog) gene of diploid Triticum monococcum L. and tenacious glume (Tg) gene of hexaploid T. aestivum L. using chromosome-specific SSR and RFLP markers. The sog gene was flanked by Xgwm71 and Xbcd120 in a 6.8 cM interval on chromosome 2A(m)S of T. monococcum whereas Tg was targeted to a 8.1 cM interval flanked by Xwmc503 and Xfba88 on chromosome 2DS of T. aestivum. Deletion bin mapping of the flanking markers assigned sog close to the centromere on 2AS, whereas Tg was mapped to the most distal region on 2DS. Both 2AS and 2DS maps were colinear ruling out the role of chromosome rearrangements for their non-syntenic positions. Therefore, sog and Tg are not true orthologues suggesting the possibility of a diverse origin.
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Affiliation(s)
- Shilpa Sood
- Department of Plant Pathology, Wheat Genetic and Genomic Resources Center, Kansas State University, Manhattan, KS 66506-5502, USA.
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Patrushev LI, Minkevich IG. The problem of the eukaryotic genome size. BIOCHEMISTRY (MOSCOW) 2009; 73:1519-52. [PMID: 19216716 DOI: 10.1134/s0006297908130117] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The current state of knowledge concerning the unsolved problem of the huge interspecific eukaryotic genome size variations not correlating with the species phenotypic complexity (C-value enigma also known as C-value paradox) is reviewed. Characteristic features of eukaryotic genome structure and molecular mechanisms that are the basis of genome size changes are examined in connection with the C-value enigma. It is emphasized that endogenous mutagens, including reactive oxygen species, create a constant nuclear environment where any genome evolves. An original quantitative model and general conception are proposed to explain the C-value enigma. In accordance with the theory, the noncoding sequences of the eukaryotic genome provide genes with global and differential protection against chemical mutagens and (in addition to the anti-mutagenesis and DNA repair systems) form a new, third system that protects eukaryotic genetic information. The joint action of these systems controls the spontaneous mutation rate in coding sequences of the eukaryotic genome. It is hypothesized that the genome size is inversely proportional to functional efficiency of the anti-mutagenesis and/or DNA repair systems in a particular biological species. In this connection, a model of eukaryotic genome evolution is proposed.
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Affiliation(s)
- L I Patrushev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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5
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Wan X, Weng J, Zhai H, Wang J, Lei C, Liu X, Guo T, Jiang L, Su N, Wan J. Quantitative trait loci (QTL) analysis for rice grain width and fine mapping of an identified QTL allele gw-5 in a recombination hotspot region on chromosome 5. Genetics 2008; 179:2239-52. [PMID: 18689882 PMCID: PMC2516094 DOI: 10.1534/genetics.108.089862] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 05/20/2008] [Indexed: 11/18/2022] Open
Abstract
Rice grain width and shape play a crucial role in determining grain quality and yield. The genetic basis of rice grain width was dissected into six additive quantitative trait loci (QTL) and 11 pairs of epistatic QTL using an F(7) recombinant inbred line (RIL) population derived from a single cross between Asominori (japonica) and IR24 (indica). QTL by environment interactions were evaluated in four environments. Chromosome segment substitution lines (CSSLs) harboring the six additive effect QTL were used to evaluate gene action across eight environments. A major, stable QTL, qGW-5, consistently decreased rice grain width in both the Asominori/IR24 RIL and CSSL populations with the genetic background Asominori. By investigating the distorted segregation of phenotypic values of rice grain width and genotypes of molecular markers in BC(4)F(2) and BC(4)F(3) populations, qGW-5 was dissected into a single recessive gene, gw-5, which controlled both grain width and length-width ratio. gw-5 was narrowed down to a 49.7-kb genomic region with high recombination frequencies on chromosome 5 using 6781 BC(4)F(2) individuals and 10 newly developed simple sequence repeat markers. Our results provide a basis for map-based cloning of the gw-5 gene and for marker-aided gene/QTL pyramiding in rice quality breeding.
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Affiliation(s)
- Xiangyuan Wan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Rajesh PN, O'Bleness M, Roe BA, Muehlbauer FJ. Analysis of genome organization, composition and microsynteny using 500 kb BAC sequences in chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:449-58. [PMID: 18504542 DOI: 10.1007/s00122-008-0789-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 05/02/2008] [Indexed: 05/08/2023]
Abstract
The small genome size (740 Mb), short life cycle (3 months) and high economic importance as a food crop legume make chickpea (Cicer arietinum L.) an important system for genomics research. Although several genetic linkage maps using various markers and genomic tools have become available, sequencing efforts and their use are limited in chickpea genomic research. In this study, we explored the genome organization of chickpea by sequencing approximately 500 kb from 11 BAC clones (three representing ascochyta blight resistance QTL1 (ABR-QTL1) and eight randomly selected BAC clones). Our analysis revealed that these sequenced chickpea genomic regions have a gene density of one per 9.2 kb, an average gene length of 2,500 bp, an average of 4.7 exons per gene, with an average exon and intron size of 401 and 316 bp, respectively, and approximately 8.6% repetitive elements. Other features analyzed included exon and intron length, number of exons per gene, protein length and %GC content. Although there are reports on high synteny among legume genomes, the microsynteny between the 500 kb chickpea and available Medicago truncatula genomic sequences varied depending on the region analyzed. The GBrowse-based annotation of these BACs is available at http://www.genome.ou.edu/plants_totals.html . We believe that our work provides significant information that supports a chickpea genome sequencing effort in the future.
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Affiliation(s)
- P N Rajesh
- U.S. Department of Agriculture, Agricultural Research Service, and Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6434, USA.
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7
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Ballvora A, Jöcker A, Viehöver P, Ishihara H, Paal J, Meksem K, Bruggmann R, Schoof H, Weisshaar B, Gebhardt C. Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments. BMC Genomics 2007; 8:112. [PMID: 17474978 PMCID: PMC3225836 DOI: 10.1186/1471-2164-8-112] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 05/02/2007] [Indexed: 11/10/2022] Open
Abstract
Background Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. Results To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Conclusion Comparative sequence analysis revealed highly conserved collinear regions that flank regions showing high variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural conservation between these distantly related plant species.
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Affiliation(s)
- Agim Ballvora
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Anika Jöcker
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Prisca Viehöver
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
- Institut für Genomforschung, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Hirofumi Ishihara
- Institut für Genomforschung, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Southern Illinois University at Carbondale, Dept. of Plant, Soil and General Agriculture, Carbondale, IL62901-4415, USA
| | - Jürgen Paal
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Khalid Meksem
- Southern Illinois University at Carbondale, Dept. of Plant, Soil and General Agriculture, Carbondale, IL62901-4415, USA
| | - Rémy Bruggmann
- GSF Forschungszentrum für Umwelt und Gesundheit, Institut für Bioinformatik, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Heiko Schoof
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Bernd Weisshaar
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
- Institut für Genomforschung, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Christiane Gebhardt
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
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Zhu W, Buell CR. Improvement of whole-genome annotation of cereals through comparative analyses. Genome Res 2007; 17:299-310. [PMID: 17284677 PMCID: PMC1800921 DOI: 10.1101/gr.5881807] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Rice is an important model species for the Poaceae and other monocotyledonous plants. With the availability of a near-complete, finished, and annotated rice genome, we performed genome level comparisons between rice and all plant species in which large genomic or transcriptomic data sets are available to determine the utility of cross-species sequence for structural and functional annotation of the rice genome. Through comparative analyses with four plant genome sequence data sets and transcript assemblies from 185 plant species, we were able to confirm and improve the structural annotation of the rice genome. Support for 38,109 (89.3%) of the total 42,653 nontransposable element-related genes in the rice genome in the form of a rice expressed sequence tag, full-length cDNA, or plant homolog from our comparative analyses could be found. Although the majority of the putative homologs were obtained from Poaceae species, putative homologs were identified in dicotyledonous angiosperms, gymnosperms, and other plants such as algae, moss, and fern. A set of rice genes (7669) lacking a putative homolog was identified which may be lineage-specific genes that evolved after speciation and have a role in species diversity. Improvements to the current rice gene structural annotation could be identified from our comparative alignments and we were able to identify 487 genes which were mostly likely missed in the current rice genome annotation and another 500 genes for structural annotation review. We were able to demonstrate the utility of cross-species comparative alignments in the identification of noncoding sequences and in confirmation of gene nesting in rice.
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Affiliation(s)
- Wei Zhu
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - C. Robin Buell
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
- Corresponding author.E-mail ; fax: (301) 838-0208
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9
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Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 2006; 35:D883-7. [PMID: 17145706 PMCID: PMC1751532 DOI: 10.1093/nar/gkl976] [Citation(s) in RCA: 845] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In The Institute for Genomic Research Rice Genome Annotation project (), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42 653 non-transposable element-related genes encoding 49 472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13 237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31 739 gene models), representing ∼50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - C. Robin Buell
- To whom correspondence should be addressed. Tel: +1 301 795 7558; Fax: +1 301 838 0208;
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10
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Martin G, Lenormand T. A GENERAL MULTIVARIATE EXTENSION OF FISHER'S GEOMETRICAL MODEL AND THE DISTRIBUTION OF MUTATION FITNESS EFFECTS ACROSS SPECIES. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb01169.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Wenzel G. Molecular plant breeding: achievements in green biotechnology and future perspectives. Appl Microbiol Biotechnol 2006; 70:642-50. [PMID: 16586104 DOI: 10.1007/s00253-006-0375-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 02/07/2006] [Indexed: 10/24/2022]
Abstract
Since one decade ago, transgenic crop plants are globally grown; in 2004, it was estimated to cover a total of 81 Mio ha in 17 countries. At present, four plant species (soybean, maize, cotton and rapeseed) dominate with two traits (herbicide tolerance and insect resistance). The traits on which research concentrates and the constructs which might come next onto the market are outlined. The procedure on how to clone such genes of interest, e.g. via map-based cloning, and some other helpful approaches of green biotechnology, like high throughput techniques and functional markers, are summarised, and a rough calculation about the market value of transgenic crops in US dollars is quoted.
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Affiliation(s)
- Gerhard Wenzel
- Plant Breeding, Center for Life and Food Sciences, Technische Universität München, Freising, Germany.
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12
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Liu Q. Computational identification and systematic analysis of the ACR gene family in Oryza sativa. JOURNAL OF PLANT PHYSIOLOGY 2006; 163:445-51. [PMID: 16455358 DOI: 10.1016/j.jplph.2005.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Accepted: 05/19/2005] [Indexed: 05/06/2023]
Abstract
Based on sequence similarity search and domain detection, nine ACT domain repeat protein-coding genes (the "ACR" genes) in rice were identified, which were mainly distributed on the chromosomes 2, 3, 4, and 8. An InterPro database search indicated that four copies of the ACT domain linearly occupied the entire polypeptide. The first three ACT domains were linked by two different sequences. However, the fourth ACT domain was extremely close to ACT3. Gene structure comparisons showed large differences in exon numbers, from three to eight, among members of the rice ACR gene family. In addition, it appeared that gene duplication might be operative when the compositions of exons and introns were analyzed. Phylogenetic analysis divided the ACR gene family into five distinct groups, and this division was generally according to the expression patterns of the ACR genes. The Arabidopsis and rice ACR proteins were clustered across together, suggesting that these ACR genes might originate from an ancient common ancestor. Notably, the identification of orthologues and paralogues would be useful for rice gene functional annotation.
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Affiliation(s)
- Qingpo Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, PR China.
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13
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Martin G, Lenormand T. A GENERAL MULTIVARIATE EXTENSION OF FISHER'S GEOMETRICAL MODEL AND THE DISTRIBUTION OF MUTATION FITNESS EFFECTS ACROSS SPECIES. Evolution 2006. [DOI: 10.1554/05-412.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Anderson LK, Lai A, Stack SM, Rizzon C, Gaut BS. Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res 2005; 16:115-22. [PMID: 16339046 PMCID: PMC1356135 DOI: 10.1101/gr.4249906] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Examining the relationships among DNA sequence, meiotic recombination, and chromosome structure at a genome-wide scale has been difficult because only a few markers connect genetic linkage maps with physical maps. Here, we have positioned 1195 genetically mapped expressed sequence tag (EST) markers onto the 10 pachytene chromosomes of maize by using a newly developed resource, the RN-cM map. The RN-cM map charts the distribution of crossing over in the form of recombination nodules (RNs) along synaptonemal complexes (SCs, pachytene chromosomes) and allows genetic cM distances to be converted into physical micrometer distances on chromosomes. When this conversion is made, most of the EST markers used in the study are located distally on the chromosomes in euchromatin. ESTs are significantly clustered on chromosomes, even when only euchromatic chromosomal segments are considered. Gene density and recombination rate (as measured by EST and RN frequencies, respectively) are strongly correlated. However, crossover frequencies for telomeric intervals are much higher than was expected from their EST frequencies. For pachytene chromosomes, EST density is about fourfold higher in euchromatin compared with heterochromatin, while DNA density is 1.4 times higher in heterochromatin than in euchromatin. Based on DNA density values and the fraction of pachytene chromosome length that is euchromatic, we estimate that approximately 1500 Mbp of the maize genome is in euchromatin. This overview of the organization of the maize genome will be useful in examining genome and chromosome evolution in plants.
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Affiliation(s)
- Lorinda K Anderson
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
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15
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Mochizuki A. An analytical study of the number of steady states in gene regulatory networks. J Theor Biol 2005; 236:291-310. [PMID: 15885706 DOI: 10.1016/j.jtbi.2005.03.015] [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: 05/06/2004] [Revised: 02/24/2005] [Accepted: 03/09/2005] [Indexed: 11/29/2022]
Abstract
Herein, I proposed a model for gene networks and studied the steady states in the dynamics both by numerical and analytical methods. In this model, mRNA and protein levels change continuously with time; each gene alters transcriptional regulation depending on the concentration of transcription factors. The dynamical behavior of continuous model is quite complex and different from that of the discrete model, the Boolean network. Large portion of steady states of this model can be classified into three types. The rough structure of gene interactions, which corresponds to Boolean function, is sufficient to predict the expression level of each gene in these types of steady states. I also determined the expected numbers of two major types of steady states observed in a randomly generated gene network. The results obtained from these formulae contradict previously accepted belief. The results are that neither gene number nor connectivity between genes increases the expected number of steady states in a random gene network. The number of steady states is very small. The number of self-regulatory genes, however, effectively increases the number of steady states in a network. These results imply that increases in gene number may not be the direct driving force for the evolution of a variety of different cell types within organisms. Instead, the number of self-regulatory genes may significantly increase cellular diversity.
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Abstract
Plant domestication ranks as one of the most important developments in human history, giving human populations the potential to harness unprecedented quantities of the earth's resources. But domestication has also played a more subtle historical role as the foundation of the modern study of evolution and adaptation. Until recently, however, researchers interested in domestication were limited to studying phenotypic changes or the genetics of simple Mendelian traits, when often the characters of most interest--fruit size, yield, height, flowering time, etc.--are quantitative in nature. The goals of this paper are to review some of the recent work on the quantitative genetics of plant domestication, identify some of the common trends found in this literature, and offer some novel interpretations of the data that is currently available.
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Cotsaftis O, Guiderdoni E. Enhancing gene targeting efficiency in higher plants: rice is on the move. Transgenic Res 2005; 14:1-14. [PMID: 15865044 DOI: 10.1007/s11248-004-4066-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Meeting the challenge of routine gene targeting (GT) in higher plants is of crucial interest to researchers and plant breeders who are currently in need of a powerful tool to specifically modify a given locus in a genome. Higher plants have long been considered the last lineage resistant to targeting technology. However, a recent report described an efficient method of T-DNA-mediated targeted disruption of a non-selectable locus in rice [Terada et al., Nat Biotechnol 20: 1030-1034 (2002)]. Though this study was an obvious breakthrough, further improvement of GT frequencies may derive from a better understanding of the natural mechanisms that control homologous recombination (HR) processes. In this review, we will focus on what is known about HR and the factors which may hamper the development of routine GT by HR in higher plants. We will also present the current strategies envisaged to overcome these limitations, such as expression of recombination proteins and refinements in the design of the transformation vector.
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Affiliation(s)
- Olivier Cotsaftis
- UMR1096 PIA, Biotrop Program, Cirad-Amis, Avenue Agropolis, F-34398 Montpellier Cedex 5, France.
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Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME. Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 2005; 47:805-18. [PMID: 15499395 DOI: 10.1139/g04-057] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expressed sequence tags (ESTs) are a valuable source of molecular markers. To enhance the resolution of an existing linkage map and to identify putative functional polymorphic gene loci in hexaploid wheat (Triticum aestivum L.), over 260,000 ESTs from 5 different grass species were analyzed and 5418 SSR-containing sequences were identified. Using sequence similarity analysis, 156 cross-species superclusters and 138 singletons were used to develop primer pairs, which were then tested on the genomic DNA of barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and wheat. Three-hundred sixty-eight primer pairs produced PCR amplicons from at least one species and 227 primer pairs amplified DNA from two or more species. EST-SSR sequences containing dinucleotide motifs were significantly more polymorphic (74%) than those containing trinucleotides (56%), and polymorphism was similar for markers in both coding and 5' untranslated (UTR) regions. Out of 112 EST-SSR markers, 90 identified 149 loci that were integrated into a reference wheat genetic map. These loci were distributed on 19 of the 21 wheat chromosomes and were clustered in the distal chromosomal regions. Multiple-loci were detected by 39% of the primer pairs. Of the 90 mapped ESTs, putative functions for 22 were identified using BLASTX queries. In addition, 80 EST-SSR markers (104 loci) were located to chromosomes using nullisomic-tetrasomic lines. The enhanced map from this study provides a basis for comparative mapping using orthologous and PCR-based markers and for identification of expressed genes possibly affecting important traits in wheat.
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Affiliation(s)
- Ju-Kyung Yu
- Department of Plant Breeding, Cornell University, 413 Bradfield Hall, Ithaca, NY 14850, USA
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19
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Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB. Comparative mapping in the Pinaceae. Genetics 2004; 168:447-61. [PMID: 15454556 PMCID: PMC1448108 DOI: 10.1534/genetics.104.028381] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Accepted: 05/27/2004] [Indexed: 11/18/2022] Open
Abstract
A comparative genetic map was constructed between two important genera of the family Pinaceae. Ten homologous linkage groups in loblolly pine (Pinus taeda L.) and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco) were identified using orthologous expressed sequence tag polymorphism (ESTP) and restriction fragment length polymorphism (RFLP) markers. The comparative mapping revealed extensive synteny and colinearity between genomes of the Pinaceae, consistent with the hypothesis of conservative chromosomal evolution in this important plant family. This study reports the first comparative map in forest trees at the family taxonomic level and establishes a framework for comparative genomics in Pinaceae.
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Affiliation(s)
- Konstantin V Krutovsky
- Institute of Forest Genetics, Pacific Southwest Research Station, US Department of Agriculture Forest Service, Davis, California 95616, USA
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20
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Yu JK, La Rota M, Kantety RV, Sorrells ME. EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 2004; 271:742-51. [PMID: 15197579 DOI: 10.1007/s00438-004-1027-3] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Accepted: 05/10/2004] [Indexed: 11/25/2022]
Abstract
Structural and functional relationships between the genomes of hexaploid wheat ( Triticum aestivum L.) (2n=6x=42) and rice (Oryza sativa L.) (2n=2x=24) were evaluated using linkage maps supplemented with simple sequence repeat (SSR) loci obtained from publicly available expressed sequence tags (ESTs). EST-SSR markers were developed using two main strategies to design primers for each gene: (1) primer design for multiple species based on supercluster analysis, and (2) species-specific primer design. Amplification was more consistent using the species-specific primer design for each gene. Forty-four percent of the primers designed specifically for wheat sequences were successful in amplifying DNA from both species. Existing genetic linkage maps were enhanced for the wheat and rice genomes using orthologous loci amplified with 58 EST-SSR markers obtained from both wheat and rice ESTs. The PCR-based anchor loci identified by these EST-SSR markers support previous patterns of conservation between wheat and rice genomes; however, there was a high frequency of interrupted colinearity. In addition, multiple loci amplified by these primers made the comparative analysis more difficult. Enhanced comparative maps of wheat and rice provide a useful tool for interpreting and transferring molecular, genetic, and breeding information between these two important species. These EST-SSR markers are particularly useful for constructing comparative framework maps for different species, because they amplify closely related genes to provide anchor points across species.
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Affiliation(s)
- J-K Yu
- Department of Plant Breeding, Cornell University, 252 Emerson Hall, NY 14853, Ithaca, USA
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21
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Tyagi AK, Khurana JP, Khurana P, Raghuvanshi S, Gaur A, Kapur A, Gupta V, Kumar D, Ravi V, Vij S, Khurana P, Sharma S. Structural and functional analysis of rice genome. J Genet 2004; 83:79-99. [PMID: 15240912 DOI: 10.1007/bf02715832] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.
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Affiliation(s)
- Akhilesh K Tyagi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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22
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Comparative Genetic Mapping in Trees: The Group of Conifers. ACTA ACUST UNITED AC 2004. [DOI: 10.1007/3-540-26538-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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23
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Wu J, Mizuno H, Hayashi-Tsugane M, Ito Y, Chiden Y, Fujisawa M, Katagiri S, Saji S, Yoshiki S, Karasawa W, Yoshihara R, Hayashi A, Kobayashi H, Ito K, Hamada M, Okamoto M, Ikeno M, Ichikawa Y, Katayose Y, Yano M, Matsumoto T, Sasaki T. Physical maps and recombination frequency of six rice chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 36:720-30. [PMID: 14617072 DOI: 10.1046/j.1365-313x.2003.01903.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We constructed physical maps of rice chromosomes 1, 2, and 6-9 with P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-specific repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR)- and RIce RetroElement 7 (RIRE7)-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.
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Affiliation(s)
- Jianzhong Wu
- Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan
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Abstract
Different approaches (including association studies) have recently been adopted for the functional characterization of allelic variation in plants and to identify sequence motifs affecting phenotypic variation. We propose the term 'functional markers' for DNA markers derived from such functionally characterized sequence motifs. Functional markers are superior to random DNA markers such as RFLPs, SSRs and AFLPs owing to complete linkage with trait locus alleles. We outline the definition, development, application and prospects of functional markers.
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Affiliation(s)
- Jeppe R Andersen
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Research Center Flakkebjerg, 4200, Slagelse, Denmark
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2447285 DOI: 10.1002/cfg.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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