Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India
Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India
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DOI：
10.1016/j.phytochem.2020.112330
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发表时间：
2020-06-01
期刊：
影响因子：
3.8
通讯作者：
Nongdam, Potshangbam
中科院分区：
文献类型：
--
作者：
Amom, Thoungamba;Tikendra, Leimapokpam;Nongdam, Potshangbam
采用随机扩增多态性DNA（RAPD）、简单重复序列（ISSR）、引物间结合位点（iPBS）和起始密码子靶向（SCoT）4种方法各10个引物，对5种重要经济竹种（Bambusa cacharensis，B. mizorameana、麻竹Dendrocalamus manipureanus、D. hamiltonii和D.产于印度东北部。40个引物分别扩增出111、115、116和138条多态性条带。通过对4个标记系统的多态信息含量（PIC）、有效多重比率（EMR）和标记指数（MI）的比较分析，发现SCoT比其他3个标记具有更高的信息量和区分能力。通过Mantel检验确定的相关值（r）范围从0.60（SCoT和RAPD）到0.83（iPBS和ISSR），表明标记之间的高度正相关。RAPD、ISSR、iPBS和SCoT标记遗传矩阵之间的对应关系表明，各标记系统在确定竹类亲缘关系上是有效的。UPGMA（Unweighted Pair Group Arithmetic Mean Method）聚类分析结果表明，不同基因型的竹种具有种特异性。除RAPD外，ISSR、iPBS和SCoT标记的树系图也显示出竹子基因型在地理来源上的密切关联。主坐标分析结果与聚类分析结果基本一致。基于植物化学研究的聚类分析不仅区分了不同的竹种，而且说明了基因型的位置特异性分组。竹类化学分析的聚类模式与DNA分子标记的聚类图相吻合。本研究建立了一种结合分子和植物化学标记的方法来确定印度东北部5种原生竹之间的遗传关系的可能性。
10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision.