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United States Department of Agriculture

Agricultural Research Service

Research Project: CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES

Location: Corn Insects and Crop Genetics Research

Title: The model legume genomes

Author
item Cannon, Steven

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: October 3, 2012
Publication Date: September 30, 2013
Citation: Cannon, S.B. 2013. The model legume genomes. In: Rose, R.J., editor. Legume Genomics: Methods and Protocols. Heidelberg, NY: Springer. p. 1-14.

Interpretive Summary: The legume plant family contains many species that are important as crops or for animal agriculture. Plants in this family are also crucial members of most ecosystems, as they are able to partner with soil bacteria to "fix" atmospheric nitrogen into a form that is directly useable by the plants as an abundant fertilizer source. This book chapter reviews the status of major research resources for this plant family. As of the time of writing, the genomes (complete collections of chromosomal DNA for an organism) have been sequenced for six legume species: soybean, common bean, chickpea, pigeonpea, and two "model legumes" used for research: Medicago truncatula and Lotus japonicus. Genome sequencing has revealed that all of these plant genomes have significant amounts of gene duplication, which presents a challenge for researchers. This review describes characteristics of and differences between these genomes, as well as on-line resources that can be used to study legumes, including SoyBase and the Legume Information System.

Technical Abstract: The primary model legumes to-date have been Medicago truncatula and Lotus japonicus. Both species are tractable both genetically and in the greenhouse, and for both, a substantial sets of tools and resources for molecular genetic research have been assembled. As sequencing costs have declined, however, additional legume genomes have been sequenced, and the funding available to crops such as soybean has enabled these to be developed to the status of genetic models in their own right. This chapter, therefore, describes a broader set of model species in the legumes, and discusses similarities and differences between the genomes sequenced to date, as well as computational resources available for various legume species. Genome structural characteristics in, for example, Medicago truncatula and Glycine max, can have large impacts on the kinds of functional genomic research that may be carried out in these species. Both of these genomes have substantial redundancy for many gene families, but the nature of the redundancy is different in the two genomes – with the redundancy typically being in the form of local gene duplications in Medicago, and in whole-genome-duplication-derived duplications in Glycine. Similar considerations (about gene environments and genome structure) will likely need to be taken into account for any model or crop species.

Last Modified: 10/1/2014
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