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Somta P, Laosatit K, Yuan X, Chen X. Thirty Years of Mungbean Genome Research: Where Do We Stand and What Have We Learned? FRONTIERS IN PLANT SCIENCE 2022; 13:944721. [PMID: 35909762 PMCID: PMC9335052 DOI: 10.3389/fpls.2022.944721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Mungbean is a socioeconomically important legume crop in Asia that is currently in high demand by consumers and industries both as dried beans and in plant-based protein foods. Marker-assisted and genomics-assisted breeding are promising approaches to efficiently and rapidly develop new cultivars with improved yield, quality, and resistance to biotic and abiotic stresses. Although mungbean was at the forefront of research at the dawn of the plant genomics era 30 years ago, the crop is a "slow runner" in genome research due to limited genomic resources, especially DNA markers. Significant progress in mungbean genome research was achieved only within the last 10 years, notably after the release of the VC1973A draft reference genome constructed using next-generation sequencing technology, which enabled fast and efficient DNA marker development, gene mapping, and identification of candidate genes for complex traits. Resistance to biotic stresses has dominated mungbean genome research to date; however, research is on the rise. In this study, we provide an overview of the past progress and current status of mungbean genomics research. We also discuss and evaluate some research results to provide a better understanding of mungbean genomics.
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Affiliation(s)
- Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Liu Q, Chang S, Hartman GL, Domier LL. Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:71-85. [PMID: 29671916 DOI: 10.1111/tpj.13931] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/12/2018] [Accepted: 03/22/2018] [Indexed: 05/14/2023]
Abstract
Glycine latifolia (Benth.) Newell & Hymowitz (2n = 40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. Here, we report the 939-Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked-reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome-scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91-bp centromere-specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. No 92-bp putative centromeric repeats, which are abundant in G. max, were detected in G. latifolia or Glycine tomentella. Annotation of the assembled genome and subsequent filtering yielded a high confidence gene set of 54 475 protein-coding loci. In comparative analysis with five legume species, genes related to defense responses were significantly overrepresented in Glycine-specific orthologous gene families. A total of 304 putative nucleotide-binding site (NBS)-leucine-rich-repeat (LRR) genes were identified in this genome assembly. Different from other legume species, we observed a scarcity of TIR-NBS-LRR genes in G. latifolia. The G. latifolia genome was also predicted to contain genes encoding 367 LRR-receptor-like kinases, a family of proteins involved in basal defense responses and responses to abiotic stress. The genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes to facilitate soybean improvement. This study also highlights the efficacy and cost-effectiveness of the application of Chromium linked-reads in diploid plant genome de novo assembly.
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Affiliation(s)
- Qiong Liu
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Sungyul Chang
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- USDA ARS, Urbana, IL, 61801, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- USDA ARS, Urbana, IL, 61801, USA
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Misra VA, Wang Y, Timko MP. A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.). BMC Genomics 2017; 18:898. [PMID: 29166879 PMCID: PMC5700742 DOI: 10.1186/s12864-017-4306-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/14/2017] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Cowpea (Vigna unguiculata (L.) Walp.) is the most important food and forage legume in the semi-arid tropics of sub-Saharan Africa where approximately 80% of worldwide production takes place primarily on low-input, subsistence farm sites. Among the major goals of cowpea breeding and improvement programs are the rapid manipulation of agronomic traits for seed size and quality and improved resistance to abiotic and biotic stresses to enhance productivity. Knowing the suite of transcription factors (TFs) and transcriptionally active proteins (TAPs) that control various critical plant cellular processes would contribute tremendously to these improvement aims. RESULTS We used a computational approach that employed three different predictive pipelines to data mine the cowpea genome and identified over 4400 genes representing 136 different TF and TAP families. We compare the information content of cowpea to two evolutionarily close species common bean (Phaseolus vulgaris), and soybean (Glycine max) to gauge the relative informational content. Our data indicate that correcting for genome size cowpea has fewer TF and TAP genes than common bean (4408 / 5291) and soybean (4408/ 11,065). Members of the GROWTH-REGULATING FACTOR (GRF) and Auxin/indole-3-acetic acid (Aux/IAA) gene families appear to be over-represented in the genome relative to common bean and soybean, whereas members of the MADS (Minichromosome maintenance deficient 1 (MCM1), AGAMOUS, DEFICIENS, and serum response factor (SRF)) and C2C2-YABBY appear to be under-represented. Analysis of the AP2-EREBP APETALA2-Ethylene Responsive Element Binding Protein (AP2-EREBP), NAC (NAM (no apical meristem), ATAF1, 2 (Arabidopsis transcription activation factor), CUC (cup-shaped cotyledon)), and WRKY families, known to be important in defense signaling, revealed changes and phylogenetic rearrangements relative to common bean and soybean that suggest these groups may have evolved different functions. CONCLUSIONS The availability of detailed information on the coding capacity of the cowpea genome and in particular the various TF and TAP gene families will facilitate future comparative analysis and development of strategies for controlling growth, differentiation, and abiotic and biotic stress resistances of cowpea.
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Affiliation(s)
- Vikram A. Misra
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
| | - Yu Wang
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
- Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232-6848 USA
| | - Michael P. Timko
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22904 USA
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Liu C, Wu J, Wang L, Fan B, Cao Z, Su Q, Zhang Z, Wang Y, Tian J, Wang S. Quantitative trait locus mapping under irrigated and drought treatments based on a novel genetic linkage map in mungbean (Vigna radiata L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2375-2393. [PMID: 28831522 DOI: 10.1007/s00122-017-2965-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
A novel genetic linkage map was constructed using SSR markers and stable QTLs were identified for six drought tolerance related-traits using single-environment analysis under irrigation and drought treatments. Mungbean (Vigna radiata L.) is one of the most important leguminous food crops. However, mungbean production is seriously constrained by drought. Isolation of drought-responsive genetic elements and marker-assisted selection breeding will benefit from the detection of quantitative trait locus (QTLs) for traits related to drought tolerance. In this study, we developed a full-coverage genetic linkage map based on simple sequence repeat (SSR) markers using a recombinant inbred line (RIL) population derived from an intra-specific cross between two drought-resistant varieties. This novel map was anchored with 313 markers. The total map length was 1010.18 cM across 11 linkage groups, covering the entire genome of mungbean with a saturation of one marker every 3.23 cM. We subsequently detected 58 QTLs for plant height (PH), maximum leaf area (MLA), biomass (BM), relative water content, days to first flowering, and seed yield (Yield) and 5 for the drought tolerance index of 3 traits in irrigated and drought environments at 2 locations. Thirty-eight of these QTLs were consistently detected two or more times at similar linkage positions. Notably, qPH5A and qMLA2A were consistently identified in marker intervals from GMES5773 to MUS128 in LG05 and from Mchr11-34 to the HAAS_VR_1812 region in LG02 in four environments, contributing 6.40-20.06% and 6.97-7.94% of the observed phenotypic variation, respectively. None of these QTLs shared loci with previously identified drought-related loci from mungbean. The results of these analyses might facilitate the isolation of drought-related genes and help to clarify the mechanism of drought tolerance in mungbean.
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Affiliation(s)
- Changyou Liu
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jing Wu
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lanfen Wang
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baojie Fan
- Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Zhimin Cao
- Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Qiuzhu Su
- Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Zhixiao Zhang
- Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Yan Wang
- Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jing Tian
- Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China.
| | - Shumin Wang
- Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Souframanien J, Reddy KS. De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L.) Hepper]. PLoS One 2015; 10:e0128748. [PMID: 26042595 PMCID: PMC4456365 DOI: 10.1371/journal.pone.0128748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/01/2015] [Indexed: 12/02/2022] Open
Abstract
Black gram [V. mungo (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.
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Affiliation(s)
- J. Souframanien
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- * E-mail:
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Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH. Chromosome Res 2015; 23:253-66. [PMID: 25634499 DOI: 10.1007/s10577-014-9464-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/22/2022]
Abstract
Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes.
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Kim SK, Nair RM, Lee J, Lee SH. Genomic resources in mungbean for future breeding programs. FRONTIERS IN PLANT SCIENCE 2015; 6:626. [PMID: 26322067 PMCID: PMC4530597 DOI: 10.3389/fpls.2015.00626] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/28/2015] [Indexed: 05/03/2023]
Abstract
Among the legume family, mungbean (Vigna radiata) has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A) and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata) has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement.
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Affiliation(s)
- Sue K. Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | | | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National UniversitySeoul, South Korea
- *Correspondence: Suk-Ha Lee, Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea,
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Bohra A, Jha UC, Kishor PBK, Pandey S, Singh NP. Genomics and molecular breeding in lesser explored pulse crops: current trends and future opportunities. Biotechnol Adv 2014; 32:1410-28. [PMID: 25196916 DOI: 10.1016/j.biotechadv.2014.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India.
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | | | - Narendra P Singh
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
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Chang S, Thurber CS, Brown PJ, Hartman GL, Lambert KN, Domier LL. Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS One 2014; 9:e99427. [PMID: 24937645 PMCID: PMC4061007 DOI: 10.1371/journal.pone.0099427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 12/22/2022] Open
Abstract
Soybean (Glycine max L. Mer.), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth.) Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib.) de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP) markers generated by genotyping by sequencing and evaluated in an F2 population and confirmed in an F5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F2 and F5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L.) chromosomes were examined by aligning SNP-containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.
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Affiliation(s)
- Sungyul Chang
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Carrie S. Thurber
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Patrick J. Brown
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Glen L. Hartman
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- United States Department of Agriculture, Agricultural Research Service, Urbana, Illinois, United States of America
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Leslie L. Domier
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- United States Department of Agriculture, Agricultural Research Service, Urbana, Illinois, United States of America
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Abstract
Legumes are the third-largest family of angiosperms, the second-most-important crop family, and a key source of biological nitrogen in agriculture. Recently, the genome sequences of Glycine max (soybean), Medicago truncatula, and Lotus japonicus were substantially completed. Comparisons among legume genomes reveal a key role for duplication, especially a whole-genome duplication event approximately 58 Mya that is shared by most agriculturally important legumes. A second and more recent genome duplication occurred only in the lineage leading to soybean. Outcomes of genome duplication, including gene fractionation and sub- and neofunctionalization, have played key roles in shaping legume genomes and in the evolution of legume-specific traits. Analysis of legume genome sequences also enables the discovery of legume-specific gene families and provides a framework for genome-wide association mapping that will target phenotypes of special importance in legumes. Translating genomic resources from sequenced species to less studied but still important "orphan" legumes will enhance prospects for world food production.
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Affiliation(s)
- Nevin D Young
- Department of Plant Pathology and Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA.
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Mensack MM, Fitzgerald VK, Ryan EP, Lewis MR, Thompson HJ, Brick MA. Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using 'omics' technologies. BMC Genomics 2010; 11:686. [PMID: 21126341 PMCID: PMC3014982 DOI: 10.1186/1471-2164-11-686] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 12/02/2010] [Indexed: 11/10/2022] Open
Abstract
Background Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers. Yet, little is known about whether these traits, which distinguish among genetically distinct types of common bean, can be evaluated using omics technologies. Results Three 'omics' approaches: transcriptomics, proteomics, and metabolomics were used to qualitatively evaluate the diversity of common bean from two Centers of Domestication (COD). All three approaches were able to classify common bean according to their COD using unsupervised analyses; these findings are consistent with the hypothesis that differences exist in gene transcription, protein expression, and synthesis and metabolism of small molecules among common bean cultivars representative of different COD. Metabolomic analyses of multiple cultivars within two common bean gene pools revealed cultivar differences in small molecules that were of sufficient magnitude to allow identification of unique cultivar fingerprints. Conclusions Given the high-throughput and low cost of each of these 'omics' platforms, significant opportunities exist for their use in the rapid identification of traits of agronomic and nutritional importance as well as to characterize genetic diversity.
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Affiliation(s)
- Meghan M Mensack
- Cancer Prevention Laboratory, Department of Horticulture, Colorado State Univ, Fort Collins, CO 80523-1173, USA.
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ZHAO D, CHENG XZ, WANG LX, WANG SH, MA YL. Integration of Mungbean ( Vigna radiata) Genetic Linkage Map. ZUOWU XUEBAO 2010. [DOI: 10.3724/sp.j.1006.2010.00932] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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ZHAO D, CHENG XZ, WANG LX, WANG SH, MA YL. Construction of Mungbean Genetic Linkage Map. ACTA AGRONOMICA SINICA 2010. [DOI: 10.1016/s1875-2780(09)60054-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yang SS, Valdés-López O, Xu WW, Bucciarelli B, Gronwald JW, Hernández G, Vance CP. Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes. BMC PLANT BIOLOGY 2010; 10:85. [PMID: 20459672 PMCID: PMC3017814 DOI: 10.1186/1471-2229-10-85] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 05/07/2010] [Indexed: 05/11/2023]
Abstract
BACKGROUND Common bean (Phaseolus vulgaris L.) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean. RESULTS To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR) analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent. CONCLUSIONS The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In addition to transcript profiling, CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
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Affiliation(s)
- S Samuel Yang
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
| | - Oswaldo Valdés-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, 62210 Cuernavaca, Mor. México
| | - Wayne W Xu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruna Bucciarelli
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
| | - John W Gronwald
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, 62210 Cuernavaca, Mor. México
| | - Carroll P Vance
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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McClean PE, Mamidi S, McConnell M, Chikara S, Lee R. Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics 2010; 11:184. [PMID: 20298570 PMCID: PMC2851600 DOI: 10.1186/1471-2164-11-184] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 03/18/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Understanding syntentic relationship between two species is critical to assessing the potential for comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively. Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species. RESULTS Genetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was approximately 120 kb/cM. approximately 15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points. CONCLUSION The collected evidence from this mapping strongly supports the duplicate history of soybean. It further provides evidence that the soybean genome was fractionated and reassembled at some point following the duplication event. These well mapped syntentic relationships between common bean and soybean will enable researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both species.
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Affiliation(s)
- Phillip E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA
- Department of Plant Sciences, Loftsgard Hall, North Dakota State University, Fargo, ND 58105, USA
| | - Sujan Mamidi
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA
| | - Melody McConnell
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA
| | - Shireen Chikara
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA
| | - Rian Lee
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA
- Department of Plant Sciences, Loftsgard Hall, North Dakota State University, Fargo, ND 58105, USA
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Galeano CH, Fernández AC, Gómez M, Blair MW. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). BMC Genomics 2009; 10:629. [PMID: 20030833 PMCID: PMC2806352 DOI: 10.1186/1471-2164-10-629] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/23/2009] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. RESULTS A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. CONCLUSION The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation between species allowed synteny comparisons to be made to sequenced genomes. This synteny analysis may support positional cloning of target genes in common bean through the use of genomic information from these other legumes.
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Affiliation(s)
- Carlos H Galeano
- Centro Internacional de Agricultura Tropical (CIAT), Apartado Aéreo 6713, Cali, Colombia
| | - Andrea C Fernández
- Centro Internacional de Agricultura Tropical (CIAT), Apartado Aéreo 6713, Cali, Colombia
| | - Marcela Gómez
- Centro Internacional de Agricultura Tropical (CIAT), Apartado Aéreo 6713, Cali, Colombia
- Current address: Laboratorio Nacional Interinstitucional de Detección y Monitoreo de Organismos Genéticamente Modificados, Instituto Colombiano Agropecuario. Km 14 Recta Tibaitatá-Mosquera, Colombia
| | - Matthew W Blair
- Centro Internacional de Agricultura Tropical (CIAT), Apartado Aéreo 6713, Cali, Colombia
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Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC PLANT BIOLOGY 2009; 9:137. [PMID: 19930676 PMCID: PMC2788553 DOI: 10.1186/1471-2229-9-137] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 11/24/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Mungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR) markers from genome shotgun sequencing of mungbean. RESULT We have generated and characterized a total of 470,024 genome shotgun sequences covering 100.5 Mb of the mungbean (Vigna radiata (L.) Wilczek) genome using 454 sequencing technology. We identified 1,493 SSR motifs that could be used as potential molecular markers. Among 192 tested primer pairs in 17 mungbean accessions, 60 loci revealed polymorphism with polymorphic information content (PIC) values ranging from 0.0555 to 0.6907 with an average of 0.2594. Majority of microsatellite markers were transferable in Vigna species, whereas transferability rates were only 22.90% and 24.43% in Phaseolus vulgaris and Glycine max, respectively. We also used 16 SSR loci to evaluate phylogenetic relationship of 35 genotypes of the Asian Vigna group. The genome survey sequences were further analyzed to search for gene content. The evidence suggested 1,542 gene fragments have been sequence tagged, that fell within intersected existing gene models and shared sequence homology with other proteins in the database. Furthermore, potential microRNAs that could regulate developmental stages and environmental responses were discovered from this dataset. CONCLUSION In this report, we provided evidence of generating remarkable levels of diverse microsatellite markers and gene content from high throughput genome shotgun sequencing of the mungbean genomic DNA. The markers could be used in germplasm analysis, accessing genetic diversity and linkage mapping of mungbean.
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Affiliation(s)
- Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Pichahpuk Uthaipaisanwong
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Juntima Chanprasert
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Worapa Seehalak
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Warunee Sommanas
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
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18
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Albrecht E, Chetelat RT. Comparative genetic linkage map of Solanum sect. Juglandifolia: evidence of chromosomal rearrangements and overall synteny with the tomatoes and related nightshades. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:831-847. [PMID: 19099284 DOI: 10.1007/s00122-008-0943-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 11/21/2008] [Indexed: 05/27/2023]
Abstract
The two nightshades Solanum ochranthum and S. juglandifolium show genetic and morphological similarities to the tomatoes (Solanum sect. Lycopersicon), but are isolated from them by strong reproductive barriers. Their genetic relationships to tomato and other Solanum species were investigated using comparative genetic linkage maps obtained from an interspecific F(2) S. ochranthum x S. juglandifolium population. Sixty-six plants were screened using a total of 132 markers--CAPs, RFLPs and SSRs--previously mapped in tomato. Twelve linkage groups were identified, generally corresponding to the expected (syntenic) tomato chromosomes, with two exceptions. Chromosome 1 was composed of two linkage groups and chromosomes 8 and 12 were connected in one large linkage group, indicating a likely reciprocal translocation differentiating the two parental genomes. The total map length comprised 790 cM, representing a 42% reduction in recombination rate relative to the tomato reference map. Transmission ratio distortion affected one-third of the genome, with 13 putative TRD loci identified on 9 out of 12 chromosomes. Most regions were collinear with the tomato reference maps, including the long arm of chromosome 10, which is inverted relative to two other tomato-like nightshades, S. lycopersicoides and S. sitiens. The results support the status of S. ochranthum and S. juglandifolium as the nearest outgroup to the tomatoes and imply they are more closely related to cultivated tomato than predicted from crossing relationships, thus encouraging further attempts at hybridization and introgression between them.
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Affiliation(s)
- Elena Albrecht
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA.
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19
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Hougaard BK, Madsen LH, Sandal N, de Carvalho Moretzsohn M, Fredslund J, Schauser L, Nielsen AM, Rohde T, Sato S, Tabata S, Bertioli DJ, Stougaard J. Legume anchor markers link syntenic regions between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis. Genetics 2008; 179:2299-312. [PMID: 18689902 PMCID: PMC2516099 DOI: 10.1534/genetics.108.090084] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 06/03/2008] [Indexed: 01/04/2023] Open
Abstract
We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of approximately 50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.
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Affiliation(s)
- Birgit Kristine Hougaard
- Laboratory of Gene Expression, Department of Molecular Biology, University of Aarhus, DK-8000, Aarhus C, Denmark
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20
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Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW. Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol 2008; 9:R57. [PMID: 18348734 PMCID: PMC2397509 DOI: 10.1186/gb-2008-9-3-r57] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 01/30/2008] [Accepted: 03/19/2008] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Legumes are the third largest family of flowering plants and are unique among crop species in their ability to fix atmospheric nitrogen. As a result of recent genome sequencing efforts, legumes are now one of a few plant families with extensive genomic and transcriptomic data available in multiple species. The unprecedented complexity and impending completeness of these data create opportunities for new approaches to discovery. RESULTS We report here a transcriptional analysis in six different organ types of syntenic regions totaling approximately 1 Mb between the legume plants barrel medic (Medicago truncatula) and soybean (Glycine max) using oligonucleotide tiling microarrays. This analysis detected transcription of over 80% of the predicted genes in both species. We also identified 499 and 660 transcriptionally active regions from barrel medic and soybean, respectively, over half of which locate outside of the predicted exons. We used the tiling array data to detect differential gene expression in the six examined organ types and found several genes that are preferentially expressed in the nodule. Further investigation revealed that some collinear genes exhibit different expression patterns between the two species. CONCLUSION These results demonstrate the utility of genome tiling microarrays in generating transcriptomic data to complement computational annotation of the newly available legume genome sequences. The tiling microarray data was further used to quantify gene expression levels in multiple organ types of two related legume species. Further development of this method should provide a new approach to comparative genomics aimed at elucidating genome organization and transcriptional regulation.
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Affiliation(s)
- Lei Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Current address: Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Hang He
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- National Institute of Biological Sciences, Beijing 102206, China
- Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, Peking University, Beijing 100871, China
| | - Juan Zhang
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Xiangfeng Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- National Institute of Biological Sciences, Beijing 102206, China
- Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, Peking University, Beijing 100871, China
| | - Sulan Bai
- College of Life Sciences, Capital Normal University, Beijing 100037, China
| | - Viktor Stolc
- Genome Research Facility, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Waraporn Tongprasit
- Genome Research Facility, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA
| | - Oliver Yu
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Xing-Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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21
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Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X. Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 2008; 9:103. [PMID: 18304330 PMCID: PMC2279124 DOI: 10.1186/1471-2164-9-103] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 02/27/2008] [Indexed: 11/16/2022] Open
Abstract
Background Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly by poor subsistence farmers. Despite its economic and social importance in the developing world, cowpea remains to a large extent an underexploited crop. Among the major goals of cowpea breeding and improvement programs is the stacking of desirable agronomic traits, such as disease and pest resistance and response to abiotic stresses. Implementation of marker-assisted selection and breeding programs is severely limited by a paucity of trait-linked markers and a general lack of information on gene structure and organization. With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing. Results We report here the sequencing and analysis of the gene-rich, hypomethylated portion of the cowpea genome selectively cloned by methylation filtration (MF) technology. Over 250,000 gene-space sequence reads (GSRs) with an average length of 610 bp were generated, yielding ~160 Mb of sequence information. The GSRs were assembled, annotated by BLAST homology searches of four public protein annotation databases and four plant proteomes (A. thaliana, M. truncatula, O. sativa, and P. trichocarpa), and analyzed using various domain and gene modeling tools. A total of 41,260 GSR assemblies and singletons were annotated, of which 19,786 have unique GenBank accession numbers. Within the GSR dataset, 29% of the sequences were annotated using the Arabidopsis Gene Ontology (GO) with the largest categories of assigned function being catalytic activity and metabolic processes, groups that include the majority of cellular enzymes and components of amino acid, carbohydrate and lipid metabolism. A total of 5,888 GSRs had homology to genes encoding transcription factors (TFs) and transcription associated factors (TAFs) representing about 5% of the total annotated sequences in the dataset. Sixty-two (62) of the 64 well-characterized plant transcription factor (TF) gene families are represented in the cowpea GSRs, and these families are of similar size and phylogenetic organization to those characterized in other plants. The cowpea GSRs also provides a rich source of genes involved in photoperiodic control, symbiosis, and defense-related responses. Comparisons to available databases revealed that about 74% of cowpea ESTs and 70% of all legume ESTs were represented in the GSR dataset. As approximately 12% of all GSRs contain an identifiable simple-sequence repeat, the dataset is a powerful resource for the design of microsatellite markers. Conclusion The availability of extensive publicly available genomic data for cowpea, a non-model legume with significant importance in the developing world, represents a significant step forward in legume research. Not only does the gene space sequence enable the detailed analysis of gene structure, gene family organization and phylogenetic relationships within cowpea, but it also facilitates the characterization of syntenic relationships with other cultivated and model legumes, and will contribute to determining patterns of chromosomal evolution in the Leguminosae. The micro and macrosyntenic relationships detected between cowpea and other cultivated and model legumes should simplify the identification of informative markers for marker-assisted trait selection and map-based gene isolation necessary for cowpea improvement.
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Affiliation(s)
- Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA.
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22
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Isemura T, Kaga A, Konishi S, Ando T, Tomooka N, Han OK, Vaughan DA. Genome dissection of traits related to domestication in azuki bean (Vigna angularis) and comparison with other warm-season legumes. ANNALS OF BOTANY 2007; 100:1053-71. [PMID: 17728336 PMCID: PMC2759210 DOI: 10.1093/aob/mcm155] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 11/28/2006] [Accepted: 05/23/2007] [Indexed: 05/17/2023]
Abstract
BACKGROUND The objective of this study was to dissect into quantitative trait loci (QTLs) the large morphological and physiological differences between cultivated azuki bean (Vigna angularis) and a wild relative and to infer the commonalities of the QTLs for domestication-related traits across the Asian Vigna and with other warm-season legumes. METHODS Two linkage maps, for the BC(1)F(1) and F(2) populations, respectively, from the same cross between azuki bean and V. nepalensis were developed. Using these linkage maps QTLs for 33 domestication-related traits were analysed and mapped. The location of mapped QTLs was compared with locations of similar QTLs in other warm-season legumes. KEY RESULTS QTLs were detected for seed-, pod-, stem- and leaf-related traits. Most traits were controlled by between two and nine QTLs but several traits, such as pod dehiscence, were controlled by single genes. QTLs for domestication-related traits were restricted to particular regions of the azuki bean genome, especially linkage groups 1, 2, 4, 7 and 9. Linkage groups 1 and 2 had QTLs for a suite of traits including pod size, germination, seed size and lower stem length. QTLs on linkage groups 7 and 9 were associated with upper stem length, maximum leaf size and pod and seed size. Pleiotropy or close linkage of genes for domestication-related traits is suggested in these regions. While some QTLs are common to azuki bean and other warm-season legumes, many are recorded for the first time in azuki bean. CONCLUSIONS QTLs for a large number of domestication-related traits have been mapped for the first time in azuki bean. QTLs with unexpected effect and new QTLs for traits such as seed size have been found. The results provide a foundation that will be useful for improvement of azuki bean and related legumes.
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Affiliation(s)
- Takehisa Isemura
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305-8602, Ibaraki, Japan
| | - Akito Kaga
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305-8602, Ibaraki, Japan
| | - Saeko Konishi
- Society for Techno-innovation of Agriculture, Forestry and Fisheries 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan
| | - Tsuyu Ando
- Society for Techno-innovation of Agriculture, Forestry and Fisheries 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan
| | - Norihiko Tomooka
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305-8602, Ibaraki, Japan
| | - Ouk Kyu Han
- Winter Cereal and Upland Crop Division, Honam Agricultural Research Institute, NICS, Rural Development Administration, #381 Songhak-dong, Iksan 570-080, Seoul, Korea
| | - Duncan A. Vaughan
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305-8602, Ibaraki, Japan
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23
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Chaitieng B, Kaga A, Tomooka N, Isemura T, Kuroda Y, Vaughan DA. Development of a black gram [Vigna mungo (L.) Hepper] linkage map and its comparison with an azuki bean [Vigna angularis (Willd.) Ohwi and Ohashi] linkage map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1261-9. [PMID: 16932883 DOI: 10.1007/s00122-006-0380-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 07/25/2006] [Indexed: 05/11/2023]
Abstract
The Asian Vigna group of grain legumes consists of six domesticated species, among them black gram is widely grown in South Asia and to a lesser extent in Southeast Asia. We report the first genetic linkage map of black gram [Vigna mungo (L.) Hepper], constructed using a BC(1)F(1) population consisting of 180 individuals. The BC(1)F(1) population was analyzed in 61 SSR primer pairs, 56 RFLP probes, 27 AFLP loci and 1 morphological marker. About 148 marker loci could be assigned to the 11 linkage groups, which correspond to the haploid chromosome number of black gram. The linkage groups cover a total of 783 cM of the black gram genome. The number of markers per linkage group ranges from 6 to 23. The average distance between adjacent markers varied from 3.5 to 9.3 cM. The results of comparative genome mapping between black gram and azuki bean show that the linkage order of markers is highly conserved. However, inversions, insertions, deletions/duplications and a translocation were detected between the black gram and azuki bean linkage maps. The marker order on parts of linkage groups 1, 2 and 5 is reversed between the two species. One region on black gram linkage group 10 appears to correspond to part of azuki bean linkage group 1. The present study suggests that the azuki bean SSR markers can be widely used for Asian Vigna species and the black gram genetic linkage map will assist in improvement of this crop.
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Affiliation(s)
- B Chaitieng
- Department of Horticulture, Faculty of Agriculture, Ubonratchathani University, Ubonratchathani, Thailand
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Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KFX, Rogers J, Quétier F, Oldroyd GE, Debellé F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A 2006; 103:14959-64. [PMID: 17003129 PMCID: PMC1578499 DOI: 10.1073/pnas.0603228103] [Citation(s) in RCA: 237] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus, provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago-Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20-30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar).
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Affiliation(s)
- Steven B. Cannon
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
- U.S. Department of Agriculture–Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, IA 50010
| | - Lieven Sterck
- Department of Plant Systems Biology (VIB), Ghent University, B-9052 Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Systems Biology (VIB), Ghent University, B-9052 Ghent, Belgium
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Foo Cheung
- Institute for Genomic Research, Rockville, MD 20850
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes–Microorganismes, Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, 31326 Castanet-Tolosan, France
| | - Xiaohong Wang
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Joann Mudge
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | | | - Thomas Schiex
- Unité de Biométrie et Intelligence Artificielle, B.P. 52627, Institut National de la Recherche Agronomique, 31326 Castanet-Tolosan, France
| | - Manuel Spannagl
- Munich Information Center for Protein Sequences Institute for Bioinformatics, Gesellschaft für Strahlung und Umweltforschung, Research Center for Environment and Health, 85764 Neuherberg, Germany
| | | | - Christine Nicholson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sean J. Humphray
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Heiko Schoof
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Klaus F. X. Mayer
- Munich Information Center for Protein Sequences Institute for Bioinformatics, Gesellschaft für Strahlung und Umweltforschung, Research Center for Environment and Health, 85764 Neuherberg, Germany
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | | | | | - Frédéric Debellé
- Laboratoire des Interactions Plantes–Microorganismes, Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, 31326 Castanet-Tolosan, France
| | - Douglas R. Cook
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616
| | - Ernest F. Retzel
- Center for Computational Genomics and Bioinformatics, Minneapolis, MN 55455; and
| | - Bruce A. Roe
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | | | - Satoshi Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yves Van de Peer
- Department of Plant Systems Biology (VIB), Ghent University, B-9052 Ghent, Belgium
| | - Nevin D. Young
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
- To whom correspondence should be addressed. E-mail:
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Phan HTT, Ellwood SR, Ford R, Thomas S, Oliver R. Differences in syntenic complexity between Medicago truncatula with Lens culinaris and Lupinus albus. FUNCTIONAL PLANT BIOLOGY : FPB 2006; 33:775-782. [PMID: 32689288 DOI: 10.1071/fp06102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 06/02/2006] [Indexed: 06/11/2023]
Abstract
Orthologous markers transferable between distantly related legume species allow for the rapid generation of genetic maps in species where there is little pre-existing genomic or EST information. We are using the model legume Medicago truncatula Gaertn. to develop such markers in legumes of importance to Australian agriculture. This will enable the construction of comparative genetic maps, help to determine patterns of chromosomal evolution in the legume family, and characterise syntenic relationships between M. truncatula and cultivated legumes. This information can then be used to identify markers that are tightly linked to the genes of interest, candidate gene(s) for a trait, and expedite the isolation of such genes. Among the Papilionoideae, we compared ESTs from the phylogenetically distant species, M. truncatula, Lupinus albus and Glycine max, to produce 500 intron-targeted amplified polymorphic markers (ITAPs). In addition to 126 M. truncatula cross-species markers from Department of Plant Pathology, University of California (USA), these markers were used to generate comparative genetic maps of lentil (Lens culinaris Medik.) and white lupin (Lupinus albus Linn.). Our results showed that 90% of the ITAPs markers amplified genomic DNA in M. truncatula, 80% in Lupinus albus, and 70% in Lens culinaris. The comparative map of Lens culinaris was constructed based on 79 ITAP markers. The Lupinus albus comparative map was developed from 105 gene-based markers together with 223 AFLP markers. Although a direct and simple syntenic relationship was observed between M. truncatula and Lens culinaris genomes, there is evidence of moderate chromosomal rearrangement. This may account for the different chromosome numbers in the two species. A more complicated pattern among homologous blocks was apparent between the Lupinus albus and M. truncatula genomes.
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Affiliation(s)
- Huyen T T Phan
- Australian Centre of Necrotrophic Plant Pathogens, State Agricultural Biotechnology Centre, Murdoch University, South Street, Murdoch, WA 6150, Australia
| | - Simon R Ellwood
- Australian Centre of Necrotrophic Plant Pathogens, State Agricultural Biotechnology Centre, Murdoch University, South Street, Murdoch, WA 6150, Australia
| | - Rebecca Ford
- BioMarka, Faculty of Land and Food Resources, The University of Melbourne, Parkville, Vic. 3010, Australia
| | - Steve Thomas
- NSW Department of Primary Industries, 161 Kite Street, Locked Bag 21, Orange, NSW 2800, Australia
| | - Richard Oliver
- Australian Centre of Necrotrophic Plant Pathogens, State Agricultural Biotechnology Centre, Murdoch University, South Street, Murdoch, WA 6150, Australia
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Shoemaker RC, Schlueter J, Doyle JJ. Paleopolyploidy and gene duplication in soybean and other legumes. CURRENT OPINION IN PLANT BIOLOGY 2006; 9:104-9. [PMID: 16458041 DOI: 10.1016/j.pbi.2006.01.007] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 01/23/2006] [Indexed: 05/06/2023]
Abstract
Two of the most important observations from whole-genome sequences have been the high rate of gene birth and death and the prevalence of large-scale duplication events, including polyploidy. There is also a growing appreciation that polyploidy is more than the sum of the gene duplications it creates, in part because polyploidy duplicates the members of entire regulatory networks. Thus, it may be important to distinguish paralogs that are produced by individual gene duplications from the homoeologous sequences produced by (allo)polyploidy. This is not a simple task, for several reasons, including the chromosomally cryptic nature of many duplications and the variable rates of gene evolution. Recent progress has been made in understanding patterns of gene and genome duplication in the legume family, specifically in soybean.
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Affiliation(s)
- Randy C Shoemaker
- USDA-ARS and Iowa State University, G401 Agronomy Hall, Ames, Iowa 50011, USA.
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Han OK, Kaga A, Isemura T, Wang XW, Tomooka N, Vaughan DA. A genetic linkage map for azuki bean [Vigna angularis (Willd.) Ohwi & Ohashi]. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1278-87. [PMID: 16193342 DOI: 10.1007/s00122-005-0046-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Accepted: 07/08/2005] [Indexed: 05/04/2023]
Abstract
To make progress in genome analysis of azuki bean (Vigna angularis) a genetic linkage map was constructed from a backcross population of (V. nepalensis x V. angularis) x V.angularis consisting of 187 individuals. A total of 486 markers-205 simple sequence repeats (SSRs), 187 amplified fragment length polymorphisms (AFLPs) and 94 restriction fragment length polymorphisms (RFLPs) -were mapped onto 11 linkage groups corresponding to the haploid chromosome number of azuki bean. This map spans a total length of 832.1 cM with an average marker distance of 1.85 cM and is the most saturated map for a Vigna species to date. In addition, RFLP markers from other legumes facilitated finding several orthologous linkage groups based on previously published RFLP linkage maps. Most SSR primers that have been developed from SSR-enriched libraries detected a single locus. The SSR loci identified are distributed throughout the azuki bean genome. This moderately dense linkage map equipped with many SSR markers will be useful for mapping a range of useful traits such as those related to domestication and stress resistance. The mapping population will be used to develop advanced backcross lines for high resolution QTL mapping of these traits.
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Affiliation(s)
- O K Han
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
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28
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Martin WJ, McCallum J, Shigyo M, Jakse J, Kuhl JC, Yamane N, Pither-Joyce M, Gokce AF, Sink KC, Town CD, Havey MJ. Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol Genet Genomics 2005; 274:197-204. [PMID: 16025250 DOI: 10.1007/s00438-005-0007-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2004] [Accepted: 05/12/2005] [Indexed: 11/30/2022]
Abstract
The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23xAC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants.
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Affiliation(s)
- William J Martin
- Agricultural Research Service, USDA, Department of Horticulture, University of Wisconsin, Madison, 53706, USA.
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Mudge J, Cannon SB, Kalo P, Oldroyd GED, Roe BA, Town CD, Young ND. Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC PLANT BIOLOGY 2005; 5:15. [PMID: 16102170 PMCID: PMC1201151 DOI: 10.1186/1471-2229-5-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 08/15/2005] [Indexed: 05/04/2023]
Abstract
BACKGROUND Recent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny tempered by rearrangements. Within the legume plant family, glimpses of synteny have also been observed. Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds. RESULTS We have uncovered two large soybean regions exhibiting synteny with M. truncatula and with a network of segmentally duplicated regions in Arabidopsis. In all, syntenic regions comprise over 500 predicted genes spanning 3 Mb. Up to 75% of soybean genes are colinear with M. truncatula, including one region in which 33 of 35 soybean predicted genes with database support are colinear to M. truncatula. In some regions, 60% of soybean genes share colinearity with a network of A. thaliana duplications. One region is especially interesting because this 500 kbp segment of soybean is syntenic to two paralogous regions in M. truncatula on different chromosomes. Phylogenetic analysis of individual genes within these regions demonstrates that one is orthologous to the soybean region, with which it also shows substantially denser synteny and significantly lower levels of synonymous nucleotide substitutions. The other M. truncatula region is inferred to be paralogous, presumably resulting from a duplication event preceding speciation. CONCLUSION The presence of well-defined M. truncatula segments showing orthologous and paralogous relationships with soybean allows us to explore the evolution of contiguous genomic regions in the context of ancient genome duplication and speciation events.
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Affiliation(s)
- Joann Mudge
- Dept of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108 USA
| | - Steven B Cannon
- Dept of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108 USA
| | - Peter Kalo
- Dept. of Disease and Stress Biology, John Innes Centre, Norwich Research Park, Colney Norwich, NR4 7UH, UK
| | - Giles ED Oldroyd
- Dept. of Disease and Stress Biology, John Innes Centre, Norwich Research Park, Colney Norwich, NR4 7UH, UK
| | - Bruce A Roe
- The Advanced Center for Genome Technology (ACGT), Stephenson Research & Technology Center, University of Oklahoma, Norman OK 73019 USA
| | - Christopher D Town
- The Institute for Genomic Research (TIGR), 9712 Medicago Center Drive, Rockville, MN 20850 USA
| | - Nevin D Young
- Dept of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, MN 55108 USA
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30
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Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S. Sequencing the genespaces of Medicago truncatula and Lotus japonicus. PLANT PHYSIOLOGY 2005; 137:1174-81. [PMID: 15824279 PMCID: PMC1088310 DOI: 10.1104/pp.104.057034] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2004] [Revised: 01/26/2005] [Accepted: 01/30/2005] [Indexed: 05/18/2023]
Affiliation(s)
- Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108, USA.
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31
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Zhu H, Choi HK, Cook DR, Shoemaker RC. Bridging model and crop legumes through comparative genomics. PLANT PHYSIOLOGY 2005; 137:1189-96. [PMID: 15824281 PMCID: PMC1088312 DOI: 10.1104/pp.104.058891] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 01/18/2005] [Accepted: 01/24/2005] [Indexed: 05/18/2023]
Affiliation(s)
- Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, USA.
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32
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Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR. Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci U S A 2004; 101:15289-94. [PMID: 15489274 PMCID: PMC524433 DOI: 10.1073/pnas.0402251101] [Citation(s) in RCA: 370] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 08/13/2004] [Indexed: 11/18/2022] Open
Abstract
Legumes are simultaneously one of the largest families of crop plants and a cornerstone in the biological nitrogen cycle. We combined molecular and phylogenetic analyses to evaluate genome conservation both within and between the two major clades of crop legumes. Genetic mapping of orthologous genes identifies broad conservation of genome macrostructure, especially within the galegoid legumes, while also highlighting inferred chromosomal rearrangements that may underlie the variation in chromosome number between these species. As a complement to comparative genetic mapping, we compared sequenced regions of the model legume Medicago truncatula with those of the diploid Lotus japonicus and the polyploid Glycine max. High conservation was observed between the genomes of M. truncatula and L. japonicus, whereas lower levels of conservation were evident between M. truncatula and G. max. In all cases, conserved genome microstructure was punctuated by significant structural divergence, including frequent insertion/deletion of individual genes or groups of genes and lineage-specific expansion/contraction of gene families. These results suggest that comparative mapping may have considerable utility for basic and applied research in the legumes, although its predictive value is likely to be tempered by phylogenetic distance and genome duplication.
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Affiliation(s)
- Hong-Kyu Choi
- Department of Plant Pathology and College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616, USA
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Kaló P, Seres A, Taylor SA, Jakab J, Kevei Z, Kereszt A, Endre G, Ellis THN, Kiss GB. Comparative mapping between Medicago sativa and Pisum sativum. Mol Genet Genomics 2004; 272:235-46. [PMID: 15340836 DOI: 10.1007/s00438-004-1055-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Accepted: 08/10/2004] [Indexed: 10/26/2022]
Abstract
Comparative genome analysis has been performed between alfalfa (Medicago sativa) and pea (Pisum sativum), species which represent two closely related tribes of the subfamily Papilionoideae with different basic chromosome numbers. The positions of genes on the most recent linkage map of diploid alfalfa were compared to those of homologous loci on the combined genetic map of pea to analyze the degree of co-linearity between their linkage groups. In addition to using unique genes, analysis of the map positions of multicopy (homologous) genes identified syntenic homologs (characterized by similar positions on the maps) and pinpointed the positions of non-syntenic homologs. The comparison revealed extensive conservation of gene order between alfalfa and pea. However, genetic rearrangements (due to breakage and reunion) were localized which can account for the difference in chromosome number (8 for alfalfa and 7 for pea). Based on these genetic events and our increasing knowledge of the genomic structure of pea, it was concluded that the difference in genome size between the two species (the pea genome is 5- to 10-fold larger than that of alfalfa) is not a consequence of genome duplication in pea. The high degree of synteny observed between pea and Medicago loci makes further map-based cloning of pea genes based on the genome resources now available for M. truncatula a promising strategy.
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Affiliation(s)
- P Kaló
- Institute of Genetics, Agricultural Biotechnology Center, Szent-Györgyi A. u. 4, 2100 Gödöllo, Hungary
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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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Abstract
The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.
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Affiliation(s)
- L S Kumar
- Plant Molecular Biology Unit, Division of Biochemical Science, National Chemical Laboratory, Pune 411008, India.
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36
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Young ND, Mudge J, Ellis THN. Legume genomes: more than peas in a pod. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:199-204. [PMID: 12667879 DOI: 10.1016/s1369-5266(03)00006-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A growing array of sequence-based tools is helping to reveal the organization, evolution and syntenic relationships of legume genomes. The results indicate that legumes form a coherent taxonomic group with frequent and widespread macro- and microsynteny. This is good news for two model legume systems, Medicago truncatula and Lotus japonicus. Indeed, both models have recently been used to clone and characterize genes for nodulation-related receptors that were originally described in legumes with more complex genomes. Studies of legume genomes have also provided insight into genome size, gene clustering, genome duplications and repetitive elements. To understand legume genomes better, it will be necessary to develop tools for studying under-represented taxa beyond the relatively small group of economically important species that have been examined so far.
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Affiliation(s)
- Nevin Dale Young
- Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, Minnesota 55108, USA.
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Murray J, Larsen J, Michaels TE, Schaafsma A, Vallejos CE, Pauls KP. Identification of putative genes in bean (Phaseolus vulgaris) genomic (Bng) RFLP clones and their conversion to STSs. Genome 2002; 45:1013-24. [PMID: 12502245 DOI: 10.1139/g02-069] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A set of 79 previously mapped bean (Phaseolus vulgaris) genomic (Bng) clones were partially sequenced. BLAST database searches detected homologies between 59 of these clones and genes from a variety of plants, especially Arabidopsis thaliana. Some matches in the database to the Bng clones included a putative P-glycoprotein-ABC transporter from Arabidopsis, an early nodulin-binding protein (ENBPI) from Medicago truncatula, a lon-protease protein from spinach, a branched-chain amino-acid aminotransferase from Arabidopsis, and a vacuolar sorting receptor (BP-80) from Pisum sativum. Additional matches were found for genes involved in isoprenoid biosynthesis, sulfur metabolism, proline biosynthesis, and floral development. Sequence tagged site (STSs) were produced for 16 of the clones, 2 of which contain simple sequence repeats (SSRs). Polymorphisms were detected for six of the STSs.
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Affiliation(s)
- J Murray
- Department of Plant Agriculture, Crop Science Division, University of Guelph, Guelph, ON N1G 2W1, Canada
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38
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Abstract
Much of our most basic understanding of genetics has its roots in plant genetics and crop breeding. The study of plants has led to important insights into highly conserved biological process and a wealth of knowledge about development. Agriculture is now well positioned to take its share benefit from genomics. The primary sequences of most plant genes will be determined over the next few years. Informatics and functional genomics will help identify those genes that can be best utilized to crop production and quality through genetic engineering and plant breeding. Recent developments in plant genomics are reviewed.
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Affiliation(s)
- S Aljanabi
- Biotechnology Department, Mauritius Sugar Industry Research Institute, Reduit, Mauritius
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Burow MD, Simpson CE, Starr JL, Paterson AH. Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species. Genetics 2001; 159:823-37. [PMID: 11606556 PMCID: PMC1461827 DOI: 10.1093/genetics/159.2.823] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Polyploidy creates severe genetic bottlenecks, contributing to the genetic vulnerability of leading crops. Cultivated peanut is thought to be of monophyletic origin, harboring relatively little genetic diversity. To introduce variability from diploid wild species into tetraploid cultivated Arachis hypogaea, a synthetic amphidiploid [[A. batizocoi K9484 x (A. cardenasii GKP10017 x A. diogoi GKP10602)](4x)] was used as donor parent to generate a backcross population of 78 progeny. Three hundred seventy RFLP loci were mapped onto 23 linkage groups, spanning 2210 cM. Chromatin derived from the two A-genome diploid ancestors (A. cardenasii and A. diogoi) comprised mosaic chromosomes, reflecting crossing over in the diploid A-genome interspecific F(1) hybrid. Recombination between chromosomes in the tetraploid progeny was similar to chromosome pairing reported for A. hypogaea, with recombination generally between chromosomes of the same subgenomic affinity. Segregation distortion was observed for 25% of the markers, distributed over 20 linkage groups. Unexpectedly, 68% of the markers deviating from expected segregation showed an excess of the synthetic parent allele. Genetic consequences, relationship to species origins, and significance for comparative genetics are discussed.
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Affiliation(s)
- M D Burow
- Department of Crop and Soil Science, University of Georgia, Athens, 30602, USA
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Day RB, McAlvin CB, Loh JT, Denny RL, Wood TC, Young ND, Stacey G. Differential expression of two soybean apyrases, one of which is an early nodulin. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2000; 13:1053-70. [PMID: 11043467 DOI: 10.1094/mpmi.2000.13.10.1053] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Two cDNA clones were isolated from soybean (Glycine soja) by polymerase chain reaction with primers designed to conserved motifs found in apyrases (nucleotide phosphohydrolase). The two cDNAs are predicted to encode for two, distinct, apyrase proteins of approximately 50 kDa (i.e., GS50) and 52 kDa (i.e., GS52). Phylogenetic analysis indicated that GS52 is orthologous to a family of apyrases recently suggested to play a role in legume nodulation. GS50 is paralogous to this family and, therefore, likely plays a different physiological role. Consistent with this analysis, GS50 mRNA was detected in root, hypocotyls, flowers, and stems, while GS52 mRNA was found in root and flowers. Neither gene was expressed in leaves or cotyledons. Inoculation of roots with Bradyrhizobium japonicum, nitrogen-fixing symbiont of soybean, resulted in the rapid (<6 h) induction of GS52 mRNA expression. The level of GS50 mRNA expression was not affected by bacterial inoculation. Western blot (immunoblot) analysis of GS50 expression mirrored the results obtained by mRNA analysis. However, in contrast to the mRNA results, GS52 protein was found in stems. Interestingly, anti-GS52 antibody recognized a 50-kDa protein found only in nodule extracts. Treatment of roots with anti-GS52 antibody, but not anti-GS50 antibody or preimmune serum, blocked nodulation by B. japonicum. Fractionation of cellular membranes in sucrose density gradients and subsequent Western analysis of the fractions revealed that GS50 colocalized with marker enzymes for the Golgi, while GS52 colocalized with marker enzymes for the plasma membrane. Restriction fragment length polymorphism (RFLP)-based mapping placed the gs52 gene on major linkage group J of the integrated genetic map of soybean. These data suggest that GS50 is likely an endo-apyrase involved in Golgi function, while GS52 is localized on the root surface and appears to play an important role in nodulation.
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Affiliation(s)
- R B Day
- Center for Legume Research, Department of Microbiology, University of Tennessee, Knoxville 37996, USA
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Grant D, Cregan P, Shoemaker RC. Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc Natl Acad Sci U S A 2000; 97:4168-73. [PMID: 10759555 PMCID: PMC18185 DOI: 10.1073/pnas.070430597] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/1999] [Indexed: 11/18/2022] Open
Abstract
Synteny between soybean and Arabidopsis was studied by using conceptual translations of DNA sequences from loci that map to soybean linkage groups A2, J, and L. Synteny was found between these linkage groups and all four of the Arabidopsis chromosomes, where GenBank contained enough sequence for synteny to be identified confidently. Soybean linkage group A2 (soyA2) and Arabidopsis chromosome I showed significant synteny over almost their entire lengths, with only 2-3 chromosomal rearrangements required to bring the maps into substantial agreement. Smaller blocks of synteny were identified between soyA2 and Arabidopsis chromosomes IV and V (near the RPP5 and RPP8 genes) and between soyA2 and Arabidopsis chromosomes I and V (near the PhyA and PhyC genes). These subchromosomal syntenic regions were themselves homeologous, suggesting that Arabidopsis has undergone a number of segmental duplications or possibly a complete genome duplication during its evolution. Homologies between the homeologous soybean linkage groups J and L and Arabidopsis chromosomes II and IV also revealed evidence of segmental duplication in Arabidopsis. Further support for this hypothesis was provided by the observation of very close linkage in Arabidopsis of homologs of soybean Vsp27 and Bng181 (three locations) and purple acid phosphatase-like sequences and homologs of soybean A256 (five locations). Simulations show that the synteny and duplications we report are unlikely to have arisen by chance during our analysis of the homology reports.
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Affiliation(s)
- D Grant
- U.S. Department of Agriculture-Agricultural Research, Service Corn Insect and Crop Genetics Research Unit, Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
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Rector BG, All JN, Parrott WA, Boerma HR. Quantitative Trait Loci for Antibiosis Resistance to Corn Earworm in Soybean. CROP SCIENCE 2000; 40:233-238. [PMID: 0 DOI: 10.2135/cropsci2000.401233x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- B. G. Rector
- USDA ARS; Insect Biology and Population Management Research Lab; P.O. Box 748 Tifton GA 31793 USA
| | - J. N. All
- Dep. of Entomology; Univ. of Georgia; Athens GA 30602-2603 USA
| | - W. A. Parrott
- Dep. of Crop and Soil Sciences; Univ. of Georgia; Athens GA 30602-7272 USA
| | - H. R. Boerma
- Dep. of Crop and Soil Sciences; Univ. of Georgia; Athens GA 30602-7272 USA
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