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Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

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Published on: January 22, 2018

Development and characterization of non-coding RNA-derived simple sequence repeat markers in coconut (Cocos nucifera

A A Sabana¹, Ginny Antony², M K Rajesh³

¹Central University of Kerala, Kasaragod, 671320, Kerala, India.

Functional & Integrative Genomics

|November 1, 2022

Summary

Researchers developed novel non-coding RNA (ncRNA)-based SSR markers for coconut molecular breeding. These markers effectively identified genetic diversity among tall and dwarf coconut accessions, aiding genetic improvement efforts.

Keywords:

Coconut Genetic diversity Non-coding RNA Polymorphic SSRs lncRNA miRNA

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Published on: July 29, 2019

Area of Science:

Genetics
Molecular Biology
Plant Breeding

Background:

Non-coding RNAs (ncRNAs) are crucial regulators of gene expression.
SSR markers are valuable tools in molecular breeding.
ncRNA-derived SSR markers offer a novel approach for genetic analysis.

Purpose of the Study:

To identify and characterize ncRNA-derived SSR markers in coconut for the first time.
To evaluate the polymorphic potential of these markers in diverse coconut accessions.
To assess the utility of ncRNA-SSR markers for genetic diversity analysis and improvement in coconut.

Main Methods:

Identification of 597 ncRNA-derived SSR markers (509 lncRNA-SSRs, 88 miRNA-SSRs).
Screening of 20 selected primers on 6 coconut accessions, with 10 showing polymorphism.
Genotyping of 96 palms from 16 accessions using 10 polymorphic ncRNA-SSR primers.

Main Results:

High polymorphism levels observed, with 2–9 alleles per marker (average 4.6).
Average heterozygosity of 0.5 and Shannon index of 1.1 indicate significant genetic variation.
Cluster analysis successfully differentiated tall and dwarf coconut accessions, grouping them into distinct clusters.

Conclusions:

ncRNA-based SSR markers are highly polymorphic and effective for assessing genetic diversity in coconut.
These markers demonstrate significant potential for molecular breeding and genetic improvement programs in coconut.
This study establishes a foundation for utilizing ncRNA-SSR markers in coconut genetic research.