Assessing genetic diversity using the first polymorphic set of EST-SSRs markers and barcoding of Moroccan saffron

Lachheb, M.; Merzougui, Soumaya El; Boudadi, Imane; Caid, Mohamed Ben El; Mousadik, Abdelhamid El; Serghini, Mohammed Amine

doi:10.1016/j.jarmap.2022.100376

Cited by 3 publications

(1 citation statement)

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“…SSRs consist of tandem units of short nucleotide motifs of 1-6 bp in length [23][24][25][26]. SSRs can be developed from both non-expressed regions and expressed regions, referred to as genomic SSRs and genic SSRs, respectively [27][28][29][30]. Unigenes from the expressed regions are the longest transcripts in genes and have been widely used for SSR marker development.…”

Section: Introductionmentioning

confidence: 99%

Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae)

2023

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Background Uraria Desv. belongs to the tribe Desmodieae (Fabaceae), a group of legume plants, some of which have medicinal properties. However, due to a lack of genomic information, the interspecific relationships, genetic diversity, population genetics, and identification of functional genes within Uraria species are still unclear. Results Using RNA-Seq, a total of 66,026 Uraria lagopodioides unigenes with a total sequence content of 52,171,904 bp were obtained via de novo assembly and annotated using GO, KEGG, and KOG databases. 17,740 SSRs were identified from a set of 66,026 unigenes. Cross-species amplification showed that 54 out of 150 potential unigene-derived SSRs were transferable in Uraria, of which 19 polymorphic SSRs were developed. Cluster analysis based on polymorphisms successfully distinguished seven Uraria species and revealed their interspecific relationships. Seventeen samples of seven Uraria species were clustered into two monophyletic clades, and phylogenetic relationships of Uraria species based on unigene-derived SSRs were consistent with classifications based on morphological characteristics. Conclusions Unigenes annotated in the present study will provide new insights into the functional genomics of Uraria species. Meanwhile, the unigene-derived SSR markers developed here will be invaluable for assessing the genetic diversity and evolutionary history of Uraria and relatives.

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