Integration of the draft sequence and physical map as a framework for genomic research in soybean (glycine max (l.) merr.) and wild soybean (glycine soja sieb. and zucc.)

Jungmin Ha, Brian Abernathy, William Nelson, David Grant, Xiaolei Wu, Henry T. Nguyen, Gary Stacey, Yeisoo Yu, Rod A Wing, Randy C. Shoemaker, Scott A. Jackson

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate map-based gene cloning. Three independent G. max BAC libraries combined with genetic and gene-based markers were used to construct a minimum tiling path (MTP) of BAC clones. A total of 107,214 clones were assembled into 1355 FPC (FingerPrinted Contigs) contigs, incorporating 4628 markers and aligned to the G. max reference genome sequence using BAC end-sequence information. Four different MTPs were made for G. max that covered from 92.6% to 95.0% of the soybean draft genome sequence (gmax1.01). Because our purpose was to pick the most reliable and complete MTP, and not the MTP with the minimal number of clones, the FPC map and draft sequence were integrated and clones with unpaired BES were added to build a high-quality physical map with the fewest gaps possible (http://soybase.org). A physical map was also constructed for the undomesticated ancestor (G. soja) of soybean to explore genome variation between G. max and G. soja. 66,028 G. soja clones were assembled into 1053 FPC contigs covering approximately 547Mbp of the G. max genome sequence. These physical maps for G. max and its undomesticated ancestor, G. soja, will serve as a framework for ordering sequence fragments, comparative genomics, cloning genes, and evolutionary analyses of legume genomes.

Original languageEnglish (US)
Pages (from-to)321-329
Number of pages9
JournalG3: Genes, Genomes, Genetics
Volume2
Issue number3
DOIs
StatePublished - Mar 2012

Fingerprint

Soybeans
Glycine
Genome
Bacterial Artificial Chromosomes
Research
Clone Cells
Fabaceae
Organism Cloning
Genes
Firearms
Genomics
Chromosomes

Keywords

  • Contig
  • Evolution
  • FingerPrinted
  • Genome
  • Genome structure
  • Sequencing
  • Whole-genome

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Genetics(clinical)

Cite this

Integration of the draft sequence and physical map as a framework for genomic research in soybean (glycine max (l.) merr.) and wild soybean (glycine soja sieb. and zucc.). / Ha, Jungmin; Abernathy, Brian; Nelson, William; Grant, David; Wu, Xiaolei; Nguyen, Henry T.; Stacey, Gary; Yu, Yeisoo; Wing, Rod A; Shoemaker, Randy C.; Jackson, Scott A.

In: G3: Genes, Genomes, Genetics, Vol. 2, No. 3, 03.2012, p. 321-329.

Research output: Contribution to journalArticle

Ha, Jungmin ; Abernathy, Brian ; Nelson, William ; Grant, David ; Wu, Xiaolei ; Nguyen, Henry T. ; Stacey, Gary ; Yu, Yeisoo ; Wing, Rod A ; Shoemaker, Randy C. ; Jackson, Scott A. / Integration of the draft sequence and physical map as a framework for genomic research in soybean (glycine max (l.) merr.) and wild soybean (glycine soja sieb. and zucc.). In: G3: Genes, Genomes, Genetics. 2012 ; Vol. 2, No. 3. pp. 321-329.
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