Dataset Information

Development and characterization of EST-SSR markers in Stipa breviflora (Poaceae).

ABSTRACT: PREMISE OF THE STUDY:Stipa breviflora (Poaceae) is one of the dominant species of the desert steppe in the eastern Eurasian grasslands. Simple sequence repeat (SSR) markers were developed for use in genetic diversity studies of this species. METHODS AND RESULTS:A total of 1954 potentially polymorphic loci were obtained by comparing transcriptome data of eight different S. breviflora individuals. We selected 81 loci to verify polymorphism and 63 loci amplified, of which 21 loci exhibited polymorphism. The number of alleles per locus varied from two to 24, the observed heterozygosity ranged from 0.083 to 0.958, and the expected heterozygosity ranged from 0.396 to 0.738. CONCLUSIONS:These newly identified SSR loci can be used for population genetic and landscape genetic studies of S. breviflora. In addition, 14 loci also amplified in six related Stipa species (S. grandis, S. krylovii, S. bungeana, S. aliena, S. gobica, and S. purpurea).

SUBMITTER: Ren J

PROVIDER: S-EPMC5400433 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Development and characterization of EST-SSR markers in <i>Stipa breviflora</i> (Poaceae).

Ren Jing J Su Zhi-Zhen ZZ Dang Zhen-Hua ZH Ding Yu Y Wang Pei-Xuan PX Niu Jian-Ming JM

Applications in plant sciences 20170412 4

<h4>Premise of the study</h4><i>Stipa breviflora</i> (Poaceae) is one of the dominant species of the desert steppe in the eastern Eurasian grasslands. Simple sequence repeat (SSR) markers were developed for use in genetic diversity studies of this species.<h4>Methods and results</h4>A total of 1954 potentially polymorphic loci were obtained by comparing transcriptome data of eight different <i>S. breviflora</i> individuals. We selected 81 loci to verify polymorphism and 63 loci amplified, of whi ...[more]

PMID: 28439477

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Project description:BackgroundElymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures.ResultsWe obtained 9.06 Gb clean sequences from the transcriptome of E. breviaristatus, generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the E. breviaristatus transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild E. breviaristatus in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2-98.3%. UPGMA analysis generally grouped species with similar genome types together.ConclusionsHere, we developed EST-SSR markers from the transcriptome of E. breviaristatus. The transferability of these markers was evaluated, and the genetic structure and diversity of E. breviaristatus were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the Elymus genus.

Dataset Information

Development and characterization of EST-SSR markers in Stipa breviflora (Poaceae).

Publications

Development and characterization of EST-SSR markers in <i>Stipa breviflora</i> (Poaceae).

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