Using of Microsatellites to Study the Genetic Polymorphisms of SRYm18 Region in Iraqi Sheep

The origin of animals is usually determined by their paternal genotypes of the genes on the Y chromosome. In addition to the genes and their polymorphisms in the genome of mitochondria that are inherited through dams. In view of the lack of studies focusing on the genes of the Y chromosome in the world and their absence in Iraq. The aim of the present study was to identify the multiple genetic polymorphisms of the SRYM18 gene in the Arabi and Awassi sheep raised in Iraq. The study was conducted in the Genetic Engineering Laboratories - College of Agriculture, University of Basra, as well as in the Basra Genome Laboratory. The amplification of the SRYM18 gene showed genetic polymorphisms and gave a gene segment of (103-880) bp. The number of alleles of the SRYm18 gene was 13 alleles in the Arabi and 16 alleles in the Awassi breeds. The equilibrium test showed that the two breeds were under equilibrium. The two breeds were identical with nine alleles, while the number of special alleles for the Arabi breed was two, while the Awassi breed was distinguished by five. The number of rare alleles reached 20, of which seven were of the Arabi breed, and 13 of them were of the Awassi breed. Mean expected heterozygosity was 0.6386 with nonsignificant Fis for Arabi breed (0.1541) but significant for Awassi breed (0.2213). Mean neutrality was close to lower bound (0.1721) and (0.1270) for Arabi and Awassi breeds respectively

Measuring drift by mean deviation: unequal breeding sex ratio revisited

When it comes to estimating the magnitude of genetic drift, there is hardly any indexes other than the effective population size. Starting from the binomial sampling distribution, this research proposed using mean deviation of allele frequency change as a direct measurement of drift, then tested it in a classical example concerning unequal breeding sex ratio. This study found that: (1) mean deviation offers a new dimension in measuring the magnitude of drift; (2) the measurement displays a half-half pattern; (3) allele frequency determines the efficacy of hitchhiking effect of rare alleles, and in what way that half-half pattern should be divided.

The Use of Genomic Information for the Conservation of Animal Genetic Diversity

The conservation of genetic diversity, both among and within breeds, is a costly process. Therefore, choices between breeds and animals within breeds are unavoidable, either for conservation in vitro (gene banks) or in vivo (maintaining small populations alive). Nowadays, genomic information on breeds and individual animals is the standard for the choices to be made in conservation. Genomics may accurately measure the genetic distances among breeds and the relationships among animals within breeds. Homozygosity at loci and at parts of chromosomes is used to measure inbreeding. In addition, genomics can be used to detect potentially valuable rare alleles and haplotypes, their carriers in these breeds and can facilitate in vivo or in vitro conservations of these genomic regions.

Identification of dwarfism loci Dw1 and Dw2 in clonal apple rootstocks using molecular markers

The paper presents the results of identification of quantitative trait loci (QTL) of Dw1 and Dw2 involved in the control of dwarf growth in clonal apple rootstocks using the molecular markers. In total, 14 forms of rootstocks were analyzed. The microsatellite markers Hi01c04, Hi04a08, CH03a09 (for the Dw1 locus), MDP0000365711, and MDP0000243703 (for the Dw2 locus) were used in the study. Analysis of the results did not reveal a relationship between the presence of a marker and the manifestation of a sign. Of the three markers of the Dw1 locus, only Hi01c04 amplifies a fragment of the expected size of 120 bp. It was found in 9 forms of rootstocks (PB-4, 57-491, 83-1-15, M9, G16, 2-12-10, 2-9-102, 4-6-5 and 70-20-20). The Hi01c04 marker was identified in both dwarf and medium-sized forms. Of the two markers of the Dw2 locus, the desired fragment is amplified in MDP0000365711. It is typical for almost all genotypes. The exception is 83-1-15, 2-12-10 and 70-20-20, which have a null allele. To assess the genetic diversity of the Dw1 and Dw2 loci, 6 microsatellite sequences Hi01c04, Hi04a08, CH03a09, CH02d08, MDP0000365711, and MDP0000243703 were used. In 14 studied samples, 29 allelic variants ranging in size from 102 bp. up to 170 bp were identified. The number of alleles per locus varied from 1 (for the MDP0000365711 locus) to 7 (for the Hi04a08 locus). No rare alleles were identified. All alleles were observed more than three times. Based on the analysis of SSR spectra, a dendrogram reflecting the similarity of the genotypes under study was built.

Microsatellite loci variability in apple cultivars developed at VIR

Background. Microsatellite (SSR) markers are now widely used both for studying genetic diversity in fruit crop collections, including apple (Malus × domestica Borkh.), and for genotyping individual accessions. The apple collection held by VIR, being the largest in Russia, contains cultivars bred at five experiment stations of VIR. These cultivars not only meet the requirements of horticulture in the region of their origin, but also are interesting as sources of valuable traits for breeding programs. However, these cultivars have not previously been studied using microsatellite markers. Materials and methods. A set of 10 SSR markers (CH02c02b, CH03d01, CH01f03b, CH02d08, CH02c02a, CH05e03, CH02c09, CHVf1, CH01h01, COL) was used for genotyping 35 apple cultivars developed at VIR and four parental forms. Fluorescently labeled PCR products were separated by capillary electrophoresis on ABI Prism 3130xl.Results. In 35 apple cultivars from VIR, 97 alleles were identified at ten studied loci. The number of alleles per locus varied from 5 (CH02c02b) to 17 (CH02c02a). The frequency of unique alleles was 26,8%, with 12,4% for rare alleles. Polymorphism information content (PIC) values varied from 0,49 (CH02c02b) to 0,91 (CH02c02a) and averaged 0,76. Expected and observed heterozygosity levels averaged 0,79 and 0,56, respectively. Cluster analysis did not reveal a clear division of cultivars according to the place of origin (experiment stations of VIR), but revealed clustering according to pedigrees.Conclusion. A high level of polymorphism was observed in 35 apple cultivars from VIR using ten SSR markers. The obtained data on the allelic composition of the studied cultivars can be used for their identification and contribute to more efficient collection management. Further studying and SSR genotyping of VIR’s apple collection and comparison with the data obtained in the presented work can help to identify the origin of cultivars with unknown pedigrees.

Comparative analysis of allele variation using allele frequencies according to sample size in Korean population

Background Allele frequency using short tandem repeats (STRs) is used to calculate likelihood ratio for database match, to interpret DNA mixture and to estimate ethnic groups in forensic genetics. In Korea, three population studies for 23 STR loci have been conducted with different sample size for forensic purposes. Objective We performed comparative analysis to determine how the difference of sample size affects the allele frequency and allele variation within same ethnic population (i.e. Korean). Furthermore, this study was conducted to check how the sampling group and multiplex kit also affect allele variation such as rare alleles and population specific alleles. Methods To compare allele variation, we used allele frequencies of three population data published from three Korean forensic research groups. Allele frequencies were calculated using different sample sizes and multiplex kits: 526, 1000, and 2000 individuals, respectively. Results The results showed the different distribution of allele frequencies in some loci. There was also a difference in the number of rare alleles observed by the sample size and sampling bias. In particular, an allele of 9.1 in the D2S441 locus was not observed in population study with 526 individuals due to multiplex kits. Conclusion Because the allele frequencies play an important role in forensic genetics, even if the samples are derived from the same population, it is important to consider the effects of sample size, sampling bias, and selection of multiplex kits in population studies.

Genetic structure of the carp population (Cyprinus carpio carpio) grown in the aquaculture in the Republic of Belarus

In this study, we presented a panel of 14 microsatellite loci (MFW1, MFW2, MFW6, MFW9, MFW10, MFW11, MFW13, MFW16, MFW20, MFW24, MFW26, MFW28, MFW29 and Cid0909), with which we studied the genetic structure of Cyprinus carpio carpio of the breed “Izobelinsky” in the Republic of Belarus. Four offshoots of carp were included in the study: two mirrory (“Smes’ zerkal’naya”, “Tri prim”) and two scaly (“Smes’ cheshujchataya”, “Stolin XVIII”).As a result, it was found that the carp breed “Izobelinsky” exhibits a high level of in-breed genetic variability. In the studied microsatellite loci, 231 alleles were identified, 62 % of the total number of alleles were rare alleles with a frequency of occurrence of less than 5.0 %. The number of effective alleles (Ne) at the loci ranged from 3.082 (MFW10) to 9.754 (MFW26). The Shannon biodiversity index (I) was 2.082 ± 0.075. The highest value of the expected heterozygosity index (He) was noted for the MFW26 locus (0.897), the lowest – for the MFW10 locus (0.676).The greatest genetic diversity is characteristic of the scaly carp “Smes’ cheshujchataya” and “Stolin XVIII”. The highest total percentage of rare alleles was determined for fishes from “Stolin XVIII”. The minimum values of this parameter were found for specimens of the carp “Smes’ zerkal’naya” and “Tri prim”.The results of this study indicate a fairly high genetic diversity of four offshoots of the carp breed “Izobelinsky”, which was established using the marker loci optimally selected for analysis. This makes it possible to differentiate the layering among themselves.

Identification and functional characterization of the extremely long allele of the serotonin transporter-linked polymorphic region

SLC6A4, which encodes the serotonin transporter, has a functional polymorphism called the serotonin transporter-linked polymorphic region (5-HTTLPR). The 5-HTTLPR consists of short (S) and long (L) alleles, each of which has 14 or 16 tandem repeats. In addition, the extralong (XL) and other rare alleles have been reported in 5-HTTLPR. Although they are more frequent in Asian and African than in other populations, the extent of variations and allele frequencies (AFs) were not addressed in a large population. Here, we report the AFs of the rare alleles in a large number of Japanese subjects (N = 2894) consisting of two cohorts. The first cohort (case-control study set, CCSS) consisted of 1366 subjects, including 485 controls and 881 patients with psychosis (bipolar disorder or schizophrenia). The second cohort (the Arao cohort study set, ACSS) consisted of 1528 elderly subjects. During genotyping, we identified 11 novel 5-HTTLPR alleles, including 3 XL alleles. One novel allele had the longest subunit ever reported, consisting of 28 tandem repeats. We named this XL28-A. An in vitro luciferase assay revealed that XL28-A has no transcriptional activity. XL28-A was found in two unrelated patients with bipolar disorder in the CCSS and one healthy subject in the ACSS who did not show depressive symptoms or a decline in cognitive function. Therefore, it is unlikely that XL28-A is associated with psychiatric disorders, despite its apparent functional deficit. Our results suggest that unraveling the complex genetic variations of 5-HTTLPR will be important for further understanding its role in psychiatric disorders.