Alleles Of Locus Research Articles

Assessment and preservation of the gene pool of the domestic <i>Kholmogorsk</i> cattle breed in the Arkhangelsk region

The article presents the results of monitoring immunogenetic studies on the origin of Kholmogory cattle to establish their breed genetic passport for the EAB locus of blood groups. The importance of determining of the breeding animals statute taking into account the forms of the identified state of erythrocyte antigens for the purpose of registration in the federal state information and analytical system of breeding resources of the Russian Federation is noted. In breeding farms of the Arkhangelsk region over the past 29 years, the total number of animals tested for the reliability of origin was 57,311. The percentage of reliability in the monitored livestock numbers varied from 86.95% (1995-2000) to 97.28% (2016-2020). To establish the genetic passport of breeding female tribal species of the breed with up to 75% Holstein bloodline approved for breeding purposes when working with Kholmogory cattle, we conducted immunogenetic testing, which revealed 46 alleles of the EAB locus. The total frequency of the EAB locus alleles in animals of groups 1-2 with specific (typical) for the Kholmogory breed and with unique alleles was 69.38%. In group 3 of animals with alleles of the approved Holstein breed, the total frequency was set at 30.6%, in group 4 with alleles of unapproved breeds – 0.02%. It was established that the concentration of alleles G2O2, B2O2, B2G2KA’B’G’O’G’’, B2E’2G’, B2O2Y2D’, Q is very low, they are found only in some individuals. The degree of homozygosity (theoretical) is 5.6%, the number of effective alleles is 17.9.

Genetic Relationships and Population Structure among Nigerian Ethnic Groups (Ibibio, Igbo, Hausa, Tiv and Yoruba) Based on Nine DNA Loci

Abstract Context: Population-specific attributes typically determine the behavior of human genotypes and traits in individuals. Examining the genetic relationships between populations presents an opportunity to observe patterns of genetic changes over time. By comparing populations, it is possible to see factors that may have sparked the evolution of a trait or genotype as well as the genetic diversity of the populations. Genetic diversity in the groups in Nigeria is still largely undefined. This can be achieved with the use of genetic markers. Aims: To determine the genetic relationships between Igbo, Ibibio, Yoruba, Tiv, and Hausa ethnic groups using nine short tandem repeat DNA markers. Settings and Design: Observational studies of 250 consenting participants. Methods and Material: Individuals of Igbo, Yoruba, Hausa, Ibibio, and Tiv were randomly sampled from their ethnic homes in Nigeria at participating institutions. DNA was extracted from blood samples using commercial DNA kits, and tested for nine autosomal short tandem repeat loci alleles using PCR and electrophoresis. The allele types and sizes were read and recorded for each locus for every individual. Statistical Analysis Used: Allelic frequencies, population pairwise genetic distances (FST and RST, analysis of molecular variance (AMOVA), and principal component analysis (PCA) were calculated using GenAlEx v6.502. Results: The fixation index (FST) was between 0.001 and 0.500 in the five populations. The estimated variation was 99.98% within individuals and 0.10% among populations. Four heterogeneous clusters were observed with three axes accounting for 32.86% variation. Conclusions: The genetic relationships closely mirrored linguistic groupings showing that language may have shaped early interaction and ultimately gene transfer between these groups.

The Relationship of Duffy Gene Polymorphism with High-Sensitivity C-Reactive Protein, Mortality, and Cardiovascular Outcomes in Black Individuals

Background: Black adults have higher incidence of all-cause mortality and worse cardiovascular disease (CVD) outcomes when compared to other U.S. populations. The Duffy chemokine receptor is not expressed on erythrocytes in a large majority of Black adults, but the clinical implications of this are unclear. Methods: Here, we investigated the relationship of Duffy receptor status, high-sensitivity C-reactive protein (hs-CRP), and mortality and incident CVD events (coronary heart disease, stroke, and heart failure) in self-identified Black members of three contemporary, longitudinal cohort studies (the Women’s Health Initiative, Jackson Heart Study, and Multi-Ethnic Study of Atherosclerosis). Data on 14,358 Black participants (9023 Duffy-null and 5335 Duffy-receptor-positive, as defined using single-nucleotide polymorphism (SNP) rs2814778) were included in this analysis. Results: Duffy null was strongly associated with higher hs-CRP (meta-analysis p = 2.62 × 10−9), but the association was largely attenuated, though still marginally significant (p = 0.005), after conditioning on known CRP locus alleles in linkage disequilibrium with the Duffy gene. In our discovery cohorts, Duffy-null status appeared to be associated with a higher risk of all-cause mortality and incident stroke, though these associations were attenuated and non-significant following adjustment for traditional risk factors including hs-CRP. Moreover, the association of Duffy-null status with mortality could not be replicated in an independent sample of Black adults from the UK Biobank. Conclusions: These findings suggest that the higher levels of hs-CRP found in Duffy-null individuals may be in part independent of CRP alleles known to influence circulating levels of hs-CRP. During the follow-up of this community-based sample of Black participants, Duffy-null status was not associated with mortality or incident CVD events independently of traditional risk factors including hs-CRP.

The inheritance pattern for the dwarf phenotype in hybrids from crosses among sunflower lines differing in alleles of the Rht1 locus

Background. Sunflower seed production is based on utilization of the heterosis effect, manifesting itself in improving both yield and plant height in hybrids. Short-stemmed lines need to be used to develop commercial hybrids with an optimum height. Molecular bases of the trait manifestation in the dwarf lines from VIR’s sunflower genetic collection have not yet been studied. Materials and methods. The material included 27 short-stemmed and 10 tall sunflower lines from VIR’s genetic collection, as well as the F1 and F2 hybrid generations derived from crossing the tall (VIR 340) and dwarf (VIR 171) genotypes. The parental lines and hybrids were phenotyped for plant height, leaf number, and internode length. Genotyping for the Rht1 locus (HaDella1 candidate gene), encoding the negative regulator of the gibberellin response, the DELLA protein, was performed using the developed CAPS marker. Results. The average plant height in the VIR 340 line over a three-year study was 162 cm, the number of leaves 29, and the internode length 6 cm. The VIR 171 line demonstrated the plant height of 66 cm, leaf number of 24, and internode length of 2.8 cm. The F1 hybrids were uniform, with the height of 180–190 cm, that indicated the dominance of the long stem trait. Analyzing the segregation in the F2 hybrid generation led to an assumption admitting the digenic control of the dwarf phenotype in the VIR 171 line. The CAPS marker G-D-1/ Bmt I was developed to identify a missense mutation T>C in the first exon of the HaDella1 gene, which results in the substitution of leucine with proline in the DELLA motif. Using the marker, the mutant Rht1 allele was identified in the VIR 171 and VIR 434 dwarf lines, similar in their origin and phenotype. The results of validation in the F2 hybrid population (VIR 340 × VIR 171) confirmed the efficiency of the G-D-1 / Bmt I marker for selecting dwarf genotypes homozygous for the Rht1 mutant allele.

Associations of the AVPR1A RS1 Microsatellite Locus with the Level of Hormones of the Anterior Pituitary Gland and Personality Traits.

The arginine vasopressin receptor gene (AVPR1A) is one of the genes affecting mental processes. The aim of this study was to search for associations of microsatellite locus RS1, which is related to the AVPR1A expression level, with the level of hormones of the anterior pituitary gland and personality traits. The study sample included Yakut men aged 18-26years (n = 121). The analysis of RS1 locus was carried out using the PCR method and sequencing of the primary nucleotide sequence. Serum hormonal levels of thyroid-stimulating hormone (TSH), follicle-stimulating hormone (FSH), luteinizing hormone (LH) and prolactin were determined by the time-resolved fluorescence immunoassay (DELFIA), plasma adrenocorticotropic hormone (ACTH) levels were determined by enzyme-linked immunosorbent assay (ELISA). In the Yakut population "short" (S) alleles of the AVPR1A RS1 locus containing ≤ 10 repeats (63%) and the corresponding SS genotypes (44.6%) were more frequent, while individuals with "long" (LL) and "heterozygous" (SL) genotypes accounted for 18.2 and 37.2%, respectively. The range of concentrations of ACTH and TSH in the group of SS genotype carriers was significantly lower than that observed in the group of LL genotype carriers (p = 0.042 and p = 0.048, respectively); the LH level was significantly higher (p = 0.029). The trend towards higher neuroticism in SS genotype carriers compared to the individuals with LL genotypes (p = 0.05) is revealed. The results obtained indicate the modulating effect of genetic variants of the AVPR1A gene on the level of anterior pituitary hormones, which could slightly affect the level of neuroticism in humans.

GCphase: an SNP phasing method using a graph partition and error correction algorithm

BackgroundThe utilization of long reads for single nucleotide polymorphism (SNP) phasing has become popular, providing substantial support for research on human diseases and genetic studies in animals and plants. However, due to the complexity of the linkage relationships between SNP loci and sequencing errors in the reads, the recent methods still cannot yield satisfactory results.ResultsIn this study, we present a graph-based algorithm, GCphase, which utilizes the minimum cut algorithm to perform phasing. First, based on alignment between long reads and the reference genome, GCphase filters out ambiguous SNP sites and useless read information. Second, GCphase constructs a graph in which a vertex represents alleles of an SNP locus and each edge represents the presence of read support; moreover, GCphase adopts a graph minimum-cut algorithm to phase the SNPs. Next, GCpahse uses two error correction steps to refine the phasing results obtained from the previous step, effectively reducing the error rate. Finally, GCphase obtains the phase block. GCphase was compared to three other methods, WhatsHap, HapCUT2, and LongPhase, on the Nanopore and PacBio long-read datasets. The code is available from https://github.com/baimawjy/GCphase.ConclusionsExperimental results show that GCphase under different sequencing depths of different data has the least number of switch errors and the highest accuracy compared with other methods.

Engineered transcription-associated Cas9 targeting in eukaryotic cells.

DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospacer target sites. Both interactions are nucleic acid sequence specific but function constitutively; thus, they provide intrinsic spatial control over DNA targeting activities but naturally lack temporal control. Here we show that engineered Cas9 fusion proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling between transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (TraCT). Engineered TraCT is enabled in eukaryotic yeast or human cells when suboptimal PAM interactions limit basal activity and when one or more nascent RNA substrates are still tethered to the actively transcribed target DNA in cis. Using yeast, we further show that this phenomenon can be applied for selective editing at one of two identical targets in distinct gene loci, or, in diploid allelic loci that are differentially transcribed. Our work demonstrates that temporal control over Cas9's targeting activity at specific DNA sites may be engineered without modifying Cas9's core domains and guide RNA components or their expression levels. More broadly, it establishes co-transcriptional RNA binding as a cis-acting mechanism that can conditionally stimulate CRISPR-Cas DNA targeting in eukaryotic cells.

The characteristic of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 alleles in Zhejiang Han population.

The Zhejiang Han population, a subgroup of the Southern Han ethnic group, resides in Zhejiang Province, situated on the southeast coast of China. In this study, we conducted HLA genotyping for 813 voluntary umbilical cord blood donors from the Zhejiang Han population, targeting 11 HLA loci, namely HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, using the next-generation sequencing method. Our analysis of the alleles and haplotypes revealed a high degree of polymorphism within these loci. A total of 289 unique HLA alleles were identified, with the HLA-B locus exhibiting the most significant diversity, while HLA-DRB4 displayed the lowest variation. Due to the inherent limitations of the sequencing method, some unresolvable alleles in the specific loci, such as HLA-DRB1, HLA-DPA1, and HLA-DPB1, were assigned as G group designation. In our comprehensive analysis across all 11 HLA loci, a total of 1204 haplotypes were estimated. The distribution of these alleles was similar to those of the Chinese Southern Han population while highly different from the Caucasian population. These findings contribute to a deeper understanding of the genetic characteristics of HLA loci within the Chinese Southern Han population.

Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association

Soybean is a crucial crop for the Brazilian economy, but it faces challenges from the biotrophic fungus Phakopsora pachyrhizi, which causes Asian Soybean Rust (ASR). In this study, we aimed to identify SNPs associated with resistance within the Rpp1 locus, which is effective against Brazilian ASR populations. We employed GWAS and re-sequencing analyzes to pinpoint SNP markers capable of differentiating between soybean accessions harboring the Rpp1, Rpp1-b and other alternative alleles in the Rpp1 locus and from susceptible soybean cultivars. Seven SNP markers were found to be associated with ASR resistance through GWAS, with three of them defining haplotypes that efficiently distinguished the accessions based on their ASR resistance and source of the Rpp gene. These haplotypes were subsequently validated using a bi-parental population and a diverse set of Rpp sources, demonstrating that the GWAS markers co-segregate with ASR resistance. We then examined the presence of these haplotypes in a diverse set of soybean genomes worldwide, finding a few new potential sources of Rpp1/Rpp1-b. Further genomic sequence analysis revealed nucleotide differences within the genes present in the Rpp1 locus, including the ULP1-NBS-LRR genes, which are potential R gene candidates. These results provide valuable insights into ASR resistance in soybean, thus helping the development of resistant soybean varieties through genetic breeding programs.

Heterogeneous genomic architecture of skeletal armour traits in sticklebacks.

Whether populations adapt to similar selection pressures using the same underlying genetic variants depends on population history and the distribution of standing genetic variation at the metapopulation level. Studies of sticklebacks provide a case in point: when colonising and adapting to freshwater habitats, three-spined sticklebacks (Gasterosteus aculeatus) with high gene flow tend to fix the same adaptive alleles in the same major loci, whereas nine-spined sticklebacks (Pungitius pungitius) with limited gene flow tend to utilize a more heterogeneous set of loci. In accordance with this, we report results of quantitative trait locus (QTL) analyses using a backcross design showing that lateral plate number variation in the western European nine-spined sticklebacks mapped to three moderate-effect QTL, contrary to the major-effect QTL in three-spined sticklebacks and different from the four QTL previously identified in the eastern European nine-spined sticklebacks. Furthermore, several QTL were identified associated with variation in lateral plate size, and three moderate-effect QTL with body size. Together, these findings indicate more heterogenous and polygenic genetic underpinnings of skeletal armour variation in nine-spined than three-spined sticklebacks, indicating limited genetic parallelism underlying armour trait evolution in the family Gasterostidae.

HLA-B5 prevalence in patients with spondyloarthritis and impact on disease phenotype: a multicentric case-control study.

The study aimed to estimate the prevalence of HLA-B51 and HLA-B52 in Lebanese patients with spondyloarthritis (SpA) compared to healthy controls (HC). We further aimed to evaluate the impact of HLA-B51 on phenotype and identify the distribution of the alleles in the HLA-B locus. A case-control study enrolled consecutive SpA patients from three rheumatology clinics in Lebanon, including axial (axSpA), peripheral SpA (pSpA), and psoriatic arthritis (PsA) and HC from blood donors. Demographic and disease data were collected through interviews and file reviews, with testing of the entire HLA-B locus using molecular techniques. The prevalence of HLA-B51 and B52 was estimated in SpA patients versus controls. Prevalence comparisons were made, and logistic regression identified factors associated with HLA-B51 in patients. Data from 120 HC and 86 SpA patients (65 axSpA, 15 pSpA, 6 PsA), mean age 25.6 and 46.4 years, respectively, showed a higher HLA-B51 prevalence in SpA (25.6%), especially axSpA (29.2%) versus HC (12.5%), p = 0.016, and a numerically higher HLA-B52 prevalence (8.1% versus 4.2%, p = 0.230). HLA-B51 correlated with recurrent oral ulcerations (OR 7.99(95%CI 2.14-29.84) and radiographic juxta-articular erosions (OR 7.65(95%CI 1.14-38.03)). HLA-B35 was the most dominant allele in both groups (18.7%), followed by HLA-B27 (15.7%) and HLA-B51 (13.4%) in SpA. HLA-B51 was identified more frequently in patients with SpA compared to HC and was associated with recurrent oral ulcerations and juxta-articular radiographic erosions. Longitudinal studies are needed to determine whether this association indicates a disease overlap or might correlate with a specific SpA phenotype.

Phenotypic characterization and gene mapping of hybrid necrosis in Triticum durum–Haynaldia villosa amphiploids

Key messagePhenotypical, physiological and genetic characterization was carried out on the hybrid necrosis gene from Haynaldia villosa, and the related gene Ne-V was mapped to chromosome arm 2VL.Introducing genetic variation from wild relatives into common wheat through wide crosses is a vital strategy for enriching genetic diversity and promoting wheat breeding. However, hybrid necrosis, a genetic autoimmunity syndrome, often occurs in the offspring of interspecific or intraspecific crosses, restricting both the selection of hybrid parents and the pyramiding of beneficial genes. To utilize the germplasms of Haynaldia villosa (2n = 2x = 14, VV), we conducted wide hybridization between durum wheat (2n = 4x = 28, AABB) and multiple H. villosa accessions to synthesize the amphiploids (2n = 6x = 42, AABBVV). This study revealed that 61.5% of amphiploids derived from the above crosses exhibited hybrid necrosis, with some amphiploids even dying before reaching maturity. However, the initiation time and severity of necrosis varied dramatically among the progenies, suggesting that there were multiple genetic loci or multiple alleles in the same genetic locus conferring to hybrid necrosis in H. villosa accessions. Genetic analysis was performed on the F2 and derived F2:3 populations, which were constructed between amphiploid STH59-1 with normal leaves and amphiploid STH59-2 with necrotic leaves. A semidominant hybrid necrosis-related gene, Ne-V, was mapped to an 11.8-cM genetic interval on the long arm of chromosome 2V, representing a novel genetic locus identified in Triticum-related species. In addition, the hybrid necrosis was correlated with enhanced H2O2 accumulation and cell death, and it was influenced by the temperature and light. Our findings provide a foundation for cloning the Ne-V gene and exploring its molecular mechanism.

Search for molecular markers of joint hypermobility

Background: Joint hypermobility (JH) is a condition that can be either benign or accompanied by pain and early development of osteoarthritis. For early verification of the risk of complications, it is necessary to study the molecular pathogenesis of various JH variants. The aim of the study: The aim of this study was to search for candidate genes involved in connective tissue metabolism and causing joint hypermobility in a form isolated or combined with connective tissue dysplasia (CTD). Materials and methods: The study involved young (21,86±0,22 y.o.) people (n=181). A clinical study was conducted for the presence of signs of JH (Beighton scale) and CTD (tables Kadurina T.I.). Further, a molecular genetic study was carried out and the search for associations of polymorphic variants of genes (vitamin D receptor (VDR), lumican (LUM), tenascin (TNXB), growth/differentiation factor 5 (GDF5), magnesium ion channel TRPM6), bone morphogenetic protein type 5 (BMP5)) and JH, CTD in isolated and combined forms. Statistical data processing was carried out by comparing qualitative features using the χ2 test, Fisher's exact test, and the χ2 test with Yates' correction for contingency tables 2x2. The strength of associations was assessed in terms of the odds ratio (Odds Ratio, OR, at p<0.05), the correction for multiple comparisons was carried out using the FDR method (Benjamin- Hochberg). Quantitative data were evaluated in pairs using the Student's t-test, the normality of distribution according to the Kolmogorov-Smirnov test. Results: Associations of the G allele and the GG genotype of the rs3734444 locus of the BMP5 gene with the presence of JH (OR=3.70 and OR=5.10), the A allele of the rs1470527 locus of the BMP5 gene and the presence of JH+CTD- (OR=8.00), the T allele and the TT genotype of the rs11144134 locus of the TRPM6 gene with JH in isolated (OR=3.00 and OR =10.19) and in the forms combined with CTD (OR=3.17 and OR=11.28), the TT genotype was also associated with the isolated form of CTD (OR=3.74). The GT genotype of the rs73611720 locus of the GDF5 gene was associated with isolated CTD (OR=4.15). No statistically significant associations were found for polymorphic variants rs11540149 (VDR), rs2268578 and rs3759222 (LUM), rs3130342 (TNXB). Conclusion: The G allele of locus rs3734444 of the BMP5 gene is a potential risk marker for JH in general, the A allele of locus rs1470527 is an isolated JH, the GT genotype of locus rs73611720 of the GDF5 gene is a marker for isolated CTD, the T allele of locus rs11144134 of the TRPM6 gene is a marker for JH combined with CTD.

Genetic drivers and cellular selection of female mosaic X chromosome loss.

Mosaic loss of the X chromosome (mLOX) is the most common clonal somatic alteration in leukocytes of femaleindividuals1,2, but little is known about its genetic determinants or phenotypic consequences. Here, to address this, we used data from 883,574 female participants across 8 biobanks; 12% of participants exhibited detectable mLOX in approximately 2% of leukocytes. Female participants with mLOX had an increased risk of myeloid and lymphoid leukaemias. Genetic analyses identified 56 common variants associated with mLOX, implicating genes with roles in chromosomal missegregation, cancer predisposition and autoimmune diseases. Exome-sequence analyses identified rare missense variants in FBXO10 that confer a twofold increased risk of mLOX. Only a small fraction of associations was shared with mosaic Y chromosome loss, suggesting that distinct biological processes drive formation and clonal expansion of sex chromosome missegregation. Allelic shift analyses identified X chromosome alleles that are preferentially retained in mLOX, demonstrating variation at many loci under cellular selection. A polygenic score including 44 allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Our results support a model in which germline variants predispose femaleindividuals to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of clonal expansion.

DRB1 locus alleles of HLA class II are associated with modulation of the immune response in different serological profiles of HIV-1/Epstein-Barr virus coinfection in the Brazilian Amazon region.

Epstein-Barr virus (EBV) infection involves distinct clinical and serological profiles. We evaluated the frequency of alleles of locus DRB1 of HLA class II in different serological profiles of EBV infection among HIV-1 infected patients. We recruited 19 patients with primary infection, 90 with serological transition and 467 with past infection by EBV, HIV-1 co-infection was 100% in primary infection and approximately 70% in other serological profiles. EBV viral load was quantified by real-time PCR, T lymphocyte quantification and cytokine level analysis were performed by flow cytometry, and HLA locus genotyping was performed by PCR-SSO. The DRB1*09 allele was associated with primary infection (p: 0.0477), and carriers of the allele showed changes in EBV viral load (p: 0.0485), CD8(+) T lymphocyte counts (p: 0.0206), double-positive T lymphocyte counts (p: 0.0093), IL-4 levels (p: 0.0464) and TNF levels (p: 0.0161). This allele was also frequent in HIV-coinfected individuals (p: 0.0023) and was related to the log10 HIV viral load (p: 0.0176) and CD8(+) T lymphocyte count (p: 0.0285). In primary infection, the log10 HIV viral load was high (p: 0.0060) and directly proportional to the EBV viral load (p: 0.0412). The DRB1*03 allele correlated with serological transition (p: 0.0477), EBV viral load (p: 0.0015), CD4(+) T lymphocyte count (p: 0.0112), CD8(+) T lymphocyte count (p: 0.0260), double-negative T lymphocyte count (p: 0.0540), IL-4 levels (p: 0.0478) and IL-6 levels (p: 0.0175). In the serological transition group, the log10 HIV viral load was high (p: 0.0060), but it was not associated with the EBV viral load (p: 0.1214). Past infection was related to the DRB1*16 allele (p: 0.0477), with carriers displaying IgG levels (p: 0.0020), CD4(+) T lymphocyte counts (p: 0.0116) and suggestive CD8(+) T count alterations (p: 0.0602). The DRB01*16 allele was also common in HIV-1 patients with past EBV infection (p: 0.0192); however, the allele was not associated with clinical markers of HIV-1 infection. Our results suggest that HLA class II alleles may be associated with the modulation of the serological profiles of the immune response to Epstein-Barr virus infection in patients coinfected with HIV-1.

Assessment of the genetic diversity of the alleles of gliadin-coding loci in common wheat (Triticum aestivum L.) collections in Kazakhstan and Russia.

The study of genetic resources using prolamin polymorphism in wheat cultivars from countries with different climatic conditions makes it possible to identify and trace the preference for the selection of the alleles of gliadine-coding loci characteristic of specific conditions. The aim of the study was to determine the "gliadin profile" of the collection of common wheat (Triticum aestivum L.) from breeding centers in Russia and Kazakhstan by studying the genetic diversity of allelic variants of gliadin-coding loci. Intrapopulation (μ ± Sμ) and genetic (H) diversity, the proportion of rare alleles (h ± Sh), identity criterion (I) and genetic similarity (r) of common wheat from eight breeding centers in Russia and Kazakhstan have been calculated. It has been ascertained that the samples of common wheat bred in Kostanay region (Karabalyk Agricultural Experimental Station, Kazakhstan) and Chelyabinsk region (Chelyabinsk Research Institute of Agriculture, Russia) had the highest intrapopulation diversity of gliadin alleles. The proportion of rare alleles (h) at Gli-B1 and Gli-D1 loci was the highest in the wheat cultivars bred by the Federal Center of Agriculture Research of the South-East Region (Saratov region, Russia), which is explained by a high frequency of occurrence of Gli-B1e (86 %) and Gli-D1a (89.9 %) alleles. Based on identity criterion (I), the studied samples of common wheat from different regions of Kazakhstan and Russia have differences in gliadin-coding loci. The highest value of I = 619.0 was found when comparing wheat samples originated from Kostanay and Saratov regions, and the lowest I = 114.4, for wheat cultivars from Tyumen and Chelyabinsk regions. Some region-specific gliadin alleles in wheat samples have been identified. A combination of Gli-A1f, Gli-B1e and Gli-Da alleles has been identified in the majority of wheat samples from Kazakhstan and Russia. Alleles (Gli-A1f, Gli-A1i, Gli-A1m, Gli-A1o, Gli-B1e, Gli-D1a, Gli-D1f, Gli-A2q, Gli-B2o, and Gli-D2a) turned out to be characteristic and were found with varying frequency in wheat cultivars in eight regions of Russia and Kazakhstan. The highest intravarietal polymorphism (51.1 %) was observed in wheat cultivars bred in Omsk region (Russia) and the lowest (16.6 %), in Pavlodar region (Kazakhstan). On the basis of the allele frequencies, a "gliadin profile" of wheat from various regions and breeding institutions of Russia and Kazakhstan was compiled, which can be used for the selection of parent pairs in the breeding process, the control of cultivars during reproduction, as well as for assessing varietal purity.

RFC1 Repeat Distribution in the Cypriot Population: Study of a Large Cohort of Patients With Undiagnosed Ataxia and Non-Disease Controls.

The intronic biallelic AAGGG expansion in the replication factor C subunit 1 (RFC1) gene was recently associated with a phenotype combining cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, as well as with late-onset ataxia. Following this discovery, studies in multiple populations extended the phenotypic and genotypic spectrum of this locus. Multiple benign and additional pathogenic configurations are currently known. Our main objectives were to study the prevalence of the pathogenic AAGGG expansion in the Cypriot population, to further characterize the RFC1 repeat locus allele distribution, and to search for possible novel repeat configurations. Cypriot undiagnosed patients, in the majority presenting at least with cerebellar ataxia and non-neurologic disease controls, were included in this study. A combination of conventional methods was used, including standard PCR flanking the repeat region, repeat-primed PCR, long-range PCR, and Sanger sequencing. Bioinformatics analysis of already available in-house short-read whole-genome sequencing data was also performed. A large group of undiagnosed patients (n = 194), mainly presenting with pure ataxia or with ataxia accompanied by neuropathy or additional symptoms, as well as a group of non-disease controls (n = 100), were investigated in the current study. Our findings include the diagnosis of 10 patients homozygous for the pathogenic AAGGG expansion and a high percentage of heterozygous AAGGG carriers in both groups. The benign AAAAGn, AAAGGn, and AAGAGn configurations were also identified in our cohorts. We also report and discuss the identification of 2 recently reported novel and possibly benign repeat configurations, AAAGGGn and AAGACn, thus confirming their existence in another distinct population, and we highlight an increased frequency of the AAAGGGn in the patient group, including a single case of homozygosity. Our findings indicate the existence of genetic heterogeneity regarding the RFC1 repeat configurations and that the AAGGG pathogenic expansion is a frequent cause of ataxia in the Cypriot population.

Effects of heat exposure from late sowing on agronomic traits and the technological quality of hexaploid wheat

Heat stress reduces wheat grain yield and affects quality traits relevant to trading and end use. In this study, 98 landraces and 152 elite hexaploid wheat varieties and breeding lines were trialled at two irrigated field sites in southern NSW to better understand heat stress responses and identify promising genotypes for heat tolerance breeding. Potential heat tolerance was defined using performance in heat-exposed late-sown (LS) plots relative to normal-sown (NS) plots, using a regression approach to calculate response indices uncorrelated with awn emergence time and performance per se in NS. The best individual responders for grain yield included genotypes from both Australia and Mexico. On average, lines selected in CIMMYT's High Temperature Wheat Yield Trials (HTWYT) performed well for yield per se in NS as well as for yield response to LS. CIMMYT lines previously selected for large grains under heat stress conditions performed well for grain size in NS and for LS responses of grain size and test weight. Dough peak resistance and time to peak resistance in a mixograph were increased by LS and these traits were positively correlated with grain protein and the occurrence of the Glu-D1d high molecular weight glutenin locus allele, respectively.

T-Cell Epitope Vaccine Prediction Analysis Targeting Phosphoprotein (P) Rabies Virus Based on the Presence of HLA-I Alleles A, B, and C Loci Throughout Southeast Asia: An Immunoinformatics Study

T cell immunity, like responses of CD4+and CD8+ T-cell, plays an important role to fight against viral infections and pathological harm. Several previous studies have shown the results that rabies virus (RABV) protein can act as an ideal receptor for rabies neuroseptic vaccine by inducing a response of T-cell. In this research, we evaluated possible vaccine epitopes based on the Rabies virus sequence and human lymphocyte antigen (HLA) distribution. First, this study used the rabies virus protein P sequence obtained from the NCBI database. Next, we predicted rabies CTL protein epitopes based on the frequency of HLA-I distribution allele locus A, B, and C in Southeast Asia region (> 1%) using Immune Epitope Database and Analysis Resource (iedb.org). Our results predict the presence of 12 epitopes of the protein P RABV. A cluster analysis of epitopes shows that seven P-protein clusters cover 97.47% of the Southeast Asian population. After a conservative epitope analysis, 8 epitopes of protein P showed protection in 11 different types of isolated Rabies virus. Finally, 4 epitopes (SQTVEEIISY119-128; RSSGIFLYNF218-227, ASGPPALEW178-186, IISYVTVNF125-133) were used to vaccinate 97.47% of people in Southeast Asia. Our results suggest that both single and combined CTL epitopes which were predicted in this study can be used as a more effective alternative vaccine against rabies virus’ infections and development

Development of PCR-based markers for identification of wheat HMW glutenin Glu-1Bx and Glu-1By alleles

BackgroundIn common wheat (Triticum aestivum L.), allelic variations in the high-molecular-weight glutenin subunits Glu-B1 locus have important effects on grain end-use quality. The Glu-B1 locus consists of two tightly linked genes encoding x- and y-type subunits that exhibit highly variable frequencies. However, studies on the discriminating markers of the alleles that have been reported are limited. Here, we developed 11 agarose gel-based PCR markers for detecting Glu-1Bx and Glu-1By alleles.ResultsBy integrating the newly developed markers with previously published PCR markers, nine Glu-1Bx locus alleles (Glu-1Bx6, Glu-1Bx7, Glu-1Bx7*, Glu-1Bx7OE, Glu-1Bx13, Glu-1Bx14(−), Glu-1Bx14(+)/Bx20, and Glu-1Bx17) and seven Glu-1By locus alleles (Glu-1By8, Glu-1By8*, Glu-1By9, Glu-1By15/By20, Glu-1By16, and Glu-1By18) were distinguished in 25 wheat cultivars. Glu-1Bx6, Glu-1Bx13, Glu-1Bx14(+)/Bx20, Glu-1By16, and Glu-1By18 were distinguished using the newly developed PCR markers. Additionally, the Glu-1Bx13 and Glu-1Bx14(+)/Bx20 were distinguished by insertions and deletions in their promoter regions. The Glu-1Bx6, Glu-1Bx7, Glu-1By9, Glu-1Bx14(−), and Glu-1By15/By20 alleles were distinguished by using insertions and deletions in the gene-coding region. Glu-1By13, Glu-1By16, and Glu-1By18 were dominantly identified in the gene-coding region. We also developed a marker to distinguish between the two Glu-1Bx14 alleles. However, the Glu-1Bx14(+) + Glu-1By15 and Glu-1Bx20 + Glu-1By20 allele combinations could not be distinguished using PCR markers. The high-molecular-weight glutenin subunits of wheat varieties were analyzed by ultra-performance liquid chromatography and sodium dodecyl sulfate–polyacrylamide gel electrophoresis, and the findings were compared with the results of PCR analysis.ConclusionsSeven Glu-1Bx and four Glu-1By allele detection markers were developed to detect nine Glu-1Bx and seven Glu-1By locus alleles, respectively. Integrating previously reported markers and 11 newly developed PCR markers improves allelic identification of the Glu-B1 locus and facilitates more effective analysis of Glu-B1 alleles molecular variations, which may improve the end-use quality of wheat.