INVESTIGATION OF THE ALLELIC COMPOSITION OF THE MA-3 MICROSATELLITE LOCUS IN SABLE (MARTES ZIBELLINA L., 1758) OF THE MIDDLE AMUR REGION: ANALYSIS OF THE COLLECTIONS OF SUCCESSIVE HUNTING SEASONS

The authors investigated the allele microsatellite locus Ma-3 composition in the Middle Amur Region sable (Martes zibellina). Three subpopulations of animals from the Bureinsky Highlands (Magan, Sutyr and Kamenushka), as well as one from the western macro slope of the Sikhote-Alin ridge (Manoma) were analyzed. The genetic material was collected for the hunting seasons of 2011/2012 – 2017/2018. Subpopulations of the northern (Magan) and middle (Sutyr) parts of the Bureinsky ridge were most similar to each other in their allele composition In the subpopulation of the Bureinsky Highlands southern part (Kamenushka) some slight differences were found. In the Manoma subpopulation, the specific allele 129 was found in hunting catches of 2012-2013 and 2017-2018. The specific allele presence in this subpopulation has proved some geographic isolation between the Sikhote Alin and the Bureinsky Highlands sable populations.

Detect and visualize tumor microsatellite instability status from next-generation sequencing data by simulating PCR techniques.

e13052 Background: Although multiplex PCR is still the golden standard technology for detecting microsatellite instability (MSI), it has some disadvantages. Firstly, its results are not quantized, and the interpretation of results can be varying for different operators. Secondly, PCR requires extra sample amount and may affect the sample amount for next-generation sequencing (NGS). So we developed a method to detect MSI status from NGS data. Methods: We developed a tool called VisualMSI, which simulates the PCR behaviors to detect the instability level of microsatellite loci. For each microsatellite locus, a pair of PCR primers are simulated by extracting the sequence from reference genome. The read pairs covering this microsatellite locus will be merged first, and then the simulated PCR primers will be mapped to the merged sequences to evaluate the inserted length. For paired tumor/normal samples, VisualMSI evaluates the earth mover's distance (EMD) between the inserted length distributions of tumor and normal. MSI status is determined by the EMD value, and is also visualized on a HTML page for manual validation. As a comparison, the MSI was also evaluated using a multiplex PCR comprising 5 loci (NR27, NR21, NR24, BAT25, and BAT26). Results: To evaluate the concordance of VisualMSI results and PCR-based results, we enrolled a group of 92 patients (39 lung cancers, 33 colorectal cancers and 20 others). For each patient, a tumor tissue sample and a blood sample were collected. White blood cells from the blood samples were also sequenced as normal control. For each patient, the 5 major MSI loci, including BAT-25, BAT-26, NR-21, NR-24 and NR-27 were evaluated by VisualMSI from NGS data, and by PCR. MSI status was categorized as MSI-H or MSI-L for each MSI locus. Finally, for the total 460 MSI loci, the VisualMSI and PCR results were concordant for 425 of them (92.39%), and were not concordant for the rest 35 (7.61%). The sensitivity is 89% (95% CI) and the specificity is 95% (95% CI), indicating that they were highly consistent. Conclusions: We developed a tool for detecting and visualizing MSI status from NGS data. The data shows that results of VisualMSI and PCR are highly concordant. This tool is now open-sourced at: https://github.com/OpenGene/VisualMSI.

Inbreeding depression level of post-larvae freshwater prawn (Macrobrachium rosenbergii) from several hatcheries in Java, Indonesia

Binur R, Pancoro A. 2017. Inbreeding depression level of post-larvae freshwater prawn (Macrobrachium rosenbergii) from several hatcheries in Java, Indonesia. Biodiversitas 18: 609-618. Inbreeding accumulation will tend to reduce genetic variation or depressed of the prawn fry produced. This problem has caused a decrease in production and quality of prawns culture in Indonesia. The purpose of this study is to measure the level of inbreeding depression prawn fry generated from several hatcheries in Java by microsatellite markers. There is four microsatellite locus to be used i.e Prk9A/T1, Prk4G/T1, TGFP16, and Mr8-88. The amplification of fourth locus using PCR with 6-carboxy-fluorescine (6-FAM) label. The number of alleles (Na) from fourth locus is Mr8-88 (11 alleles), TGFP16 (10 alleles), Prk4G/T1 (9 alleles), dan Prk9A/T1 (5 alleles), respectively. The level of polymorphism locus from highest to lowest is locus Prk4G/T1 (0.703), Prk9A/T1 (0.507), TGFP16 (0.410), and Mr8-88 (0.370), respectively. Inbreeding depression level of postlarvae (PL) M. rosenbergii tend to moderate with BBI Ciamis (He 0.444), BBUG Samas (He 0.514), LRPTBPAT Sukamandi (He 0.519), and UPBL Probolinggo (He 0.530), respectively. AMOVA analysis showed about 8.0% genetic variation among populations. From these results, it can be concluded that the PL produced indicated have been depressed. Post-larvae prawns produced from fourth hatcheries is not recommended to be a broodstock but can be used for cultivation for farmers.

Allelic state at the microsatellite locus Xgwm261 marking the dwarfing gene Rht8 in Egyptian bread wheat (Triticum aestivum L.) genotypes released from 1947 to 2004

Rht8 is widely used in dry environments such as Mediterranean regions where it increases plant adaptability. Variation at the Gatersleben wheat microsatellite Xgwm261 locus, whose 192-bp allele closely linked to the dwarfing gene Rht8, on chromosome 2D within 0.6 cM, was used to screen thirty Egyptian bread wheat genotypes released from (1947-2004) to assess the variation at this locus. There were three microsatellite allelic variants based on size. Screening of this wheat collection showed that the three alleles Xgwm261-165, Xgwm261-174 and Xgwm261-192 bp were the most frequent. The highest allele frequency was observed for a Xgwm261-165 bp fragment (65.52%) followed by a Xgwm261-174 bp fragment (24.14%). However, the allele frequency of a Xgwm261-192 bp fragment among these wheat genotypes was 10.34%. The percentage distribution of dwarfing alleles for the microsatellite locus Xgwm261 in the Egyptian wheat breeding programs was 30, 20, 20 and 30% for the wheat breeding program Giza, Sakha, Gemmiza and Sids, respectively. PIC for Xgwm261 was 0.527. Genetic heritage of Egyptian genotypes at the microsatellite locus Xgwm261 is consequence of new parental components usage, carriers short plant and early maturity attributes and consequent selection progeny with these traits in breeding programs. The present study will be helpful in characterization Egyptian wheat genotypes, as well as in accurate selection of parents for wheat breeding program in Egypt.