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.)

G3: Genes, Genomes, Genetics

David Grant⁵  William Nelson¹  Scott A. Jackson⁴  Gary Stacey²  Jungmin Ha³  Henry T. Nguyen²  Brian Abernathy⁴  Randy C. Shoemaker⁵  Yeisoo Yu¹  Xiaolei Wu²  Rod A. Wing¹ 

[1] BIO5 Institute, University of Arizona, Tucson, Arizona 85721BIO5 Institute, University of Arizona, Tucson, Arizona 85721BIO5 Institute, University of Arizona, Tucson, Arizona 85721;National Center for Soybean Biotechnology, Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211National Center for Soybean Biotechnology, Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211National Center for Soybean Biotechnology, Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211;Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana 47907Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana 47907Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana 47907;Institute of Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602Institute of Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602Institute of Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602;United States Department of Agriculture–Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011United States Department of Agriculture–Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011United States Department of Agriculture–Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011

关键词: FingerPrinted Contig;    whole-genome sequencing;    genome structure;    genome evolution;   

DOI  :  10.1534/g3.111.001834

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

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 547 Mbp 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.

【 授权许可】

Unknown