Genotyping Of Loci Research Articles

The effect of SOX4 gene 3\u2032UTR polymorphisms on osteoporosis

ObjectiveThis study aimed to explore the correlation between the SRY-related high-mobility-group box gene 4 (SOX4) 3′ untranslated region (UTR) single nucleotide polymorphism (SNP) and osteoporosis susceptibility.MethodsThe study recruited 330 osteoporosis patients (the case group) and 330 non-osteoporosis patients (the control group) in Sichuan Chengdu First People’s Hospital and Zibo Central Hospital from August 2016 to August 2019. Sanger sequencing was used to analyze the genotypes of SOX4 gene rs79958549, rs139085828, and rs201335371 loci. Multi-factor dimensionality reduction (MDR) was used to analyze the interaction between the SOX4 gene rs79958549, rs139085828, and rs201335371 loci and the clinical characteristics of the subjects.ResultsThe risk of osteoporosis in the carriers of A allele at SOX4 rs79958549 was 5.40 times that in the carriers of the G allele (95% CI 3.25–8.96, P < 0.01). The risk of osteoporosis in the carriers of the A allele at SOX4 rs139085828 was 1.68 times that in the carriers of the G allele (95% CI 1.45–1.85, P < 0.01). The risk of osteoporosis in the carriers of the T allele at SOX4 rs201335371 was 0.54 times that in the carriers of the C allele (95% CI 0.43–0.69, P < 0.01). The SOX4 gene rs79958549, rs139085828, and rs201335371 A-A-C haplotype (OR = 5.14, 95% CI 2.45–10.57, P < 0.01) were associated with increased risk of osteoporosis and G-G-T haplotype was significantly associated with decreased risk of osteoporosis (OR = 0.48, 95% CI 0.38–0.62, P < 0.01). The interaction among the factors of sex, smoking, drinking, rs79958549, rs201335371 was the best model for osteoporosis prediction, and the risk for osteoporosis in ‘high-risk combination’ was 2.74 times that of ‘low-risk combination’ (95% CI 1.01–7.43, P = 0.04). Multiple logistic regression analysis revealed that the risk factors for osteoporosis were BMD (OR = 5.85, 95% CI 2.88–8.94, P < 0.01), T score (OR = 8.54, 95% CI 5.66–10.49, P < 0.01), Z score (OR = 3.77, 95% CI 2.15–8.50, P < 0.01), rs79958549 SNP (OR = 6.92, 95% CI 3.58–8.93, P < 0.01), and rs139085828 SNP (OR = 2.36, 95% CI 1.85–4.27, P < 0.01). The protective factor for osteoporosis was rs201335371SNP (OR = 0.48, 95% CI 0.32–0.75, P < 0.01).ConclusionThe SOX4 gene SNPs rs79958549, rs139085828, and rs201335371 loci were significantly associated with osteoporosis risk.

Predicting Pathogenicity of CDH1 Gene Variants in Patients with Early-onset Diffuse Gastric Cancer from Western Mexico.

Early-onset diffuse gastric cancer (EODGC) occurs at or before 50 years of age. Pathogenic mutations and germline deletions in the CDH1 gene (E-cadherin) are well-documented genetic factors associated with the causes of EODGC. The objective of the study was to study CDH1 germline variants and their potential functional impact in patients with EODGC in a Mexican population. We studied seven EODGC patients from a biomedical research center in western Mexico. Variants were identified by Sanger sequencing and multiplex ligation-dependent probe amplification. The DeepSEA and SNPClinic v.1.0 software and the Ensembl (1000 Genomes Project, 1kGP) and ClinVar databases were used to predict functional single-nucleotide polymorphisms (SNPs). The genetic admixture of the Mexican patients was corroborated by 22 short tandem repeat loci genotyping and structure analysis. We found 12 germline CDH1 variants in all EODGC patients, and all of them are considered as polymorphisms: rs34561447, rs5030625, rs16260, rs1330727101, rs28372783, rs942269593, rs3743674, rs1801552, rs34939176, rs33964119, rs3556654, and rs1801026. The prediction of regulatory SNPs in the promoter suggests a role for a retrovirus in EODGC that induces the transcription of interferon-related genes through toll-like receptor-interferon response factor 3 signaling, as three SNPs in the CDH1 promoter alter three binding sites for this transcription factor. In addition, SNPs rs28372783 and rs1801026 could alter upstream stimulatory factors 1 (USF1)/USF2-mediated telomerase-dependent lymphocyte activation in EODGC. Other interesting result is a CTCF-dependent shorter CDH1 isoform lacking exon 14, probably due to exon-skipping mediated by rs33964119. Classical pathogenic germline mutations in the CDH1 gene were not found in these 7 EODGC patients. However, the in silico approaches revealed the possible involvement of a retrovirus and a shorter E-cadherin isoform in EODGC. Nevertheless, further in vitro and in vivo assays are needed to confirm these predictions.

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

The availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.

Population structure of Phytophthora infestans (Mont.) de Bary in Ethiopia

Late blight disease caused by an Oomycete Phytophthora infestans is a major constraint to potato production and is causing significant yield losses in Ethiopia. This study was conducted to characterize the genetic diversity of the pathogen population in the major potato growing regions Awi, East Hararghe, South Gondar, West Arsi, West Gojjam and West Shewa in Ethiopia. In total 138 P. infestans isolates were collected using FTA cards in 2017, genotyped using 12-plex SSR markers and characterized for the mitochondrial haplotype. The genotypic patterns were compared to those of reference isolates from the EU2_A1 and US-1 clonal lineages. The population structure analysis using discriminant analysis of principal components (DAPC) and STRUCTURE indicated that most of the Ethiopian isolates were similar to the EU2_A1, while a second cluster of isolates was formed that was clearly different from EU2_A1 as well as the US-1 reference isolates. This new genotype was characterized by private alleles in the SSR D13 locus. We named this new genotype as ET-1 lineage. All isolates had the same mitochondrial haplotype (Ia). EU2_A1 was dominant clonal lineage in all locations except West Arsi which was dominated with ET-1 lineage. The old US-1 lineage was not discovered among the Ethiopian samples which suggest that it has been displaced. The West Arsi, West Gojjam and West Shewa populations were found to contain the highest genetic diversity, with the greatest number of multi locus genotypes (MLGs) and a higher diversity index compared to the other locations. The findings of this study establish a baseline of the pathogen population diversity in Ethiopia. Continuous tracking of P. infestans population in both potato and tomato is recommended to monitor the changes and migration patterns.

Distinct evolutionary trajectories of MHC class I and class II genes in Old World finches and buntings.

Major histocompatibility complex (MHC) genes code for key proteins of the adaptive immune system, which present antigens from intra-cellular (MHC class I) and extra-cellular (MHC class II) pathogens. Because of their unprecedented diversity, MHC genes have long been an object of scientific interest, but due to methodological difficulties in genotyping of duplicated loci, our knowledge on the evolution of the MHC across different vertebrate lineages is still limited. Here, we compared the evolution of MHC class I and class II genes in three sister clades of common passerine birds, finches (Fringillinae and Carduelinae) and buntings (Emberizidae) using a uniform methodological (genotyping and data processing) approach and uniform sample sizes. Our analyses revealed contrasting evolutionary trajectories of the two MHC classes. We found a stronger signature of pervasive positive selection and higher allele diversity (allele numbers) at the MHC class I than class II. In contrast, MHC class II genes showed greater allele divergence (in terms of nucleotide diversity) and a much stronger recombination (gene conversion) signal. Gene copy numbers at both MHC class I and class II evolved via fluctuating selection and drift (Brownian Motion evolution), but the evolutionary rate was higher at class I. Our study constitutes one of few existing examples, where evolution of MHC class I and class II genes was directly compared using a multi-species approach. We recommend that re-focusing MHC research from single-species and single-class approaches towards multi-species analyses of both MHC classes can substantially increase our understanding MHC evolution in a broad phylogenetic context.

Y-Chromosome Haplogroup Diversity in Khazar Burials from Southern Russia

Genetic studies of archaeological burials open up new possibilities for investigating the cultural-historical development of ancient populations, providing objective data that can be used to investigate the most controversial problems of archeology. In this work, we analyzed the Y-chromosomes of nine skeletons recovered from elite burial mounds attributed to the 7th–9th centuries of the Khazar Khaganate in the modern Rostov region. Genotyping of polymorphic microsatellite loci of the Y chromosome made it possible to establish that among the nine skeletons studied, three individuals had R1a Y-haplogroup, two had C2b, and one each had G2a, N1a, Q, and R1b Y-haplogroups. Such results were noteworthy for the mixture of West Eurasian and East Asian paternal lineages in these samples. The Y-chromosome data are consistent with the results of the craniological study and genome-wide analysis of the same individuals in showing mixed genetic origins for the early medieval Khazar nobility. These findings are not surprising in light of the history of the Khazar Khaganate, which arose through its separation from the Western Turkic Khaganate and establishment in the North Caucasus and East European steppes.

Response of Egg Number to Selection of Different Genotypes of 24-bp Insertion-Deletion Locus in the Promoter of Prolactin Gene of Papua Local Chickens

This study aims to estimate the response of the number of eggs produced up to 240 days of age (EN240) to the selection of Papua local chickens (PLC) with different genotypes from the 24-bp Indel cPRLp locus. A total of 68 PLCs were taken randomly from several breeders in Manokwari as the basic population for selection (G0). Genotype identification of the 24-bp Indel cPRLp locus was performed G0. Based on the distribution of these genotypes, mating pairs were randomly formed G0-II, G0-DD and G0-ID to produce G1-II, G1-DD, and G1-Control (G0-ID offspring). Heritability of EN240 in G1-II and G1-DD populations were estimated in full-sib (single pairs mating). Individual selection based on breeding value EN240 was carried out on G1-II (♀) and G1-DD (♀) to form the selection generation (GS): GS-II (♀) and GS-DD (♀). Selection was also carried out on G1-II (♂) and G1-DD (♂) based on body weight at 240 days (BW240) to become selected GS-II (♀) and GS-DD (♀) mating partners. GS-Control was also formed through 25% random sampling from G1-Control (♂ and ♀). GS mating resulted in the second generation (G2): G2-II, G2-DD, and G2-Control. Age at first laying (AFL), EN240, and mean egg weight (EWA) in hens of G1, GS, and G2 were recorded. Response to selection for EN240 was calculated by two methods predicted selection response (Rp) and actual selection response (Rr). Both methods of calculation yield positive and high values. In actual response (Rr), PLC in II genotypes group are more responsive to the selection treatment than DD genotype group. Selection increase EN240 impact accelerate of AFL and lower the EWA, because of their negative genetic correlation.

Ecology and population structure of some indigenous geese breeds and the impact of four GH and Pit-1 SNPs on their body weights.

This study aims to determine the genetic correlation using nine microsatellite markers to reconstruct the history of some indigenous geese populations, along with the use of four single nucleotides polymorphisms (SNPs) to investigate their correlation with the geese body weight. Microsatellite markers are mainly used to provide updated information on changes in the population structure of geese breeds. The eight goose populations reported 24% private alleles specific for each population. Expected heterozygosity (He) ranged from 0.46 to 0.70. Three breeds were reported highly polymorphic. Inbreeding coefficient (Fis) revealed that three breeds were in a minimum level of extinction danger, while one breed was in a potential endangered situation. Phylogenetic tree, principal component analysis (PCA), and self-organizing map (SOM) were constructed using MATLAB to study the population distribution and relationship among these breeds. Four SNPs were detected, two SNPs at GH gene exon (C123T and C158T), and two SNPs at Pit-1 gene exons (G161A and T282G). Four SNP loci were reported to have a significant effect on geese body weight. They were CT genotype for C123T locus, TT genotype for C158T locus, GG genotype for G161A locus, and GG genotype for T282G locus.

Single Marker Association with Mastitis Incidence of Three Microsatellite Loci, BM1258, BM1443 and BM1818, in Egyptian Buffalo

To detect the linkage between single markers of microsatellite type and mastitis incidence in Egyptian buffalo three markers (BM1258, BM1443 and BM1818) and one hundred twenty-three lactating animals were used. The selected animals were tested using Modified White Side Test (MWT) to screen animals for mastitis. Non-denatured polyacrylamide gel was used to determine the sizes of the PCR amplified products using reference animal to verify the allelic sizes obtained. For each marker, the frequencies of alleles and genotypes for both positive and negative animal groups were compared by using the chi-square test and the Fisher's exact test. The odds ratios calculated as an estimate of relative risk of mastitis incidence associated with each microsatellite genotypes. A positive mastitis test reaction (MWT) was revealed in 19.5% of total samples. For BM1258, BM1443, and BM1818, the number of alleles was found to be 4, 3 and 5, respectively. The polymorphism in all three studied loci was high (PIC>0.5). The genetic parameters of these loci, including observed and expected heterozygosity, were estimated using full characterizations of this set of three polymorphic loci. The polymorphic information content, heterozygosity, and number of successful alleles of the studied loci showed that BM1443 had the lowest variability and BM1818 had the highest variability, with 0.597 and 0.757, respectively. The overall effects of the three studied markers on mastitis incidence were significantly (P<0.05) different. The genotypes combination ‘72/79’, ‘74/74’, and ‘79/82’ at BM1258 loci; ‘78/78’ and ‘88/88’ at BM1443 loci, were observed only in the mastitis free animals. On the other hand, BM4505 loci genotypes were found in the positive populations except the combination of genotypes 134/134, 134/140 and 134/144 animals. The information observed in the present study, could be valuable for improving mastitis resistance in Egyptian buffalo breeds through using molecular tools

Insights into genetic variants within sheep IGF2BP1 and their association with litter size

Abstract Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays a crucial role in cellular growth, proliferation, and embryonic development by regulating mRNA stability. IGF2BP1 has been recently found to be located on a new 194.6-kb interval of the fecundity gene FecL. A total of nine insertion/deletion (InDel) variations within IGF2BP1 were identified in 916 adult Australian White sheep, and three were polymorphic: a 5-bp InDel in a downstream region, 9-bp InDel in intron 4, and 15-bp InDel in intron 2. Association analyses indicated that both the 5-bp and 9-bp InDel mutations were significantly associated with litter size at 2nd gestation. The heterozygous genotype (ID) of the 5-bp InDel locus and homozygous insertion genotype (II) of the 9-bp InDel locus were associated with large litter size. Moreover, the combined genotype ID-II of the 5-bp and 9-bp InDel genotypes was identified as the best genotype. These findings will pave the way for future research on marker-assisted selection of reproductive traits in sheep breeding.

Root Rot Resistance Locus PaLAR3 Is Delivered by Somatic Embryogenesis (SE) Pipeline in Norway Spruce (Picea abies (L.) Karst.)

Research Highlights: The Norway spruce somatic embryogenesis (SE) pipeline is suitable for multiplication of material with root rot resistance traits. Background and Objectives: Heterobasidion root rot is the economically most severe forest pathogen in Europe, reducing the benefit of planting elite forest material. In this study, the SE-propagation ability of elite Norway spruce material carrying root rot resistance traits was studied. Materials and Methods: We analyzed the presence of the root rot resistance locus PaLAR3B among 80 Finnish progeny-tested Norway spruce plus-trees used for SE-plant production as well as in 241 SE lines (genotypes) derived from them. Seven full-sib families with lines having either AA, AB, or BB genotype for PaLAR3 locus were further studied for their SE-plant propagation ability. Results: The results indicate that 47.5% of the studied elite trees carry the PaLAR3B allele (45% are heterozygous and 2.5% homozygous). The resistance allele was present among the SE lines as expected based on Mendelian segregation and did not interfere with somatic embryo production capacity. All embryos from PaLAR3 genotypes germinated well and emblings were viable in the end of first growing season. However, in three families, PaLAR3B homo- or heterozygotes had 23.2% to 32.1% lower viability compared to their respective hetero- or PaLAR3A homozygotes. Conclusions: There is no trade-off between root rot resistance locus PaLAR3B and somatic embryo production ability, but the allele may interfere with Norway spruce embling establishment.

Triple null mutations in starch synthase SSIIa gene homoeologs lead to high amylose and resistant starch in hexaploid wheat

BackgroundLack of nutritionally appropriate foods is one of the leading causes of obesity in the US and worldwide. Wheat (Triticum aestivum) provides 20% of the calories consumed daily across the globe. The nutrients in the wheat grain come primarily from the starch composed of amylose and amylopectin. Resistant starch content, which is known to have significant human health benefits, can be increased by modifying starch synthesis pathways. Starch synthase enzyme SSIIa, also known as starch granule protein isoform-1 (SGP-1), is integral to the biosynthesis of the branched and readily digestible glucose polymer amylopectin. The goal of this work was to develop a triple null mutant genotype for SSIIa locus in the elite hard red winter wheat variety ‘Jagger’ and evaluate the effect of the knock-out mutations on resistant starch content in grains with respect to wild type.ResultsKnock-out mutations in SSIIa in the three genomes of wheat variety ‘Jagger’ were identified using TILLING. Subsequently, these loss-of function mutations on A, B, and D genomes were combined by crossing to generate a triple knockout mutant genotype Jag-ssiia-∆ABD. The Jag-ssiia-∆ABD had an amylose content of 35.70% compared to 31.15% in Jagger, leading to ~ 118% increase in resistant starch in the Jag-ssiia-∆ABD genotype of Jagger wheat. The single individual genome mutations also had various effects on starch composition.ConclusionsOur full null Jag-ssiia-∆ABD mutant showed a significant increase in RS without the shriveled grain phenotype seen in other ssiia knockouts in elite wheat cultivars. Moreover, this study shows the potential for developing nutritionally improved foods in a non-GM approach. Since all the mutants have been developed in an elite wheat cultivar, their adoption in production and supply will be feasible in future.

Роль полиморфных вариантов генов ADIPOQ, MTHFR, PON1, KCNJ11, TCF7L2, ITLN1 и PPARG в увеличении риска развития ожирения в Кыргызской Республике

Цель исследования - оценить вклад полиморфных вариантов g.15661G&gt; T (ген ADIPOQ), p.A222V (ген MTHFR), p.Q192R (ген PON1), p.K23E (ген KCNJ11), g.53341C&gt;T (ген TCF7L2), p.V109D (ген ITLN1) и p.P12A (ген PPARG) в развитие ожирения для лиц кыргызской национальности. Исследование было проведено по типу «случай-контроль» и включало 130 пациентов с ожирением (мужчин - 65 (50,0%), женщин - 65 (50,0%)). Группа сравнения - 115 человек без ожирения, метаболических нарушений и сердечно-сосудистых заболеваний в анамнезе (мужчин - 62 (53,9%), женщин - 53 (46,1%). Генотипирование осуществляли методом ПЦР-ПДРФ. Анализ межгенных взаимодействий проводился с использованием программы MDR 3.0.2. Маркерами развития ожирения в кыргызской популяции являются аллель V и генотип VV локуса p.A222V (MTHFR), а также аллель K и генотип KK локуса p.K23E (KCNJ11). При наличии генетического профиля AV (p.A222V, MTHFR) / EK (p.K23E, KCNJ11) вероятность развития ожирения возрастает более чем в 3 раза, ОШ=3,49, 95% ДИ=[1,44-8,45], p=0,001. In this study, we investigated whether polymorphisms g.15661G&gt;T (ADIPOQ), p.A222V (MTHFR), p.Q192R (PON1), p.K23E (KCNJ11), g.53341C&gt;T (TCF7L2), p.V109D (ITLN1) and p.P12A (PPARG) are associated with obesity in the Kyrgyz population. We genotyped 245 nonrelated adults Kyrgyz individuals. 130 patients (male - 65 (50,0%), female - 65 (50,0%) with obesity and 115 non-obese control subjects (male - 62 (53,9%), female - 53 (46,1%). Genotyping of single-nucleotide polymorphism was performed by PCR-RFLP method. Analysis of intergenic interactions conducted with MDR v.3.0.2 program. Тhe V allele and the VV genotype of the p.A222V locus (MTHFR), as well as the K allele and the KK genotype of the p.K23E locus (KCNJ11) increase risk of obesity in the Kyrgyz population. Subjects having the VV genotype of p.A222V locus (MTHFR) and KK genotype of the p.K23E locus (KCNJ11) had 3-fold [OR = 3,49 (1,44-8,45); p = 0,001] higher risk of developing compared with subjects carrying neither of these genotypes.

Cape Feather Coloration Signals Different Genotypes of the Most Polymorphic MHC Locus in Male Golden Pheasants (Chrysolophus pictus).

Simple SummaryOrnamental feather coloration in birds is deemed an honest signal of male quality, but is seldom embodied at the functional genetic level. The major histocompatibility complex is involved in the immune response, thereby affecting an organism’s fitness. Here, we tested the hypothesis that the coloration of the cape feather signals genetic quality in the male golden pheasant. We measured brightness, chroma, and hue as the main parameters to quantify color differences. Then, we investigated the genotypes of all major histocompatibility complex loci associated with adaptive immunity. The results showed that heterozygosity of the most polymorphic major histocompatibility complex locus was positively related with the brightness and chroma of cape feathers. Our study suggested that cape feather coloration might signal different genotypes of the most polymorphic major histocompatibility complex locus in male golden pheasants.Ornamental feather coloration is usually a reflection of male quality and plays an important role during courtship, whereas the essence of male quality at the genetic level is not well understood. Major histocompatibility complex (MHC)-based mate choice has been observed in various vertebrates. Here, we investigated the relationship between the coloration of cape feathers and the MHC genotypes in golden pheasants (Chrysolophus pictus). We found that feather coloration differed sharply among different individuals (brightness: 1827.20 ± 759.43, chroma: 1241.90 ± 468.21, hue: 0.46 ± 0.06). Heterozygous individuals at the most polymorphic MHC locus (IA2) had brighter feathers than homozygous individuals (Z = −2.853, p = 0.004) and were more saturated in color (Z = −2.853, p = 0.004). However, feather coloration was not related to other MHC loci or to overall genetic heterozygosity (p > 0.050). Our study suggested that coloration of cape feathers might signal IA2 genotypes in golden pheasants.

АЛЛЕЛЬНЫЙ ПОЛИМОРФИЗМ ГЕНА КАППА-КАЗЕИНА (CSNЗ) У БЫКОВ-ПРОИЗВОДИТЕЛЕЙ ЧЕРНО-ПЁСТРОЙ ПОРОДЫ

The leading role in increasing dairy cow performance is played by seed bulls; 90-96% of the herd genetic progress depends on them. This is due to the fact that for this group of animals the genetic evaluation of the individuals used is reliably carried out and the worst andmoderate animals in terms of breeding qualities are most intensively culled from reproduction. Therefore, when pure-breeding and choosing seed bulls for the herd, the information on the genotypes of milk protein alleles, in particular the kappa-casein gene (CSN3), should be taken into account. The experimental studies were carried out in the livestock breeding operation of the AO “Plempredpriyatiye Barnaulskoye”. It has been found that the prevailing genotype in the Black Pied seed bulls is the CSNAA genotype; its frequency reaches 0.578; the alternative CSN3ВB genotype is found in single ani-mals. The allele A accounts for 0.756, and B -0.245. Among the Black Pied seed bulls, no statistically significant shift in genetic equilibrium was found for any of the three genotypes of kappa-casein gene locus. The studies of the polymorphism of the kappa-casein gene in the seed bulls taking into account their line belonging have revealed that only in the Vis Back Ideal line there is a BB genotype asso-ciated with the processing properties of milk, while it lacks in the bulls of the Montwick Chieftain and Reflection Sover-ing lines. The genotype CSN3AA prevails in the seed bulls of all lines; the highest frequency occurs in the Reflection Sovering line -0.625, and the lowest in the Vis Back Ideal line -0.542. The differences in the allele frequencies be-tween the lines, apparently, are associated with the peculi-arities of the origin of the seed bulls and the direction of the selective breeding work with the Black Pied cattle.

Application of Multiple Short Tandem Repeat Loci for Rapid Diagnosis of Down Syndrome and Edward Syndrome.

Chromosomal diseases with chromosomal abnormalities are one of the most common genetic diseases in humans, including abnormal numbers and structural abnormalities. Patau syndrome (also known as trisomy 13), Edward syndrome (also called trisomy 18), and Down syndrome (also known as trisomy 21) are all clinically fatal diseases caused by abnormal numbers of autosomes. However, there is no reliable and effective cure for chromosomal diseases, mainly relying on fast and accurate prenatal diagnosis technology to reduce the rate of birth defects. Fluorescent-labeled primers were designed and then used in fluorescence quantitative polymerase chain reaction (FQ-PCR) composite amplification, capillary electrophoresis typing, and gene fragment analysis technology to detect 64 amniotic fluid samples, which were indicated high risks of trisomy 18 and 21 by non-invasive prenatal diagnostic technology (NIPT). The results are compared with the results of karyotype analysis and chromo-some copy variations (CNVs). Sixty-four samples were determined by FQ-PCR technology with the help of short tandem repeat (STR) regarded as molecular marker (STR-FQ-PCR), the result showed 61 cases of chromosomal aneuploidy were positive, including 14 cases of Edward syndrome and 47 cases of Down syndrome. A total of 460 STR locus genotypes were detected, containing 84 STR locus genotypes of Edward syndrome and 376 STR locus genotypes of Down syndrome. Chromosome karyotype analysis showed that the detected samples were all chromosomal aneuploidy. Among them were 15 cases of trisomy 18, including 14 cases of homozygous type and 1 case of chimeric type, 49 cases of trisomy 21, consisting of 47 cases homozygous type and 2 cases chimeric type. Sixty-two cases of chromosomal aneuploidy were detected by CNVs with 14 cases of trisomy 18 and 48 cases of trisomy 21. The detectable rate of STR-FQ-PCR technology is 95.31% while the karyotype analysis is the highest with 100%. For non-chimera and non-structural abnormal samples, the coincidence rate of results between STR-FQ-PCR technology and karyotype analysis was 100%. All above manifested the application of multiple STR loci for rapid diagnosis of Down syndrome and Edward syndrome has high clinical value.

Association of gene polymorphism with menorrhagia combined with thyroid pathology

Purpose of the study: to establish the frequency of alleles and genotypes of GP IIIa gene polymorphism in adolescent girls with uterine bleeding that is concomitant thyroid pathology and conduct a thorough genetic analysis of patients.Materials and methods. 70 teenage girls with puberty menorrhagia were surveyed. Study groups: I (main) – 30 teenage girls with puberty menorrhagia against the background of thyroid gland pathology, II group (comparison) – 40 teenage girls diagnosed with puberty menorrhagia. Control group consist of 25 almost healthy teenage girls. GP IIIa gene polymorphism (PLA1/PLA2) was studied once using PCR polymerase chain reaction.Results. A1/A2 polymorphism of the GP IIIa gene in adolescent girls with menorrhagia against the background of thyroid pathology indicates the likely prevailing frequency of individuals with “favorable” A1 allele over such with A2A2 genotype with and without pathology: in 12.3 and 9 times respectively. In adolescents without concomitant pathology A1A1 genotype was observed 11.7% more frequently than those with thyroid disease and 15.0% more often than in the control group. Distribution of genotypes of the GP IIIa gene polymorphous locus corresponded to the expected Hardy-Weinberg population balance, both in general and separately in the surveyed groups.Conclusions. In adolescents with menorrhagia without thyroid pathology A1A1 genotype occur 11.7% more frequently than in girls with thyroid diseases and 15.0% more often than in the control group. Relative frequency of A1A2- genotype is 9.2% in girls with menorrhagia and thyroid pathology, and A2A2 genotype by 2.5% over such in adolescents of comparison groups. Thus, risk factors for uterine bleeding with existing thyroid pathology in adolescent girls may depend on gene polymorphism.

Association of leptin gene polymorphisms with predisposition of cattle to ketosis

Leptin is a hormone produced by adipocytes — cells of adipose tissue, involved in the regulation of eating behavior, affecting the reproductive function, as well as the growth and Constitution of animals. In certain physiological conditions in cows, intensive use of their own fat reserves leads to excessive appearance of volatile fatty acids in the blood, which, in turn, become «satiety signals» and lead to a reduction in feed consumption. At this point, the genetic characteristics of the animal associated with the regulation of metabolism, eating behavior, contributing to or preventing the possible development of ketosis become particularly important. The aim of the research is to determine the possible influence of the leptin locus genotype (y7f, a80v, R25C polymorphisms) on the frequency of ketosis in cattle. We have genotyped Holstein breeding bulls (PCR/RFLP) belonging to WWS (USA) based on the A80V, R25C, and Y7F loci of the leptin gene, which were evaluated by their daughters and «ketosis resistance coefficients» (Wellness trait index (WT$) ketosis) were determined with a high level of confidence. It was found that the group of breeding bulls with the AARRYY genotype is distinguished by a significantly higher average index of «daughters' resistance to ketosis» compared to the AARCYY and AVCCYY groups, which may indicate that the AARRYY genotype in breeding bulls is one of the genetic factors protecting their daughters from the development of ketosis. In addition, 150 Holstein cows were genotyped using the same loci, of which 50 had ketosis and 100 were healthy. In the group of healthy Holstein cows, compared with the group of animals with ketosis and hepatopathology, the AARCYY genotype was three times more common.

Associations of content and gene polymorphism of macrophage inhibitory factor-1 and chronic hepatitis C virus infection.

BACKGROUNDThe expression of macrophage inhibitory factor-1 (MIC-1) is increased in peripheral blood of patients with chronic hepatitis and liver cirrhosis. However, whether MIC-1 gene polymorphism is correlated with relevant diseases is not yet reported.AIMTo explore the correlation between gene polymorphism in MIC-1 exon region and chronic hepatitis C virus (HCV) infection.METHODSThis case-control study enrolled 178 patients with chronic hepatitis C (CHC) in the case group, and 82 healthy subjects from the same region who had passed the screening examination comprised the control group. The genotypes of rs1059369 and rs1059519 loci in the MIC-1 gene exon were detected by DNA sequencing. Also, the MIC-1 level, liver function metrics, liver fibrosis metrics, and HCV RNA load were determined. Univariate analysis was used to compare the differences and correlations between the two groups with respect to these parameters. Multivariate logistic regression was used to analyze the independent relevant factors of CHC.RESULTSThe plasma MIC-1 level in the CHC group was higher than that in the control group (P < 0.05), and it was significantly positively correlated with alanine aminotransferase, aspartate aminotransferase (AST), type III procollagen N-terminal peptide (known as PIIINP), type IV collagen, and HCV RNA (P < 0.05), whereas negatively correlated with total protein and albumin (P < 0.05). The genotype and allele frequency distribution at the rs1059519 locus differed between the two groups (P < 0.05). The allele frequency maintained significant difference after Bonferroni correction (Pc < 0.05). Logistic multiple regression showed that AST, PIIINP, MIC-1, and genotype GG at the rs1059519 locus were independent relevant factors of CHC (P < 0.05). Linkage disequilibrium (LD) was found between rs1059369 and rs1059519 loci, and significant difference was detected in the distribution of haplotype A-C between the CHC and control groups (P < 0.05). Meanwhile, we found the MIC-1 level trend to increase among rs1059519 genotypes (P = 0.006) and the level of MIC-1 in GG genotype to be significantly higher than CC genotype (P = 0.009, after Bonferroni correction).CONCLUSIONPlasma MIC-1 level was increased in CHC patients and correlated with liver cell damage, liver fibrosis metrics, and viral load. The polymorphism at the MIC-1 gene rs1059519 locus was correlated with HCV infection, and associated with the plasma MIC-1 level. G allele and GG genotype may be an important susceptible factor for CHC.

Polymorphism of DMRT3 Gene and Its Association with Body Measurements in Horse Breeds

The double sex and mab-3-related transcription factor 3 gene (DMRT3) placed on chromosome 23 of equine. This gene codes a major transcription factor in the spinal cord complex encompasses regulating motion of vertebrates. It is implicated in a neural network for the synchrony of the moving apparatus that governs limb motion. The aim of this study was to determine polymorphism of DMRT3 gene in Iranian exotic and native horse breeds (Persian Arab, Akhal teke, Yamut, Kurd, Dareshouri, Caspian, Taleshi) using of PCR-RFLP technique and its correlation with body measurements. DNA was extracted from blood samples of 374 horses and a 485-bp fragment within the horse DMRT3 gene was synthesized applying specific primers. The PCR products were digested with DdeI restriction enzyme at 37??C overnight, and the resulting products were separated by the 3.5% agarose gel and visualized by ethidium bromide staining. Body measurements and gene association analyses were performed using a statistical model containing the fixed effects of breed, sex and the animal genotype for the DMRT3 locus. In all of the studied populations two genotypes, CC and AC, were observed while AA was not observed. Frequencies of C and A alleles were 0.97 and 0.03%, respectively. The AC genotype was only observed in Iranian native breeds including Turkmen (Akhal teke), Turkmen (Yamut), Dareshouri, Kurd and Caspian, while the other 12 remained breeds had only CC genotype. Number of observed alleles, number of effective alleles, observed heterozygosity, expected heterozygosity, Shanon???s index, Nei???s index and fixation index (Fis) for all studied breeds were 2.00, 1.06, 0.06, 0.06, 0.14, 0.06 and 0.10, respectively. A UPGMA dendrogram based on the Nei???s standard genetic interval between studied breeds displayed distinct clusters for Iranian native and exotic breeds. Statistical association analysis of two observed genotypes with body measurements showed that the studied mutation has no effect on body measurements.