Abstract
The accessibility to public sequence information has paved the way for development of new genomic resources and its cross transferability among closely related genera. In the present study, the nucleotide and EST sequences derived from nine different species of Eleusine were utilized for identifying microsatellite markers and their transferability in E. coracana. The frequency and distribution of repeat motifs of Di, tri, tetra and penta-nucleotide repeats were compared across species. The nucleotide/EST sequences, classified based on their function, were majorly involved in abiotic stress followed by carbohydrate biosynthesis in all the species. Of 2133 primers designed, tri-nucleotide repeats were more abundant (1043) followed by repeats in compound format (963). A highest number of 1660 primer pairs were identified in E. coracana subsp. coracana and nearly 50% of which contained compound repeats, majorly comprising of di-nucleotides. The frequency of microsatellite repeats and the number of primers designed per sequence were maximum in E. kigeziensis (138%) followed by E. floccifolia (126%) while the same was minimum in E. coracana subsp. africana (53%). While the transferability of microsatellites derived from other Eleusine species to cultivated coracana species ranged from 50 to 100%, the primers derived from cultivated species were more informative than from that of wild relatives.
Highlights
With the availability of limited genomic resources in a species, utilization of information from closely related species and wild relatives plays pivotal role in the development of genomic resources and its application
The expressed sequence tag (EST) from coracana sub species were functionally related to abiotic stress including drought / salt stress tolerance followed by developing seed cDNAs
Whereas in case of africana sub species and other Eleusine species, majority of the ESTs were related to carbohydrate biosynthesis including both photosynthesis and starch biosynthesis followed by internal transcribed spacer (ITS) regions of ribosomal RNAs (Figure 1)
Summary
With the availability of limited genomic resources in a species, utilization of information from closely related species and wild relatives plays pivotal role in the development of genomic resources and its application. Studies have shown that certain chromosome segments are conserved among related taxa allowing development of common markers. In spite of new advancements in DNA markers like SNPs, microsatellite markers called as simple sequence repeats (SSRs) are still the markers of choice for various molecular genetic studies including genome mapping, DNA fingerprinting, genetic diversity, population structure and phylogeny studies. This preference is due to the advantages
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