Mitochondrial DNA variation in natural populations of Japanese larch (Larix kaempferi)

Abstract

Levels of genetic variation within and among natural populations of Japanese larch [Larix kaempferi (Lamb.) Carrière] were evaluated by Restriction Fragment Length Polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) obtained from 209 individuals representing 14 natural populations distributed across most of the species’ natural range in central Japan. Polymorphisms were screened by two RFLP techniques: Southern hybridization of mitochondrial gene probes and Polymerase Chain Reaction (PCR)-RFLP analysis of sequence-tagged sites. However, obvious polymorphism was only detected around the coxIII gene, following digestion with the EcoRI restriction enzyme, in the Southern hybridization analysis. Five haplotypes were identified across the 14 populations, with 11 populations exhibiting little or no genetic variation. Within-population genetic variation was low (HS = 0.158), while population differentiation was substantial (a standardized genetic differentiation measure, G’ST = 0.581). The northernmost, marginal population on Mt. Manokamidake made a significant contribution to the total detected genetic variation. The mtDNA variation displayed geographic structure despite the restricted natural distribution of Japanese larch. Results of this study should be useful for establishing criteria for the genetic conservation and management of natural populations of the species.

Utility of the Mitochondrial Genome in Plant Taxonomic Studies

“…Universal primers were defined in conserved regions (exons) and were used to amplify mtDNA regions with conserved microsynteny. Polymorphism in amplified fragment has been revealed with various methods: PCR-RFLP (Boonruangrod et al, 2008;Godbout et al, 2005;San Jose-Maldia et al, 2009;Moriguchi et al, 2009;Naydenov et al, 2007), RFLP-SSR (Burban and Petit, 2003;Godbout et al, 2005;Jaramillo-Correa et al, 2003), mtDNA-SSR (Hosaka and Sanetomo, 2009), the variable number of tandem repeats (VNTR) in minisatelite regions (Bastien et al, 2003;Fievet et al, 2007;Honma et al, 2011;Yoshida et al, 2012), and finally in DNA sequences (Avtzis and Aravanopoulos, 2011;Eckert et al, 2008;Edwards et al, 2005;Goodall-Copestake et al, 2010;Gugger et al, 2011). The choice of the candidate loci was limited and was depending on the taxonomic level addressed by the phylogenetic study.…”