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Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes

Angioi, Simonetta Agostina and Desiderio, Francesca and Rau, Domenico and Bitocchi, Elena and Attene, Giovanna and Rapa, Roberto (2009) Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes. Plant Biology, Vol. 11 , p. 598-612. eISSN 1438-8677. Article.

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DOI: 10.1111/j.1438-8677.2008.00143.x

Abstract

Chloroplast microsatellites (cpSSRs) provide a powerful tool to study the genetic variation and evolution of plants. We have investigated the usefulness of 39 primer pairs tagging cpSSR loci on a set of eight different genera of Leguminosae (Papilionoideae subfamily) and five species belonging to the genus Phaseolus. Thirty-six 'universal' primer pairs were retrieved from the literature, one was re-designed and a further two were designed de novo. The cpSSR loci analysed were highly polymorphic across the individuals examined. Twenty-seven primer pairs were polymorphic in the overall sample, 18 within Phaseolus, and 16 in both P. vulgaris and P. coccineus. Analysis of the plastome sequences of four Leguminosae species (obtained from GenBank) showed that in the loci targeted by universal primer pairs: (i) the originally tagged cpSSRs can be lost; (ii) other cpSSRs can be present; and (iii) polymorphism arises not only from differences in the numbers of cpSSR repeats, but often from other insertion/deletion events. Multilocus linkage disequilibrium analysis suggests that homoplasy is not a major problem in our dataset, and principal component analysis indicates intelligible relationships among the species considered. Our study demonstrates that this set of chloroplast markers provides a useful tool to study the diversity and the evolution of several legumes, and particularly P. vulgaris and P. coccineus.

Item Type:Article
ID Code:1757
Status:Published
Refereed:Yes
Uncontrolled Keywords:Domestication, genetic diversity, Leguminosae, molecular markers, Phaseolus
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/07 Genetica agraria
Divisions:001 Università di Sassari > 01 Dipartimenti > Scienze agronomiche e genetica vegetale agraria
Publisher:Blackwell / Wiley
eISSN:1438-8677
Copyright Holders:© 2008 German Botanical Society and The Royal Botanical Society of the Netherlands
Additional Information:Pubblicato online il 22 dicembre 2008.
Deposited On:18 Aug 2009 10:06

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