A STRATEGY FOR DEVELOPMENT OF MICROSATELLITE MARKERS FOR LESS STUDIED ORGANISMS BASED ON EST-SSRS OF WELL STUDIED ORGANISMS WITHIN SAME FAMILY: CASE STUDY ON (PROSOPIS JULIFLORA L.) LEGUME PLANT

ADNAN A.S. AL-ASBAHI¹*, FATIMA AHMED ALHADI^2
1Department of Biology (Biotechnology and Molecular Genetics), Faculty of Sciences, Sana’a University, P. O. Box 14686, Sana’a, Republic of Yemen
²Department of Biology (Plant Physiology-Ecology), Faculty of Sciences, Sana’a University, Sana’a, Republic of Yemen
* Corresponding Author : adnanasbahi@yahoo.com

Received : 20-11-2010     Accepted : 14-12-2010     Published : 04-04-2011
Volume : 2     Issue : 1       Pages : 11 - 20
J Crop Sci 2.1 (2011):11-20
DOI : http://dx.doi.org/10.9735/0976-8920.2.1.11-20

Keywords : Prosopis juliflora, Expressed Sequence Tag (EST), Simple Sequence Repeat (SSR), CAP3 software, Unigenes
Conflict of Interest : None declared

It is widely known that publicly available expressed sequence tags (ESTs) markers for a certain organism, are used for development of simple sequence repeats (SSRs) for that organism. SSRs have been used in a wide range of applications in genetic studies. However, many plants, animals and microbe species have only limited number of (ESTs) markers available in the databases such as, mesquite desert plant species (Prosopis juliflora). Available small amount of ESTs for Prosopis juliflora can be compared with those of well-studied legume species in both less and well-studied species for further analysis and usage as traditional SSR markers for genomic comparative studies with minimal amount of money and time required for genotyping accompanied with high level of transferability and polymorphism than what expected by using anonymous SSR or ESTs derived SSR randomly selected from closely related species or genera. Prosopis juliflora ESTs downloaded from Genbank were clustered into different unigenes, each of which represents ESTs of same and relevant function. Then, they were analyzed for the presence of various SSR classes in these EST unigenes knowm as (EST-SSRs) unigenes in order to assess sequence, length, repetitious folds, distribution and relative abundance of different SSR motifs of mono, di-, tri-, tetra-, and penta-nucleotide contained in these ESTs. Comparative analysis of (EST-SSRs) in Prosopis juliflora with those of well-studied legumes, such as Medicago truncatula, Glycine max and Lotus japonicus resulted in identification the SSR repeat motif categories existing in high frequency rates within those legume species. These SSR regarded as promising SSRs markers used as cross genera were tested in P. juliflora based on primer pairs of anonymous SSR of the well-studied species, Medicago, through PCR that have shown transferability of these markers into P. juliflora as cross-genera SSR markers. The developed anonymous SSR markers of loci across family would offer an opportunity in cheap and fast genotyping of less studied organisms such as Prosopis legume species that suffers from poor genome resources.

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