Development and characterization of 20 novel EST-SSR markers for Pteroceltis tatarinowii, a relict tree in China

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

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.

Potential geographic distribution of relict plant Pteroceltis tatarinowii in China under climate change scenarios

Pteroceltis tatarinowii (Pteroceltis: Ulmaceae) is a deciduous tree that has a cultivation history of more than 2000 years in China. As an excellent afforestation tree species and rare and endangered tertiary relic plant, P. tatarinowii has high ecological protection value. Due to the forest destruction caused by predatory logging and natural environmental factors, the population of P. tatarinowii in China has decreased significantly. In this study, the potential geographical distribution of P. tatarinowii in China under climate change was predicted using MaxEnt model and ArcGIS based on 223 effective distribution points of P. tatarinowii and 11 environmental variables. The results showed that: (1) the prediction accuracy of MaxEnt model was extremely high, and the areas under curve (AUC) value of the training data was 0.936; The area of the potential suitable habitat area of P. tatarinowii under current climate condition was 180.84×10⁴ km², and mainly located in the central and southeast regions of China. (2) The domain environmental variables affecting the potential geographical distribution of P. tatarinowii were min temperature of coldest month (12.1~22.7°C), isothermality (26.6~35.8), mean diurnal range 6.9~9.3°C and precipitation of wettest month (189.5 ~955.5 mm). (3) In 2050s and 2070s, compared with current (4.19×10⁴ km²), the area of highly suitable habitat will increase by 0.2%-0.3% (RCP2.6) and 1.22%-3.84% (RCP8.5) respectively. while the poorly, moderately and total suitable habitats will decrease. The gravity center of P. tatarinowii showed a trend of migration to higher latitudes and northern regions in the future. These results will provide theoretical basis for cultivation management and resource protection of P. tatarinowii.

De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae)

Zelkova schneideriana Hand.-Mazz. of the Ulmaceae family is a Tertiary relict and economically deciduous tree species endemic to Central and Southern China. In this study, we performed a transcriptome sequencing of Z. schneideriana using high-throughput sequencing approach to detect polymorphic expressed sequence tag-simple sequence repeats (EST-SSR) markers. A total of 3,235 microsatellite loci were detected from 53,517 unigenes. A set of 30 microsatellite markers were randomly selected to validate in 41 individuals from three populations, of which 10 were polymorphic. The number of alleles per locus ranged from 3 to 11. The observed heterozygosity and expected heterozygosity ranged from 0.366 to 0.829 and 0.439 to 0.848, respectively. These polymorphic SSR primers showed good transferability across different Zelkova species, and are valuable for future studies on genetic diversity, conservation, phylogeography, and species delimitation in Z. schneideriana, as well as other Zelkova species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02968-5.

Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide

White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover.