Nucleotide variation at the methionine synthase locus in an endangered tree species, Fokienia hodginsii (Cupressaceae) in Vietnam

Abstract

Nucleotide variation at the methionine synthase (MetE) locus within and among populations of an endangered forest tree Fokienia hodginsii in Vietnam was investigated in the present study. A total of 12 populations were sampled across Vietnam. The length of the sequenced locus varied from 1567 to 1559 bp. A total of 42 polymorphic sites were detected among samples. Overall, nucleotide diversity was estimated to be 0.00499 and 0.00692 at the total (ð_tot) and silent sites (ð_silent) in the pool, respectively. Nucleotide diversity within populations varied from 0.00300 to 0.00521 at the total and 0.00357 to 0.00666 at silent sites. The estimates of nucleotide diversity were lower in the 4 populations located in central and southern Vietnam (0.00300 to 0.00380) in comparison with the northern populations (ranging from 0.00399 to 0.00543). Overall estimates of genetic differentiation among 12 populations were low (F_ST = 0.093 and K_ST* = 0.078), even though both values were highly significant (P < 0.001). Pairwise analysis among 12 populations showed significant genetic differentiation as evaluated by F_ST and Snn but not significant as evaluated by K_ST*. Analysis of genetic clustering using BAPS provided the best support for all 144 sequences belonging to the same genetic cluster. The implication of the results revealed in this study in the genetic conservation of F. hodginsii was discussed.

Key words: Population genetics, conservation, forest, methionine synthase (MetE), structure.