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Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum.

ABSTRACT: BACKGROUND:Stenotaphrum secundatum is 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 of S. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm 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. secundatum accessions. RESULTS:Based on seven types of phenotypic data, the 49?S. secundatum accessions 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 the S. secundatum accessions are highly diverse. S. secundatum could 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 among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum. Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum. The SNPs identified in this study could be used to distinguish S. secundatum accessions.

SUBMITTER: Luo Y

PROVIDER: S-EPMC7425169 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum.

Luo Ying Y Zhang Xiujie X Xu Jiahong J Zheng Yao Y Pu Shouqin S Duan Zhizhen Z Li Zhihao Z Liu Guodao G Chen Jinhui J Wang Zhiyong Z

BMC genetics 20200812 1

<h4>Background</h4>Stenotaphrum secundatum is 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 of S. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, ...[more]

PMID: 32787786

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Project description:The current classification of sporadic Creutzfeldt-Jakob disease (sCJD) includes six major clinicopathological subtypes defined by the physicochemical properties of the protease-resistant core of the pathologic prion protein (PrPSc), defining two major PrPSc types (i.e., 1 and 2), and the methionine (M)/valine (V) polymorphic codon 129 of the prion protein gene (PRNP). How these sCJD subtypes relate to the well-documented phenotypic heterogeneity of genetic CJD (gCJD) is not fully understood. We analyzed molecular and phenotypic features in 208 individuals affected by gCJD, carrying 17 different mutations, and compared them with those of a large series of sCJD cases. We identified six major groups of gCJD based on the combination PrPSc type and codon 129 genotype on PRNP mutated allele, each showing distinctive histopathological characteristics, irrespectively of the PRNP associated mutation. Five gCJD groups, named M1, M2C, M2T, V1, and V2, largely reproduced those previously described in sCJD subtypes. The sixth group shared phenotypic traits with the V2 group and was only detected in patients carrying the E200K-129M haplotype in association with a PrPSc type of intermediate size ("i") between type 1 and type 2. Additional mutation-specific effects involved the pattern of PrP deposition (e.g., a "thickened" synaptic pattern in E200K carriers, cerebellar "stripe-like linear granular deposits" in those with insertion mutations, and intraneuronal globular dots in E200K-V2 or -M"i"). A few isolated cases linked to rare PRNP haplotypes (e.g., T183A-129M), showed atypical phenotypic features, which prevented their classification into the six major groups. The phenotypic variability of gCJD is mostly consistent with that previously found in sCJD. As in sCJD, the codon 129 genotype and physicochemical properties of PrPSc significantly correlated with the phenotypic variability of gCJD. The most common mutations linked to CJD appear to have a variable and overall less significant effect on the disease phenotype, but they significantly influence disease susceptibility often in a strain-specific manner. The criteria currently used for sCJD subtypes can be expanded and adapted to gCJD to provide an updated classification of the disease with a molecular basis.

Dataset Information

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum.

Publications

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum.

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