Dendrocalamus hamiltonii is a giant bamboo species native to Indian subcontinent with high economic importance. Nevertheless, highly outcross nature and flowering once in decades impose severe limitation in its propagation. Identification and mixed cultivation of genetically diverse genotypes may assist successful breeding and natural recombination of desirable traits. Characterization of existing genetic diversity and population structure are indispensable for efficient implementation of such strategies, which is facing a major challenge due to non-availability of sequence-based markers for the species. In this study, 8121 EST-SSR markers were mined from D. hamiltonii transcriptome data. Among all, tri-repeats were most represented (52%), with the abundance of CCG/CGG repeat motif. A set of 114 polymorphic markers encompassing epigenetic regulators, transcription factors, cell cycle regulators, signaling, and cell wall biogenesis, detected polymorphism and interaction (in silico) with important genes, that might have role in bamboo growth and development. Genetic diversity and population structure of the three D. hamiltonii populations (72 individuals) revealed moderate to high-level genetic diversity (mean alleles per locus: 5.8; mean PIC: 0.44) using neutral EST-SSR markers. AMOVA analysis suggests maximum diversity (59%) exists within population. High genetic differentiation (G_st = 0.338) and low gene flow (N_m = 0.49) were evident among populations. Further, PCoA, dendrogram, and Bayesian STRUCTURE analysis clustered three populations into two major groups based on geographical separations. In future, SSR marker resources created can be used for systematic breeding and implementation of conservation plans for sustainable utilization of bamboo complex.

中文翻译：

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发现和利用EST-SSR标记资源进行亚热带竹Dendrocalamus hamiltonii的遗传多样性和种群结构分析。

Dendrocalamus hamiltonii是印度次大陆特有的巨大竹种，具有重要的经济意义。然而，高度异质的自然和数十年来开花的植物在其繁殖上受到严重限制。遗传多样性基因型的鉴定和混合培养可以帮助成功繁殖和自然重组所需性状。现有遗传多样性和种群结构的表征对于有效实施此类战略是必不可少的，由于无法获得基于序列的标记物，该战略面临着重大挑战。在这项研究中，从D. hamiltonii转录组数据中提取了8121个EST-SSR标记。其中，三重复最多（52％），并带有丰富的CCG / CGG重复基序。一组114个多态性标记，包括表观遗传调控因子，转录因子，细胞周期调控因子，信号传导和细胞壁生物发生，检测到多态性以及与重要基因的相互作用（计算机模拟），这些基因可能与竹子的生长发育有关。使用中性EST-SSR标记，三个D. hamiltonii种群（72个个体）的遗传多样性和种群结构显示了中度至高级的遗传多样性（每个基因座平均等位基因：5.8；平均PIC：0.44）。AMOVA分析表明，人群中存在最大多样性（59％）。高遗传分化（G _st  = 0.338）和低基因流（N _m = 0.49）在人群中很明显。此外，PCoA，树状图和贝叶斯结构分析根据地理分隔将三个人口分为两个主要群体。将来，创建的SSR标记资源可用于系统育种和实施保护计划，以实现竹群的可持续利用。