基于mtDNA和cpDNA序列的甘薯栽培种及近缘野生种分析

王崇; 王连军; 田小海; 雷剑; 柴沙沙; 焦春海; 杨新笋

doi:10.7671/j.issn.1001-411X.202011026

基于mtDNA和cpDNA序列的甘薯栽培种及近缘野生种分析

Analyses of Ipomoea batatas cultivated species and wild relatives based on mtDNA and cpDNA sequences

摘要

摘要:
目的利用线粒体DNA(Mitochondrial DNA，mtDNA)序列和叶绿体DNA(Chloroplast DNA，cpDNA)matK序列对甘薯Ipomoea batatas栽培种及近缘野生种进行分子鉴定和亲缘关系分析，为甘薯栽培种和近缘野生种的种质鉴定、保护及开发利用提供理论依据。

方法以3个甘薯栽培种及8个近缘野生种为材料，采用CTAB法提取基因组DNA，通过PCR扩增mtDNA序列和cpDNA matK序列，使用DnaSP 6.0对序列进行核苷酸多态性、单倍型多样性等特征分析，并基于邻接法构建3个甘薯栽培种及8个近缘野生种的系统发育进化树。

结果 5个mtDNA序列和cpDNA matK序列经测序、比对、拼接后，长度为6 713 bp，GC占比在47.79%~48.31%之间。合并序列的单倍型数量、核苷酸多态性、变异位点数量、单一突变位点数量、简约信息位点数量和插入/缺失位点数量分别为9、0.003 25、69、39、30和111。中性检验显示，合并序列差异不显著(P>0.10)，遵循中性进化模型。3个甘薯栽培种及8个近缘野生种间的遗传距离在0.000 00~0.005 84之间，平均遗传距离0.003 26，遗传多样性较低；按照亲缘关系被分为2大类，各大类内部亲缘关系较近。

结论本研究采用的序列可对甘薯栽培种和近缘野生种进行准确的鉴定区分，为甘薯近缘野生种的进化和利用提供参考和理论指导。

Abstract:
Objective To conduct molecular identification and genetic relationship analysis of Ipomoea batatas cultivated species and wild relatives based on mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) matK sequences, and provide theoretical bases for germplasm identification, protection, development and utilization.

Method Three cultivated species and eight wild relatives were used as materials, from which total DNA was extracted by the CTAB method. Their mtDNA and cpDNA matK sequences were amplified by PCR. DnaSP 6.0 was used to analyze nucleotide diversity, haplotype diversity and other characteristics. The phylogenetic tree of three cultivated species and eight wild relatives was constructed based on the neighbor-joining method.

Result The length of five mtDNA regions and one cpDNA region was 6 713 bp after sequencing, alignment and splicing, the GC proportion was 47.79%−48.31%, and the haplotype number, nucleotide diversity, variable site number, singleton variable site number, parsimony informative site number, insertion/deletion site number were 9, 0.003 25, 69, 39, 30, 111, respectively. The neutrality test showed there was no significant difference between Tajima’sD values at the level of P>0.10, which indicated that variation of those regions followed neutral theory of molecular evolution. The genetic distances among three cultivated species and eight wild relatives ranged from 0.000 00 to 0.005 84, with an average genetic distance of 0.003 26, indicating low genetic diversity. The phylogenetic tree divided the 11 species into two categories with close genetic relationship within the category.

Conclusion The sequences used in this study can accurately identify I. batatas cultivated species and wild relatives, and provide references and theoretical guidance for the evolution and utilization of I. batatas wild relatives.

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