Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): First microsatellite database (OpSatdb)
| Autor: | Mary Rani K L, G. Ravichandran, Bhagya H P, Naveen Kumar P, Ravi K. Mathur, Sarika Sahu, P. Anitha, Kalyana Babu B |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Genotype Population Quantitative Trait Loci lcsh:Medicine Biology Arecaceae Palm Oil computer.software_genre Elaeis guineensis Genome Article 03 medical and health sciences 0302 clinical medicine Gene mapping Databases Genetic education lcsh:Science Synteny Expressed Sequence Tags education.field_of_study Expressed sequence tag Genetic diversity Multidisciplinary Polymorphism Genetic Database lcsh:R food and beverages Chromosome Mapping Molecular Sequence Annotation biology.organism_classification 030104 developmental biology Microsatellite lcsh:Q computer 030217 neurology & neurosurgery Genome Plant Microsatellite Repeats |
| Zdroj: | Scientific Reports Scientific Reports, Vol 9, Iss 1, Pp 1-9 (2019) |
| ISSN: | 2045-2322 |
| Popis: | The availability of large expressed sequence tag (EST) and whole genome databases of oil palm enabled the development of a data base of microsatellite markers. For this purpose, an EST database consisting of 40,979 EST sequences spanning 27 Mb and a chromosome-wise whole genome databases were downloaded. A total of 3,950 primer pairs were identified and developed from EST sequences. The tri and tetra nucleotide repeat motifs were most prevalent (each 24.75%) followed by di-nucleotide repeat motifs. Whole genome-wide analysis found a total of 245,654 SSR repeats across the 16 chromosomes of oil palm, of which 38,717 were compound microsatellite repeats. A web application, OpSatdb, the first microsatellite database of oil palm, was developed using the PHP and MySQL database (https://ssr.icar.gov.in/index.php). It is a simple and systematic web-based search engine for searching SSRs based on repeat motif type, repeat type, and primer details. High synteny was observed between oil palm and rice genomes. The mapping of ESTs having SSRs by Blast2GO resulted in the identification of 19.2% sequences with gene ontology (GO) annotations. Randomly, a set of ten genic SSRs and five genomic SSRs were used for validation and genetic diversity on 100 genotypes belonging to the world oil palm genetic resources. The grouping pattern was observed to be broadly in accordance with the geographical origin of the genotypes. The identified genic and genome-wide SSRs can be effectively useful for various genomic applications of oil palm, such as genetic diversity, linkage map construction, mapping of QTLs, marker-assisted selection, and comparative population studies. |
| Databáze: | OpenAIRE |
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