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Protocols in ecological and environmental plant physiology

 

Article << Previous     |     Next >>   Contents Vol 40(7)

Revisiting an important component of plant genomes: microsatellites

Caihua Gao A , Xiaodong Ren A , Annaliese S. Mason B , Jiana Li A , Wei Wang A , Meili Xiao A and Donghui Fu C D

A Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
B Centre for Integrative Legume Research and School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Qld, Australia.
C Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
D Corresponding author. Email: fudhui@163.com

Functional Plant Biology 40(7) 645-661 http://dx.doi.org/10.1071/FP12325
Submitted: 31 October 2012  Accepted: 16 January 2013   Published: 11 February 2013


 
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Abstract

Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.

Additional keywords: evolution, microsatellite distribution, microsatellite function, microsatellite variation.


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