Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Fabio Brusco,Matteo Martina,Davide Gulino,Flavio Portis,Ezio Portis,Lorenzo Barchi,Alberto Acquadro,Sergio Lanteri,Mario Rabaglio

doi:10.3390/ijms23063126

Fabio Brusco, Matteo Martina + Show 7 more

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https://doi.org/10.3390/ijms23063126

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Abstract

Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.

Highlights

Anemone genus belongs to the Ranunculaceae family and the nowadays most cultivated species (A. coronaria L., A. hortensis L., and A. pavoniana Lam.) originated in the Mediterranean basin
We generated the first draft for genome sequence of A. coronaria, and we report on the massive microsatellite loci identification following its genome-wide survey
The development of a draft genome assembly of Anemone coronaria L. represents the first step toward genomic studies in poppy anemone

Summary

Introduction

Anemone genus belongs to the Ranunculaceae family and the nowadays most cultivated species (A. coronaria L., A. hortensis L., and A. pavoniana Lam.) originated in the Mediterranean basin. A. coronaria L., known as poppy anemone, is an herbaceous, perennial crop cultivated both as a cut-flower and garden plant [1]. It is a diploid species characterized by 16 chromosomes (2n = 2x = 16), but some of the commercial varieties are tetraploid. Due to protogyny, and highly heterozygous [3]. Self-pollination is possible, the species is characterized by marked inbreeding depression [4], which precludes the obtainment of pure lines suitable for the production of F1 hybrid seeds. Commercial cultivars are produced by inter-crossing of selected heterozygous plants and show variable levels of internal genetic variability. Growers plant rhizomes, which are generated after one season of nursery cultivation [5]

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