TU-DAMD employment for molecular characterization of Salvia judaica and Salvia palaestina species

Genetic diversity in perennial Salvia judaica Boiss (Judean sage) and Salvia palaestina Benth (Palestinian sage) species using touch-up directed amplification of minisatellite region DNA (TU-DAMD) has been performed in two separated sets; in the first set (set A) the initial annealing temperature was increased from 50 °C to 55 °C, whereas, in the second one (set B), it increased from 55 °C to 60 °C by 0.5 °C/cycle during the first 10 PCR amplification cycles. Fifteen DAMD primers have been tested for each set. Set (A) produced 89.39% polymorphism level (P%) with polymorphic information content (PIC) average of 0.33 and marker index (MI) average of 3.96. Whereas, in set (B) these values were recorded to be 94.02%, 0.34 and 3.98 for P%, PIC and MI, respectively. Data showed that the two mentioned sets successfully highlighted high polymorphism level between the two studied Salvia sp. This work studies genetic diversity of S. judaica and S. palaestina species using TU-DAMD test as a novel molecular marker.

Genetic diversity and relationships among salvia species by ISSR markers

Species identification is fundamentally important within the fields of conservation, biology, biogeography and ecology. Salvia species are herbaceous, biennial or annual, strongly aromatic. Inter-Simple sequence repeats (ISSR) molecular markers were used for evaluate genetic diversity and relationship analysis of 30 Salvia species. Ten selected ISSR primers amplified 116 loci, respectively, of which all were polymorphic. The obtained average polymorphism information content 0.39, average band informativeness 10.5 and the marker index 3.1 revealed high genetic diversity prevailing among Salvia accessions. The dendrogram was constructed based on ISSR separated the individuals into sub-clusters in accordance with their species. Our results indicated that ISSR markers can be used as a reliable and informative technique for evaluation of genetic diversity and relationships among Salvia species. The objectives of present study are: 1) can ISSR markers identify Salvia species, 2) what is the genetic of these taxa in Iran, and 3) to investigate the species inter-relationship?

PENGEMBANGAN METODE PENANDA ISOZYME PADA TREMBESI

Fifty samples of raintree from Sangatta, the capital city of Kutai Timur Regency, East Kalimantan were analyzed using isozyme markers to determine the characteristics of the banding pattern. The use of isozymes was intended as a biochemical marker for genetic diversity analysis. This study aimed to determine the enzyme system that could be used to determine genetic diversity of raintree. The enzyme systems used were diaphorase, esterase, and peroxidase. Polymorphism assessments were carried out on the parameters of expected heterozygosity (H), polymorphism information content (PIC), effective multiplex ratio (E), marker index (MI), discriminanting power (D), and Resolving (R). Among the three enzyme systems used, diaphorase showed consistent performance against each of the parameters assessed, with a value of H =0.475; PIC = 0.362; E =6.1; MI = 2,2; D = 0.63: and R = 4.44. However, esterase had the highest multiplex effective ratio (E = 6.16). Therefore, diaphorase is the best isozyme marker that can be used to analyze the genetic diversity of raintree.

Comprehensive analysis of Japanese population history by detecting ancestry-marker polymorphisms without using ancestral genomic information

Modern Japanese are considered to derive from a mixture of two major ancestral populations: the indigenous Jomon people and immigrants from continental East Asia. Since most of the existing methods for detecting genetic components from ancestral populations require their genomes, ancestral genomic components in Japanese could not detected so far due to the lack of precisely sequenced ancient Jomon genomes. To overcome the difficulty, we developed a reference-free detection method using a novel summary statistic, the ancestry-marker index (AMI). We applied the AMI to modern Japanese samples from the 1000 Genomes Project and identified 208,648 ancestry-marker SNPs that were likely derived from the Jomon people (Jomon-derived SNPs). Comparing the Jomon allele score detected in this study with modern Japanese and two ancient Jomon individuals showed that the Jomon derived SNPs were detected with high accuracy by the AMI in real data, and that the Jomon derived SNPs were detected by several tens of times from a single Jomon individual by the AMI. The analysis of Jomon-derived SNPs in 10,842 modern Japanese individuals recruited from all the 47 prefectures of Japan showed that the genetic differences among the prefectures were mainly caused by differences in the admixture proportion of the Jomon people, due to the difference of population size of immigrants in the final Jomon to the Yayoi period. We also confirmed the presence of the Jomon alleles around phenotype associated SNPs characteristic of East Asians to clarify whether these phenotypes of modern Japanese were derived from the Jomon people.

Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration

Drought and desertification are the major environmental constraints facing the Sahelian agro-ecosystems for decades. Assessing genetic diversity of native tree species is critical to assist ecosystems restoration efforts. Here we describe genetic diversity and structure of seven Balanites aegyptiaca L. natural populations distributed across the Sahelian-Saharan zone of Mauritania using 16 polymorphic ISSR primers. These generated 505 polymorphic bands. Polymorphism information content (PIC) varied from (0.13–0.29) with an average 0.23, marker index (MI) averaged 7.3 (range 3.3–10.3) and resolving power (RP) ranged from (4.53–14.6) with an average 9.9. The number of observed alleles (Na) ranged from (0.62–1.39), Effective number of alleles (Ne) varied from (1.26–1.37), Shannon’s information index (I) ranged from (0.25–0.36). AMOVA analysis showed that 80% of the genetic variation was fined within populations, which is supported by a low level of genetic differentiation between population (GST = 0.21) and an overall estimate of gene flow among populations (Nm = 1.9). The dendrogram based on Jaccard's similarity coefficient and the structure analysis divided the seven populations into two main clusters in which two populations from the Saharan zone were grouped. Our results provide baseline data for genetic conservation programs of this Sahelian neglected crop and with an important econ-ecological role.