Allelism Tests Research Articles

Influence of the CYP2J2 Gene Polymorphisms on Chronic Obstructive Pulmonary Disease Risk in the Chinese Han Population

IntroductionCytochrome P450 (CYP) 2J2 is a major enzyme that controls epoxyeicosatrienoic acids biosynthesis, which may play a role in chronic obstructive pulmonary disease (COPD) development. In this study, we aimed to assess the influence of CYP2J2 polymorphisms with COPD susceptibility. Material and methodsA case–control study enrolled 313 COPD cases and 508 controls was to investigate the association between CYP2J2 polymorphisms and COPD risk. Agena MassARRAY platform was used to genotype CYP2J2 polymorphisms. Odds ratios (OR) and 95% confidence intervals (CI) were calculated to evaluate the association between CYP2J2 polymorphisms and COPD risk. ResultsWe observed rs11207535 (homozygote: OR=0.08, 95%CI=0.01–0.96, p=0.047; recessive: OR=0.08, 95%CI=0.01–0.94, p=0.044), rs10889159 (homozygote: OR=0.08, 95%CI=0.01–0.92, p=0.043; recessive: OR=0.08, 95%CI=0.01–0.90, p=0.040) and rs1155002 (heterozygote: OR=1.63, 95%CI=1.13–2.36, p=0.009; dominant: OR=1.64, 95%CI=1.15–2.35, p=0.006; additive: OR=1.45, 95%CI=1.09–1.92, p=0.011) were significantly associated with COPD risk. Allelic tests showed T allele of rs2280274 was related to a decreased risk of COPD and T allele of rs1155002 was associated with an increased COPD risk. Stratified analyses indicated the effects of CYP2J2 polymorphisms and COPD risk were dependent on gender and smoking status (p<0.05). Additionally, two haplotypes (Ars11207535Crs10889159Trs1155002 and Ars11207535Crs10889159Crs1155002) significantly decreased COPD risk. ConclusionIt suggested CYP2J2 polymorphisms were associated with COPD susceptibility in the Chinese Han population.

A Major QTL Located in Chromosome 8 of Cucurbita moschata Is Responsible for Resistance to Tomato Leaf Curl New Delhi Virus.

Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite whitefly transmitted begomovirus, responsible since 2013 of severe damages in cucurbit crops in Southeastern Spain. Zucchini (Cucurbita pepo) is the most affected species, but melon (Cucumis melo) and cucumber (Cucumis sativus) are also highly damaged by the infection. The virus has spread across Mediterranean basin and European countries, and integrated control measures are not being enough to reduce economic losses. The identification of resistance genes is required to develop resistant cultivars. In this assay, we studied the inheritance of the resistance to ToLCNDV previously identified in two Cucurbita moschata accessions. We generated segregating populations crossing both resistant pumpkins, an American improved cultivar Large Cheese (PI 604506) and an Indian landrace (PI 381814), with a susceptible C. moschata genotype (PI 419083). The analysis of symptoms and viral titers of all populations established the same monogenic recessive genetic control in both resistant accessions, and the allelism tests suggest the occurrence of alleles of the same locus. By genotyping with a single nucleotide polymorphism (SNP) collection evenly distributed along the C. moschata genome, a major quantitative trait locus (QTL) was identified in chromosome 8 controlling resistance to ToLCNDV. This major QTL was also confirmed in the interspecific C. moschata × C. pepo segregating populations, although C. pepo genetic background affected the resistance level. Molecular markers here identified, linked to the ToLCNDV resistance locus, are highly valuable for zucchini breeding programs, allowing the selection of improved commercial materials. The duplication of the candidate region within the C. moschata genome was studied, and genes with paralogs or single-copy genes were identified. Its synteny with the region of chromosome 17 of the susceptible C. pepo revealed an INDEL including interesting candidate genes. The chromosome 8 candidate region of C. moschata was also syntenic to the region in chromosome 11 of melon, previously described as responsible of ToLCNDV resistance. Common genes in the candidate regions of both cucurbits, with high- or moderate-impact polymorphic SNPs between resistant and susceptible C. moschata accessions, are interesting to study the mechanisms involved in this recessive resistance.

Genetic analysis of Aegilops tauschii-derived seedling resistance to leaf rust in synthetic hexaploid wheat

Seedling resistance to leaf rust available in the synthetic hexaploid wheat line Syn137 was characterised by means of cytogenetic and linkage mapping. Monosomic analysis located a single dominant gene for leaf rust resistance on chromosome 5D. Molecular mapping not only confirmed this location but also positioned the gene to the distal part of the long arm of chromosome 5D. A test of allelism showed that the gene, tentatively named LrSyn137, is independent but closely linked to Lr1. It appears that Syn137 is occasionally heterogeneous for Lr1 since the analysis of the Lr1-specific marker RGA567-5 in the genetic mapping population indicated the presence of Lr1. Syn137 represents another source of genetic variation that can be useful for the diversification of leaf rust resistance in wheat cultivars.

The SNP rs560426 Within ABCA4-ARHGAP29 Locus and the Risk of Nonsyndromic Oral Clefts.

Nonsyndromic oral clefts are common birth defect with complex etiology. In the present study, we attempt to further validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. We performed allelic transmission disequilibrium test analysis, on 10 eligible single nucleotide polymorphisms (SNPs) and SNP haplotypes using the Family-Based Association Test. The study sample consisted of 334 case-parent trios of nonsyndromic oral clefts from Taiwanese population, separated into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO) groups. We found only the SNP rs560426 within the ABCA4 gene showed strong association with NSCPO (P = .03498; Permuted P = .05382). No association between other 9 selected SNPs in ABCA4-ARHGAP29 region and the risk of nonsyndromic oral clefts was found. For the haplotype analyses, we found only haplotype T-C (rs570926 and rs3789431) in ABCA4 block 2 showed significant association with nonsyndromic NSCL/P in these Taiwanese trios. We used a family-based analysis in 334 Taiwanese case-parent trios to validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. This study provides a new evidence for an association between the intron variant rs560426 within ABCA4 and nonsyndromic cleft palate which may contribute their regulatory role in craniofacial development.

Evaluation of HLA-B 57:01 and its effect on antiretroviral therapy in patients with human immunodeficiency virus infection: Experience of a University Hospital

Aim: Before the decision to start abacavir (ABC), which is a member of the antiretroviral therapy (ART) combinations, the presence of the HLA-B*57:01 allele gene should be investigated in case of hypersensitivity to the drug. In recent years, many clinics tend to conduct “treat now” policy for HIV therapy. We aimed to evaluate HLA-B*57:01 test results and its effect on the initiation time of ART, combination and changing of ART. Materials and Methods: HLA-B*57:01 screening test was evaluated retrospectively in the HIV-infected patients admitted to Inonu University Faculty of Medicine Department of Infectious Diseases and Clinical Microbiology between January 2019 and December 2019. Moreover, the time frame of HLA-B*57:01 tests were evaluated along with the HIV confirmation test completion time. It was evaluated whether there was any effect on the start of treatment and treatment change. Results: Of the 47 HIV-positive patients 44 (93.6%) were male and 3 (6.4%) were female whose HLA-B*57:01 allele was screened. The mean age ± SD of these 47 patients was 37.7 ± 13.5 years. HLA-B*57:01 gene positivity was not detected in any of our cases. After HLA-B*57:01 test detection, ten (21%) of these patients were treated with ABC sulfate plus dolutegravir sodium plus lamivudine. Five of the patients were naive patients, while the other five patients were treatment experienced. HLA-B*57: 01 allele test completion time of the patients (mean ± SD) was 4.02 ± 2.35 days. HLA-B*57:01 completion time did not differ statistically in patients with and without treatment change (p=0.243). Conclusion: HIV infected individuals should be started to treat with ART soon after their diagnosis. To detect the HLA-B*57:01 allele in genomic DNA is important in this period. The fact that this procedure can be performed in centers following HIV-infected patients will positively affect the process of starting treatment.

A study of crown rust resistance in historical and modern oat cultivars representing 120 years of Polish oat breeding

The objective of this paper was to measure resistance to Puccinia coronata f.sp. avenae (Pca) in a set of 63 previously uncharacterised new and historical oat cultivars representing 120 years of Polish oat breeding. The distinctiveness of the obsolete and modern gene pools led to the expectation that the earlier cultivars could be a valuable source of useful resistance genes discarded during subsequent breeding. The plant material was tested at the seedling stage using 14 Pca pathotypes and at the adult plant stage under natural infection conditions in 3 years of field observations. In all, 23 genotypes displayed an immune response to at least one Pca pathotype in the test at the seedling stage, however, most of them were susceptible to crown rust infection in the field. The most resistant, presenting immunity to 9 out of 14 P. coronata isolates, was Celer. The infection profile of this cultivar corresponded to the pattern of reference line Pc39. An allelism test confirmed that the resistance of both the Pc39 line and Celer is conditioned by either the same locus or by tightly linked genes. The infection analysis also demonstrated that some of the newest cultivars (Elegant, Komfort and Harnaś) showed a relatively high level of resistance in each year of field trials, despite being completely susceptible at the seedling stage. Further research will be required to evaluate the source, durability and suitability of this resistance. The study did not find any novel resistance to crown rust in the historic cultivars. However, results provide a new insight into adult plant stage resistance in Polish modern cultivars. The resistance of these cultivars is the result of many years of selection in breeding programs and provides an excellent base for future work.

Phenotypic, genetic, and molecular function of msc-2, a genic male sterile mutant in pepper (Capsicum annuum L.).

Bulked segregant analysis and fine mapping delimited the pepper genic male sterile (msc-2) locus into a 336kb region on chromosome 5. A strong candidate gene, Capana05g000766, a homolog of AtMS1, was indentified in this region. Genic male sterility (msc-2) is used to produce hybrid seeds in Northern China. However, no co-segregated markers have been reported or candidate genes controlling this trait have been cloned. Here, bulked segregant analysis and genotyping of an F2 population and a 18Q5431AB line were employed to fine map msc-2, which was delimited to a 336kb region. In this region, Capana05g000766 was a homolog of AtMS1, which encodes a plant homeodomain finger involved in tapetum development. A "T" deletion in the Capana05g000766 locus leads to a premature stop codon, which may cause a loss-of-function mutation. Real-time PCR analysis revealed that Capana05g000766 was an anther-specific gene and down-regulation of the gene resulted in male sterility. Therefore, Capana05g000766 was identified as the strongest candidate gene for the msc-2 locus. Allelism tests showed that msc-1 and msc-2 were nonallelic, and bimolecular fluorescence complementation analysis indicated that the two genes did not interact directly with each other at the protein level. As msc-1 and msc-2 are homologs of AtDYT1 and AtMS1 in Arabidopsis, they may play similar roles in tapetum development in genic male sterile peppers, and Msc-1 might be up stream of Msc-2 in the regulation of other genes involved in tapetum development.

General regression model: A "model-free" association test for quantitative traits allowing to test for the underlying genetic model.

Most genome-wide association studies used genetic-model-based tests assuming an additive mode of inheritance, leading to underpowered association tests in case of departure from additivity. The general regression model (GRM) association test proposed by Fisher and Wilson in 1980 makes no assumption on the genetic model. Interestingly, it also allows formal testing of the underlying genetic model. We conducted a simulation study of quantitative traits to compare the power of the GRM test to the classical linear regression tests, the maximum of the three statistics (MAX), and the allele-based (allelic) tests. Simulations were performed on two samples sizes, using a large panel of genetic models, varying genetic models, minor allele frequencies, and the percentage of explained variance. In case of departure from additivity, the GRM was more powerful than the additive regression tests (power gain reaching 80%) and had similar power when the true model is additive. GRM was also as or more powerful than the MAX or allelic tests. The true simulated model was mostly retained by the GRM test. Application of GRM to HbA1c illustrates its gain in power. To conclude, GRM increases power to detect association for quantitative traits, allows determining the genetic model and is easily applicable.

Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea)

Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR; Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.

Pairing and Exchanging between Daypyrum villosum Chromosomes 6V#2 and 6V#4 in the Hybrids of Two Different Wheat Alien Substitution Lines.

Normal pairing and exchanging is an important basis to evaluate the genetic relationship between homologous chromosomes in a wheat background. The pairing behavior between 6V#2 and 6V#4, two chromosomes from different Dasypyrum villosum accessions, is still not clear. In this study, two wheat alien substitution lines, 6V#2 (6A) and 6V#4 (6D), were crossed to obtain the F1 hybrids and F2 segregating populations, and the testcross populations were obtained by using the F1 as a parent crossed with wheat variety Wan7107. The chromosomal behavior at meiosis in pollen mother cells (PMCs) of the F1 hybrids was observed using a genomic in situ hybridization (GISH) technique. Exchange events of two alien chromosomes were investigated in the F2 populations using nine polymerase chain reaction (PCR) markers located on the 6V short arm. The results showed that the two alien chromosomes could pair with each other to form ring- or rod-shaped bivalent chromosomes in 79.76% of the total PMCs, and most were pulled to two poles evenly at anaphase I. Investigation of the F2 populations showed that the segregation ratios of seven markers were consistent with the theoretical values 3:1 or 1:2:1, and recombinants among markers were detected. A genetic linkage map of nine PCR markers for 6VS was accordingly constructed based on the exchange frequencies and compared with the physical maps of wheat and barley based on homologous sequences of the markers, which showed that conservation of sequence order compared to 6V was 6H and 6B > 6A > 6D. In the testcross populations with 482 plants, seven showed susceptibility to powdery mildew (PM) and lacked amplification of alien chromosomal bands. Six other plants had amplification of specific bands of both the alien chromosomes at multiple sites, which suggested that the alien chromosomes had abnormal separation behavior in about 1.5% of the PMCs in F1, which resulted in some gametes containing two alien chromosomes. In addition, three new types of chromosome substitution were developed. This study lays a foundation for alien allelism tests and further assessment of the genetic relationship among 6V#2, 6V#4, and their wheat homoeologous chromosomes.

ITGAM is a risk factor to systemic lupus erythematosus and possibly a protection factor to rheumatoid arthritis in patients from Mexico.

ITGAM has consistently been associated with susceptibility to systemic lupus erythematosus (SLE) in many ethnically diverse populations. However, in populations with higher Amerindian ancestry (like Yucatan) or highly admixed population (like Mexican), ITGAM has seldom been evaluated (except few studies where patients with childhood-onset SLE were included). In addition, ITGAM has seldom been evaluated in patients with rheumatoid arthritis (RA). Here, we evaluated whether four single nucleotide polymorphisms (SNPs), located within ITGAM, were associated with SLE and RA susceptibility in patients from Mexico. Our study consisted of 1,462 individuals, which included 363 patients with SLE (292 from Central Mexico and 71 from Yucatan), and 621 healthy controls (504 from Central Mexico and 117 from Yucatan). Our study also included 478 patients with RA from Central Mexico. TaqMan assays were used to obtain the genotypes of the four SNPs: rs34572943 (G/A), rs1143679 (G/A), rs9888739 (C/T), and rs1143683 (C/T). We also verified the genotypes by Sanger sequencing. Fisher's exact test and permutation test were employed to evaluate the distribution of genotype, allele, and haplotype between patients and controls. Our data show that all four ITGAM SNPs are significantly associated with susceptibility to SLE using both genotypic and allelic association tests (corrected for multiple testing, but not for population stratification). A second study carried out in patients from Yucatan, a southeastern part of Mexico (with a high Amerindian ancestry), also replicated SLE association with all four SNPs, including the functional SNP, rs1143679 (OR = 24.6 and p = 9.3X10-6). On the other hand, none of the four SNPs are significant in RA after multiple testing. Interestingly, the GACC haplotype, which carries the ITGAM rs1143679 (A) minor allele, showed an association with protection against RA (OR = 0.14 and p = 3.0x10-4). Our data displayed that ITGAM is a risk factor to SLE in individuals of Mexican population. Concurrently, a risk haplotype in ITGAM confers protection against RA.

Gb8, a new gene conferring resistance to economically important greenbug biotypes in wheat.

A new greenbug resistance gene Gb8 conferring broad resistance to US greenbug biotypes was identified in hard red winter wheat line PI 595379-1 and was mapped to the terminal region of chromosome 7DL. Greenbug [Schizaphis graminum (Rondani)] is a worldwide insect pest that poses a serious threat to wheat production. New greenbug resistance genes that can be readily used in wheat breeding are urgently needed. The objective of this study was to characterize a greenbug resistance gene in PI 595379-1, a single plant selection from PI 595379. Genetic analysis of response to greenbug biotype E in an F2:3 population derived from a cross between PI 595379-1 and PI 243735 indicated that a single gene, designated Gb8, conditioned resistance. Linkage analysis placed Gb8 in a 2.7-Mb interval in the terminal bin of chromosome 7DL (7DL3-082-1.0), spanning 595.6 to 598.3Mb in the Chinese Spring IWGSC RefSeq version 1.0 reference sequence. Gb8 co-segregated with a newly developed SSR marker Xstars508, positioned at 596.4Mb in the reference sequence. Allelism tests showed that Gb8 was different from three permanently named genes on the same chromosome arm and the estimated genetic distance between Gb8 and Gb3 was 15.35 ± 1.35cM. Gb8 can be directly used in wheat breeding to enhance greenbug resistance.

Transethnic associations among immune-mediated diseases and single-nucleotide polymorphisms of the aryl hydrocarbon response gene ARNT and the PTPN22 immune regulatory gene

BackgroundBecause immune responses are sensitive to environmental changes that drive selection of genetic variants, we hypothesized that polymorphisms of some xenobiotic response and immune response genes may be associated with specific types of immune-mediated diseases (IMD), while others may be associated with IMD as a larger category regardless of specific phenotype or ethnicity. ObjectiveTo examine transethnic gene-IMD associations for single nucleotide polymorphism (SNP) frequencies of prototypic xenobiotic response genes—aryl hydrocarbon receptor (AHR), AHR nuclear translocator (ARNT), AHR repressor (AHRR) — and a prototypic immune response gene, protein tyrosine phosphatase, non-receptor type 22 (PTPN22), in subjects from the Environmental Polymorphisms Registry (EPR). MethodsSubjects (n = 3731) were genotyped for 14 SNPs associated with functional variants of the AHR, ARNT, AHRR, and PTPN22 genes, and their frequencies were compared among African Americans (n = 1562), Caucasians (n = 1838), and Hispanics (n = 331) with previously reported data. Of those genotyped, 2015 EPR subjects completed a Health and Exposure survey. SNPs were assessed via PLINK for associations with IMD, which included those with autoimmune diseases, allergic disorders, asthma, or idiopathic pulmonary fibrosis. Transethnic meta-analyses were performed using METAL and MANTRA approaches. ResultsARNT SNP rs11204735 was significantly associated with autoimmune disease by transethnic meta-analyses using METAL (odds ratio, OR [95% confidence interval] = 1.29 [1.08–1.55]) and MANTRA (ORs ranged from 1.29 to 1.30), whereas ARNT SNP rs1889740 showed a significant association with autoimmune disease by METAL (OR = 1.25 [1.06–1.47]). For Caucasian females, PTPN22 SNP rs2476601 was significantly associated with autoimmune disease by allelic association tests (OR = 1.99, [1.30–3.04]). In Caucasians and Caucasian males, PTPN22 SNP rs3811021 was significantly associated with IMD (OR = 1.39 [1.12–1.72] and 1.50 [1.12–2.02], respectively) and allergic disease (OR = 1.39 [1.12–1.71], and 1.62 [1.19–2.20], respectively). In the transethnic meta-analysis, PTPN22 SNP rs3811021 was significantly implicated in IMD by METAL (OR = 1.31 [1.10–1.56]), and both METAL and MANTRA suggested that rs3811021 was associated with IMD and allergic disease in males across all three ethnic groups (IMD METAL OR = 1.50 [1.15–1.95]; IMD MANTRA ORs ranged from 1.47 to 1.50; allergic disease METAL OR = 1.58 [1.20–2.08]; allergic disease MANTRA ORs ranged from 1.55 to 1.59). ConclusionsSome xenobiotic and immune response gene polymorphisms were shown here, for the first time, to have associations across a broad spectrum of IMD and ethnicities. Our findings also suggest a role for ARNT in the development of autoimmune diseases, implicating environmental factors metabolized by this pathway in pathogenesis. Further studies are needed to confirm these data, assess the implications of these findings, define gene-environment interactions, and explore the mechanisms leading to these increasingly prevalent disorders.

New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX.

At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors (“nodulation factors”) are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2A allele (for “Sym2 Afghan”, as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2E allele (for “Sym2 European”). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2A, as has been confirmed by an allelism test with Sym2A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this “Tajik” allele of LykX differs from the “European” one by a single nucleotide polymorphism leading to an R75P change in the receptor part of the putative protein. Thus, our new data are in agreement with the hypothesis concerning the identity of LykX and the elusive Sym2 gene.

Rare variants in SLC6A4 cause susceptibility to major depressive disorder with suicidal ideation in Han Chinese adolescents and young adults

BackgroundSuicidal ideation (SI) is the most serious symptom of major depressive disorder (MDD) and considered an extreme state. The serotonin transporter gene (SLC6A4) plays a significant role in MDD and suicide pathophysiology. Previous studies have revealed an association between common variants of SLC6A4 with the risk of MDD and suicide. However, very few studies have so far focused on the degree to which rare variants of SLC6A4 are responsible for the depression observed in adolescent and young adult suicide patients. The aim of this study was to examine the impact of common and rare variants of SLC6A4 on the risk of Han Chinese adolescents and young adults suffering MDD with SI. MethodsTargeted sequencing of the SLC6A4 gene was conducted using FastTarget technology in Han Chinese adolescents and young adults, of which 74 were MDD patients with SI and 150 were healthy controls. Gene-based association analyses of rare variants were performed using enrichment analysis and a cumulative allele test. An allele association study was performed against common variants. ResultsAfter sequencing and bioinformatics analysis, a total of 15 single nucleotide variants (SNVs) were detected in the targeted regions from all participants, including 9 common and 6 rare variants. Among these, 5 rare variants were identified within the study group. Enrichment analysis of rare variants demonstrated a statistical difference (p = 0.042) between the study and control groups. Using cumulative allele analysis, alternative alleles in the SLC6A4 gene exhibited an association with MDD patients with SI (cumulative allele: OR = 10.18, 95% CI = 1.18–87.32, p = 0.017). No significant association was found between the 9 common SLC6A4 variants and MDD patients with SI. ConclusionsOur results suggest that rare variants of SLC6A4 may contribute to a genetic risk of adolescents and young adults suffering MDD with SI.

Localization of rust resistance genes in old local Russian flaxes by methods of classical genetics

Flax rust, a disease that destroyed a significant portion of the yield before the creation of resistant varieties, is currently defeated, but it can cause new outbreaks as identical resistance genes are used in breeding. Since only one of the allelic genes can be introduced into a variety, the aim of this work is to identify genes for resistance to the disease in lines selected during the evaluation of old Russian flaxes from the VIR collection. The original accessions were added to the collection in 1922, that is, before the release of breeding varieties, so their genes are of natural origin. The analysis was performed on an artificial infectious background by methods of classical genetics, including the test for allelism. Nine monogenic lines with the original R genes were crossed to tester varieties for six loci: K, L, M, N, P, and Q. F2 hybrids in the phase of cotyledon leaves were inoculated with monopustule clones of the fungus, not virulent to any of evaluated genes. Gene allelism was checked by the absence of the segregation. It was exactly proven that R genes of the k-716 line from the Pskov kryazh (gc-32) and the k-780 accession from the Minsk oblast (gc-33) were located in the P locus, the gene of the k-846 line from the Ivanovo-Voznesensk oblast (gc-39) was in the M locus, and the gene of the k-834 line from the Vladimir oblast (gc-38) probably belonged to the K locus. The segregation in the crosses of all testers to the k-630 line from the Simbirsk oblast (gc-25) showed that its gene was not allelic to any of the known loci. Probably, there was a formerly unknown locus. The location of the other genes failed to be identified due to the linkage between loci N and P and the presence of several resistance genes in some lines. The gene in gc-9 was in either M or K locus; and the genes of gc-34, gc-40, and gc-46 were located in P or K. Since all the evaluated genes were original, the genes of these lines were different alleles of the identified loci.

Variabilidad genética neutral y presencia de mecanismos de resistencia en Myzus persicae (Hemiptera: Aphididae), provenientes de diferentes hospedantes en Chile central

Myzus persicae es considerado la tercera plaga de importancia económica de varios cultivos en Chile. Su variabilidad genética es influenciada por la disponibilidad del hospedante primario. Este insecto ha adquirido resistencia a la mayoría de los insecticidas utilizados para su control. El presente trabajotuvo como objetivo evaluar la diversidad genética y la presencia de mecanismos de resistencia de M. persicae en cultivos como duraznero y pimentón. El estudio se realizó en doce localidades: seis en la región de O'Higgins y seis en la región del Maule en Chile central. Para evaluar la diversidad genética neutral, se utilizaron siete marcadores microsatélites, y la identificación de mecanismos se realizó mediante ensayos de discriminación alélica. La mayor diversidadgenética se presentó en poblaciones del duraznero &gt; 0,80 en promedio. En pimentón y arvenses, esta diversidad fue 0,36 en promedio. La frecuencia de individuos con mecanismos de resistencia fue baja y en forma predominantemente heterocigota en los hospedantes evaluados, lo que sugiere que la forma de reproducción sexual del áfido influye en los niveles de resistencia a insecticida. La presencia de mecanismos de resistencia en M. persicae dependedel hospedante, región geográfica y momento de muestreo en el que son evaluados. Existe suficiente evidencia de que las poblaciones de M. persicae están compuestas por muy pocos grupos genéticos, presentando diferentes dinámicas de resistencia a insecticidas en la misma temporada agrícola.

Identification of a New Powdery Mildew Resistance Gene pmDHT at or Closely Linked to the Pm5 Locus in the Chinese Wheat Landrace Dahongtou.

Chinese wheat landrace Dahongtou was resistant to 35 of 38 tested Chinese isolates of Blumeria graminis f. sp. tritici at the seedling stage. Genetic analysis of the F2 populations and their derived F2:3 families of crosses of Dahongtou with the susceptible varieties Mingxian 169 and Huixianhong indicated that the resistance of Dahongtou to B. graminis f. sp. tritici isolate E09 was conferred by a single recessive gene, tentatively designated as pmDHT. The gene was mapped to chromosome arm 7BL and flanked by markers Xwmc526/XBE443877 and Xgwm611/Xwmc511 at genetic distances of 0.8 and 0.3 cM, respectively. The chromosomal position of pmDHT was similar to the multi-allelic Pm5 locus on 7BL. Allelism tests with crosses of Dahongtou with Fuzhuang 30 (Pm5e) and Xiaobaidong (mlxbd) indicated that pmDHT was allelic to both Pm5e and mlxbd. However, pmDHT showed a different pattern of resistance to the 38 B. graminis f. sp. tritici isolates compared with wheat lines with Pm5a, Pm5b, Pm5e, mlxbd, and PmHYM and also differed from PmSGA. Thus, pmDHT was identified most likely as a new allele or at least a closely linked gene of the Pm5 locus. This gene can be transferred into susceptible wheat cultivars/lines and pyramided with other resistance genes through marker-assisted selection to improve powdery mildew resistance.

Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles: A GeT-RM Collaborative Project

Pharmacogenetic testing increasingly is available from clinical and research laboratories. However, only a limited number of quality control and other reference materials currently are available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories (Camden, NJ), has characterized 179 DNA samples derived from Coriell cell lines. Testing included the recharacterization of 137 genomic DNAs that were genotyped in previous Genetic Testing Reference Material Coordination Program studies and 42 additional samples that had not been characterized previously. DNA samples were distributed to volunteer testing laboratories for genotyping using a variety of commercially available and laboratory-developed tests. These publicly available samples will support the quality-assurance and quality-control programs of clinical laboratories performing CYP2D6 testing.

Gene-edited murine cell lines for propagation of chronic wasting disease prions

Prions cause fatal infectious neurodegenerative diseases in humans and animals. Cell culture models are essential for studying the molecular biology of prion propagation. Defining such culture models is mostly a random process, includes extensive subcloning, and for many prion diseases few or no models exist. One example is chronic wasting disease (CWD), a highly contagious prion disease of cervids. To extend the range of cell models propagating CWD prions, we gene-edited mouse cell lines known to efficiently propagate murine prions. Endogenous prion protein (PrP) was ablated in CAD5 and MEF cells, using CRISPR-Cas9 editing. PrP knock-out cells were reconstituted with mouse, bank vole and cervid PrP genes by lentiviral transduction. Reconstituted cells expressing mouse PrP provided proof-of-concept for re-established prion infection. Bank voles are considered universal receptors for prions from a variety of species. Bank vole PrP reconstituted cells propagated mouse prions and cervid prions, even without subcloning for highly susceptible cells. Cells reconstituted with cervid PrP and infected with CWD prions tested positive in prion conversion assay, whereas non-reconstituted cells were negative. This novel cell culture platform which is easily adjustable and allows testing of polymorphic alleles will provide important new insights into the biology of CWD prions.