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Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers

Ngoot-Chin T, Zulkifli MA, van de Weg E, Zaki NM, Serdari NM, Mustaffa S, et al.

Planta, 2021 Feb 05;253(2):63.
PMID: 33544231 DOI: 10.1007/s00425-021-03567-7

MAIN CONCLUSION: Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Oil palm produces a quarter of the world's total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker-trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker-trait association analyses.

Matched MeSH terms: Ploidies*
Dysplasia and DNA ploidy to prognosticate clinical outcome in oral potentially malignant disorders

Sathasivam HP, Nayar D, Sloan P, Thomson PJ, Odell EW, Robinson M

J Oral Pathol Med, 2021 Feb;50(2):200-209.
PMID: 33151583 DOI: 10.1111/jop.13121

BACKGROUND: Oral potentially malignant disorders are a clinical conundrum as there are no reliable methods to predict their behaviour. We combine conventional oral epithelial dysplasia grading with DNA ploidy analysis to examine the validity of this approach to risk assessment in a cohort of patients with known clinical outcomes.
METHODS: Sections from diagnostic biopsies were assessed for oral epithelial dysplasia using the WHO grading system, and DNA ploidy analysis was performed using established methods. Patients reviewed for a minimum of 5 years who did not develop oral squamous cell carcinoma were classified as "non-transforming" cases. Patients that developed oral squamous cell carcinoma ≥ 6 months after the initial diagnostic biopsy were classified as having "malignant transformation."
RESULTS: Ninety cases were included in the study. Seventy cases yielded informative DNA ploidy results. Of these 70 cases, 31 progressed to cancer. Oral epithelial dysplasia grading and DNA ploidy status were both significantly associated with clinical outcome (P

Matched MeSH terms: Ploidies
Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific

Kreike CM, Van Eck HJ, Lebot V

Theor Appl Genet, 2004 Aug;109(4):761-8.
PMID: 15156282

The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia,Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were grouped according to their country of origin, to their ploidy level (diploid or triploid) and to their habitat--cultivated or wild. Gene diversity within these groups and the genetic distance between these groups were computed. Dendrograms were constructed using UPGMA cluster analysis. In each country, the gene diversity within the groups of wild genotypes was the highest compared to the diploid and triploid cultivars groups. The highest gene diversity was observed for the wild group from Thailand (0.19), the lowest for the diploid cultivars group from Thailand(0.007). In Malaysia there was hardly any difference between the gene diversity of the cultivars and wild groups, 0.07 and 0.08, respectively. The genetic distances between the diploid cultivars groups ranges from 0.02 to 0.10, with the distance between the diploid accessions from Thailand and Malaysia being the highest. The genetic distances between the wild groups range from 0.05 to 0.07. First, a dendrogram was constructed with only the diploids cultivars from all countries. The accessions formed clusters largely according to the country from which they originated. Two major groups of clusters were revealed, one group assembling accessions from Asian countries and the other assembling accessions from the Pacific. Surprisingly, the group of diploid cultivars from Thailand clustered among the Pacific countries. Secondly,a dendrogram was constructed with diploid cultivated,triploid cultivated and wild accessions. Again the division of the accessions into an Asian and a Pacific gene pool is obvious. The presence of two gene pools for cultivated diploid taro has major implications for the breeding and conservation of germplasm.

Matched MeSH terms: Ploidies
Fulltext Prognostic Implications of DNA Repair, Ploidy and Telomerase in the Malignant Transformation Risk Assessment of Leukoplakia

Thomas G, Tr S, George S P, Somanathan T, Sarojam S, Krishnankutti N, et al.

Asian Pac J Cancer Prev, 2020 Feb 01;21(2):309-316.
PMID: 32102504 DOI: 10.31557/APJCP.2020.21.2.309

BACKGROUND: Although leukoplakia shows a higher risk for malignant transformation to oral cancer, currently there are no clinically relevant biomarker which can predict the potentially high risk leukoplakia. This study aimed to investigate the genetic alterations such as DNA ploidy, telomerase expression and DNA repair capacity as predictive markers of malignant transformation risk of leukoplakia.
METHODS: The study was initiated in September 2005 and patients were followed up to March 2014. Two hundred patients with oral leukoplakia, 100 patients with oral cancer and 100 healthy, age and sex matched adults with normal oral mucosa as controls were recruited. The DNA ploidy content was measured by high resolution flow cytometry, level of telomerase expression was identified by TRAP assay and intrinsic DNA repair capacity was measured by mutagen induced chromosome sensitivity assay of cultured peripheral blood lymphocytes. The Chi-square test or Fisher's Exact test was used for comparison of categorical variables between biomarkers. A p value less than or equal to 0.05 was considered as statistically significant. Analysis was performed with SPSS software version 16. Logistic regression was used to find the association between the dependent and three independent variables.
RESULTS: There was significant difference in the distribution of ploidy status, telomerase activity and DNA repair capacity among control, leukoplakia and oral cancer group (p<0.001). When the molecular markers were compared with histological grading of leukoplakia, both DNA ploidy analysis and telomerase activity showed statistical significance (p<0.001). Both aneuploidy and telomerase positivity was found to coincide with high-risk sites of leukoplakia and were statistically significant (p.

Matched MeSH terms: Ploidies*
Phylogeny of Hopea (Dipterocarpaceae) inferred from chloroplast DNA and nuclear PgiC sequences

Choong CY, Wickneswari R, Norwati M, Abbott RJ

Mol Phylogenet Evol, 2008 Sep;48(3):1238-43.
PMID: 18280183 DOI: 10.1016/j.ympev.2008.01.004
Matched MeSH terms: Ploidies
Glutathione S-transferase activities in African catfish injected with β-naphthoflavone: effects of ploidy, gender, dose, and sampling time

Karami A, Courtenay SC

Environ Monit Assess, 2015 Nov;187(11):681.
PMID: 26452505 DOI: 10.1007/s10661-015-4906-7

Glutathione S-transferases (GST) are considered among the most controversial biomarkers of water pollutants in fish with little known about factors influencing their activities. The objective of this study was to investigate how gender, dose, ploidy, and sampling time alter hepatic GST activities in African catfish (Clarias gariepinus) following β-naphthoflavone (β-NF) injection. Newly matured male and female diploid and triploid fish were intraperitoneally (i.p.) injected with 0, 15, or 75 mg/kg of β-NF, and livers were excised 24, 48, and 72 h post-injection. Results showed that hepatic GST activities were significantly inhibited by both doses of β-NF. Inhibition was greater in females than males, but no significant differences were observed between diploid and triploid fish. Enzymatic activities differed over time with lowest levels 72 h post-injection. These results extend our understanding of GST activity in fish and highlight the necessity of considering confounding factors when comparing different studies.

Matched MeSH terms: Ploidies
Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels

Ng KK, Lee SL, Koh CL

Mol Ecol, 2004 Mar;13(3):657-69.
PMID: 14871369

Analyses of the spatial distribution pattern, spatial genetic structure and of genetic diversity were carried out in two tropical tree species with contrasting breeding systems and different ploidy levels using a 50-ha demographic plot in a lowland dipterocarp forest in Peninsular Malaysia. Shorea leprosula is a diploid and predominantly outcrossed species, whereas S. ovalis ssp. sericea is an autotetraploid species with apomictic mode of reproduction. Genetic diversity parameters estimated for S. leprosula using microsatellite were consistently higher than using allozyme. In comparisons with S. leprosula and other tropical tree species, S. ovalis ssp. sericea also displayed relatively high levels of genetic diversity. This might be explained by the lower pressure of genetic drift due to tetrasomic inheritance, and for autotetraploids each locus can accommodate up to four different alleles and this allows maintenance of more alleles at individual loci. The observed high levels of genetic diversity in S. ovalis ssp. sericea can also be due to a random retention of more heterogeneous individuals in the past, and the apomictic mode of reproduction might be an evolutionary strategy, which allows the species to maintain high levels of genetic diversity. The spatial distribution pattern analyses of both species showed significant levels of aggregation at small and medium but random distribution at the big diameter-class. The decrease in magnitude of spatial aggregation from small- to large-diameter classes might be due to compensatory mortality during recruitment and survival under competitive thinning process. Spatial genetic structure analyses for both species revealed significant spatial genetic structure for short distances in all the three diameter-classes. The magnitude of spatial genetic structure in both species was observed to be decreasing from smaller- to larger-diameter classes. The high spatial genetic structuring observed in S. ovalis ssp. sericea at the small-diameter class is due primarily to limited seed dispersal and apomictic mode of reproduction. The similar observation in S. leprosula, however, can be explained by limited seed and pollen dispersal, which supports further the fact that the species is pollinated by weak fliers, mainly of Thrips and Megalurothrips in the lowland dipterocarp forest.

Matched MeSH terms: Ploidies
Fulltext Potentially malignant disorders of the oral cavity: current practice and future directions in the clinic and laboratory

Dionne KR, Warnakulasuriya S, Zain RB, Cheong SC

Int J Cancer, 2015 Feb 1;136(3):503-15.
PMID: 24482244 DOI: 10.1002/ijc.28754

Despite commendable progress in the prevention, detection, and treatment of a wide variety of solid tumor types, oral squamous cell carcinoma (OSCC) remains a significant health burden across the globe. OSCC carcinogenesis involves accumulation of genetic alterations that coincide with the multistep malignant transformation of normal oral epithelium. OSCC is often first diagnosed at late stages of the disease (advanced regional disease and/or metastasis). Delayed diagnosis precludes successful treatment and favorable outcomes. In clinical practice, opportunities exist to identify patients with oral potentially malignant disorders (OPMDs), which precede the development of cancer. This review addresses the current status of laboratory and clinical research on OPMDs, with emphasis on leukoplakia and erythroplakia. OSF is also presented, though there is a paucity of published studies on this disorder. We focus on findings that could translate into earlier diagnosis and more efficacious treatment of those lesions with significant malignant potential. We explore how markers of OPMD malignant transformation might be implemented into current diagnostic practice to help clinicians objectively stratify patients into treatment/follow-up groups according to relative risk. We provide an overview of recently concluded and ongoing OPMD chemoprevention trials. We describe laboratory OPMD models that can be used to not only to reveal the genetic and molecular intricacies of oral cancer but also to develop novel screening methods and therapeutic approaches. Finally, we call for targeted screening programs of at-risk populations in order to facilitate diagnosis and treatment of OPMD and early OSCC.

Matched MeSH terms: Ploidies