Simple sequence repeat (SSR) markers play an important role in genetic and molecular breeding programs, especially for non‐model species. We identified SSRs from expressed sequence tags (EST‐SSRs) and whole genome sequences (gSSRs), by analysing the transcriptome and genome of the Mongolian sea buckthorn (Hippophae rhamnoides subsp. mongolica) cultivar ‘Sunny’. Using the same number of loci, EST‐SSRs showed higher transferability to Hippophae than gSSRs, and phylogenetic trees based on EST‐SSRs demonstrated higher resolution for classifying Hippophae species and subspecies into clades, possibly due to high conservatism and/or existence of adaptive divergence between species/subspecies in coding sequence regions. In contrast, parentage analyses showed that gSSRs were more effective at resolving parentage than EST‐SSRs due to higher level of polymorphism in gSSRs. The markers developed in this study can be used in the identification and pedigree reconstruction of species/subspecies of sea buckthorn, while their usage in clarifying phylogenetic relationship among species remains to be discussed. The comparison between EST‐SSRs and gSSRs would provide insight into the trade‐off between differentiation and polymorphism in marker selection for breeding programs.

中文翻译：

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系统发育和谱系重建的基因组SSR和EST-SSR标记—沙棘的比较

简单序列重复（SSR）标记在遗传和分子育种计划中，特别是对非模型物种，起着重要作用。我们确定了SSR标记从表达序列标签（EST-SSRS）和全基因组序列（gSSRs），通过分析蒙古沙棘的转录和基因组（沙棘亚种木）品种“阳光”。使用相同数量的基因座，EST-SSRs向沙棘的转移能力比gSSRs高，并且基于EST-SSRs的系统树证明了对沙棘进行分类的分辨率更高物种和亚种进入进化枝，可能是由于高度保守和/或在编码序列区域中物种/亚种之间存在适应性差异。相反，亲子关系分析显示，由于gSSRs中的多态性较高，因此gSSR比EST-SSRs更有效地解决了亲子关系。在这项研究中开发的标记可用于沙棘的物种/亚种的鉴定和系谱重建，而它们在阐明物种之间的系统发生关系方面的用途仍有待讨论。EST-SSR和gSSR之间的比较将提供有关育种程序标记选择中分化与多态性之间权衡的见解。