Abstract
Molecular markers provide a useful method for genotype characterization and allow a high precision determination of the genetic relationship between cultivars and varieties. A system based on DNA sequences—which is known as DNA barcoding—will choose one or several standard loci which can be sequenced and compared to differentiate between species. In this research, the ITS, matK, and trnH-psbA sequences were evaluated for the molecular identification of seven F. carica genotypes, generating complete sequences for the first two loci, but unable to produce bidirectional sequences by using the trnH-psbA sequence. The ITS sequence presented the highest variation rates, while the phylogeny constructed with the matK sequence obtained the highest percentage of solved monophyletic groups. Through Pearson’s correlation analysis, it was possible to determine the existence of a significant correlation between the ITS region and psbA-trnH, and the matK and psbA-trnH sequences, but not between ITS and matK. The phylogenies constructed with the ITS + matK barcodes and ITS + matK + psbA-trnH presented the highest percentage for resolution. However, considering the cost efficiency and the facilitated recovery by using PCR, the matK + ITS combination is recommended.
Highlights
Fig (Ficus carica L.) has been an emblematic fruit tree since ancient times, associated to the beginning of horti-How to cite this paper: Castro, C., Hernandez, A., Alvarado, L. and Flores, D. (2015) DNA Barcodes in Fig Cultivars (Ficus carica L.) Using ITS Regions of Ribosomal DNA, the psbA-trnH Spacer and the matK Coding Sequence
Different DNA analysis methods have allowed a precise identification of the different genotypes, and they can be classified into three basic types [4]. One of these categories corresponds to methods which are not based on polymerase chain reaction (PCR), where it is possible to find, for example, restriction fragment length polymorphism analysis (RFLP) and the variable number tandem repeats (VNTRs)
The aim of this research was to evaluate the use of ITS regions of ribosomal DNA, the psbA-trnH spacer, and the matK sequence as markers for molecular identification through DNA barcoding of different Ficus carica L. accessions present at the Centro de Investigaciónen Biotecnología of InstitutoTecnológico de Costa Rica
Summary
Fig (Ficus carica L.) has been an emblematic fruit tree since ancient times, associated to the beginning of horti-How to cite this paper: Castro, C., Hernandez, A., Alvarado, L. and Flores, D. (2015) DNA Barcodes in Fig Cultivars (Ficus carica L.) Using ITS Regions of Ribosomal DNA, the psbA-trnH Spacer and the matK Coding Sequence. Morphological, physiological, and agronomical performance parameters are frequently used in fig trees in order to establish the descriptors required for the identification of existing genotypes, with the parameters related to leaves and fruits being the most selective These traits are very sensitive and are dependent upon environmental conditions; the number of descriptors is limited and in some cases; it does not allow separating the phenotypes in different groups [2] [3]. Different DNA analysis methods have allowed a precise identification of the different genotypes, and they can be classified into three basic types [4] One of these categories corresponds to methods which are not based on polymerase chain reaction (PCR), where it is possible to find, for example, restriction fragment length polymorphism analysis (RFLP) and the variable number tandem repeats (VNTRs). The third category is the one where a PCR with a specific objective is used, enumerating the microsatellite markers (SSR) and the inter-single sequence repeats (ISSR)
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