At present, the available SSR markers of elm (Ulmus) have been seriously deficient, which can not meet the needs of molecular marker-assisted breeding and evaluation of germplasm resources. In this study, transcriptome data of Ulmus pumila were used as materials to develop EST-SSR markers of elms. EST-SSR markers were also classified according to gene function for the first time. In this study, 8288 perfect and 569 compound SSR loci were detected from 17,624 EST sequences (36,609,384 bp). Most of the perfect SSR sequences were based on short sequence lengths of 10–22 bp. The most common SSR repeat units were A/T (3330, 40.18%), AG/CT (1211, 14.61%), and AAG/CTT (568, 6.85%). All EST-SSR loci were function classified based on the Cluster of Orthologous Groups (COG) database. There were substantial differences in the type and proportion of SSR repeat units among the functional classes. Most EST-SSR loci were located in gene-coding regions. Ninety pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-nine primers were verified with clear bands. The number of alleles per locus (Na) ranged from 2 to 6; the number of effective alleles (Ne) ranged from 1.061 to 3.261; the observational heterozygosity (Ho) and expected heterozygosity (He) ranged from 0 to 0.968 and 0.112 to 0.651, respectively. The clustering pattern is consistent with traditional taxonomy that provides a molecular basis for the classification of elm. There were differences in the effective amplification and percentage of polymorphic loci among different functional SSR loci. The analysis of 880 primer combinations showed that markers within a single COG group were less effective than across groups. This study clarified the importance of SSR primer selection for clustering results. This study developed a large number of SSR markers in elm, providing effective markers for molecular marker-assisted breeding, genetic mapping, and other related research.

目前，榆树可用SSR标记（榆）一直严重不足，不能满足分子的需要标记辅助育种和种质资源的评价。在这项研究中，Ulmus pumila的转录组数据用作开发榆树EST-SSR标记的材料。EST-SSR标记也首次根据基因功能进行分类。在这项研究中，从17,624个EST序列（36,609,384 bp）中检测到8288个Perfect和569个复合SSR基因座。大多数完美的SSR序列都是基于10-22 bp的短序列长度。最常见的SSR重复单元是A / T（3330，40.18％），AG / CT（1211，14.61％）和AAG / CTT（568，6.85％）。所有EST-SSR基因座均基于直系同源群（COG）数据库进行功能分类。在功能类别之间，SSR重复单元的类型和比例存在实质性差异。大多数EST-SSR基因座位于基因编码区。随机选择90对，并使用聚合酶链反应扩增进行测试验证。用清晰的条带验证了49个引物。每个基因座的等位基因数量（Na）为2至6；有效等位基因（Ne）的数量为1.061至3.261；观察杂合度（Ho）和预期杂合度（He）的范围分别从0到0.968和0.112到0.651。聚类模式与传统分类法一致，后者为榆树的分类提供了分子基础。不同功能的SSR基因座的有效扩增和多态性基因座的百分比存在差异。对880种引物组合的分析表明，单个COG组内的标记物不如跨组有效。这项研究阐明了SSR引物选择对聚类结果的重要性。这项研究在榆树中开发了大量SSR标记，为分子标记辅助育种，遗传作图和其他相关研究提供了有效的标记。