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

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.