Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (N_A) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (H_O) and expected (H_E) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96–84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.

Erythrophleum fordii Oliv. is a valuable rosewood species indigenous to the tropical and warm sub-tropical zones of Vietnam, Laos, and South China. The natural forests have been heavily fragmented mostly due to over-exploitation and over-utilization, and alteration to croplands and fast-growing plantations. Therefore, it has been included in the IUCN Red List of Endangered Species as an endangered species. In the present study, genetic diversity and population genetic structure of 11 populations were estimated by SSR makers in South China. Five high polymorphic loci were studied with a total of 34 alleles, among which, seven were private alleles. The mean number of alleles per locus (A), the mean number of efficient alleles per locus (Ae), the observed (Ho) and expected (He) heterozygosity, and Shannon’s index (I) of the 11 populations were 3.40, 2.31, 0.52, 0.56, and 0.90, respectively. Correlation analysis between genetic parameters and geographical factors showed that He and I were in significant negative correlation with longitude, indicating that genetic diversity of E. fordii reduced gradually from West to East in south China. F_IS of eight populations with above five samples was on average 0.01, most loci conformed to Hardy-Weinberg equilibrium in these populations; their genetic differentiation coefficient (F_ST) was 0.18, indicating that genetic differentiation among populations was relatively low and there existed 18% genetic variation among populations. Gene flow (Nm) between these populations was 1.28. The Mantel test showed that genetic distance was not significantly correlated with geographical distance (p > 0.05). It was concluded that populations with high genetic diversity or private alleles, especially Longmen, Wuming and Pingxiang populations should be a priority for in situ conservations, meanwhile more populations and as many families as possible in each population should be collected for ex situ conservations of germplasm resources of this species in the future.