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Croatian Medical Journal logoLink to Croatian Medical Journal
. 2007 Aug;48(4):556–562.

Forensic Botany: Potential Usefulness of Microsatellite-based Genotyping of Croatian Olive (Olea europaea L.) in Forensic Casework

Snježana Štambuk 1, Davorka Sutlović 2, Pavle Bakarić 3, Sandra Petričević 1, Šimun Anđelinović 2
PMCID: PMC2080570  PMID: 17696311

Abstract

Aim

To assess genotyping with microsatellite-based markers of the olive (Olea europaea L.) for potential application of olive as legal case evidence, with regard to the degree of variability within the Croatian olive genomic pool and to the effectiveness of the chosen set of microsatellite-based markers in revealing olive divergence.

Methods

The total of 44 autochthonous Croatian olive specimens were subjected to genotyping with 16 previously described and developed microsatellite-based markers. According to previous morphological analyses, 44 specimens were classified into 30 cultivars with the exception of an additional, previously unassigned specimen.

Results

Genotyping of 44 specimens distinguished a total of 44 different genotype profiles by 16 microsatellite-based loci. Average expected heterozigosity amounted to 0.758, which points to significant diversity of Croatian olives.

Conclusion

Croatian olive genotyping showed strong varietal discrimination up to the single tree and considerable potential application of olive as evidence in investigation of crime, accident, and suicide circumstances.


Forensic botany is the study of plants and plant material with the purpose of presenting the plant evidence in court. It includes a number of disciplines, such as plant anatomy and systematics palynology, plant ecology, limnology, plant chemistry, and plant molecular biology (1). In spite of its high potential in assessing the legal case evidence, only a few cases of plant forensic investigation applying DNA profiling, when a suspect was linked to the crime scene, were described (2,3). Plant DNA profiling serves to identify the origin of detected plant material connected to a crime, suicide, or accident, and hence, it may contribute to identifying the location(s) where the event took place (primary scene), recent location of the body, whether a victim had been transferred or moved (secondary scene), and whether a suspect was present at a crime or accident scene (4,5). DNA profiling is also employed in solving the issues of narcotics and drug enforcement, as well as of unauthorized commercialization of some plants.

Microsatellite-based genotyping, due to its great reproducibility and high degree of certainty in assigning the origin of a biological material that serves as legal case evidence, represents one of the most reliable DNA profiling methods in forensic investigation (6).

Microsatellites, short tandem repeats (STR) or simple sequence repeats (SSR) consist of a number of tandemly repeated short DNA sequences (1-6 base pairs long). They are distributed throughout the eukaryotic genome. In addition, microsatellites are multiallelic due to their high intraspecies variability and are easily amenable to polymerase chain reaction (PCR)-based analysis. Both characteristics make them the DNA markers of choice for human DNA profiling analyses. However, microsatellite-based markers found their way of wider application in different branches of animal and plant sciences.

Olea europaea L. is a diploid, outcrossing species. Cultivated olives have been reproduced mainly by vegetative propagation and sporadically by cross-breeding, which resulted in the creation of a number of varieties due to accidental crosses between cultivated forms or between wild and cultivated forms, but also due to accumulation of mutations, along with local selection of outstanding individuals. Hence, most olive cultivars have a local origin. More than 2000 cultivars have been documented in the Mediterranean region by means of their morphology (7).

At present, microsatellite-based DNA sequences are the most appropriate genetic markers used in olive cultivar characterization and classification. Many microsatellites have been isolated from olives and their respective primer pairs have been developed (8-14).

Due to their mainly local origin, specific olive cultivars are indigenous to specific geographical areas. In addition, the same cultivars grown in different environmental conditions have different genotype profiles. Both olive characteristics ensure their relevance in the assessment of the location of origin of the olive sample in question.

Olive trees are abundant in Croatia. In order to assess the application potential of Croatian olive DNA profiling in forensic investigations, we genotyped the total of 44 specimens that comprise 30 cultivars and their 13 varieties, as well as one unassigned olive specimen.

Material and methods

Plant material

Forty-four autochthonous Croatian olive specimens Olea europaea subsp. europaea var. europaea (30 cultivars and their 13 varieties, as well as one unassigned olive specimen) from the south of Croatia, the native area of their cultivation, were selected for this study (Figure 1).

Figure 1.

Figure 1

Analyzed olive specimens and native areas of their cultivation. The oval indicates geographical location of olive specimens in Croatia, sampled in this study.

DNA extraction

Total DNA was isolated from young olive leaves and flower buds, following an already published olive DNA isolation method (15), with several modifications. Young olive leaves and buds were washed by 4% sodium hypochlorite and 0.2 g of plant tissue was ground into liquid nitrogen and incubated in 4 mL of prewarmed CTAB buffer [2%(w/v) CTAB, 100 mM Tris-HCl pH 8, 1.4 M NaCl, 40 mM EDTA pH 8, 0.5% SDS, 6% (w/v) PVP, 0.2%(v/v) 2-mercaptoethanol]. The samples were incubated at 65°C for an hour and a half and mixed gently several times. Equal volume of chloroform-isoamyl alcohol [24:1 (v/v)] was added to the mix and centrifuged twice (incubated for 20 minutes and centrifuged at 8000 rpm for 10 minutes). After the RNase digestion, samples were purified by phenol-chloroform-isoamyl alcohol [25:24:1 (v/v)] and further precipitated by 2 M ammonium-acetate and 2/3 (v/v) isopropanol. DNA was further washed by water using Centricon Centrifugal Filter Devices (with YM-100 MW membrane-Amicon; Millipore, Billerica, MA, USA) in order to remove polyphenols and pigments soluble in water.

Quantification of olive DNA was performed by spectrophotometar (Ultrospec 2000, Pharmacia Biotech (Biochrom) Ltd. Cambridge, UK).

Primers and microsatellite-based marker analysis

Olive specimens were characterized with the following 16 microsatellite-based markers: UDO99-008, UDO99-012, UDO99-019, UDO99-024, UDO99-028, UDO99-031, UDO99-039, UDO99-043 (11), ssrOeUA-DCA3, ssrOeUA-DCA8, ssrOeUA-DCA9, ssrOeUA-DCA10, ssrOeUA-DCA14, ssrOeUA-DCA16 (9), EMO2, and EMO3 (12).

Polymerase chain reactions were carried out in a volume of 12.5 μL, containing 1.5 mM MgCl2 for all ssrOeUA markers and EMO2 and EMO3; 2 mM MgCl2 for all UDO99 markers except UDO99-008; and 2.5 mM MgCl2 for UDO99-008 marker; 0.2 mM of each dNTP (Applied Biosystems, Foster City, CA, USA), GeneAmp 10×PCR Buffer II (1.25 μL for ssrOeUA-DCA3, ssrOeUA-DCA14, and ssrOeUA-DCA16; 1.5 μL for ssrOeUA-DCA8, ssrOeUA-DCA9, ssrOeUA-DCA10, EMO2, EMO3, UDO99-019, and UDO99-043; 1.75 μL for UDO99-008, UDO99-012, UDO99-024, UDO99-028, UDO99-031, and UDO99-039 markers; Applied Biosystems), primers, and 0.25 U AmpliTaq Gold DNA polymerase (Applied Biosystems). PCR reactions were performed in Applied Biosystems thermocyclers 9600 and 9700 under the following conditions: a step of 10 minutes at 95°C, followed by 35 cycles of 45 seconds at 94°C, 1 minute at the appropriate annealing temperature of the primer, and 1 minute at 72°C, and a final extension at 72°C for 30 minutes.

PCR products were analyzed in an automated sequencer (ABI Prism 310 Genetic Analyzer, Software v3.2, Applied Biosystems) and fragment lengths were determined using Genescan 500 Liz internal size standard (Applied Biosystems).

All PCR reactions were repeated three times if the results were perfectly concordant, and up to six times if there was a discrepancy in the first three amplifications, until obtaining at least three concordant results. Such discrepancies occurred on the average in 25% cases of total amplifications for each microsatellite-based marker, but were resolved in further three amplifications.

Data analysis

The expected heterozygosity (HE) of each locus was calculated according to the formula HE=n(1-Σpi2)/(n-1), where pi is the frequency of the i-th allele and n is the number of gene copies in the sample for the given locus (16).

Expected and observed heterozygosities were calculated considering that specimens with only one amplified product for the given locus were homozygotes for that locus. Hence, heterozygosities reported here might have been underestimated in cases when null alleles occurred.

Results

Genotyping analysis was performed on the total of 44 different olive samples, and the total of 163 amplified polymorphic products were obtained after applying 16 previously developed primer pairs used for amplification of microsatellite-based markers (Table 1). The absence of any amplified product occurred only once, ie in genotyping one cultivar applying marker UDO99-028 (Table 2).

Table 1.

Composition, size range, and number of alleles detected in 44 olive specimens; observed (Ho) and expected heterozygosity (HE)

Locus
Repeat motif
Size range (bp)
No. of polymorphic alleles
Ho
HE
(GA)n repeats:
ssrOeUA-DCA3 (HB)19 (229-252) 8 0.932 0.836
ssrOeUA-DCA8 (HB)18 (124-154) 9 0.932 0.811
ssrOeUA-DCA9 (HB)23 (152-209) 10 0.886 0.829
ssrOeUA-DCA10 (UB)14(HB)17 (153-241) 20 0.750 0.910
EMO2 (AG)5-G-(GA)10 (184-244) 14 ND* ND*
(CA)n repeats:
UDO99-008 (AC)13 (155-166) 7 0.273 0.792
UDO99-012 (GT)10 (155-166) 5 0.659 0.610
UDO99-031 (TG)21 (TATG)6 (107-151) 9 0.455 0.583
UDO99-043 (GT)12 (171-219) 13 0.886 0.746
ssrOeUA-DCA14 (DB)18B6(UBB)7 (145-191) 11 ND* ND*
EMO3 (CA)7 (203-214) 9 0.841 0.841
(GA)n and (CA)n compound repeats:
ssrOeUA-DCA16 (HU)13(HB)29 (124-182) 12 0.886 0.815
(CA)n or (GT)n and (TA)n compound repeats:
UDO99-019 (GT)20(AT)5 ( 99-163) 6 0.636 0.499
UDO99-024 (CA)11(TA)2(CA)4 (166-195) 9 0.682 0.747
UDO99-028 (CA)23(TA)3 (126-176; 0) 10 0.886 0.831
UDO99-039 (AT)5(GT)11 (106-186) 12 ND* ND*
Total 164
Average 10.25 0.747 0.758

*Ho and HE were not determined since some specimens yielded three different amplified products.

Table 2.

The lengths of DNA sequences (bp) encompassing 16 microsatellites as a results of genotyping 44 different Croatian olive specimens*

Markers
Cultivars U-008 U-012 U-019 U-024 U-028 U-031 U-039 U-043 DCA3 DCA14 DCA16 DCA8 DCA9 DCA10 EMO2 EMO3
Resulja 165 155/157 129/143 172/186 134/151 108/137 177/180 175/177 236/250 170/178 152 136/154 164/188 208/217 184/210/225 203/212
Grozdulja 164 155/160 129/154 179/184 172 108/146 156/177 181 229/246 187 152 124/134 205/207 153/194 219/225/230 210
Pačica 165 155 129 172/186 151/172 148 180 175/177 236/246 170/187 157/161 136/138 205/207 163/213 219/225/230 211/212
Pontoguza 160/165 155/164 129/143 172/186 151/172 108 177/180 177/215 229/246 187 127/157 134/136 164/207 215/239 220/225 211/212
Paštrica 160/165 155/164 129/143 172/186 151/172 108 177/180 177/215 229/246 187 127/157 134/136 164/207 215/239 219/225 208/212
Sitnica 1 160 155/164 129/143 172/186 134/172 108 178 179/215 229/236 184/187 152/157 124/134 205/207 159/239 219/225 203/212
Sitnica 2 162 155/164 129/143 172/186 134/172 108 178 179/215 229/236 187 152/157 124/134 207/209 159/239 219/225 203/212
Grozdača 166 155 129/143 184/186 134/151 110 179/184 177/179 229/246 178/187 152/179 134/136 164/205 155/239 225 203/210
Dužica 166 155 129 166/186 NA 108 106 177/179 246/250 178 157/182 136 164/184 217 224/225 208
Bjelica 1 163/165 155/164 129 184 132/153 108/151 106/177 177/179 229/240 153/175/187 152/157 130/134 205/207 153/237 219/223/230 210/211
Bjelica 2 163/165 155/164 129 184 132/153 108/151 106/179 179 229/240 153/175/187 152/157 130/134 205/207 153/237 219/225/230 211
Bjelica 3 163/165 155/164 129 184 132/153 108/151 106/177 179/181 229/240 153/175/187 152/157 130/134 197/207 153/237 220/225/230 210
Mezanica 1 160/166 155/166 129 186 134/151 110 177/180 177/179 240/250 178/191 124/126 136/138 174/196 155/237 202/225/230 208/211
Mezanica 2 160/166 155/166 129 186 134/151 110 177/180 177/179 240/250 178/187 124/126 136/138 174/196 155/239 202/224/228 208/211
Lastovka 155/164 157/164 99/129 184/188 134 108 106/179 171/219 229 187 152/157 130/138 188/196 153/195 211/219/244 210/213
Uljarica 1 164 155/164 129/163 184 134/141 108/151 106/177 179/217 229/240 180/187 152/157 126/134 174 239 202/210/223 211
Uljarica 2 164 155/164 129/163 184 134/141 108/151 106/177 179/217 229/240 180/187 152/157 126/134 174 239 201/210/223 211/212
Uljarica 3 164 155/164 129/163 184 134/141 108/151 106/177 179/217 229/240 178/187 152/157 126/134 152/174 158/239 202/210/223 211/212
Vel. Lastovka 165 155/166 129/143 172/186 126/134 108 178/180 177/215 229/250 187/189 157/177 134/136 164/205 157/239 202/225/230 208/212
Želudarica 165 155 129 166/186 126/153 108 106 177/179 242/250 178/187 124/127 130/136 164/205 155 225/230 210/211
Murgulja 165 155/164 129/143 186 126/172 108 106/177 179/213 236/246 178/187 152 124/136 164/207 159/217 220/225 203/208
Trsteno Olive 163 157/166 99/129 181/184 176 108/137 175/177 189/219 242/252 145/153/175 124/163 130/140 188/207 153/175 210/225/230 212/214
Zuzorka 160 155/164 129/143 172/186 134/172 108 178 179/215 229/236 187 152/157 124/134 205/207 159/241 219/225/230 203/211
Žabarka 165 155 129 186/195 134/172 108 144/177 175/179 229/250 153/176/187 177 134/140 164/188 220 220/225/240 208
Levantinka 166 155 129 186 151/153 110/151 177/186 179/183 236 178/187 152/176 124/134 164/207 177/215 225/230 208/211
Jeruzalemka 165 155 99/129 172/186 172 108/137 123/138 175/179 229/246 145/178 152/157 136/140 184/207 159/217 220 208/212
Crnica 166 155/164 129/143 186 151/172 108 106/179 177/179 236/246 187 152/176 124/136 196/207 155/239 202/219/230 203/208
Lumbardeška 1 165 155 129/143 172/186 134/151 108 177/180 177/179 236/250 178/187 152/177 134/136 164/205 217 225/230 208/212
Lumbardeška 2 165 155 129/143 171/186 134/151 108 177/180 177/179 236/250 178/187 152/177 134/136 164/205 217 225 208/212
Konavoska 166 155/164 129/143 186 134/151 108 106/177 177/179 236/250 187 157/177 136 196/205 155/159 202/225/230 210
Dubravka 165 155 129 166/186 126/153 108 106 177/179 242/250 178/187 124/127 130/136 164/205 155 225/230 210/211
Krvavica 166 155/164 129/143 186 126/172 108 106/177 179/211 236/248 178/187 127/152 124/136 164/207 159/215 220/225 203/208
Polituša 166 155 113/129 172/186 151/172 107/148 180 175/177 236/246 170/187 157/161 136/138 205/207 163/215 220/225/230 211/212
Puizica 1 164 157/166 129 166/186 134/162 124/151 177 179 240/252 170/187 146/152 134/148 174 169/237 202/224 206/212
Puizica 2 164 157/166 129 166/186 134/162 124/151 177 179 240/252 170/187 152 134/148 174 169/237 202/223 206/212
Šljivača 166 155 113/129 172/186 151/172 107/148 180 179 236/246 170/187 157/161 136/138 205/207 163/215 219/225/230 210/211
Piculja 1 155/164 157/166 129 166/181 153/172 108/144 106/123/138 179/185 229/242 170/187 124/146 124/130 174/205 153/212 202/225/230 206/209
Piculja 2 155/164 157/166 129 166/181 153/172 108/151 106/123/138 179/185 229/242 170/187 124/146 124/130 174/205 153/215 202/225/230 206/209
Piculja 3 155/164 157/166 129 166/181 153/172 108/151 106/123/138 179/185 229/242 170/187 124/146 124/130 174/205 153/212 202/225/230 206/209
Piculja 4 155/164 157/166 113/129 166/181 153/172 108/151 106/123/138 179/185 229/242 170/187 124/146 124/130 174/197 153/212 202/225/230 206/209
Šipan Mezanica 164 155/164 129/163 184 134/141 108/151 106/177 179/217 229/240 180/187 152/157 126/134 174 158/239 202/210/223 211/212
Oblica 1 166 155 129/143 172/186 134/151 108 177/180 177/179 236/250 178/187 152/176 134/136 164/205 217 225/230 208/211
Oblica 2 166 155 129/143 172/186 134/151 108 177/180 177/179 250 178/187 152/176 134/136 164/205 217 225 208/212
Oblica 3 166 155 129/143 172/186 134/151 108 177/180 177/179 236/250 178/187 152/176 134 164/205 217 225/230 208/212

*Abbreviations: U-No. refer to UDO99-No.; DCANo. refer to ssrOeUA-DCANo.; NA – no amplified product.

The allele size ranges and the total number of alleles, as well as the expected and observed heterozygosities for each locus are presented in Table 1. The average expected heterozygosity amounted to 0.758.

An electropherogram of microsatellite-based olive DNA, serving as an illustration of the amplified products obtained in this study, is demonstrated in the Figure 2.

Figure 2.

Figure 2

The electropherogram of olive DNA obtained in this study by applying UDO99-024 microsatellite-based marker (internal size standard – LIZ 500). X-axis indicates fragment lenght (bp), while Y-axis indicates relative flourescent units (RFU) that are proportional to the amount of PCR product.

Three microsatellite-based primer pairs (UDO99-039, ssrOeUA-DCA14, and EMO2) amplified three different products for some cultivars (UDO99-039 for all four Piculja varieties, ssrOeUA-DCA14 for all three Bjelica varieties, as well as for two cultivars – Trsteno Olive and Žabarka, and EMO2 for 25 out of 44 specimens), thus increasing their power of discrimination of genotyped olive specimens.

Discussion

By genotyping more than one different specimen of the same olive cultivar denominations we have demonstrated that it is possible to distinguish among different intracultivar varieties by means of a set of 16 microsatellite-based markers.

In our study, 164 polymorphic alleles were characterized using 16 microsatellite-based markers over 44 different specimens and 30 denominations defined previously by agronomic and morphological means (17,18). In comparison, in the study employing 14 microsatellite-based markers over 130 specimens comprising 67 different denominations, 135 alleles were detected (19), while in the study employing 12 microsatellite-based markers over 50 specimens comprising 34 different cultivars, 119 alleles were detected (20). Furthermore, in the study applying 15 microsatellite-based markers over 47 cultivars, 124 alleles were detected (9), while in the study applying 7 microsatellite-based markers over 23 cultivars, 45 polymorphic alleles were detected (12). Finally, in our study the average expected heterozygosity amounted to 0.758, while in other studies it amounted to 0.679 (19), 0.760 (20), 0.693 (9), 0.648 (12), and 0.681 (13). Hence, comparable levels of genetic variability were observed in other studies as well. In addition, we showed that the applied set of microsatellite-based markers efficiently resolved all the cases of intracultivar variability, which points to a high potential of 16 chosen microsatellite-based markers in revealing olive genetic diversity.

The mechanism of the occurrence of three different microsatellite-based alleles amplified by one primer pair is not elucidated, but might be ascribed to chromosome rearrangements (21), genome fusions (22,23), or “chimerism” (24).

Microsatellite-based olive genotyping application is justified in solving criminal and civil cases by its ability to assign olive DNA to an individual tree and at the same time by its capability of yielding the same molecular profile for the same tree due to the olive microsatellite somatic stability.

General reproducibility of microsatellite-based genotyping data among laboratories should result in a comprehensive olive genotyping database that might be searched in case of a need to assign the origin of the found plant material connected to crime or accident or suicide scene.

In conclusion, we demonstrated that Croatian olive cultivar genotyping using 16 microsatellite-based markers may provide the possibility of olive specimen identification up to the individual tree and may open the possibility of their successful application in forensic investigations.

Acknowledgements

This research was supported by a grant from the Croatian Ministry of Science, Education, and Sports (grant No. 141-2160800-0333). We gratefully acknowledge the provision of samples by Franko Marinović and Antun Kotlar from the Croatian Agricultural Extension Institute (CAEI) of Dubrovačko-neretvanska County. Equipment was provided by the Laboratory of Forensic and Clinical Genetics, headed by Prof Šimun Anđelinović, Split university Hospital.

Disclaimer

Snježana Štambuk is an employee of SMS – Food Development Center, Klis, Croatia. SMS - Food Development Center participated to the financing of the experimental work, organized sampling and contributed to designing the work.

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