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Cross-taxon transferability of sugarcane expressed sequence tags derived microsatellite (EST-SSR) markers across the related cereal grasses

  • Ram Baran SinghEmail author
  • Balwant Singh
  • Ram Kushal Singh
Original Article
  • 6 Downloads

Abstract

Sugarcane is a crop of economic importance providing sugar and bioenergy resource which has a substantial contribution to the national GDP of India as well as other countries. Genomes of the several grasses have co-evolved which share large-scale synteny and genome collinearity; hence it is possible to employ EST-SSR markers of one grass species for genetic study of other related species. A set of sixty potentially informative EST-derived microsatellite (SSR) markers were employed to examine their cross-taxa transferability across the limit of taxonomic boundaries of different grass genomes. The high (96.6%) rate of SSRs cross-transferability observed in genus Saccharum followed by Erianthus (93.3%), Narenga (88.3%), Sclerostachya (86.3%), and Miscanthus (83.3%). Relatively lower rates of cross amplification were observed in other cereal crops including Sorghum bicolor, Pennisetum glaucum, Zea mays, Triticum aestivum, Oryza sativa, and Avena sativa. Cross-transferable EST-SSR markers were utilized to evaluate phylogenetic relationships among genus Saccharum, closely related genera of Saccharum complex, and other allied cereal grasses. The polymorphic information content values ranged from 0.35 to 0.95, with an average of 0.71. Such a high rates of cross-taxa transferability of the EST-SSRs make them a potent tool for genetic studies and comparative genomics across wide evolutionary distances within and across genera along with technologically simplicity and cost effectiveness. EST-SSRs will facilitate to devise potent tools for genetic improvement through advance molecular breeding of such crops for high grain productivity and better quality. They will especially be useful for the orphan grass species, which contribute a major part of the global food security.

Keywords

Expressed sequence tags (ESTs) Saccharum complex Saccharum species Saccharum related genera Genetic diversity Cross-taxa transferability 

Abbreviations

EST-SSRs

Expressed sequence tags derived simple sequence repeats

FAOSTAT

Food and Agriculture Organization of the United Nations-Statistics Division

5′ UTR

Five prime untranslated regions

3′ UTR

Three prime untranslated regions

hnRNA

Heterogeneous nuclear RNA

MISA

MIcroSAtellite Identification Tool

Notes

Acknowledgements

Authors are thankful to Director, Sugarcane Research Institute, Shahjahanpur, India for conferring necessary accessories to perform this study.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest directly or indirectly and informed consent to publish this study.

Supplementary material

13562_2019_502_MOESM1_ESM.docx (26 kb)
Supplementary material 1 (DOCX 25 kb)

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.I.K. Gujral Punjab Technical UniversityJalandharIndia
  2. 2.Swami Satyanand College of Management and TechnologyAmritsarIndia
  3. 3.Sugarcane Research InstituteUttar Pradesh Council of Sugarcane ResearchShahjahanpurIndia

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