SNP discovery in Cryptomeria japonica var. sinensis using restriction-site associated DNA sequencing (RAD-seq）

Our study is the first to explore the genetic composition of ancient
Cryptomeria trees across distribution range in China. Background and
Objectives: Cryptomeria japonica var. sinensis is a native forest species
of China; it is widely planted in the south of the country to create
forests and for wood production. Unlike Cryptomeria in Japan, genetic
Chinese Cryptomeria has seldom been studied, although there is ample
evidence of its great ecological and economic value. Materials and
Methods: Because of overcutting, natural populations are rare in the wild.
In this study, we investigated seven ancient tree populations to explore
the genetic composition of Chinese Cryptomeria through ddRAD-seq
technology. Results: The results reveal lower genetic variation but higher
genetic differentiation (Ho=0.143, FST=0.1204) than Japanese Cryptomeria
(Ho=0.245, FST=0.0455). The 86% within-population variation is based on
analysis of molecular variance (AMOVA). Significant excess heterozygosity
was detected in three populations and some outlier loci were found; these
were considered to be the consequence of selection or chance. STRUCTURE
analysis and dendrogram construction divided the seven ancient tree
populations into four groups corresponding to the geographical provinces
in which the populations are located, but there was no obvious correlation
between genetic distance and geographic distance. Demographic history
analysis conducted by a Stairway Plot showed that the effective population
size of Chinese Cryptomeria had experienced a continuing decline from the
mid-Pleistocene to the present. Our findings suggest that strong genetic
drift caused by climate fluctuation and intense anthropogenic disturbance
together contributed to the current low diversity and structure.
Considering the species’ unfavorable conservation status, strategies are
urgently required to preserve the remaining genetic resources.