Comparative genetic diversity studies of Shorea curtisii (dipterocarpaceae)

An assessment using SSR and DAMD markers

W. S. Ho, R Wickneswari V Ratnam, M. C. Mahani, Shukor Md. Nor

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Genetic diversity of Shorea curtisii from different age cohorts, namely, seedlings, saplings and adult trees were determined using six SSR loci and 33 DAMD loci. To quantify genetic diversity in S. curtisii we used standard genetic diversity measures for SSR data, and both phenotypic and genotypic methods with null-allele frequency corrected for deviation from Hardy-Weinberg equilibrium (HWE) with SSR markers for DAMD data. Results showed that the genetic diversity measured using DAMD genotypic method was lower than those derived from SSR data based on the same set of samples. This suggests that DAMD allele frequencies corrected from HWE deviation using fixation index derived from SSR data may be underestimated. The genetic distance matrix generated from SSR data was significantly correlated with DAMD genotype data (r = 0.990, p < 0.05), indicating a similar genetic structure of S. curtisii being depicted by both marker types among the age cohorts tested. The relationship between sample size and genetic diversity measures demonstrated a threshold level, i.e. n = 20 and n = 30 for seedlings and saplings respectively, and n = 15 and n = 20 for adult trees revealed by SSR and DAMD markers respectively. Genetic diversity measures dropped drastically below these levels. These results further imply that a highly heterogeneous population was observed in 5. curtisii from each age cohort. Collectively, both SSR and DAMD markers have good genome coverage in the S. curtisii genome.

Original languageEnglish
Pages (from-to)22-35
Number of pages14
JournalJournal of Tropical Forest Science
Volume18
Issue number1
Publication statusPublished - Jan 2006

Fingerprint

Dipterocarpaceae
Shorea
genetic variation
sapling
saplings
Seedlings
Gene Frequency
gene frequency
allele
genome
seedling
Genome
loci
null alleles
seedlings
Genetic Structures
Sample Size
genetic structure
genetic distance
fixation

Keywords

  • DNA analyses
  • Genetic distance
  • Hill dipterocarp forest
  • Polymorphisms
  • Tropical timber species

ASJC Scopus subject areas

  • Agricultural and Biological Sciences (miscellaneous)

Cite this

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title = "Comparative genetic diversity studies of Shorea curtisii (dipterocarpaceae): An assessment using SSR and DAMD markers",
abstract = "Genetic diversity of Shorea curtisii from different age cohorts, namely, seedlings, saplings and adult trees were determined using six SSR loci and 33 DAMD loci. To quantify genetic diversity in S. curtisii we used standard genetic diversity measures for SSR data, and both phenotypic and genotypic methods with null-allele frequency corrected for deviation from Hardy-Weinberg equilibrium (HWE) with SSR markers for DAMD data. Results showed that the genetic diversity measured using DAMD genotypic method was lower than those derived from SSR data based on the same set of samples. This suggests that DAMD allele frequencies corrected from HWE deviation using fixation index derived from SSR data may be underestimated. The genetic distance matrix generated from SSR data was significantly correlated with DAMD genotype data (r = 0.990, p < 0.05), indicating a similar genetic structure of S. curtisii being depicted by both marker types among the age cohorts tested. The relationship between sample size and genetic diversity measures demonstrated a threshold level, i.e. n = 20 and n = 30 for seedlings and saplings respectively, and n = 15 and n = 20 for adult trees revealed by SSR and DAMD markers respectively. Genetic diversity measures dropped drastically below these levels. These results further imply that a highly heterogeneous population was observed in 5. curtisii from each age cohort. Collectively, both SSR and DAMD markers have good genome coverage in the S. curtisii genome.",
keywords = "DNA analyses, Genetic distance, Hill dipterocarp forest, Polymorphisms, Tropical timber species",
author = "Ho, {W. S.} and {V Ratnam}, {R Wickneswari} and Mahani, {M. C.} and {Md. Nor}, Shukor",
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T1 - Comparative genetic diversity studies of Shorea curtisii (dipterocarpaceae)

T2 - An assessment using SSR and DAMD markers

AU - Ho, W. S.

AU - V Ratnam, R Wickneswari

AU - Mahani, M. C.

AU - Md. Nor, Shukor

PY - 2006/1

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N2 - Genetic diversity of Shorea curtisii from different age cohorts, namely, seedlings, saplings and adult trees were determined using six SSR loci and 33 DAMD loci. To quantify genetic diversity in S. curtisii we used standard genetic diversity measures for SSR data, and both phenotypic and genotypic methods with null-allele frequency corrected for deviation from Hardy-Weinberg equilibrium (HWE) with SSR markers for DAMD data. Results showed that the genetic diversity measured using DAMD genotypic method was lower than those derived from SSR data based on the same set of samples. This suggests that DAMD allele frequencies corrected from HWE deviation using fixation index derived from SSR data may be underestimated. The genetic distance matrix generated from SSR data was significantly correlated with DAMD genotype data (r = 0.990, p < 0.05), indicating a similar genetic structure of S. curtisii being depicted by both marker types among the age cohorts tested. The relationship between sample size and genetic diversity measures demonstrated a threshold level, i.e. n = 20 and n = 30 for seedlings and saplings respectively, and n = 15 and n = 20 for adult trees revealed by SSR and DAMD markers respectively. Genetic diversity measures dropped drastically below these levels. These results further imply that a highly heterogeneous population was observed in 5. curtisii from each age cohort. Collectively, both SSR and DAMD markers have good genome coverage in the S. curtisii genome.

AB - Genetic diversity of Shorea curtisii from different age cohorts, namely, seedlings, saplings and adult trees were determined using six SSR loci and 33 DAMD loci. To quantify genetic diversity in S. curtisii we used standard genetic diversity measures for SSR data, and both phenotypic and genotypic methods with null-allele frequency corrected for deviation from Hardy-Weinberg equilibrium (HWE) with SSR markers for DAMD data. Results showed that the genetic diversity measured using DAMD genotypic method was lower than those derived from SSR data based on the same set of samples. This suggests that DAMD allele frequencies corrected from HWE deviation using fixation index derived from SSR data may be underestimated. The genetic distance matrix generated from SSR data was significantly correlated with DAMD genotype data (r = 0.990, p < 0.05), indicating a similar genetic structure of S. curtisii being depicted by both marker types among the age cohorts tested. The relationship between sample size and genetic diversity measures demonstrated a threshold level, i.e. n = 20 and n = 30 for seedlings and saplings respectively, and n = 15 and n = 20 for adult trees revealed by SSR and DAMD markers respectively. Genetic diversity measures dropped drastically below these levels. These results further imply that a highly heterogeneous population was observed in 5. curtisii from each age cohort. Collectively, both SSR and DAMD markers have good genome coverage in the S. curtisii genome.

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