Olive (Olea europaea L. subsp. europaea, var. europaea) belongs to the Oleaceae family and is an evergreen plant native to the Mediterranean Basin. Genotyping of olive germplasm collections is a very complex task due to the bad knowledge of cultivar denominations, the high intra-specie and intra-cultivar variability. At the moment, the di-nucleotide SSR markers are more used, but while showing a high level of polymorphism present also many problems related to difficult discrimination of neighboring alleles. The availability of olive genome sequence has allowed us their intensive screening to search for polynucleotide microsatellite regions with long core repeats, potentially polymorphic among cultivars. For this purpose, we chose Genome-wide Microsatellite Analyzing Tool Package(GMATA) that integrate SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enable simultaneously display SSR markers with other genome features. The analysis has performed following the search parameters for repetitive elements in class I (≥20 base pairs [bp]) and discarding di-nucleotide SSR motivs.Unit size/ minimum number of repeats are defined as 3/7, 4/5, 5/4, and 6/4, and the maximum length of interruption between adjacent SSR has set to 5 bp. In order to evaluate and isolate only the high polymorphic SSR markers among those predicted, about 50 potential of them are preliminary tested in three different cultivars. In the future, only the more polymorphic SSR markers will be validated in at least 100 cultivars.

Development and evaluation of polymorphic genomic-SSR markers in olive (Olea europaea L.)

REGINA T. M. R.;
2019

Abstract

Olive (Olea europaea L. subsp. europaea, var. europaea) belongs to the Oleaceae family and is an evergreen plant native to the Mediterranean Basin. Genotyping of olive germplasm collections is a very complex task due to the bad knowledge of cultivar denominations, the high intra-specie and intra-cultivar variability. At the moment, the di-nucleotide SSR markers are more used, but while showing a high level of polymorphism present also many problems related to difficult discrimination of neighboring alleles. The availability of olive genome sequence has allowed us their intensive screening to search for polynucleotide microsatellite regions with long core repeats, potentially polymorphic among cultivars. For this purpose, we chose Genome-wide Microsatellite Analyzing Tool Package(GMATA) that integrate SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enable simultaneously display SSR markers with other genome features. The analysis has performed following the search parameters for repetitive elements in class I (≥20 base pairs [bp]) and discarding di-nucleotide SSR motivs.Unit size/ minimum number of repeats are defined as 3/7, 4/5, 5/4, and 6/4, and the maximum length of interruption between adjacent SSR has set to 5 bp. In order to evaluate and isolate only the high polymorphic SSR markers among those predicted, about 50 potential of them are preliminary tested in three different cultivars. In the future, only the more polymorphic SSR markers will be validated in at least 100 cultivars.
978-88-904570-9-8
Olea europaea, SSR, bionformatics, genotyping
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/20.500.11770/302500
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