Genetic improvement in coconut relies on exploiting the vast existing diversity among coconut accessions. Robust molecular markers are a pre-requisite for efficient characterization of genetic diversity. Microsatellites or simple sequence repeats (SSRs), mined from expressed sequence tags (ESTs), constitute an important resource for analysis of genetic diversity as they are abundant, polymorphic and represent function regions of the genome. We have identified a total of 318,528 putative EST-SSRs from 130,942 unigenes utilizing a leaf transcriptome dataset of coconut. Among the EST-SSRs, dinucleotide repeats were abundant (219,912; 69.04%) followed by trinucleotide (70,722; 22.2%) and tetra-nucleotide repeats (6281; 1.9%). Among the dinucleotide repeat motifs, the dominant repeat was AG/CT (35.87%), followed by AT/AT (18.59%), while the dominant trinucleotide repeat was AAG/CTT (4.59%). One hundred and twenty EST-SSR primer pairs were designed and utilized to amplify six DNA samples of coconut accessions. Fifty primers (41.7%) produced reproducible polymorphic fragments of expected sizes, from which a total of 10 primers were selected for the diversity assessment in 186 palms of 50 coconut accessions, comprising of 25 each of tall and dwarf accessions. A total of 137 alleles were detected with an average of 13.7 alleles per SSR locus. The number of alleles observed at each locus in the data set ranged from 7 to 22. All the loci showed 100% polymorphism with respect to the samples screened. The average observed heterozygosity was 0.46. The PIC values ranged from 0.79 (CnKGDEST129 and CnKGDEST100) to 0.91 (CnKGDEST117 and CnKGDEST122) with a mean value of 0.85, indicating the capacity of the EST-SSR markers to detect high levels of polymorphism. The cluster analysis revealed that accessions were generally clustered based on their relative similarity and irrespective of their geographic origins. The present study demonstrates the usefulness of transcriptome sequencing as a rapid and cost-effective methodology for the development of molecular markers. The EST-SSR markers generated through this study constitute useful and reliable tools for assessment of genetic diversity and marker-assisted selection in coconut.

椰子的遗传改良依赖于利用椰子种之间广泛的现有多样性。强大的分子标记是有效表征遗传多样性的先决条件。从表达的序列标签（EST）中提取的微卫星或简单序列重复序列（SSR），构成了分析遗传多样性的重要资源，因为它们丰富，多态且代表了基因组的功能区域。我们已经利用椰子的叶片转录组数据集从130,942个单基因中鉴定出总共318,528个EST-SSR。在EST-SSR中，二核苷酸重复序列丰富（219,912; 69.04％），其次是三核苷酸重复序列（70,722; 22.2％）和四核苷酸重复序列（6281; 1.9％）。在二核苷酸重复序列基序中，主要重复序列是AG / CT（35.87％），其次是AT / AT（18.59％），而主要的三核苷酸重复序列是AAG / CTT（4.59％）。设计了一百二十个EST-SSR引物对，并用于扩增六个椰子种质的DNA样品。五十个引物（41.7％）产生了预期大小的可再现多态性片段，从中选择了10个引物，用于186个棕榈树（50个椰子种）中的多样性，其中每个种高低矮种都包括25个。总共检测到137个等位基因，每个SSR基因座平均13.7个等位基因。在数据集中每个基因座处观察到的等位基因数目范围为7至22。相对于筛选的样品，所有基因座均显示100％多态性。观察到的平均杂合度为0.46。PIC值范围为0.79（CnKGDEST129和CnKGDEST100）到0.91（CnKGDEST117和CnKGDEST122），平均值为0.85，表明EST-SSR标记检测高水平多态性的能力。聚类分析表明，种质通常基于它们的相对相似性而被聚类，而与它们的地理起源无关。本研究证明了转录组测序作为开发分子标记物的快速且经济有效的方法的有用性。通过这项研究产生的EST-SSR标记构成了评估椰子遗传多样性和标记辅助选择的有用和可靠的工具。本研究证明了转录组测序作为开发分子标记物的快速且经济有效的方法的有用性。通过这项研究产生的EST-SSR标记构成了评估椰子遗传多样性和标记辅助选择的有用和可靠的工具。本研究证明了转录组测序作为开发分子标记物的快速且经济有效的方法的有用性。通过这项研究产生的EST-SSR标记构成了评估椰子遗传多样性和标记辅助选择的有用和可靠的工具。