Joy Nisha, Prasanth V P, Soniya E V
Plant Molecular Biology Lab, Rajiv Gandhi Centre for Biotechnology, Poojappura, Thiruvananthapuram 695014, India.
Genetica. 2011 Aug;139(8):1033-43. doi: 10.1007/s10709-011-9605-x. Epub 2011 Aug 28.
The genotypes of black pepper are morphologically and genotypically highly diverse and carry all the cumulative variations inherited and maintained through generations. The present study describes the Simple Sequence Repeat (SSR) or microsatellite based assessment of genetic diversity among forty popular genotypes and four different species of black pepper in Southern region of India. For isolation of SSR primers, our earlier attempts with enrichment strategies like 'Triplex affinity capture' did not extract a single SSR primer due to close proximity of restriction sites to the SSR motif. Hence we developed a 'Sequential Reverse Genome Walking (SRGW)' strategy with better enrichment efficiency of 72% that generated seven new SSR primers. Genotyping precisely discriminated majority of genotypes which indicated that the SSR primers are very informative. A total of 62 alleles with an average of 15.5 alleles over 4 loci were identified. All the SSR primers showed an average Polymorphism Information Content (PIC) value of 0.85. The estimated average Shared Allele Frequency ranged between 1.57 and 20.12%. The PCA plot revealed four closely related individual groups and identified Karimunda, Wild pepper and a local landrace 'local b' as the most divergent genotypes. Cluster analysis exposed the genetic relatedness between hybrids and selections with other known cultivars. The introduction of black pepper from South India to Malaysia was emphasized from the observation of genetic similarity of Malaysian cultivar 'Kuching' with other indigenous popular cultivars. The study was first to portray the precise genetic relatedness among the major indigenous genotypes of black pepper.
黑胡椒的基因型在形态学和基因层面具有高度多样性，承载着历代遗传并保留下来的所有累积变异。本研究描述了基于简单序列重复（SSR）或微卫星的印度南部地区40个常见基因型和4种不同黑胡椒品种的遗传多样性评估。为了分离SSR引物，我们早期采用“三重亲和捕获”等富集策略的尝试，由于限制酶切位点与SSR基序距离过近，未能提取到一条SSR引物。因此，我们开发了一种“顺序反向基因组步移（SRGW）”策略，其富集效率更高，达72%，并产生了7条新的SSR引物。基因分型能够精确区分大多数基因型，这表明SSR引物具有很高的信息量。共鉴定出62个等位基因，4个位点平均有15.5个等位基因。所有SSR引物的平均多态信息含量（PIC）值为0.85。估计的平均共享等位基因频率在1.57%至20.12%之间。主成分分析图显示了4个密切相关的个体组，并确定卡里蒙达、野生胡椒和一个地方品种“本地b”为最具差异的基因型。聚类分析揭示了杂种和选种与其他已知品种之间的遗传相关性。通过观察马来西亚品种“古晋”与其他本土流行品种的遗传相似性，强调了黑胡椒从印度南部引入马来西亚的情况。该研究首次描绘了黑胡椒主要本土基因型之间精确的遗传相关性。
