Development and characterization of microsatellite loci for Ficus hirta (Moraceae)

High genetic diversity and low population differentiation of a medical plant Ficus hirta Vahl., uncovered by microsatellite loci: implications for conservation and breeding

BACKGROUND

Wuzhimaotao (Radix Fici Hirtae) originates from the dry root of Ficus hirta (Moraceae), which is widely known as a medical and edible plant distributed in South China. As the increasing demand for Wuzhimaotao, the wild F. hirta has been extremely reduced during the past years. It is urgent to protect and rationally develop the wild resources of F. hirta for its sustainable utilization. However, a lack of genetic background of F. hirta makes it difficult to plan conservation and breeding strategies for this medical plant. In the present study, a total of 414 accessions of F. hirta from 7 provinces in southern China were evaluated for the population genetics using 9 polymorphic SSR markers.

RESULTS

A mean of 17.1 alleles per locus was observed. The expected heterozygosity (He) varied from 0.142 to 0.861 (mean = 0.706) in nine SSR loci. High genetic diversity (H_e = 0.706, ranged from 0.613 to 0.755) and low genetic differentiation among populations (G'_ST = 0.147) were revealed at population level. In addition, analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (96.2%) was significantly higher than that among populations (3.8%). Meanwhile, the three kinds of clustering methods analysis (STRUCTURE, PCoA and UPGMA) suggested that the sampled populations were clustered into two main genetic groups (K = 2). Mantel test showed a significant correlation between geographic and genetic distance among populations (R² = 0.281, P < 0.001). Pollen flow, seed flow and/or geographical barriers might be the main factors that formed the current genetic patterns of F. hirta populations.

CONCLUSIONS

This is a comprehensive study of genetic diversity and population structure of F. hirta in southern China. We revealed the high genetic diversity and low population differentiation in this medicinal plant and clarified the causes of its current genetic patterns. Our study will provide novel insights into the exploitation and conservation strategies for F. hirta.

Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification

BACKGROUND

Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species.

RESULTS

Sixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva.

CONCLUSIONS

The 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.

Systems biology approach in plant abiotic stresses

Plant abiotic stresses are the major constraint on plant growth and development, causing enormous crop losses across the world. Plants have unique features to defend themselves against these challenging adverse stress conditions. They modulate their phenotypes upon changes in physiological, biochemical, molecular and genetic information, thus making them tolerant against abiotic stresses. It is of paramount importance to determine the stress-tolerant traits of a diverse range of genotypes of plant species and integrate those traits for crop improvement. Stress-tolerant traits can be identified by conducting genome-wide analysis of stress-tolerant genotypes through the highly advanced structural and functional genomics approach. Specifically, whole-genome sequencing, development of molecular markers, genome-wide association studies and comparative analysis of interaction networks between tolerant and susceptible crop varieties grown under stress conditions can greatly facilitate discovery of novel agronomic traits that protect plants against abiotic stresses.

Development of 14 polymorphic microsatellite loci for Ficus tikoua (Moraceae)

PREMISE OF THE STUDY

Polymorphic microsatellite markers were developed to facilitate studies on the fine-scale population genetic structure of Ficus tikoua (Moraceae), a prostrate shrub known to have highly restricted gene flow.

METHODS AND RESULTS

Microsatellite primers were developed using the biotin-streptavidin capture method and scanned for polymorphism within 76 individuals sampled from three natural F. tikoua populations. Fourteen loci were shown to be polymorphic, with allele numbers ranging from three to 16. The observed and expected heterozygosity in the three populations ranged from 0 to 1 and from 0 to 0.87, respectively. Substantial divergence was found among the populations at some loci. All loci can be successfully amplified in at least eight other Ficus species, indicating good transferability within the genus.

CONCLUSIONS

The 14 microsatellite loci will be a helpful tool for assessing the fine-scale genetic structure of F. tikoua.