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

• Published in: Plants
• Main Authors: Shuang Wang, Ying Wang, Jingbo Zhou, Pan Li, Hungwei Lin, Ye Peng, Lipeng Yu, Yunyan Zhang, Zhongsheng Wang
• Format: Article in Journal/Newspaper
• Language: English
• Published: MDPI AG 2022
• Subjects: Sassafras tzumu; Arctic Tertiary relict plant; nuclear microsatellite; genetic diversity; population structure; population differentiation; Botany; QK1-989; Arctic
• Online Access: https://doi.org/10.3390/plants11202706; https://doaj.org/article/0ed76b401cd34a159be27109e9acd762

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 ( F ST = 0.286) of six wild populations of S. tzumu were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity ( H E ) of 0.430 at the species level and H E 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 ( N m = 0.625), a relatively high degree of inbreeding ( F IS = 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 ...