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Article

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

1
Department of Plants, Soils and Climate, Utah State University, Logan, UT 84322, USA
2
Center for Integrated BioSystems (CIB), Utah State University, Logan, UT 84322, USA
3
Department of Computer Science, Utah State University, Logan, UT 84322, USA
*
Author to whom correspondence should be addressed.
Genes 2020, 11(12), 1486; https://doi.org/10.3390/genes11121486
Received: 13 November 2020 / Revised: 23 November 2020 / Accepted: 26 November 2020 / Published: 10 December 2020
(This article belongs to the Section Plant Genetics and Genomics)
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. Citrus is the world’s most widely cultivated fruit crop. We have implemented a microsatellite database, citSATdb, having the highest number (~1,296,500) of putative SSR markers from the genus Citrus, 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. citSATdb represents a comprehensive source of markers for developing/implementing new approaches for molecular breeding, required to enhance Citrus productivity. The potential polymorphic SSR markers identified by cross-species transferability could be used for genetic diversity and population distinction in other species. View Full-Text
Keywords: SSR; citrus; marker-assisted selection; database; microsatellites; genomics; plant breeding and genetics SSR; citrus; marker-assisted selection; database; microsatellites; genomics; plant breeding and genetics
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MDPI and ACS Style

Duhan, N.; Meshram, M.; Loaiza, C.D.; Kaundal, R. citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement. Genes 2020, 11, 1486. https://doi.org/10.3390/genes11121486

AMA Style

Duhan N, Meshram M, Loaiza CD, Kaundal R. citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement. Genes. 2020; 11(12):1486. https://doi.org/10.3390/genes11121486

Chicago/Turabian Style

Duhan, Naveen, Manish Meshram, Cristian D. Loaiza, and Rakesh Kaundal. 2020. "citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement" Genes 11, no. 12: 1486. https://doi.org/10.3390/genes11121486

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