Gadissa Fekadu, Tesfaye Kassahun, Dagne Kifle, Geleta Mulatu
Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Box 1176, Addis Ababa, Ethiopia.
Department of Biology, Madda Walabu University, Box 247, Bale Robe, Ethiopia.
BMC Genet. 2018 Oct 11;19(1):92. doi: 10.1186/s12863-018-0682-z.
Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia.
Twenty polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers were developed for P. edulis based on EST sequences of P. barbatus deposited in the GenBank. These markers were used for genetic diversity analyses of 287 individual plants representing 12 populations, and a total of 128 alleles were identified across the entire loci and populations. Different parameters were used to estimate the genetic diversity within populations; and gene diversity index (GD) ranged from 0.31 to 0.39 with overall mean of 0.35. Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with only 3% of the total variation accounted for variation among populations. Likewise, cluster and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and the reproductive biology of the crop.
These newly developed EST-SSR markers are highly polymorphic within P. edulis and hence are valuable genetic tools that can be used to evaluate the extent of genetic diversity and population structure of not only P. edulis but also various other species within the Lamiaceae family. Among the 12 populations studied, populations collected from Wenbera, Awi and Wolaita showed a higher genetic diversity as compared to other populations, and hence these areas can be considered as hot spots for in-situ conservation as well as for identification of genotypes that can be used in breeding programs.
食用香茶菜（Plectranthus edulis (Vatke) Agnew，当地称为埃塞俄比亚迪尼奇或埃塞俄比亚土豆）是埃塞俄比亚本土经济上最重要的可食用块茎作物之一。评估种群内部和种群之间的遗传多样性程度是育种和保护措施的首要且最重要的步骤之一。因此，本研究旨在利用来自埃塞俄比亚不同农业生态区的样本评估该作物的遗传多样性和种群结构。
基于保存在GenBank中的毛喉鞘蕊花（P. barbatus）的EST序列，为食用香茶菜开发了20个基于表达序列标签的多态性简单序列重复（EST-SSR）标记。这些标记用于对代表12个种群的287株个体植物进行遗传多样性分析，在整个位点和种群中总共鉴定出128个等位基因。使用不同参数估计种群内的遗传多样性；基因多样性指数（GD）范围为0.31至0.39，总体平均值为0.35。分子方差分层分析（AMOVA）显示种群分化显著但程度较低，种群间变异仅占总变异的3%。同样，聚类和STRUCTURE分析并未将种群分为截然不同的簇，这可能归因于历史和当代的基因流动以及该作物的繁殖生物学特性。
这些新开发的EST-SSR标记在食用香茶菜内具有高度多态性，因此是有价值的遗传工具，不仅可用于评估食用香茶菜的遗传多样性程度和种群结构，还可用于评估唇形科内的各种其他物种。在所研究的12个种群中，与其他种群相比，从温贝拉、阿维及沃莱塔采集的种群显示出更高的遗传多样性，因此这些地区可被视为原地保护以及鉴定可用于育种计划的基因型的热点地区。
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