Development of a new set of genic SSR markers in the genus Gentiana: in silico mining, characterization and validation

Malhotra, Era Vaidya; Jain, Rishu; Bansal, Sangita; Mali, Suresh Chand; Sharma, Neelam; Agrawal, Anuradha

doi:10.1007/s13205-021-02969-4

Cited by 2 publications

(1 citation statement)

References 49 publications

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“…Numerous primer sequences have been published, with high repeatability being a common feature. Consequently, SSR technology has been widely used in genetic studies into plants and animals (Vieira et al,2016;Rajesh et al, 2021;Malhotra et al, 2021;Yang et al, 2021) . SSR sequence analysis and mining has thus become a fundamental process in structural genomics research.…”

Section: Introductionmentioning

confidence: 99%

Development and Application of a Novel Simple Sequence Repeat Mining Algorithm Based on Regular Expression

Zhen-guo

Geng

et al. 2022

Preprint

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Simple sequence repeats (SSRs) are molecular genetic markers that are powerful tools in genomics studies; SSR markers are routinely mined as a part of genetic workflows. Here, we developed a novel SSR mining algorithm based on regular expression that can reduce the complexity of commonly used SSR mining software. We used the following SSR mining regular expression: ({i, j}?) (\1) {k}, where i and j denote the minimum and maximum lengths of the motifs of the SSR sequence, respectively, and k is the minimum number of repeat motifs. From this SSR mining algorithm, we developed an SSR sequence analysis software (named "regexSSRw") that is capable of mining eligible SSR loci from FASTA format sequences; regexSSRw can be accessed at https://github.com/renm79/rgxSSRw. This SSR mining algorithm can aid a range of applications, from being used by programmers in the development of SSR mining software to being implemented by scholars into their SSR marker workflow.

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Section: Introductionmentioning

confidence: 99%

Development and Application of a Novel Simple Sequence Repeat Mining Algorithm Based on Regular Expression

Zhen-guo

Geng

et al. 2022

Preprint

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Development and characterization of novel EST-SSR markers for Gentiana straminea Maxim., a traditional Tibetan herb in China and cross-amplification in related species

Cheng,

Lin,

Zhou

et al. 2024

Plant Genet. Resour.

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Gentiana straminea Maxim. (Gentianaceae) is an important traditional Tibetan herb that is mainly distributed on the Qinghai-Tibetan Plateau. Despite its agricultural and pharmacological importance, there remains a paucity of microsatellite markers, particularly expressed sequence tag-simple sequence repeat (EST-SSR) markers, available for this local endemic species. In this study, based on previous Illumina transcriptome data of G. straminea, a total of 96 EST-SSR markers were initially designed and tested. Thirty-two of 96 loci (33.33%) were successfully amplified and verified for validation. Among them, 10 were polymorphic and had clear bands. The polymorphism information content values were 0.09–0.799, the number of alleles per locus ranged from 3 to 14, and the levels of observed and expected heterozygosity were 0.078–0.722 and 0.238–0.884, respectively, which suggested a high level of information. Moreover, cross-amplification was successful for 10 loci in two other related species, Gentiana macrophylla Pallas and Gentiana dahurica Fischer. These EST-SSR markers provide a valuable tool for investigating the genetic diversity related to quantitative traits and population genetic studies on G. straminea and related species in sect. Cruciata Gaudin.

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Development of a new set of genic SSR markers in the genus Gentiana: in silico mining, characterization and validation

Cited by 2 publications

References 49 publications

Development and Application of a Novel Simple Sequence Repeat Mining Algorithm Based on Regular Expression

Development and Application of a Novel Simple Sequence Repeat Mining Algorithm Based on Regular Expression

Development and characterization of novel EST-SSR markers for Gentiana straminea Maxim., a traditional Tibetan herb in China and cross-amplification in related species

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