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Phenotypic and molecular marker analysis uncovers the genetic diversity of the grassStenotaphrum secundatum

文献类型： 外文期刊

作者： Luo, Ying 1 ; Zhang, Xiujie 1 ; Xu, Jiahong 1 ; Zheng, Yao 1 ; Pu, Shouqin 1 ; Duan, Zhizhen 1 ; Li, Zhihao 1 ; Liu, Guod 1 ;

作者机构： 1.Hainan Univ, Key Lab Genet & Germplasm Innovat Trop Special Fo, Engn Res Ctr Rare & Precious Tree Species Hainan, Coll Forestry,Minist Educ, Haikou 570228, Hainan, Peoples R China

2.Hainan Univ, Coll Forestry, Hainan Biol Key Lab Germplasm Resources Trop Spec, Haikou 570228, Hainan, Peoples R China

3.Chinese Acad Trop Agr Sci, Haikou 570228, Hainan, Peoples R China

关键词： Stenotaphrum secundatum; Phenotype; Molecular markers; Single-nucleotide polymorphism; Genetic diversity

期刊名称：BMC GENETICS （ 影响因子：2.797； 五年影响因子：3.263 ）

ISSN： 1471-2156

年卷期： 2020 年 21 卷 1 期

页码：

收录情况： SCI

摘要： Background Stenotaphrum secundatumis an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity ofS. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification ofS. secundatumgermplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49 S. secundatumaccessions. Results Based on seven types of phenotypic data, the 49 S. secundatumaccessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers (h = 0.47,I = 0.66) and ISSR markers (h = 0.45,I = 0.64) supports the notion that theS. secundatumaccessions are highly diverse.S. secundatumcould be divided into three classes based on the evaluated molecular markers. Conclusions Phenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation amongS. secundatumaccessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification ofS. secundatum. Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity inS. secundatum. The SNPs identified in this study could be used to distinguishS. secundatumaccessions.

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