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

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

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC-end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.

Original languageEnglish (US)
Pages (from-to)572-581
Number of pages10
JournalGenome
Volume44
Issue number4
DOIs
StatePublished - 2001
Externally publishedYes

Fingerprint

Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Soybeans
Restriction Fragment Length Polymorphisms
Microsatellite Repeats
restriction fragment length polymorphism
microsatellite repeats
soybeans
genomics
Nucleic Acid Repetitive Sequences
Genome
genome
Medicago truncatula
Surveys and Questionnaires
Protein Databases
repetitive sequences
Expressed Sequence Tags
Genomics
expressed sequence tags
Computational Biology

Keywords

  • Contig
  • Glycine max
  • Physical map
  • Sequencing

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biotechnology
  • Genetics
  • Genetics(clinical)

Cite this

Marek, L. F., Mudge, J., Darnielle, L., Grant, D., Hanson, N., Paz, M., ... Shoemaker, R. C. (2001). Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome, 44(4), 572-581. https://doi.org/10.1139/gen-44-4-572

Soybean genomic survey : BAC-end sequences near RFLP and SSR markers. / Marek, Laura Fredrick; Mudge, Joann; Darnielle, Laura; Grant, David; Hanson, Nadja; Paz, Margie; Yan, Huihuang D; Denny, Roxanne; Larson, Karin; Foster-Hartnett, Dawn; Cooper, Anne; Danesh, Dariush; Larsen, Dana; Schmidt, Tina; Staggs, Rod; Crow, John A.; Retzel, Ernest; Young, Nevin D.; Shoemaker, Randy C.

In: Genome, Vol. 44, No. 4, 2001, p. 572-581.

Research output: Contribution to journalArticle

Marek, LF, Mudge, J, Darnielle, L, Grant, D, Hanson, N, Paz, M, Yan, HD, Denny, R, Larson, K, Foster-Hartnett, D, Cooper, A, Danesh, D, Larsen, D, Schmidt, T, Staggs, R, Crow, JA, Retzel, E, Young, ND & Shoemaker, RC 2001, 'Soybean genomic survey: BAC-end sequences near RFLP and SSR markers', Genome, vol. 44, no. 4, pp. 572-581. https://doi.org/10.1139/gen-44-4-572
Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M et al. Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome. 2001;44(4):572-581. https://doi.org/10.1139/gen-44-4-572
Marek, Laura Fredrick ; Mudge, Joann ; Darnielle, Laura ; Grant, David ; Hanson, Nadja ; Paz, Margie ; Yan, Huihuang D ; Denny, Roxanne ; Larson, Karin ; Foster-Hartnett, Dawn ; Cooper, Anne ; Danesh, Dariush ; Larsen, Dana ; Schmidt, Tina ; Staggs, Rod ; Crow, John A. ; Retzel, Ernest ; Young, Nevin D. ; Shoemaker, Randy C. / Soybean genomic survey : BAC-end sequences near RFLP and SSR markers. In: Genome. 2001 ; Vol. 44, No. 4. pp. 572-581.
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