Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki.
Genet Mol Res
; 12(3): 2841-51, 2013 Jan 09.
Article
in En
| MEDLINE
| ID: mdl-23359055
We developed and characterized expressed sequence tags (ESTs)-simple sequence repeats (SSRs) and targeted region amplified polymorphism (TRAP) markers to examine genetic relationships in the persimmon genus Diospyros gene pool. In total, we characterized 14 EST-SSR primer pairs and 36 TRAP primer combinations, which were amplified across 20 germplasms of 4 species in the genus Diospyros. We used various genetic parameters, including effective multiplex ratio (EMR), diversity index (DI), and marker index (MI), to test the utility of these markers. TRAP markers gave higher EMR (24.85) but lower DI (0.33), compared to EST-SSRs (EMR = 3.65, DI = 0.34). TRAP gave a very high MI (8.08), which was about 8 times than the MI of EST-SSR (1.25). These markers were utilized for phylogenetic inference of 20 genotypes of Diospyros kaki Thunb. and allied species, with a result that all kaki genotypes clustered closely and 3 allied species formed an independent group. These markers could be further exploited for large-scale genetic relationship inference.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Microsatellite Repeats
/
Expressed Sequence Tags
/
Diospyros
Country/Region as subject:
Asia
Language:
En
Journal:
Genet Mol Res
Journal subject:
BIOLOGIA MOLECULAR
/
GENETICA
Year:
2013
Document type:
Article
Affiliation country:
China
Country of publication:
Brazil