Genome-wide assessment of population genetic and demographic history in Magnolia odoratissima based on SLAF-seq

Magnolia odoratissima is a highly threatened species, with small distribution and scattered populations due to habitat fragmentation and human activity. In this study, the genetic diversity and population structure of the five remaining natural populations and two cultivated populations of M. odoratissima were analyzed using single nucleotide polymorphisms (SNPs) derived from specific-locus amplified fragment sequencing. A total of 180,650 SNPs were identified in seventy M. odoratissima individuals. The Nei’s and Shannon-Wiener diversity index across all M. odoratissima population were 0.35 and 0.51, respectively, while the observed heterozygosity (Ho) and expected heterozygosity (He) were 0.27 and 0.34, respectively. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. The FST and AMOVA indicated that high genetic differentiation exists among populations, and a phylogenetic neighbor-joining tree, Bayesian model–based clustering and discriminant function analysis of principal component all divided the M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations. Demographic history inferences indicated show that three clusters of M. odoratissima experienced at least three bottlenecks and resulted in a decrease of effective population size. Our results suggest that three distinct evolutionary significant units should be set up to conserve this critically endangered species.