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X. He, F. Li, J. Shi and S. Gan

References B rondani , R. P. V., E. R. W illiams , C. B rondani and D. G rattapaglia (2006): A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biol. 6 : 20. F aria , D. A., E. M. C. M amani , G. J. P appas , D. G rattapaglia (2011): Genotyping systems for Eucalyptus based on tetra-, penta-, and hexanucleotide repeat EST microsatellites and their use for individual fingerprinting and assignment tests. Tree Genet. Genomes 7 : 63–77. F aria , D. A

Open access

Li-Wei Gao and Guo-Liang Wang

Abstract

Lung cancer (LC), which includes small-cell lung carcinoma (SCLC) and non-small-cell lung carcinoma (NSCLC), is common and has a high fatality rate. This study aimed to reveal the prognostic mechanisms of LC. GSE30219 was extracted from the Gene Expression Omnibus (GEO) database, and included 293 LC samples and 14 normal lung samples. Differentially expressed genes (DEGs) were identified using the Limma package, and subjected to pathway enrichment analysis using DAVID. MicroRNAs (miRNAs) targeting the DEGs were predicted using Webgestalt. Cytoscape software was used to build a protein-protein interaction (PPI) network and to identify significant network modules. Survival analysis was conducted using Survminer and Survival packages, and validation was performed using The Cancer Genome Atlas (TCGA) dataset. The good and poor prognosis groups contained 518 DEGs. miR-190, miR-493, and miR-218 for the upregulated genes and miR-302, miR-200, and miR-26 for the downregulated genes were predicted. Three network modules (module 1, 2, and 3) were identified from the PPI network. CDK1, MCM10, and NDC80 were the core nodes of module 1, 2, and 3, respectively. In module 1, CDK1 interacted with both CCNB1 and CCNB2. Additionally, CDK1, CCNB1, CCNB2, MCM10, and NDC80 expression levels correlated with clinical survival and were identified as DEGs in both GSE30219 and the TCGA dataset. miR-190, miR-493, miR-218, miR-200, and miR-302 might act in LC by targeting the DEGs. CDK1, CCNB1, CCNB2, MCM10, and NDC80 might also influence the prognosis of LC.

Open access

C. Navarro, S. Cavers, N. Colpaert, G. Hernandez, P. Breyne and A. J. Lowe

Abstract

In Mesoamerica, tropical dry forest is a highly threatened habitat, and species endemic to this environment are under extreme pressure. The tree species, Lonchocarpus costaricensis is endemic to the dry northwest of Costa Rica and southwest Nicaragua. It is a locally important species but, as land has been cleared for agriculture, populations have experienced considerable reduction and fragmentation. To assess current levels and distribution of genetic diversity in the species, a combination of chloroplast-specific (cpDNA) and whole genome DNA markers (amplified fragment length polymorphism, AFLP) were used to fingerprint 121 individual trees in 6 populations. Two cpDNA haplotypes were identified, distributed among populations such that populations at the extremes of the distribution showed lowest diversity. A large number (487) of AFLP markers were obtained and indicated that diversity levels were highest in the two coastal populations (Cobano, Matapalo, H = 0.23, 0.28 respectively). Population differentiation was low overall, FST = 0.12, although Matapalo was strongly differentiated from all other populations (FST = 0.16-0.22), apart from Cobano (FST = 0.11). Spatial genetic structure was present in both datasets at different scales: cpDNA was structured at a range-wide distribution scale, whilst AFLP data revealed genetic neighbourhoods on a population scale. In general, the habitat degradation of recent times appears not to have yet impacted diversity levels in mature populations. However, although no data on seed or saplings were collected, it seems likely that reproductive mechanisms in the species will have been affected by land clearance. It is recommended that efforts should be made to conserve the extant genetic resource base and further research undertaken to investigate diversity levels in the progeny generation.

Open access

A. C. Coelho, M. B. Lima, D. Neves and A. Cravador

Abstract

The genetic variability of cork oak (Quercus suber, L.) in Portugal was evaluated by AFLP using five primer combinations. Three hundred and thirteen trees from three geographically contrasting regions exhibited a high level of genetic variation. The genetic profile of each individual is composed of 291 loci, randomly positioned in the genome and consists of monomorphic and polymorphic fragments. Similarities and dissimilarities among the individuals were quantitatively evaluated by numerical taxonomy. The overall sample shows a proportion of AFLP polymorphic markers of 71%, denoting a high level of variability. Ninety percent of the polymorphic markers identified in cork oak genotypes are uniformly distributed throughout the cork oak populations of Algarve, Alentejo and Trás-os-Montes regions. The coefficients of genetic similarity vary from 0.61 to 0.88 implying that 60% of fragments found are common. A sample of 52 holm oak [Quercus ilex subsp. rotundifolia (Lam.)] trees from overlapping areas was also analysed by AFLP with the same five primer combinations. However the codification of markers together with those selected on cork oak profiles was feasible with only one primer combination due to an apparent much higher polymorphism. AFLP and numerical taxonomy analysis enabled to differentiate the taxa and showed that the level of similarity observed between the profiles of the individuals from holm oak species was lower than that observed in cork oak, implying that apparently the degree of polymorphism is higher in Q. ilex subsp. rotundifolia than that quantified in Q. suber. A Bayesian approach was used to assess Q. suber total genetic diversity (Ht = 0.2534, P < 0.001) of which 1.7% (Fst = 0.0172, P < 0.001) was assigned to differences among populations. Analysis of molecular variance (AMOVA) showed that most genetic variation is comprised within populations (96%) while 3.6% is among populations (Φst = 0.036, P < 0.001). Differences among populations within geographic regions account for 2.6% (Φsc = 0.026, P < 0.001) of the total variation and only 1.3% (Φct = 0.013, P = 0.007) is attributed to variation among regions denoting little differentiation of populations over a range of 700 km.

Open access

Nicoleta P. Berbec, Sorina M.F. Papuc, Andreea C.D.F. Tutulan-Cunita, Silvana M. Angelescu, Anca I. Lupu and Aurora A. Arghir

Abstract

De novo acute myeloid leukemias (AML) represent a heterogeneous group of clonal hematopoietic disorders in which chromosomal abnormalities are detected in a majority of patients. At present, cytogenetic changes are recognized as important diagnostic markers and prognosis determinants. Complex karyotype changes are associated with resistance to treatment and unfavorable evolution. We report on an AML case with complex karyotype changes characterized by molecular genetic techniques (fluorescence in situ hybridization - FISH and array-based comparative genomic hybridization - array-CGH) and an extremely poor outcome. A 72 year-old female patient was admitted for genetic investigations with a clinical diagnosis of AML. Classical and molecular cytogenetic tests as well as array-CGH were performed. Complex chromosomal abnormalities were identified at diagnosis, consisting of genomic imbalances involving chromosomes 6, 7, 9, and 17. AML with complex karyotype changes is a heterogeneous disease, as a variety of genomic abnormalities are detected, involving virtually all chromosomes. The pathogenesis of AML with complex karyotype is poorly understood. The complexity of karyotypic changes in our case highlights the importance of using complementary genetic investigation in order to obtain a comprehensive view of AML genome.

Open access

O. Lepais, V. Léger and Sophie Gerber

References CHIKHI, L. and M. BRUFORD (2005): Mammalian population genetics and genomics, pp. 539-584. In: Mammalian Genomics, edited by A. RUVINSKY and J. MARSHALL Graves, CAB International. DUMOLIN, S., B. DEMESURE and R. J. PETIT (1995): Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theoretical and Applied Genetics 91: 1253-1256. GERBER, S., P. CHABRIER and A. KREMER (2003): FaMoz: a software for parentage analysis using dominant, codominant

Open access

D. Torres-Dini, A. C. P. Nunes, A. Aguiar, N. Nikichuk, C. Centurión, M. Cabrera, M. L. T. Moraes, M. D. V. Resende and A. M. Sebbenn

References Aguiar AV de, Teixeira-Freitas DMA, de Almeida Filho JE, Sousa VA, Resende MDV, Silva-Junior OB, Grattapaglia D (2015) Genomic prediction of growth traits in Pinus taeda using genome-wide sequence-based DArT-seq markers. In: IUFRO TREE Biotechnol Conference 2015, Florence, Italy: Forests: the importance to the planet and society. Balmelli G, Resquin F (2005) Evaluación productiva de origenes de Eucalyptus globulus en zonas litoral y norte. Serie Técnica INIA 149:1–19. Balmelli G, Resquin F (2008) Evaluación productiva de especies de

Open access

C. G. Jones, J. A. Plummer, E. L. Barbour and M. Byrne

References ALDRICH, P. R. and J. DOEBLEY (1992): Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor: Theor. Appl. Genet. 85: 293-302. ANONYMOUS (2003): Geology of Timor Leste. (United Nations Economic and Social Commission for Asia and the Pacific (UNESCAP) www.unescap.org/esd/water/publications/mineral/amrs/vol17: Bangkok) AUSTERLITZ, F., S. MARIETTE, N. MACHON, P.-H. GOUYON and B. GODELLE (2000): Effects of colonization processes on genetic diversity

Open access

D. Gömöry, L. Paule, D. Krajmerová, I. Romšáková and J. Piecka

trials at sites in England and Wales. Forestry 76: 385-399. DOYLE, J. J. and J. L. DOYLE (1987): A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11-15. EDMANDS, S. and C. C. TIMMERMAN (2003): Modeling factors affecting the severity of outbreeding depression. Cons. Biol. 17: 883-892. ELLISON, C. K. and R. S. BURTON (2008): Interpopulation hybrid breakdown maps to the mitochondrial genome. Evolution 62: 631-638. ERIXON, P. and B. OXELMAN (2008): Reticulate or

Open access

Eduardo P. Cappa and Michael U. Stoehr

trials is enhanced by including a spatially correlated residual. Can J For Res 31:1887-1893. Available at http://dx.doi.org/10.1139/cjfr-31-11-1887 Costa e Silva J, Potts BM, Dutkowski GW (2006) Genotype by environment interaction for growth of Eucalyptus globulus in Australia. Tree Genet Genomes 2:61–75. Available at http://dx.doi.org/10.1007/s11295-005-0025-x Ding M, Tier B, Dutkowski GW (2008) Multi-environment trial analysis for Pinus radiata. New Zeal J For Sci 38:143-159 Dutkowski GW, Costa e Silva J, Gilmour AR, Lopez GA (2002) Spatial