Cross-amplification and Characterization of Polymorphic Microsatellite Markers From Acacia (Senegalia) mellifera and Acacia brevispica to Acacia senegal (L.) Willd.

Abstract

The NERC and CEH trade marks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner.Cross-amplification and characterization of polymorphic microsatellite markers from Acacia (Senegalia) mellifera and Acacia brevispica to Acacia senegal (L.) Willd. to 0.800 (Ame03). Cross amplification of these loci represents a potential source of codominant marker and will be useful in the study of genetic diversity, structure, gene flow and breeding systems of this important Acacia species. IntroductionAcacia senegal (L) Willd. is a multipurpose agro-forestry tree, native to the arid and semi-arid lands of Sub-Saharan Africa but found as far as the Indian sub-continent. It grows to a height of 5-12 m, with a trunk up to 30 cm in diameter (Fagg & Allison 2004) and is valued for gum arabic production, as well as secondary agricultural roles, such as restoring soil fertility and providing fuel and fodder (Ballal et al. 2005). It is also essential in sand dune fixation and is preferred in bush-fallow rotation and intercropping Despite its ecological and economic importance, little progress has been made in developing sets of molecular markers for genetic studies.Microsatellites are among the best classes of markers for studying genetic processes in natural populations because they are abundant, co-dominant, interspersed throughout the genome, possess high resolution power and polymorphism (Chase et al. 1996). Their development, however, requires a significant investment (Fernandez et al. 2000); therefore, when markers have been developed in taxonomically related species, it is worthwhile testing for cross-amplification. In this brief preliminary study thirty-four microsatellite primers developed from A. mellifera and A. brevispica were tested for cross-amplification in A. senegal. Materials and Methods Microsatellite loci screeningGenomic DNA was isolated from leaves following a modified CTAB procedure . These loci were then tested for polymorphism and reproducibility. Polymorphism testingThe final set of loci was screened for polymorphism using a set of 30 DNA samples (3 samples per population from 10 populations). PCR was carried out as described above and products separated on 0.25 mm denaturing polyacrylamide gels containing 10%Ammonium Persulfate (APS), tetramethylethylenediamine (TEMED)-Omnipur and 8 % acrylamide (Gene-PAGE plus)-Amresco and electrophoresed using 1 X TBE buffer on a Li-Cor IR 2 4200 DNA sequencer. Band sizes were determined by referencing standard IRD800, 50-350 bp and 50-700 bp ladder (Khasa et al. 2005). Loci that were polymorphic and informative were then selected as a set of A. senegal markers for further studies. ResultsOut of the 34 loci screened, 11 were selected for polymorphism screening with a larger number of DNA samples while others failed to amplify or showed poor amplification (Table S1). During the screening, 7 loci (Table 1) showed positive amplification and unambiguous pattern...

Genetic consequences of anthropogenic disturbances and population fragmentation in Acacia senegal

“…DNA quantification was performed through Bio-photometer readings and comparison with low DNA mass ladder (Invitrogen) in 1 % agarose gel. Polymerase chain reaction (PCR) amplifications of 12 polymorphic microsatellite loci (Assoumane et al 2009;Omondi et al 2010a) for all the individuals and populations were performed following the procedure described by Hanaoka et al (2012). Capillary fragment electrophoresis of PCR products were scored against an internal standard (600 Liz size standards) on an ABI 3500 genetic analyser, and genotype data scored using GeneMapper 5.0 software (Applied Biosystems, CA, USA).…”