: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Species for Germplasm Characterization and Crop Improvement

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2020 Dec 16

PMID 33321957

Citations 10

Authors

Naveen Duhan

Manish Meshram

Cristian D Loaiza

Rakesh Kaundal

Affiliations

Soon will be listed here.

Abstract

Microsatellites or simple sequence repeats (SSRs) are popular co-dominant markers that play an important role in crop improvement. To enhance genomic resources in general horticulture, we identified SSRs in the genomes of eight citrus species and characterized their frequency and distribution in different genomic regions. is the world's most widely cultivated fruit crop. We have implemented a microsatellite database, , having the highest number (~1,296,500) of putative SSR markers from the genus , represented by eight species. The database is based on a three-tier approach using MySQL, PHP, and Apache. The markers can be searched using multiple search parameters including chromosome/scaffold number(s), motif types, repeat nucleotides (1-6), SSR length, patterns of repeat motifs and chromosome/scaffold location. The cross-species transferability of selected markers can be checked using e-PCR. Further, the markers can be visualized using the Jbrowse feature. These markers can be used for distinctness, uniformity, and stability (DUS) tests of variety identification, marker-assisted selection (MAS), gene discovery, QTL mapping, and germplasm characterization. represents a comprehensive source of markers for developing/implementing new approaches for molecular breeding, required to enhance productivity. The potential polymorphic SSR markers identified by cross-species transferability could be used for genetic diversity and population distinction in other species.

Citing Articles

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