Development of potential dbEST-derived microsatellite markers for genetic evaluation of sugarcane and related cereal grasses

Autor: Ram Kushal Singh, Balwant Singh, Ram Baran Singh
Rok vydání: 2019
Předmět:
Zdroj: Industrial Crops and Products. 128:38-47
ISSN: 0926-6690
Popis: Sugarcane expressed sequence tags (ESTs) database (db) offers a great opportunity for developing functional molecular markers associated with the desirable agronomic traits. The aim of the present study was to develop informative simple sequence repeat (SSR) markers in sugarcane using sugarcane expressed sequence tags (ESTs), characterization with respect to their abundance, distribution, variability, and to test their competence in genetic diversity. A total of 361 EST-SSR markers were developed and screened for their ability to detect polymorphism across the wide range of sugarcane germplasm. Among the developed SSRs, TNRs containing motifs were predominant with a frequency of 55%, which followed by TtNRs (22%), PNRs (11%), DNRs (7%), and HNRs (5%). Gene Ontology and homology search was conducted to establish the relevancy of SSRs in functional genomics. Resulting, ∼39% SSRs were found to be functional and confirmed homology with different proteins and transcription factors involved in gene expression. A set of 96 polymorphic primer pairs was used to evaluate genetic diversity among Saccharum species, related genera and cross amplification in other cereal grasses. A total of 710 alleles were generated which ranged from 2 to 15 with an average of 7.40 alleles per locus and showed 100% polymorphism. Polymorphism information content (PIC) value was ranged from 0.35 to 0.91 with an average of 0.71. Majority of the markers developed in current study were related to sucrose metabolism, stress physiology, plant immune responses, signal transduction, biosynthesis of secondary metabolites, ATP generation, growth and other biochemical process. The high degree of polymorphism, cross-species amplification and genetic diversity assessed with these SSR markers suggested their utility for genome mapping, QTL analysis, comparative genomics, gene-based association studies, and marker-assisted selection in sugarcane. Moreover, these informative EST-SSRs described here would enrich existing repertoire of genetic resources for sugarcane and also other related taxa constitute the important secondary genepool for sugarcane genetic improvement.
Databáze: OpenAIRE
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