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.

基于非编码 RNA (ncRNA) 的 SSR 标记在分子育种中非常有用，因为 ncRNA 在基因调控中起着重要作用。在本研究中，我们首次在椰子中鉴定出 597 个 ncRNA 衍生的 SSR 标记，包括 509 个长链非编码 RNASSR (lncRNASSR) 和 88 个微 RNASSR (miRNASSR)。其中，选择了 20 个引物（lncRNA-SSR 和 miRNA-SSR 各 10 个），在 6 个椰子种质上进行筛选，50% 产生了多态性片段。这 10 个多态性引物用于对 16 个椰子种质的 96 个棕榈树进行基因分型，每个种质包含 8 个高和矮的种质。每个 SSR 标记的等位基因数量从 2 到 9 个不等，每个位点平均有 4.6 个等位基因。平均杂合度和Shannon指数分别为0.5和1.1，表明ncRNA-SSRs具有较高的多态性水平。基于距离的聚类分析表明，所有高大和矮小的种质都被区分并分组在不同的聚类中。该研究证明了基于 ncRNA 的 SSR 标记可用于评估椰子的遗传多样性和遗传改良。