Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer.

Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.

A genetic analysis of taoyuan pig and its phylogenetic relationship to eurasian pig breeds.

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan's early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value (FIS) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high FST values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.

Molecular adsorption at silica/CH3CN interface probed by using evanescent wave cavity ring-down absorption spectroscopy: determination of thermodynamic properties.

Evanescent wave cavity ring-down absorption spectroscopy is applied to measure the thermodynamic properties of the surface adsorption for neutral trans-4-[4-(dibutylamino)styryl]-1-(3-sulfopropyl) pyridinium (DP) and charged trans-4-[4-(dibutylamino)styryl]-1-methylpyridinium iodide (DMP+ I-) at the silica/CH3CN interface, where the interfacial density is determined by measurement of absorbance. The bulk concentration dependence of the surface density may be characterized with a Langmuir isotherm model, which yields saturated surface density, equilibrium constant, and free energy of adsorption of (7.0 +/- 0.3) x 10(13) cm(-2), (1.3 +/- 0.2) x 10(4) M(-1), and -23.5 +/- 0.4 kJ/mol for DP and (8.9 +/- 0.3) x 10(12) cm(-2), (2.6 +/- 0.7) x 10(4) M(-1), and -25.2 +/- 0.6 kJ/mol for DMP+ I-, respectively. The surface density of the isolated silanol groups may then be estimated in terms of the molecular probe results. The absorption contribution from the bulk solution is a factor of approximately 10(1)-10(2) smaller than the total absorbance measured such that subtraction of the bulk contribution leads to negligible change of the thermodynamic properties. The DP is adsorbed to the SiOH sites by forming hydrogen bonds, while the DMP+ cation is bound to the SiO- sites by electrostatic attraction. Surface forces are also probed by addition of triethylamine (TEA), which is competitive with DP for the silanol sites. When the TEA concentration is increased, the DP surface density is found to decrease, whereas the DMP+ surface density increases. The obtained thermodynamic properties are generally consistent with those measured by second harmonic generation spectroscopy. However, when a tetramethylammonium ((CH3)4N+ Cl-) salt is added, the DMP+ cation behaves differently between these two methods. Formation of an electrical double layer may account for the difference.