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

Publisher: Springer Country of Publication: Germany NLM ID: 100939343 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1438-7948 (Electronic) Linking ISSN: 1438793X NLM ISO Abbreviation: Funct Integr Genomics Subsets: MEDLINE

Original Publication: Berlin : Springer, c2000-

Cocos*/genetics ; Genetic Variation*; Microsatellite Repeats ; Polymorphism, Genetic ; RNA, Untranslated/genetics

Non-coding RNA (ncRNA)-based SSR markers are highly useful in molecular breeding as ncRNAs play a significant role in gene regulation. In the present study, for the first time in coconut, we have identified 597 ncRNA-derived SSR markers, including 509 long non-coding RNASSRs (lncRNASSRs) and 88 micro RNASSRs (miRNASSRs). Of these, 20 primers (10 each from lncRNA-SSR and miRNA-SSR) were selected, screened on 6 coconut accessions, and 50% produced polymorphic fragments. These 10 polymorphic primers were used for genotyping 96 palms of 16 coconut accessions, comprising eight tall and dwarf accessions each. The number of alleles ranged from 2 to 9 per SSR marker, with an average of 4.6 alleles per locus. The average heterozygosity and Shannon index were 0.5 and 1.1, respectively, suggesting that ncRNA-SSRs show high polymorphism level. Distance-based cluster analyses revealed that all the tall and dwarf accessions were differentiated and grouped in different clusters. The study demonstrates the usefulness of ncRNA-based SSR markers for assessing genetic diversity and genetic improvement in coconut.
(© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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internal fund Central University of Kerala; Project No. 1000761030 ICAR-CPCRI

Keywords: Coconut; Genetic diversity; Non-coding RNA; Polymorphic SSRs; lncRNA; miRNA

0 (RNA, Untranslated)

Date Created: 20221101 Date Completed: 20221129 Latest Revision: 20221129

20240105

10.1007/s10142-022-00911-2

36318348