Abstract P4-08-07: Correlation of Oncotype Dx Recurrence Score and Luminal Subtypes of Breast Cancer

Background: Molecular subtypes of breast cancer have been characterized by gene expression analysis. Luminal subtypes are hormone receptor (HR) positive and Her2/neu negative. Immunohistochemistry (IHC) has been used as a surrogate test for gene expression. Ki67 is a proliferation marker that identifies high-risk subtype of luminal breast cancer. Recently, the proposed Ki67 index (KI) of 14% was suggested as a cut-off to distinguish between luminal A and luminal B tumors (JNCI. 2009;101:736-750). The oncotype dx (ODx) is a 21- gene test that provides prognostic and predictive information in early stage HR-positive breast cancer patients. The test is reported as low (<18), intermediate (18-30) and high (>30) risk recurrence scores (RS)

Design: We investigated the relationship between ODx RS and luminal subtypes of breast cancers using the KI of 14% as the cut-off for distinguishing luminal A and B tumors. Biomarker analysis (ER, PR, Her2/neu, Ki67 and p53) was performed as part of the diagnostic work-up using standard IHC procedures. Scoring was done by automated image analysis. Her2/neu FISH was performed on all IHC 2+ and 3 + results.

Pathologic parameters such as, tumor size, grade, and presence of LVI were evaluated. Ploidy was performed by the Autocyte system (Tripath) on Feulgen stained paraffin sections.

Results: We identified 106 patients with HR positive breast cancer who were tested for ODx from February 2006 to May 2010. 85/106 had Ki67 data available for analysis. 46/85 (54%) were luminal A and 39/85 (46%) luminal B tumors. The mean KI in luminal A was 6.93% versus 31.1% in luminal B (P<0.0001). The mean tumor size was 1.94 and 1.92 cm in luminal A and B respectively. Grade 1, 2 and 3 comprised 28/85 (32.9%), 49 (57.6%) and 8 (9.41%) of all tumors respectively. Of the grade1 tumors, 75% were luminal A, and grade 3 tumors were predominantly luminal B (p=0.013). LVI was present in 16 cases, 11 (68.8%) in luminal B and 5/16 (31.2%) in luminal A tumors (p=0.0416). Luminal A tumors were predominantly diploid 30/45 (66.6%) and luminal B were mostly aneuploid 21/32 (65.6%) (p=0.019). The overall mean RS in luminal A and B tumors was 14.67 and 20.15 respectively (P<0.0004). Luminal A tumors had low RS in 32/46 (66.6%). and luminal B tumors had predominantly intermediate/high RS in 23/39 (62.1%) (p=0.0082). ER Allred Scores were 7.1 and 7.3 and percent positivity was 88.1% and 91% respectively for luminal A and B subtypes. PR Allred scores were 5.6 and 5.8, and percent positivity was 62.1 and 52.9% for A and B tumors respectively. Information regarding treatment was available in 72 cases. 19 (26.3%) were treated by a combination of chemo and anti-hormonal therapy and 53 (73.6%) were treated by anti hormonal therapy alone, 8 of the 19 (42.1%) luminal A patients received combination therapy versus 11 (57.8%) in the luminal B category (p=0.277).

Conclusion: Ki67 is a useful marker that showed significant correlation with RS by ODx. Luminal A tumors are more likely to be low grade, diploid with low RS compared to luminal B tumors. Ki67 in conjunction with other pathologic parameters may serve as a surrogate marker for the ODx RS.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-08-07.

Abstract P4-08-10: Correlation of Oncotype Dx Recurrence Score with Histologic Parameters, Biomarker Expression and KI-67 Index

Background: Oncotype Dx (ODx) is a 21-gene RT-PCR based assay that provides prognostic and predictive information in patients with hormone receptor (HR) positive breast cancer. The test predicts the likelihood of disease recurrence in the form of a recurrence score (RS), which is categorized into low, intermediate and high-risk types. We examined the relationship between ODx RS and histologic parameters, DNA ploidy, tumor markers (ER, PR, Her2, Ki67, p53) expression by immunohistochemistry (IHC).

Design: We identified 106 patients with HR-positive invasive breast cancer who were tested for ODx from the department files. Pathologic variables such as, tumor size, grade, histologic type, lymphovascular invasion (LVI) were reviewed. Tumor markers ER, PR, Her2, p53 expression, Ki67 index (KI) and ploidy were performed as part of the patient's diagnostic work-up using standard procedures. Scoring was done by automated image analysis. Results of biomarker expression were compared to the ODx RS. All Her2neu 3+ and 2+ results by IHC were confirmed by FISH. Ploidy was performed by the Autocyte system (Tripath) on Feulgen stained sections. Oncotype RS was reported as low (<18), intermediate (18-30) and high risk (>30).

Results: Mean tumor size was 1.96 cm. Of the 106 cases, 87 (82%), 14 (13.2%) and 2(1.8%) were ductal, lobular and mixed types respectively. Grade 1, 2 and 3 comprised 35 (33.0%), 62 (58.4%) and 9 (8.5%) respectively. Twenty-one (19.8%) had LVI. Oncotype RS was low in 56 (52.8%), intermediate in 45 (42.4%) and high in 5 (4.7%). Mean tumor size in low RS group was 2.2 cm versus 1.6 cm in the intermediate/high RS group (p <0.05). There was no significant association of grade and LVI with RS. ER Allred score was 7.2, 7.2 and 8.0 and percent positivity was 88.0%, 91.1% and 96.3% in low, intermediate and high RS respectively (p=0.6325). The PR Allred score was 6.0, 5.3 and 3.5 and percent positivity was 64.7%, 51.8% and 16.6% in low, intermediate and high RS respectively (p=0.0432). There was 100% concordance between ER by IHC and ODx. Concordance for PR was 71/75 (94.6%). The four discordant PR results by ODx had mean score of 20% by IHC. The mean KI was 14.4%, 21.8% and 25.6% in low, intermediate and high RS respectively (p=0.0248). Low KI (<14%) and high KI (>14%) showed significant correlation with RS (p=0.0055). Her2neu IHC was negative in 43/49 (87.7%) and borderline in 6/49 (12.2%) and all were negative by FISH. Her2 FISH showed 100% (44/44) concordance with Her2 results by ODx. There was no association between DNA ploidy and RS (p=0.7143). P53 expression showed no significant correlation with RS (p=0.2602). Patients in the intermediate/high RS group were more likely to be treated with a combination of chemo plus anti-hormonal therapy (P<0.0001) and radiation (P<0.05) compared to the low RS group.

Conclusions: This study shows a complete concordance between ER IHC and Her2 FISH with RT-PCR by ODx. Low PR scores and high KI predict

high RS by ODx. There is a significant association between KI and ODx RS. Ki67 index identifies low and high RS groups, which correspond to the luminal A, and B subtypes of breast cancer respectively.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-08-10.

Hybrid x-ray/optical luminescence imaging: characterization of experimental conditions

PURPOSE

The feasibility of x-ray luminescence imaging is investigated using a dual-modality imaging system that merges x-ray and optical imaging. This modality utilizes x-ray activated nanophosphors that luminesce when excited by ionizing photons. By doping phosphors with lanthanides, which emit light in the visible and near infrared range, the luminescence is suitable for biological applications. This study examines practical aspects of this new modality including phosphor concentration, light emission linearity, detector damage, and spectral emission characteristics. Finally, the contrast produced by these phosphors is compared to that of x-ray fluoroscopy.

METHODS

Gadolinium and lanthanum oxysulfide phosphors doped with terbium (green emission) or europium (red emission) were studied. The light emission was imaged in a clinical x-ray scanner with a cooled CCD camera and a spectrophotometer; dose measurements were determined with a calibrated dosimeter. Using these properties, in addition to luminescence efficiency values found in the literature for a similar phosphor, minimum concentration calculations are performed. Finally, a 2.5 cm agar phantom with a 1 cm diameter cylindrical phosphor-filled inclusion (diluted at 10 mg/ml) is imaged to compare x-ray luminescence contrast with x-ray fluoroscopic contrast at a superficial location.

RESULTS

Dose to the CCD camera in the chosen imaging geometry was measured at less than 0.02 cGy/s. Emitted light was found to be linear with dose (R(2)= 1) and concentration (R(2)= 1). Emission peaks for clinical x-ray energies are less than 3 nm full width at half maximum, as expected from lanthanide dopants. The minimum practical concentration necessary to detect luminescent phosphors is dependent on dose; it is estimated that subpicomolar concentrations are detectable at the surface of the tissue with typical mammographic doses, with the minimum detectable concentration increasing with depth and decreasing with dose. In a reflection geometry, x-ray luminescence had nearly a 430-fold greater contrast to background than x-ray fluoroscopy.

CONCLUSIONS

X-ray luminescence has the potential to be a promising new modality for enabling molecular imaging within x-ray scanners. Although much work needs to be done to ensure biocompatibility of x-ray exciting phosphors, the benefits of this modality, highlighted in this work, encourage further study.

Molecular and chemical mechanisms involved in aphid resistance in cultivated tomato

*An integrated approach has been used to obtain an understanding of the molecular and chemical mechanisms underlying resistance to aphids in cherry-like tomato (Solanum lycopersicum) landraces from the Campania region (southern Italy). The aphid-parasitoid system Macrosiphum euphorbiae-Aphidius ervi was used to describe the levels of resistance against aphids in two tomato accessions (AN5, AN7) exhibiting high yield and quality traits and lacking the tomato Mi gene. *Aphid development and reproduction, flight response by the aphid parasitoid A. ervi, gas chromatography-mass spectrometry headspace analysis of plant volatile organic compounds and transcriptional analysis of aphid responsive genes were performed on selected tomato accessions and on a susceptible commercial variety (M82). *When compared with the cultivated variety, M82, AN5 and AN7 showed a significant reduction of M. euphorbiae fitness, the release of larger amounts of specific volatile organic compounds that are attractive to the aphid parasitoid A. ervi, a constitutively higher level of expression of plant defence genes and differential enhancement of plant indirect resistance induced by aphid feeding. *These results provide new insights on how local selection can offer the possibility of the development of innovative genetic strategies to increase tomato resistance against aphids.

Ciliary blood flow and aqueous humor production

Aqueous humor production is a metabolically active process sustained by the delivery of oxygen and nutrients and removal of metabolic waste by the ciliary circulation. This article describes our investigations into the relationship between ciliary blood flow and aqueous humor production. The results presented indicate that there is a dynamic relationship between ciliary blood flow and aqueous humor production, with production being blood flow independent above a critical level of perfusion, and blood flow dependent below it. The results also show that the plateau portion of the relationship shifts up or down depending on the level of secretory stimulation or inhibition, and that oxygen is one critical factor provided by ciliary blood flow. Also presented is a theoretical model of ocular hydrodynamics incorporating these new findings.

Hypertension is a factor associated with chronic daily headache

Chronic daily headache (CDH) is one of the more frequently observed headache syndromes at major tertiary care centers. CDH is defined as headache occurring >15 days/month. Different mechanisms are involved in the development of CDH but what factors specifically contributing to the transformation from episodic into CDH remain largely unknown. Analgesic overuse is commonly identified as the most important factor for such transformation. Hypertension, allergy, asthma, arthritis, diabetes, obesity and hypothyroidism were associated with CDH in clinical series. The objective of this study is to identify risk factors of chronicity in patients with headache. A total of 1,483 consecutive patients were studied. We collected information on age, gender, headache type and comorbidity. Patients were divided into three diagnostic groups: migraine and tension-type headache (CTT) diagnosis were made according to ICHD-II, and CDH fulfilling the Proposal Headache Classification for Chronic Daily Headache described by Silberstein and Lipton (in Chronic daily headache including transformed migraine, chronic tension-type headache, and medication overuse, 2001). We used descriptive statistics and Chi-square test. Our data show that age, gender and headache onset were similar in the three groups. Diabetes, hypercolesterolaemia, smoke and cardiopathy prevalence did not differ in the three groups (P > 0.05). Hypertension prevalence in CDH group (16.2%) was significantly higher than in the other two groups (migraine 7.3%; CTT 6.6%; P < 0.01). There were no differences (P > 0.05) in hypertension prevalence between CDH with and without medication overuse. CDH patients (mean age 41.8 +/- 14) referred to the Headache Center later than migraine and CTT patients (mean age 37 +/- 12) (P > 0.05). According to previous studies we found that hypertension is more frequent in CDH than in migraine and CTT. Examining this result it is possible to conclude that there exists an association between CDH and hypertension, but not that a causal relationship necessarily exists. Considering the other somatic conditions we did not find any correlation. The potential role of somatic comorbidity in CDH has to be studied in further clinical trials.

A viral chitinase enhances oral activity of TMOF

In this study we investigate the combined effect on Heliothis virescens (Lepidoptera, Noctuidae) larvae of Aedes aegypti-Trypsin Modulating Oostatic Factor (Aea-TMOF), a peptide that inhibits trypsin synthesis by the gut, impairing insect digestive function, and Autographa californica nucleopolyhedrovirus Chitinase A (AcMNPV ChiA), an enzyme that is able to alter the permeability of the peritrophic membrane (PM). Aea-TMOF and AcMNPV ChiA were provided to the larvae by administering transgenic tobacco plants, co-expressing both molecules. Experimental larvae feeding on these plants, compared to those alimented on plants expressing only one of the two molecules considered, showed significantly stronger negative effects on growth rate, developmental time and mortality. The impact of AcMNPV ChiA on the PM of H. virescens larvae, measured as increased permeability to molecules, was evident after five days of feeding on transgenic plants expressing ChiA. This result was confirmed by in vitro treatment of PM with recombinant ChiA, extracted from the transgenic plants used for the feeding experiments. Collectively, these data indicate the occurrence of a positive interaction between the two transgenes concurrently expressed in the same plant. The hydrolytic activity of ChiA on the PM of tobacco budworm larvae enhances the permeation of TMOF molecules to the ectoperitrophic space, and its subsequent absorption. The permeation through the paracellular route of Aea-TMOF resulted in a spotted accumulation on the basolateral domain of enterocytes, which suggests the occurrence of a receptor on the gut side facing the haemocoel. The binding of the peptide, permeating at increased rates due to the ChiA activity, is considered responsible for the enhanced insecticide activity of the transgenic plants expressing both molecules. These data corroborate the idea that ChiA can be effectively used as gut permeation enhancer in oral delivery strategies of bioinsecticides targeting haemocoelic receptors.

Purification and characterization of a viral chitinase active against plant pathogens and herbivores from transgenic tobacco

The Autographa californica nucleopolyhedrovirus chitinase A (AcMNPV ChiA) is a chitinolytic enzyme with fungicidal and insecticidal properties. Its expression in transgenic plants enhances resistance against pests and fungal pathogens. We exploited tobacco for the production of a biologically active recombinant AcMNPV ChiA (rChiA), as such species is an alternative to traditional biological systems for large-scale enzyme production. The protein was purified from leaves using ammonium sulfate precipitation followed by anion exchange and gel-filtration chromatography. Transgenic plants produced an estimated 14 mg kg(-1) fresh leaf weight, which represents 0.2% of total soluble proteins. The yield of the purification was about 14% (2 mg kg(-1) fresh leaf weight). The comparison between the biochemical and kinetic properties of the rChiA with those of a commercial Serratia marcescens chitinase A indicated that the rChiA was thermostable and more resistant at basic pH, two positive features for agricultural and industrial applications. Finally, we showed that the purified rChiA enhanced the permeability of the peritrophic membrane of larvae of two Lepidoptera (Bombyx mori and Heliothis virescens) and inhibited spore germination and growth of the phytopatogenic fungus Alternaria alternata. The data indicated that tobacco represents a suitable platform for the production of rChiA, an enzyme with interesting features for future applications as "eco-friendly" control agent in agriculture.

Systemin-dependent salinity tolerance in tomato: evidence of specific convergence of abiotic and biotic stress responses

Plants have evolved complex mechanisms to perceive environmental cues and develop appropriate and coordinated responses to abiotic and biotic stresses. Considerable progress has been made towards a better understanding of the molecular mechanisms of plant response to a single stress. However, the existence of cross-tolerance to different stressors has proved to have great relevance in the control and regulation of organismal adaptation. Evidence for the involvement of the signal peptide systemin and jasmonic acid in wound-induced salt stress adaptation in tomato has been provided. To further unravel the functional link between plant responses to salt stress and mechanical damage, transgenic tomato (Lycopersicon esculentum Mill.) plants constitutively expressing the prosystemin cDNA have been exposed to a moderate salt stress. Prosystemin over-expression caused a reduction in stomatal conductance. However, in response to salt stress, prosystemin transgenic plants maintained a higher stomatal conductance compared with the wild-type control. Leaf concentrations of abscissic acid (ABA) and proline were lower in stressed transgenic plants compared with their wild-type control, implying that either the former perceived a less stressful environment or they adapted more efficiently to it. Consistently, under salt stress, transgenic plants produced a higher biomass, indicating that a constitutive activation of wound responses is advantageous in saline environment. Comparative gene expression profiling of stress-induced genes suggested that the partial stomatal closure was not mediated by ABA and/or components of the ABA signal transduction pathway. Possible cross-talks between genes involved in wounding and osmotic stress adaptation pathways in tomato are discussed.

Cost-Benefit Analysis of Post-Lumpectomy Treatment in Elderly Women

Introduction In this era of rising cost of medical care, it is difficult to decide how to treat patients (pts). Specifically, with elderly pts who have small breast cancers (BC), there are many options. The NSABP B21 study looked at the need for breast radiotherapy (RT) after lumpectomy in node - pts with invasive BC &lt;=1 cm, by speculation that tamoxifen (tam) might be as effective as radiotherapy (RT) in reducing in breast tumor recurrence (IBTR). Pts were randomly assigned to tam, RT/placebo or RT/tam. IBTR rates were similar in the 2 groups of pts aged &gt;=70 who received tam or RT alone. The CALGB also looked at this question in pts &gt;= 70 with stage 1, node -, ER+ BC by randomly assigning them to tam or tam/RT. The only difference between the 2 groups was the rate of IBTR, which was 1% in the tam/RT group and 4% in the tam group. There was no differences in mastectomy for local recurrences, distant metastases, or 5 year OS. With the addition of aromatase inhibitors (AI), the IBTR rate in this cohort would be smaller. Based on these studies, we undertook a cost-benefit analysis of RT vs tam vs AI in pts &gt;=70 with node -, ER+, stage 1 BC.MethodsThe 3 adjuvant treatment (tx) methods considered were conventional whole breast RT (28 fractions) alone, anastrozole (1mg Qday x 5 years), & tam (20mg Qday x 5 yrs). Rates of IBTRs were extrapolated from the CALGB 5 year data as a basis, the NSABP B21 trial relative risks (9.3% RT alone vs 16.5% Tam alone), & the ATAC trial relative risks (1.5% RT+Tam vs 1.0% RT+AI). Rates of contralateral breast cancers (CBC) were similarly estimated. Costs of outpatient tx was estimated using Medicare Part B reimbursements as a surrogate. Drug costs were taken from prices from Drugstore.com. All breast failures (CBC + IBTRs) were assumed treated with mastectomy alone. Costs associated with mastectomy were estimated using Medicare Part B reimbursements for surgical costs and associated Part A inpatient prospective payments. Total cost for each tx was calculated by the formula C = FC + TC, where C= total cost, FC= failure associated cost (failure rate x mastectomy cost), and TC = tx cost.ResultsThe results for estimation of failure rates at 5 years is shown in Table 1.Table 1 IBTRCBCTotal Breast FailuresRT alone2.25%3.07%5.32%AI alone2.67%0.74%3.41%Tam Alone4.00%1.25%5.25% The cost of mastectomy was $10,037.08.The results for total cost are shown in Table 2.Table 2 Treatment CostFailure Associated CostTotal CostRT alone$11,717.70$533.97$12,251.67AI alone$18,645.14$342.26$18,987.40Tam alone$1,013.28$526.95$1,540.23 DiscussionWe consider costs of initial tx and tx of local failure. Tam alone would be the tx of choice if simply considering this total cost. However, if side effects associated with each tx is considered, then the cost for each would need to be increased accordingly. For example, in NSABP P1 trial, 3 pts died from PE on tam. If a cost were estimated for these deaths (beyond the scope of this abstract), the total cost for tam would be much higher.ConclusionsThe results from adjuvant tx after breast conserving surgery in older women with early stage BC have been excellent. In an era of steadily increasing health care costs, the cost-to-benefit ratio should be one of the factors taken into consideration when deciding tx options.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1074.

Anti-Breast Cancer Activity of a Novel Strategy of Targeting Autophagy Induced by Pan-HDAC Inhibitor and Acetylated Hsp70

During the in vivo growth of breast cancers, hypoxia, deprivation of nutrients, acidosis and increased reactive oxygen species collectively induce the metabolic and protein-misfolding/denaturing stress. This increases the levels of heat shock proteins (hsp) and induces autophagy to avoid cell death. Autophagy is a conserved catabolic pathway in which cytoplasmic macromolecules and organelles are sequestered in autophagosomes, which fuse with lysosomes for protein degradation and amino acid recycling. Elevated levels of hsp70 and hsp90 promote protein re-folding and prevent protein aggregation. Increase in hsp70 levels are also known to inhibit both intrinsic and extrinsic pathway of apoptosis. In our present studies, we have determined that the in vitro stress induced by nutrient withdrawal or treatment with pan-HDAC inhibitor (HDI) panobinostat (PS) (Novartis Pharmaceuticals) results in hyperacetylation of hsp70, which induces autophagy of the cultured breast cancer MB-231 and MCF-7 cells. The initial steps of autophagy include vesicle nucleation, vesicle expansion to form the phagophore, edges of which fuse to form the autophagosome. This process is triggered by a lipid kinase (PI3KC3) signaling complex, consisting of Vps34, Vps15, and autophagy associated genes (ATG) 6 and ATG14, that mediates vesicle nucleation. We have determined that hyperacetylated hsp70 significantly enhances the stability and activity of VPS34, which leads to binding of VPS34 to Beclin1 (ATG6). Hyperacetylated hsp70 also recruits the PHD domain containing E3 ligase for sumoylation, KAP1, to induce the sumoylation of VPS34 by SUMO-1. This was documented by confocal immunostaining with fluorescence-conjugated anti-VPS34 and anti-SUMO-1 antibodies, as well as by biochemical determination of in vitro and in vivo sumoylation of VPS34. PS treatment also induced LC3II accumulation and formation of authophagosomes, the latter determined morphologically by electron microscopy. PS-induced, KAP-1 dependent sumoylation of VPS34 and downstream autophagosome formation were abrogated by siRNA to hsp70. Also, VPS34 expression was attenuated and the processing of LC3 was inhibited in cells from the hsp70 knockout as compared to the control mice. Importantly, we also determined that, as compared to treatment with each agent alone, co-treatment with PS and the inhibitor of autophagy 3-methl-adenosine (3-MA) or chloroquine significantly enhanced cell death of breast cancer MB-231 and SUM159T cells. Furthermore, the in vivo role of hyperacetylated hsp70 in autophagy induced during growth of the orthotopically implanted MB-231 xenografts in the mammary fat pads of NOD/SCID mice was also established. In cohorts of mice, following growth to a size of 100, 200, 500 and 1000 cu mm, tumor cell-lysates demonstrated tumor size-dependent increase in the intracellular levels of hyperacetylated hsp70, Beclin1 and LC3 II. Collectively, these novel findings suggest that, stress-induced heat shock response and increase in acetylated hsp70 promotes autophagy. Our findings also demonstrate that in established breast cancers autophagy can be selectively targeted by co-treatment with a pan-HDAC inhibitor and an inhibitor of autophagy to eliminate breast cancer cells.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3124.

Treatment of early breast cancer

Surgical intervention for breast cancer has continually evolved. The current review reports on updates from the pivotal trials, examines areas of controversy, and explores possible future directions.

Relationships of Campanian olive cultivars: comparative analysis of molecular and phenotypic data

Estimation of the genetic relatedness of traditional olive cultivars with genetic markers and phenotypic data enables progress in plant breeding, management of genetic resources, and protection of both breeders' rights and certified premium products. We used amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and quantitative and qualitative morphological traits, including characteristics recommended for variety registration, to study genetic diversity and relationships in the olive at different levels. The 14 varieties analyzed, which are used for the production of Protected Denomination of Origin extra-virgin olive oil, represent the most important cultivars in the Campania region of Italy and typify a regional diversity characteristic of traditional olive cultivation. The genetic distances obtained with the two DNA marker systems were significantly correlated, as were those obtained by quantitative and qualitative traits. A lower but significant correlation was also observed between distances based on molecular markers and quantitative traits, but qualitative traits, even if sampled in high numbers, failed to describe the pattern of molecular similarity. Our data imply that the type and the number of phenotypic traits scored can greatly influence the outcome of the analysis, and care should be taken when qualitative and quantitative data are combined. Furthermore, the data indicate that the two molecular marker systems are useful for investigating genetic relationships, but they may also be used to complement and assist the traditional registration of varieties. We propose that since the information provided by molecular and morphological marker systems in olive is different, they should serve different purposes.

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

Background

Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits.

Results

Fruits of Coratina, a widely cultivated variety characterized by a very high phenolic content, and Tendellone, an oleuropein-lacking natural variant, were used as starting material for monitoring the transcriptome. Four different cDNA libraries were sequenced, respectively at the beginning and at the end of drupe development. A total of 261,485 reads were obtained, for an output of about 58 Mb. Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface.

Conclusion

Massively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development. Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.