Soybean Genomics Research Program Strategic Plan
2011; Crop Science Society of America; Volume: 4; Issue: 1 Linguagem: Inglês
10.3835/plantgenome2011.12.0001
ISSN1940-3372
AutoresRoger Boerma, Richard F. Wilson, Ed Ready,
Tópico(s)Plant pathogens and resistance mechanisms
ResumoThis strategic plan builds on the soybean communities’ previous efforts (October, 1999; July, 2001; May, 2003; July, 2005; and May, 2007) to review progress on the development and deployment of soybean genomic resources. The results are impressive (see Soybean Genomics Research Program Accomplishments Report, 2010, available at http://soybase.org/SoyGenStrat2007/SoyGenStratPlan2008-2012-Accomplishments%20v1.6.pdf [verified 17 Mar. 2011]). For example, in the last 5 yr the soybean research community has produced a genetic linkage map with over 5500 mapped markers spanning the entire 2296 cM soybean genome. A set of 1536 SNP markers that are evenly distributed across the 20 linkage groups was developed for whole genome analysis of polymorphisms in both elite North American cultivars and breeding lines. In addition, an expanded array of 50,000 SNPs is under development which will be used to create haplotype maps of over 18,000 accessions of the USDA soybean germplasm collection. This research is scheduled for completion in late 2010 and the SNP haplotype map of each accession will be placed on the HapMap Browser on SoyBase. Large-scale shotgun sequencing of the soybean cultivar Williams 82 was completed late in 2008 by the U.S. Department of Energy Joint Genome Institute (DOE-JGI) and recently reported in the scientific journal Nature (Schmutz et al., 2010). The present soybean assembly (Glyma.1.01) captured approximately 975 Mbp of its 1100 Mbp genome. The gene set integrates ∼1.6 million ESTs with homology and predicts 66,153 protein-coding loci available at http://www.phytozome.net/soybean (verified 17 Mar. 2011). Soybean researchers have developed several microarray technologies for gene expression studies. The GeneChip Soybean Genome Array is commercially available for studying gene expression (http://www.affymetrix.com/products_services/arrays/specific/soybean.affx#1_1 [verified 17 Mar. 2011]). This GeneChip contains 37,500 Glycine max transcripts, 15,800 Phytophthora sojae transcripts, and 7500 Heterodera glycines transcripts. The achievement of milestones in previous strategic plans for soybean genomic research have advanced soybean to its current status as a crop model for translational genomics. Simply stated, soybean genomic resources in hand will accelerate the ability of plant breeders to enhance soybean productivity, pest resistance, and nutritional quality. However, many secrets of the soybean genome have yet to be revealed. To continue to make informed decisions it was critical to capture the consensus wisdom of leading soybean researchers on the next logical steps in the development and utilization of soybean's genomic resources. On 27–28 July 2010 Roger Boerma chaired a workshop sponsored by the United Soybean Board in St. Louis MO that brought together 44 eminent soybean researchers in the areas of genomic sequencing, gene function, transformation/transgenics, and translational genomics. The purpose of the Workshop was to develop a strategy for achieving the critical soybean genomic resources and information required to accelerate the rate of yield gain and addition of value to U.S. soybean cultivars. A consensus was reached on a number of high priority performance measures or research objectives. In addition the anticipated outcomes of successfully achieving these performance measures are included in the final plan. Overall, two issues emerged as being critically important or overarching issues: (i) Provide additional support staff for continued development and population of SoyBase, and (ii) Development of a genetic repository/distribution center for soybean mutants/transgenic lines. The enhancement of SoyBase was deemed important for all four Strategic Goals. The genetic repository/distribution center was broadly supported by Workshop participants. Listed below is an outline of the four Strategic Goals and their respective Performance Measures. Within each Goal, the Performance Measures are listed in order of importance. 1.1: Ensure the accuracy of reference sequence assembly. 1.2: Capturing and leveraging existing genetic diversity in soybean germplasm. 1.3: Improving bioinformatic resources for genomic analysis and practical applications. 1.4: Reveal function of targeted genome sequences to facilitate gene discovery and application. 1.5: Leveraging genomic information from Phaseoloids and other species. 1.6: Determine the role of epigenetics in soybean improvement. 2.1: Develop comprehensive gene expression data for soybean. 2.2: Develop near isogenic lines (NIL) to help reveal genetic mechanisms that mediate useful traits. 2.3: Develop an improved infrastructure to facilitate genome annotation. 2.4: Achieve high-definition genomic characterization of biological mechanisms and regulatory systems in soybean. 2.5: Use functional genomic methods to characterize transcription regulated pathways. 2.6: Advance gene modification technologies to help associate candidate genes with a discrete phenotype. 2.7: Create a saturated transposon insertion population with defined flanking sequences that can be used to identify mutants by BLAST sequence comparison. 2.8: Implement outreach opportunities for education and use of genomic databases. 2.9: Develop an ORFeome library from agronomically important genes and gene families. 3.1: Establish of a soybean genetic repository and distribution center. 3.2: Develop next-generation transformation and targeting technologies and utilize these transgenic approaches to help elucidate gene function and deploy genes of interest. 4.1: Develop analytical approaches to characterize soybean germplasm diversity based on the SoyHapMap 1.0 data to identify parental lines for breeding purposes. 4.2: Discover gene/QTL for qualitative traits and develop tightly linked DNA markers. 4.3: Discover gene/QTL for quantitative traits and develop tightly linked DNA markers. 4.4: Develop and populate a user-friendly database of validated QTL for use in marker assisted breeding applications. 4.5: Define the molecular genetic signatures of selection in 70+ years of U.S. soybean breeding by use of the 50,000 SNP Illumina Infinium Assay. 4.6: Define optimum breeding models for different breeding situations using in silico analysis. The chromosome-scale draft assembly of the soybean (Glycine max L. Merr.) genome is an outcome of a dynamic, technology driven, and timely strategic process whose origin may be traced formally to the Soybean Genomics White Paper (Boerma et al., 2000). That January 2000 document was a product of a 21–22 Oct. 1999 meeting of 17 experts in plant genomics, DNA markers, plant transformation, and bioinformatics. A consensus was reached on research priorities in the area of soybean genomics. Milestones included: (i) doubling Simple Sequence Repeat (SSR) markers within 3 yr; (ii) expansion of Single Nucleotide Polymorphism (SNP) markers to 10,000 within 3 to 5 yr; (iii) improving the efficiency of soybean transformation; (iv) tagging 80% of the genes in the soybean genome within 3 to 5 yr; (v) integration of genetic, physical, and transcript maps of soybeans within 3 to 5 yr; and (vi) employing comparative genomics to define the structure and attributes of the soybean genome. It became mutually beneficial to establish research coalitions to improve the efficiency of genomic investigations among related species. For this reason, the U.S. Legume Crops Genomics Initiative (LCGI) was organized under the auspices of the American Soybean Association, United Soybean Board, National Peanut Foundation, USA Dry Pea and Lentil Council, the National Dry Bean Council, and the Alfalfa Council to facilitate communication and cooperation among scientists with an interest in genomic research on soybean, peanut, pea and lentil, common bean, alfalfa, and model-legume crops. LCGI was founded on the premise that the development of an integrated legume genomics research system would enhance ability to leverage information across legume crops and model species and the first workshop was convened on 30–31 July 2001 at Hunt Valley, MD. Twenty-six legume scientists developed a white paper (Boerma et al., 2001) that outlined high-priority research in the areas of: (i) genome sequencing of strategic legume species; (ii) physical map development and refinement; (iii) functional analysis: transcriptional and genetic; (iv) development of DNA markers for comparative mapping and breeding; (v) characterization and utilization of legume biodiversity; and (vi) development of a legume data resource. The nature of this cooperative interaction not only ensured timely research progress in all legume crops associated with the Initiative, but also enhanced the competitive position of the LCGI within the framework of the National Plant Genome Initiative, which is coordinated by the Interagency Working Group on Plant Genomics, Committee on Science, National Science and Technology Council. Implementation of a coordinated effort for research and development of genomics across the legume family facilitated progress in the model species Medicago truncatula and Lotus japonicus and in soybean (Glycine max), and accentuated the need to transfer genomic information from the model species to cool-season pulses [pea (Pisum sativum), lentil (Lens culinaris), chickpea (Cicer arietinum), field bean (Vicia faba)], and warm-season food legumes [peanut (Arachis hypogea), common bean (Phaseolus vulgaris)], and forage legumes [alfalfa (Medicago sativa), clover (Trifolium spp.)]. This mission was codified further by (i) a third white paper, entitled: Legumes as a Model Plant Family: Genomics for Food and Feed; and (ii) by the publication of the monograph, Legume Crop Genomics. The white paper was an outcome of the CATG (Cross-legume Advances through Genomics) conference on 14–15 Dec. 2004 in Sante Fe, NM with funding from the National Science Foundation (Plant Genome Research Program) and the USDA (National Research Initiative). About 50 individuals in attendance represented the respective legume communities as well as various funding agencies. The objectives of the conference were to: (i) identify a unifying goal for an international cross-legume genome project; (ii) identify cross-cutting themes to help integrate the different legume crop genomics programs, including a unified legume genomics information system, nutritional and health-related aspects of legumes, and detailed synteny and comparative genomics of legumes; and (iii) outline specific components and milestones for the initiative. These deliberations identified four tiers of legume species, each with specific genomic resources to be developed. Based on phylogenetic arguments, and particularly the degree of synteny, two major foci of legumes were identified, the hologaleginoid clade or cool-season legumes and the phaseoloid/millettioid clade or warm-season legumes. In each of these two foci, one or two reference species were identified, M. truncatula and L. japonicus in the former and soybean in the latter. Development of a full range of genomics resources, including sequencing of the entire genome, was the highest priority for these reference species. For a second group, common bean and peanut, a broad range of genomic resources were recommended, including a physical map, BAC-end sequencing and marker development, anchoring of the genetic and physical map, ESTs of the major organs, chip resources, and sequencing of gene rich regions. A third group consisted of all other legume crops in the two foci, including pea, lentil, chickpea, field bean, clover, cowpea (Vigna unguiculata), and pigeon pea (Cajanus cajan). For these legumes, translational genomic tools were to be developed, principally for cross-legume markers, species-specific recombinant inbred lines, genetic maps, EST and BAC libraries. A fourth group included other legumes not in the two main foci, such as members of the basal legume clades. An abbreviated version of this white paper was published. (Gepts et al. 2005). As each of the legume crop communities began to amass critical genomic resources, it became necessary for each community to develop priorities that were crop specific. The strategic foundation for soybean genomics research was laid on 20–21 May 2003, when 19 researchers participated in a workshop. The scientists reviewed the current status of soybean genomic research and reached consensus on a strategic framework for outlining research priorities and significant near-term milestones. This input was captured in the Strategic Plan for Soybean Genomics 2003–2007. (available at http://soybase.org/SoyGenStrat2005/Soy_Genome_Strat_Plan_2005.html [verified 17 Mar. 2011]) Coordination of plan implementation was delegated through election of the Soybean Genetic Executive Committee (SoyGEC). The SoyGEC took action to move forward aggressively on genomic resources including physical mapping, EST anchoring, and functional genomic resources. The SoyGEC (http://soybase.org/resources/soygec.php [verified 17 Mar. 2011]) also initiated strategies to proactively communicate soybean research community priorities to representatives of federal granting agencies, and encouraged coordination of dedicated research teams to solve soybean problems of national and international importance. A National Science Foundation (NSF)-sponsored workshop was held in St. Louis on 21 Oct. 2003 to take an inventory of the current genomic resources in soybean, identify areas where more data were needed, and to set a research a strategy to advance soybean genomics research. Special attention was focused on research opportunities provided by unique aspects of soybean biology. The workshop included academic, governmental, and industrial scientists covering a wide variety of specialties related to both basic and applied research on soybean, along with scientists from outside the soybean field who provided general expertise in genomics and represented a wealth of experience garnered from other genomic projects. Representatives from federal funding agencies and soybean commodity groups participated as observers. This workshop extended and further defined the findings from earlier workshops, which had surveyed the status and priority goals for soybean & legume genomics (see http://soybase.org/Genetic_Resources/Soybean_Genetic_Resources.html [verified 17 Mar. 2011]) (Stacey et al., 2004). Action to address the need for bioinformatic resources was taken by the National Center for Genome Research (NCGR) and USDA, ARS, NPS when the U.S. Congress established the Model Plant Initiative (MPI) to use bioinformatics to leverage genomic information from model plant species. The Legume Information System (LIS), a joint NCGR and ARS effort, was one of the first projects in support of the MPI to demonstrate the integration of genomic information from Arabidopsis thaliana, Medicago truncatula and Lotus japonicus to important agronomic legumes, e.g., soybean, alfalfa, pea, dry beans. Since its inception, LIS development has been guided by ideas and suggestions from the legume research communities. Based on user needs, USDA-ARS and NCGR developed a plan to amplify the power of this information resource for identification of candidate genes, unique genes, and evolutionary relationships among genes for crop improvement. It was agreed to utilize LIS as a foundation for a Comparative Legume Biology (CLB) Program. CLB expanded LIS from a passive data management system to a platform for novel data analysis and visualization tools. With the emergence of high throughput biotechnologies and bioinformatics, comparative biology enabled more sophisticated analyses of genomic sequences, genomic maps, micro-arrays, protein arrays, metabolic arrays, genetic regulatory networks, and biochemical and whole organism phenotypes. The SoyGEC convened the first assessment of research performance against the Strategic Plan for Soybean Genomics 2003–2007 on 19–20 July 2005 in St. Louis, MO. Presentations provided updates on the current status of soybean resources and related genomics technologies. Stakeholder input was generated in facilitated discussion groups to assess the status of soybean genomics, identify needs, and identify milestones to achieve objectives. The discussion groups included the general areas of Functional Genomics A (Transcriptome and Proteome), Functional Genomic B (Reverse Genetics), Physical and Genetic Maps, and Bioinformatics. Several topics received overwhelming support in all group reports. A high quality physical map in Williams 82 and integration with the physical map of ‘Forrest’ was a very high priority. A whole-genome sequence was an expectation of the research community. The need for standardization of protocols, terminologies and ontologies was evident as interactions among groups and among research communities expand. Finally, there was urgent need to establish long-term facilities that have the capability to archive, maintain, generate and provide biological resources. Overall, there was consensus that the ongoing research was on target, if not ahead of schedule, and still relevant to the goals and objectives of the Strategic Plan for Soybean Genomics 2003–2007. On 20 Jan. 2006 the USDA and DOE announced plans to share resources and coordinate the study of plant and microbial genomics. The soybean genome was first on the list for sequencing. Dr. Ari Patrinos, DOE Associate Director for SBER, directed the Joint Genome Institute (JGI) to carry out the work with the Stanford Human Genome Center. A Genome Strategic Planning Workshop to consider research goals and priorities for the next 5-yr programmatic cycle was convened by the SoyGEC in St. Louis, MO on 30–31 May 2007 by James Specht (University of Nebraska-Lincoln). This workshop was attended by 48 experts in diverse genomic areas. Whereas previous soybean strategic plans had dealt with preparation for the eventual sequencing of the genome, the announcement that the soybean genome would be sequenced by DOE-JGI necessitated a reassessment of strategic objectives for the next research plan. Jeremy Schmutz, Stanford, the leader of the DOE-JGI soybean sequence assembly effort reported that the work was proceeding exceptionally well, despite the ancient polyploidy of a now well-diploidized soybean. A 4X shotgun genome sequence of the genome had been developed and a draft assembly had been created. This assembly was being evaluated to determine the optimal means for obtaining the final goal of an 8X coverage. The 8X sequence was slated to be completed by the end of 2007, with a final assembly expected to be completed in mid-2008. A gratifying number of objectives and milestones identified in the 2005 Plan had been achieved on schedule. The number of SNPs and STSs proposed for discovery and development was exceeded. Inbred mapping resources (RILs) were developed. Transformation technologies had improved and various gene knock-out systems were working. USB and NSF funding enabled work on physical and transcript maps. Bioinformatic resources and staffing had more than doubled, in time to receive the whole genome shotgun sequence. These technological developments and the diminishing cost of many genomic-based technologies were taken into full account in the development of the Strategic Plan for Soybean Genomics 2008–2012. The SoyGEC reached out to colleagues abroad at the first meeting of the International Soybean Genome Consortium at he NIAS in Tsukuba, Japan on 20 April 2007. This ongoing association has helped leverage resources for soybean genomic research in Japan, Korea, China, and the USA. This current report summarizes the most recent strategic plan for soybean genomics research. This plan was developed at a workshop held on 27–28 July 2010 in St. Louis MO. The workshop was convened by Roger Boerma and included 44 soybean researchers in the areas of genomic sequencing, gene function, transformation/transgenics, and translational genomics. The purpose of the workshop was to develop a consensus strategy for achieving the critical soybean genomic resources and information required to accelerate the rate of yield gain and addition of value to U.S. soybean cultivars. This plan, Soybean Genomics Research Program Strategic Plan: Implementing Research to Meet 2012–2016 Strategic Milestones documents the high priority Performance Measures or research objectives, and anticipated outcomes of successfully achieving Strategic Goals for soybean genomic research in the next 5 yr. Within each Goal, the Performance Measures are listed in order of importance. Performance Measure 1.1: Ensure the accuracy of reference sequence assembly. Quality control is essential for useful reassembly of genome sequences. Accuracy of the reference genome impacts the effectiveness of all subsequent investigations of gene discovery, identification of gene function, comparative genomics, and characterization of the nature of genetic diversity in soybean. The first chromosome scale draft sequence of Glycine max is of very high quality. However, there are regions within the genome that remain ambiguous. These regions may contain genes that are important to soybean improvement. Therefore, research is needed to correct portions of the assembly. · Closure of remaining gaps in sequence contigs/scaffolds. · Correction of the order and orientation of improperly aligned scaffolds/contigs. · Optical maps to orient contigs/scaffolds and estimate gaps sizes and place unanchored sequence contigs. · Additional clone libraries targeted to span gaps and/or to help orient contigs/scaffolds. · New sequencing technologies to generate long-range sequence reads. Performance Measure 1.2: Capturing and leveraging existing genetic diversity in soybean germplasm. Genotypic diversity is the basis for genetic enhancement of soybean. Linkage disequilibrium and other statistical measures suggest that much of the variation for useful traits within the USDA germplasm collection remain untapped because of the difficulties in effectively identifying genetic differences. However, advances in DNA sequencing technology will enable the high-definition characterization of genotypic differences among germplasm accessions, cultivars, and breeding lines. · Resequencing a subset of the U.S. germplasm collection (including the ancestral land races) that captures greater than 90% of the genetic variation in G. max will access genetic diversity on a base-pair to base-pair level. · Haplotype maps of the entire USDA G. max and G. soja collections to identify rare, potentially valuable genes/alleles. · De novo sequencing (near reference level sequencing) of up to 10 selected G. max lines to estimate presence-absence variation (PAV), copy number variants (CNV), genes that are not present in the reference genome, and other structural variation. Performance Measure 1.3: Improving bioinformatic resources for genomic analysis and practical applications. As a consequence of advances in sequencing technology, the amount of the soybean genomic and associated data is growing at exponential rates. Data storage limitations are now eclipsed by problems that limit the curator's ability to compile, analyze, and interpret data in a useful and timely manner. There is a need for expansion of an integrated database for use by all researchers, including breeders, to enhance the utility of genome sequence data. · Criteria for decision tools for parental selection and distinguishing genotypes during breeding population development (See Goal 4). · Software, protocols, and database support for sequence-based genotyping. · Expansion of SoyBase to completely integrate all relevant information using almost any concept as an entry point. For example starting with a gene name or function, a user should be able to quickly find the position(s) of that gene on the genetic and sequence maps, information about that gene, and links to the scientific literature for more details. Performance Measure 1.4: Reveal function of targeted genome sequences to facilitate gene discovery and application. High-definition mapping of DNA sequences in quantitative trait loci (QTL) enables the construction of allele specific markers for genetic traits. However, many genes may be present in a QTL region. Association of candidate gene sequences with a specific biological function or response not only facilitates marker development, but also expands knowledge of the biological mechanisms that mediate agricultural traits in soybean. Accurate annotation of the reference sequence is needed to improve the efficiency and utility of gene discovery. · Definition of entire gene families, 5’ to 3’, and alternative transcripts. · Validated gene models with Transcription Start Sites (TSSs) for 20,000 genes. · Refined accuracy of the transposon element database (TEdb) to recover genes embedded in transposable elements. · Refined annotation of pseudogenes (e.g., truncated or early stop codons) that may have transcriptional evidence. · Definition of regulatory elements (transcription factor binding sites, micro RNAs, etc.) that control gene expression. · Annotation of known promoter elements for all identified motifs, prediction of unknown elements, and identification of co-regulated genes. · Small RNA sequences from a range of tissues to understand the role of small RNAs in gene regulation. · Functional annotation of soybean gene sets to facilitate gene discovery and genetic improvement. · Collection and integration of functional information for all published gene mutant/descriptions. · Collection and integration of transcriptome data with genetic and genomic resources in SoyBase, the USDA-ARS soybean genetic database (http://soybase.org). Performance Measure 1.5: Leveraging genomic information from Phaseoloids and other species. Phaseolus vulgaris (dry bean) and Vigna unguiculata (cowpea) are diploid species with synteny to soybean. Phaseolus and Vigna both diverged from Glycine about 19–23 MYA, and may be very useful for the discovery of genes for protection against abiotic stresses in soybean. Genome sequencing of both species is underway. The perennial Glycine species are also of interest because of the nature of polyploidy in Glycine as a whole, and thus for understanding the duplicated nature of the soybean genome. These species diverged from soybean (and its progenitor, G. soja) around 5 MYA. The perennial species constitute the secondary germplasm pool for soybean, and may provide traits such as drought tolerance and rust resistance. · Identification of genetic variability for nutritional traits in common bean and cowpea that may be applicable to soybean. · Discovery of the genes or quantitative trait loci (QTL) with DNA markers to facilitate transfer to elite cultivars. · Sets of SNP panels specific to appropriate populations of common bean and cowpea. · Genetically and chromosomally stable interspecific populations between soybean and G. tomentella for resequencing and identification of diploids with resistance to pest and pathogens. Performance Measure 1.6: Determine the role of epigenetics in soybean improvement. Epigenetics represents non-Mendelian inheritance of phenotypic traits. This area of plant biology is poorly understood. However, a growing body of knowledge suggests a hierarchical stratification in the regulation of gene expression that involves a complex interaction among gene products. · Enhanced knowledge base for understanding the role of epigenetics in mediating gene expression. · Understanding the contribution of epigenetic phenomena to phenotypic diversity. Performance Measure 2.1: Develop comprehensive gene expression data for soybean. Current annotation of the soybean genome suggests at least 45,000 protein encoding genes. While genome sequencing reveals all of the genes present within an organism, it cannot tell us what specific gene products are needed for different cellular pathways, tissues, or organs. For example, leaves and roots contain the same DNA, yet their very different structures are the result of differences in gene expression. It is laborious to examine the expression of genes on a gene-by-gene basis. Fortunately, new high-throughput sequencing platforms provide a rapid and sensitive means to survey gene expression. Limited soybean gene expression atlases are now available and have already been utilized to study the expression of some genes. However, these resources need to be expanded to include many more specific tissues and, more importantly, environmental treatments, especially those of agronomic importance (e.g., drought or insect predation). The availability of a comprehensive, soybean expression atlas that encompasses all such tissues and treatments would be an invaluable resource for the study of soybean gene function. · An improved soybean gene atlas developed from RNA-seq approaches, which includes a comprehensive list of all expressed soybean genes, alternative splice products, and the identification of co-regulated genes and gene networks. · RNA-seq data representing 100 different tissues and treatments. · A standardized methodology for submitting data toward the whole soybean genome annotation effort. Performance Measure 2.2: Develop near isogenic lines (NIL) to help reveal genetic mechanisms that mediate useful traits. The application of the full repertoire of functional genomic tools to soybean promises to yield new and important insights that can be mined for soybean improvement. However, these tools can be fully utilized only in well controlled experiments that minimize experimental variation, include replication, and provide rigorous statistical analysis. An important variable is genotypic variation. However, this can be reduced by the use of NILs varying only in key alleles that control important agronomic traits. The availability of such NILs is essential for soybean to fully benefit from the m
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