Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (Sassafras tzumu) Revealed by Novel Nuclear Microsatellite (nSSR) Markers

Abstract

Sassafras tzumu (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of S. tzumu are still lacking and remain largely unclear. Here, we predicted 16,215 candidate polymorphic nuclear microsatellite (nSSR) loci from the assembled nucleus databases of six geographic-distant individuals of S. tzumu via CandiSSR. Among these nSSRs, the di- (75.53%) and tri-nucleotide (19.75%) repeats were the most abundant, and 27 new polymorphic SSRs were developed and characterized in 136 individuals from six natural populations of S. tzumu. The majority of the above 27 SSRs (24 loci, 88.89%) presented moderate polymorphism (mean PIC = 0.356), and the transferability of these markers in other Sassafras species was high (85.19%). A moderately low level of genetic diversity and a high variation (FST = 0.286) of six wild populations of S. tzumu were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity (HE) of 0.430 at the species level and HE ranging from 0.195 to 0.387 at the population level. Meanwhile, a bottleneck effect was shown in two populations. Consistent with the results of the principal coordinate analysis (PCoA) and phylogenetic trees, structure analysis optimally divided these six S. tzumu populations into two clusters, and the further strong population subdivision appeared from K = 2 to K = 5, which corresponded to two evolutionarily significant units (ESUs). Moreover, the significant correlation between genetic and geographic distance was tested by the Mantel test (r = 0.742, p = 0.006), clarifying the effect about isolation by distance (IBD), which could be possibly explained by the low gene flow (Nm = 0.625), a relatively high degree of inbreeding (FIS = 0.166), a relatively large distribution, and mountainous barriers. Above all, our research not only enlarged the useful genetic resources for future studies of population genetics, molecular breeding, and germplasm management of S. tzumu and its siblings but also contributed to proposing scientific conservation strategies and schemes for the better preservation of S. tzumu and other Sassafras (Lauraceae) species.

Genetic structure of an endangered species Ormosia henryi in southern China, and implications for conservation

“…In southern China, there are several major mountains (e.g., Wuyi Mountains, Nanling Mountains) that might serve as physical barriers to prevent the gene exchange between populations. Strong IBD patterns have been found in many other tree species in this region, such as Castanopsis fargesii [ 37 ], Schima superba [ 38 ] and Sassafras tzumu [ 39 ] . On the other hand, no significant effects of IBE were detected by either Mantel tests or MMRR analysis.…”

Environment influences the genetic structure and genetic differentiation of Sassafras tzumu (Lauraceae)

“…Presently, investigations pertaining to the genetic diversity and genetic structure of S. tzumu populations predominantly center around the analysis of genetic diversity utilizing isoenzymes and the development of microsatellite loci [ 14 , 16 – 18 ]. Wang et al [ 17 ] used 27 polymorphic nSSRs of S. tzumu to conduct genetic diversity, genetic structure analysis and mantel tests, thus providing corresponding theoretical basis for the protection and utilization of S. tzumu . A study conducted an analysis of the genetic structure of three diminutive natural populations of S. tzumu in Hubei Province, wherein the findings explicated that the proportion of polymorphic loci in the three populations stood at 49.5%.…”