Soybean genomic survey: BAC-end sequences near RFLP and SSR markers

Marek, Laura F.; Mudge, Joann; Darnielle, Laura; Grant, David; Hanson, Nadja; Paz, Margie M.; Yan, Huihuang; Denny, Roxanne; Larson, Karin; Foster‐Hartnett, Dawn; Cooper, Anne; Danesh, D.; Larsen, Dana; Schmidt, Tina; Staggs, Rod; Crow, John A.; Retzel, Ernest; Young, Nevin D.; Shoemaker, Randy C.

doi:10.1139/g01-052

Cited by 61 publications

(51 citation statements)

References 31 publications

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“…The studies also suggested that the repetitive sequences were not evenly interspersed among single-copy sequences and clustering appeared to be similar to that found in wheat (Triticum aestivum) and rye (Secale cereale; Flavell and Smith, 1976;Smith and Flavell, 1977). Analysis of data generated from BAC end sequences suggests that although some regions are predominantly gene-rich or repetitive-rich, most loci contain a mixture of repetitive and genic sequences (Marek et al, 2001).…”

Section: Current Status Of Soybean Genomicsmentioning

confidence: 53%

“…The global gene space of soybean is not yet defined. However, gene-rich regions have been observed in soybean (Marek et al, 2001) using hypomethylated RFLPs as signatures of genic regions as compared to SSRs. Of more than 2,000 BAC-end sequences examined, RFLP-associated sequences had only one-half as many repetitive sequences and 50% more genic sequences compared with SSR-associated sequences.…”

Section: Current Status Of Soybean Genomicsmentioning

confidence: 99%

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National Science Foundation-Sponsored Workshop Report. Draft Plan for Soybean Genomics

et al. 2004

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Recent efforts to coordinate and define a research strategy for soybean (Glycine max) genomics began with the establishment of a Soybean Genetics Executive Committee, which will serve as a communication focal point between the soybean research community and granting agencies. Secondly, a workshop was held to define a strategy to incorporate existing tools into a framework for advancing soybean genomics research. This workshop identified and ranked research priorities essential to making more informed decisions as to how to proceed with large scale sequencing and other genomics efforts. Most critical among these was the need to finalize a physical map and to obtain a better understanding of genome microstructure. Addressing these research needs will require pilot work on new technologies to demonstrate an ability to discriminate between recently duplicated regions in the soybean genome and pilot projects to analyze an adequate amount of random genome sequence to identify and catalog common repeats. The development of additional markers, reverse genetics tools, and bioinformatics is also necessary. Successful implementation of these goals will require close coordination among various working groups.

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Section: Current Status Of Soybean Genomicsmentioning

confidence: 53%

Section: Current Status Of Soybean Genomicsmentioning

confidence: 99%

National Science Foundation-Sponsored Workshop Report. Draft Plan for Soybean Genomics

et al. 2004

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“…More than 750 SSR and RFLP markers were used to identify BAC clones in soybean. The markers anchor these BACs to the consensus molecular genetic map for soybean (Marek et al, 2001;Foster-Hartnett, et al, 2002). Almost 60% of the end sequences from BACs identified by both types of markers produce significant similarity in BLAST database searches.…”

Section: Building An Infrastructure Of Bac Contigs Anchored To the Gementioning

confidence: 99%

“…A marker-anchored Marek et al, 2001;Shultz et al, 2001) physical map of the soybean genome derived from large insert clones (Marek and Shoemaker, 1997;Danesh et al, 1998;Meksem et al, 2000) has been constructed and refined (C. Wu, personal communication). There are currently four routes available to access the data sets.…”

Section: Community Access To Project Resourcesmentioning

confidence: 99%

“…The sequences associated with a contig represent a second route of entry to the physical map. Selecting the NCBI button next to a marker allows the DNA sequences associated with that marker to be displayed (Iqbal et al, 2001;Marek et al, 2001). These include primer sequences, allele sequences, BAC end sequences, and sequence-tagged sites linked to clone plate addresses within that contig.…”

Section: Community Access To Project Resourcesmentioning

confidence: 99%

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Summaries of Legume Genomics Projects from around the Globe. Community Resources for Crops and Models

2003

Plant Physiol.

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Edited by Kathryn A. VandenBosch and Gary Stacey, Monitoring Editors, Plant PhysiologyGenomic research has and will continue to revolutionize plant biology. It is clear that the adoption of Arabidopsis as a model species has done much to speed the development of plant genomics and to hasten our increased understanding of basic plant biology. However, Arabidopsis is not an "omniscient" model because this plant does not encompass all of the diverse physiological, developmental, and environmental processes seen throughout the plant kingdom. Thus, to study these other processes and to bring the genomic revolution to crop species, additional genomic resources must be developed in other plants.Over the past several years, this realization has led to the adoption of the model species concept to the study of legumes. Unlike Arabidopsis, legumes develop important and interesting symbioses with nitrogen (N)-fixing rhizobia and with mycorrhizal fungi. They also exhibit interesting differences in secondary metabolism, pod development, and other processes that cannot be adequately modeled with Arabidopsis. The impetus for the development of legume models has come primarily from researchers interested in the rhizobium-legume symbiosis. Because of this, two models, not one, have been developed: Lotus japonicus and Medicago truncatula. In reality, these two models have evolved due to the energy of their proponents but, scientifically, they can also be justified because they exhibit two developmental systems for nodulation as well as other differences. L. japonicus forms determinate nodules, in which the root subepidermal cortical cells initiate nodule formation and a persistent, terminal nodule meristem does not develop. In contrast, M. truncatula nodules initiate from the division of inner cortical cells and continue to grow from a terminal, persistent meristem. As can be seen by the summaries below, both legume model species are now well established with a large number of laboratories involved. Therefore, in the long run, legume biology can only benefit by a comparison of the results between these models and legume crop plants.In contrast to the effort focused on the legume models, with the possible exception of soybean (Glycine max), significantly smaller efforts exist to study the genomics of legume crop species. This is unfortunate because it remains to be seen just how much of the information developed from legume models can be directly applied to the improvement of legume crops.It is clear that legume biology is rapidly undergoing a revolutionary transformation due to the application of genomic methods. The future is exceedingly bright, and one would expect rapid progress in our understanding of basic plant processes and the unique aspects of legume physiology and development.The edited summaries below represent the currently funded genomic activities focused on legume models and crops. For convenience, these are listed by relevant species, although similar trends and interests are apparent throughout.

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