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Transcriptome Assembly and Identification of EST-SSR Markers in Crocus Sativus

Document Type : Research Paper

Authors

1 MSc in Agricultural Biotechnology, Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Mashhad, Iran.

2 Associate Professor, Crop and Horticultural Science Research Department, Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Mashhad, Iran.

3 Assistant Professor, Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Iran.

Abstract

Crocus sativus is a triploide plant and propagating by vegetative propagation. Therefore, trait segregation and genetic diversity are limited in this plant. EST-SSR markers have some priority, for example co-dominant inheritance, locus specific and highly polymorphic against all other markers. Due to the availability of transcriptome data, it is possible to develop EST-SSR markers and polymorphism studies in saffron. Development of EST-SSR markers in C. sativus make it possible to study genetic diversity and molecular polymorphism in different genotypes. In order to develop EST-SSR marker for C. sativus, we downloaded public available C. sativus RNA-seq data. Quality control and preprocessing of raw reads were done using FastQC and Trimmomatic tools, respectively. We performed de novo transcriptome assembly using RNA-Bloom. CD-HIT-EST was used in order to reduce redundancy in transcriptome assembly. The assembly quality was evaluated using the BUSCO software and completeness of transcriptome assembly was 90%. After achieving to high quality transcriptome assembly of C. sativus, EST-SSRs were identified by MISA tool. The EST-SSRs primers were designed using Primer3. 35459 SSR-containing sequences were detected and primer pairs were designed for them. Ten EST-SSR primer pairs were randomly selected to amplify C. sativus DNA. Seven pairs of the primers (70%) generated clear and reproducible bands with the expected size. These EST-SSR markers can be functional and useful for C. sativus genetic studies.

Keywords

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References
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Saffron Agronomy and Technology
Volume 10, Issue 1 - Serial Number 35
April 2022
Pages 41-49
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