BackgroundIdentification of high resolving DNA-based markers is of paramount importance to unlock the potential of genetic diversity and selection of unique accessions of Capsicum annuum L., within Cross River and Ebonyi States of Nigeria, for breeding and conservation. Therefore, we comparatively explored the effectiveness of start codon targeted (SCoT) and directed amplified minisatellite DNA (DAMD) markers for diversity analysis of the accessions. Fifteen accessions were collected for DNA extraction and amplifications with the markers.ResultsDendrograms from SCoT and DAMD categorized the accessions into five and three genetic groups, respectively, while the principal component analysis identified five genetic clusters, each from the markers. The average values of allele, gene diversity and polymorphic information content detected with SCoT and DAMD demonstrate that the two markers were effective and efficient, especially, SCoT in genetic diversity study of the accessions of pepper. Number of polymorphic loci (NPL) and percentage polymorphic loci (PPL) from SCoT (NPL = 64, PPL = 80.00–95.73%) and DAMD (NPL = 56, PPL = 53.33–86.67%) were high, but higher in SCoT markers. Other effective genetic parameters (effective number of alleles, Nei’s genetic diversity and Shannon’s information indices) identified with the two marker systems elucidated the allelic richness, rich genetic diversity within the populations and informative nature of the markers, especially SCoT. The intraspecific genetic diversity, interspecific genetic diversity, and coefficient of differentiation obtained with SCoT and DAMD further exposed the genetic structure with more genetic divergence within than among the populations of the accessions. Estimate of gene flow from the SCoT markers was 3.8375 and 0.6.2042 for the DAMD markers. The estimate of gene flow values from the markers indicated extensiveness with SCoT (Nm = 3.8375) and extremely extensive with DAMD (Nm = 6.2042) among the populations.ConclusionThis study shows that SCoT markers may be more useful and informative than DAMD in measuring genetic diversity and differentiation of the accessions of the genus Capsicum. Genetic parameters obtained with SCoT showed that the accessions from Cross River were more genetically diverse than the ones from Ebonyi State. Therefore, SCoT may be a preferred marker in evaluating genetic diversity for improvement and conservation of this spicy crop, C. capsicum.

中文翻译：

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通过起始密码子靶向和定向扩增小卫星 DNA 标记揭示辣椒的遗传多样性和结构

背景识别基于高分辨率 DNA 的标记对于释放遗传多样性的潜力以及选择尼日利亚克罗斯河州和埃博尼州的辣椒独特种质进行育种和保护至关重要。因此，我们比较探讨了起始密码子靶向（SCoT）和定向扩增小卫星DNA（DAMD）标记对种质多样性分析的有效性。收集了 15 个种质，用于 DNA 提取和标记扩增。结果 SCoT 和 DAMD 的树状图分别将种质分为 5 个和 3 个遗传组，而主成分分析则确定了 5 个遗传簇，每个遗传簇都来自标记。SCoT和DAMD检测的等位基因、基因多样性和多态性信息含量的平均值表明这两个标记是有效和高效的，特别是SCoT在辣椒种质遗传多样性研究中。SCoT（NPL = 64，PPL = 80.00–95.73%）和 DAMD（NPL = 56，PPL = 53.33–86.67%）的多态性位点（NPL）数量和百分比多态性位点（PPL）较高，但 SCoT 标记物较高。用两个标记系统鉴定的其他有效遗传参数（有效等位基因数、Nei's遗传多样性和Shannon's信息指数）阐明了等位基因丰富度、群体内丰富的遗传多样性和标记的信息性质，特别是SCoT。通过SCoT和DAMD获得的种内遗传多样性、种间遗传多样性和分化系数进一步揭示了种质群体内比群体间遗传差异更大的遗传结构。SCoT 标记的基因流估计为 3.8375，DAMD 标记的基因流估计为 0.6.2042。对标记的基因流值的估计表明，在人群中，SCoT (Nm = 3.8375) 具有广泛性，而 DAMD (Nm = 6.2042) 则极其广泛。结论本研究表明，在测量遗传多样性方面，SCoT 标记可能比 DAMD 更有用、信息更丰富。以及辣椒属种质的分化。通过 SCoT 获得的遗传参数表明，来自克罗斯河的材料比来自埃博尼州的材料更具遗传多样性。因此，SCoT 可能是评估遗传多样性以改进和保护这种辛辣作物辣椒的首选标记。