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

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.

Genome-Wide Development of Polymorphic Microsatellite Markers and Genetic Diversity Analysis for the Halophyte Suaeda aralocaspica (Amaranthaceae)

“…After performing the analysis, we discovered that the frequency of SSRs in S. aralocaspica's entire genome was 393.37 SSRs/Mb. This amount was significantly higher when compared to Anemone coronaria (65.52 SSRs/Mb), Solanum melongena (120 SSRs/Mb), and Triticum aestivum (36.68 SSRs/Mb) [27][28][29]. Therefore, it can be inferred that SSRs were abundant in the whole genome of S. aralocaspica.…”

Identifying potential ligand molecules EGFR mediated TNBC targeting the kinase domain-identification of customized drugs through in silico methods

“…The genetic variations of EGFR have been collected from the database of single nucleotide polymorphisms( 26 ). The variants were further analyzed using an ensemble variant effect predictor (VEP)( 27 ). The functional domains of the protein have been identified using Expasy Prosite( 28 ).…”

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

“…In plant breeding, the development of molecular marker databases has been extensively promoted in economically important plants such as Sesamum indicum (Dossa et al, 2017), Vicia faba (Mokhtar et al, 2020), Nicotiana spp. (Wang et al, 2018), legumes species (n = 13) (Duan and Kaundal, 2021), horticultural species (n = 112) (Song et al, 2021), and Anemone coronaria (Martina et al, 2022).…”

“…In plant breeding, the development of molecular marker databases has been extensively promoted in economically important plants such as Sesamum indicum (Dossa et al, 2017), Vicia faba (Mokhtar et al, 2020), Nicotiana spp . (Wang et al, 2018), legumes species (n = 13) (Duan and Kaundal, 2021), horticultural species (n = 112) (Song et al, 2021), and Anemone coronaria (Martina et al, 2022). Since the usage is based on a graphical user interface, the database offers the breeders, a user-friendly path for rapid identification of molecular markers without a pre-requisite expertise in command line scripting.…”