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Lentil (Lens culinaris Medik.) is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB), caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers have been developed from three recombinant inbred line (RIL) populations. The IH × NF map contained 460 loci across 1461.6 cM, while the IH × DIG map contained 329 loci across 1302.5 cM and the third map, NF × DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across seven linkage groups (LGs), with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs) explaining 52 and 69% of phenotypic variation for resistance to infection in the IH × DIG and IH × NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted the phenotypic responses with high levels of accuracy (~86%), and therefore have the potential to be widely adopted in lentil breeding programs. The availability of RIL-based maps, a consensus map, and validated markers linked to AB resistance provide important resources for lentil improvement.

Background As one of the most common body malignant cancers, skin cancers contain a group of highly heterogeneous tumors with different malignant potential, prognosis and treatment methods. Despite the progress in the treatment of skin cancers worldwide, the overall prognosis is still poor. Recent studies indicated single nucleotide polymorphisms (SNPs) of interleukin-6 (IL-6), including 174G/C and 597G/A, might be associated with susceptibility to skin cancer. This meta-analysis aims to clarify the relationship between IL-6 gene polymorphisms and skin cancers. Methods Eligible studies were identified from searching PubMed, Embase, Web of Science and Cochrane. Pooled odds ratio (OR) and corresponding 95% confidence interval (CI) were obtained for the relationships between IL-6 174G/C and 597G/A polymorphisms and skin cancer using random-effects models. For the included studies, the Newcastle-Ottawa scale (NOS) score was calculated to assess study quality. Heterogeneity tests, sensitivity analysis, and publication bias assessments were also performed. Trim-and-fill method was used when publication bias existed aiming to adjusting OR. All data were analyzed in R (version 4.0.2). Results This meta-analysis included 1,705 cases and 1,987 controls for 174G/C polymorphism (10 publications), and 968 cases and 998 controls for 597G/A polymorphism (3 publications). No elevated risk of skin cancer was found in all comparisons for 174G/C polymorphism: CC vs. GC + GG, OR =1.03 (95% CI: 0.81–1.31); GC + CC vs. GG, OR =1.16 (95% CI: 0.96–1.39); CC vs. GG, OR =1.14 (95% CI: 0.86–1.53); GC vs. GG, OR =1.16 (95% CI: 0.99–1.37); C vs. G, OR =1.07 (95% CI: 0.92–1.24). Then we performed subgroup analysis based on publication year, the cancer type, sample size, NOS score. Significant differences were observed in the subgroup of publication year before 2010 (GC + CC vs. GG, OR =1.255, P=0.012; GC vs. GG, OR =1.277, P=0.01), while there is no statistical significance in the subgroup of publication year after 2010 (P>0.05 for all comparisons). After publication bias adjustment, the results further suggested that 174G/C polymorphism is not associated with the risk of skin cancer. No elevated risk of skin cancer was found in the comparisons for 597G/A polymorphism. Discussion Current evidence showed that IL-6 gene polymorphisms might not be associated with the susceptibility to skin cancer.

Tissue inhibitors of metalloproteinases (TIMPs) play a crucial role in endogenous angiogenesis besides the regulation of matrix metalloproteinase (MMP) activity. Associations between TIMP-2 gene polymorphisms and the risk of retinopathy of prematurity (ROP) were examined. Premature infants born between 2009 and 2018 were included. Five single-nucleotide polymorphisms (SNPs) of TIMP-2 were analyzed with real-time polymerase chain reaction (PCR). Multivariate logistic regression was applied to model associations between TIMP-2 polymorphisms and ROP susceptibility and severity. The GA+AA genotype in individuals with the TIMP-2 polymorphism of rs12600817 was associated with a higher risk of ROP (odds ratio [OR]: 1.518, 95% confidence interval [CI]: 1.028–2.242) compared with their wild-type genotypes. The AA genotype (OR: 1.962, 95% CI: 1.023–3.762) and the AA+GA genotype (OR: 1.686, 95% CI: 1.030–2.762) in individuals with the rs12600817 polymorphism had higher risks of severe, treatment-requiring ROP relative to their wild-type counterparts. In patients with treatment-requiring ROP, the AG+GG genotypes in the TIMP-2 polymorphism of rs2889529 were correlated with the treatment response (p = 0.035). The TIMP-2 polymorphism of rs12600817 help in predicting ROP risks in preterm infants, while the polymorphism of rs2889529 can serve as a genetic marker in evaluating the ROP treatment response.

Background: Chronic hepatitis C is characterized by a progressive deterioration of liver function and is involved in metabolic complications, such as hepatic steatosis. Objective: The aim of this study was to investigate the role of host and viral characteristics associated with -493G/T (rs1800591), I128T (rs3816873), Q95H (rs61733139), and Q244E (rs17599091) Single Nucleotide Polymorphisms (SNPs) in the Microsomal Triglyceride Transfer Protein (MTTP) gene on hepatic steatosis in chronic hepatitis C. Methods: SNPs were genotyped by PCR-RFLP and analyzed in combination with host and viral characteristics by multiple logistic regression in different genetic models of inheritance. Results: The authors analyzed 236 patients with chronic hepatitis C, and 53% had hepatic steatosis. The mutated allele frequencies were > 5%, and the genotypes were in Hardy-Weinberg equilibrium (p ≥ 0.05). It was observed that patients with HCV genotype 3 infection (OR = 2.74, 95% CI 1.24‒6.06, p = 0.013), female sex (OR = 2.28, 95% CI 1.21‒4.28, p = 0.011) and moderate- and high-intensity liver inflammatory activity (A2-A3) (OR = 3.61, 95% CI 1.86‒7.01, p < 0.001) alone exhibited a higher risk of steatosis. The results of multiple logistic regression analysis for interaction showed that for the -493G/T SNP, when the GT/TT genotype (dominant model) and the GT genotype (codominant model) were each combined with HCV genotype 3 infection, an 11.51-fold (95% CI 2.08‒63.59, p = 0.005) and a 15.69-fold (95% CI 2.46‒99.85, p = 0.004) increased risk of steatosis, respectively, was observed. For the I128T SNP, when both the IT/TT genotype (dominant model) and the IT genotype (codominant model) were combined with HCV genotype 3 infection, an 8.51-fold (95% CI 1.59‒45.54, p = 0.012) and an 8.40 fold (95% CI 1.51‒46.91, p = 0.015) increased risk of steatosis, respectively, was observed. Conclusion: The present study showed that the viral genotype combined with the -493G/T and I128T SNPs in the MTTP gene influences hepatic steatosis.

Cerebral Cavernous Malformation (CCM) is a cerebrovascular disease of genetic origin affecting 0.5% of the population and characterized by abnormally enlarged and leaky capillaries that predispose to seizures, neurological deficits, and intracerebral hemorrhage (ICH). CCM occurs sporadically or is inherited as dominant condition with incomplete penetrance and highly variable expressivity. Three disease genes have been identified: KRIT1 (CCM1), CCM2 and CCM3. Previous results demonstrated that loss-of-function mutations of CCM genes cause pleiotropic effects, including defective autophagy, altered reactive oxygen species (ROS) homeostasis, and enhanced sensitivity to oxidative stress and inflammatory events, suggesting a novel unifying pathogenetic mechanism, and raising the possibility that CCM disease onset and severity are influenced by the presence of susceptibility and modifier genes. Consistently, genome-wide association studies (GWAS) in large and homogeneous cohorts of patients sharing the familial form of CCM disease and identical mutations in CCM genes have led to the discovery of distinct genetic modifiers of major disease severity phenotypes, such as development of numerous and large CCM lesions, and susceptibility to ICH. This review deals with the identification of genetic modifiers with a significant impact on inter-individual variability in CCM disease onset and severity, including highly polymorphic genes involved in oxidative stress, inflammatory and immune responses, such as cytochrome P450 monooxygenases (CYP), matrix metalloproteinases (MMP), and Toll-like receptors (TLR), pointing to their emerging prognostic value, and opening up new perspectives for risk stratification and personalized medicine strategies.

Type 2 diabetes mellitus (T2DM) is a metabolic disorder characterized by elevated blood glucose levels and is influenced by both genetic and environmental factors. It is treated with various classes of oral antidiabetic drugs, however, response to treatment is highly variable with patients failing to achieve adequate glycemic control. Treatment response variability has been associated with single nucleotide polymorphisms (SNPs) which influence the pharma-cokinetics and pharmacodynamics of drug(s). The aim of this study was to evaluate the genetic association of 17 SNPs and the response to metformin therapy in patients diagnosed with diabetes from the indigenous Nguni population of South Africa. One hundred and forty indigenous African patients diagnosed with T2DM were recruited and genotyped using the MassARRAY® system. Therapeutic response of patients was ascertained by a change in Hb A1c. Two SNPs (rs1801282 and rs6265) were monomorphic. All other variants were within the Hardy-Weinberg equilibrium (HWE). The T allele of the SLC variant rs316009 [odds ratio (OR) = 0.25, 95% confidence interval (95% CI) = 0.01-0.09, p value = 0.044] and the CT genotype of the PCK1 variant rs4810083 (OR = 2.80, 95% CI = 1.01-7.79, p value = 0.049) were associated with an improved response to treatment after adjustment. No association was observed with post Bonferroni correction. Moreover, this study provides important additional data regarding possible associations between genetic variants and metformin therapy outcomes. In addition, this is one of the first studies providing genetic data from the understudied indigenous sub-Saharan African populations.

Background Proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains (NLR) make up one of most important resistance (R) families for plants to resist attacks from various pathogens and pests. The available transcriptomes of limber pine (Pinus flexilis) allow us to characterize NLR genes and related resistance gene analogs (RGAs) in host resistance against Cronartium ribicola, the causal fungal pathogen of white pine blister rust (WPBR) on five-needle pines throughout the world. We previously mapped a limber pine major gene locus (Cr4) that confers complete resistance to C. ribicola on the Pinus consensus linkage group 8 (LG-8). However, genetic distribution of NLR genes as well as their divergence between resistant and susceptible alleles are still unknown. Results To identify NLR genes at the Cr4 locus, the present study re-sequenced a total of 480 RGAs using targeted sequencing in a Cr4-segregated seed family. Following a call of single nucleotide polymorphisms (SNPs) and genetic mapping, a total of 541 SNPs from 155 genes were mapped across 12 LGs. Three putative NLR genes were newly mapped in the Cr4 region, including one that co-segregated with Cr4. The tight linkage of NLRs with Cr4-controlled phenotypes was further confirmed by bulked segregation analysis (BSA) using extreme-phenotype genome-wide association study (XP-GWAS) for significance test. Local tandem duplication in the Cr4 region was further supported by syntenic analysis using the sugar pine genome sequence. Significant gene divergences have been observed in the NLR family, revealing that diversifying selection pressures are relatively higher in local duplicated genes. Most genes showed similar expression patterns at low levels, but some were affected by genetic background related to disease resistance. Evidence from fine genetic dissection, evolutionary analysis, and expression profiling suggests that two NLR genes are the most promising candidates for Cr4 against WPBR. Conclusion This study provides fundamental insights into genetic architecture of the Cr4 locus as well as a set of NLR variants for marker-assisted selection in limber pine breeding. Novel NLR genes were identified at the Cr4 locus and the Cr4 candidates will aid deployment of this R gene in combination with other major/minor genes in the limber pine breeding program.

The availability of large-scale genomic data resources makes it very convenient to mine and analyze genes that are related to important agricultural traits in rice. Pan-genomes have been constructed to provide insight into the genome diversity and functionality of different plants, which can be used in genome-assisted crop improvement. Thus, a pan-genome comprising all genetic elements is crucial for comprehensive variation study among the heat-resistant and -susceptible rice varieties. In this study, a rice pan-genome was firstly constructed by using 45 heat-tolerant and 15 heat-sensitive rice varieties. A total of 38,998 pan-genome genes were identified, including 37,859 genes in the reference and 1141 in the non-reference contigs. Genomic variation analysis demonstrated that a total of 76,435 SNPs were detected and identified as the heat-tolerance-related SNPs, which were specifically present in the highly heat-resistant rice cultivars and located in the genic regions or within 2 kbp upstream and downstream of the genes. Meanwhile, 3214 upregulated and 2212 downregulated genes with heat stress tolerance-related SNPs were detected in one or multiple RNA-seq datasets of rice under heat stress, among which 24 were located in the non-reference contigs of the rice pan-genome. We then mapped the DEGs with heat stress tolerance-related SNPs to the heat stress-resistant QTL regions. A total of 1677 DEGs, including 990 upregulated and 687 downregulated genes, were mapped to the 46 heat stress-resistant QTL regions, in which 2 upregulated genes with heat stress tolerance-related SNPs were identified in the non-reference sequences. This pan-genome resource is an important step towards the effective and efficient genetic improvement of heat stress resistance in rice to help meet the rapidly growing needs for improved rice productivity under different environmental stresses. These findings provide further insight into the functional validation of a number of non-reference genes and, especially, the two genes identified in the heat stress-resistant QTLs in rice.

Background. Personalized therapy is becoming increasingly popular in oncological scenarios, not only based on molecular pharmacological targets, but also preventing any drug–drug–gene interaction (DDGI), which could lead to severe toxicities. Single nucleotide polymorphisms (SNPs), the individual germline sequence variations in genes involved in drug metabolism, are correlated to interindividual response to drugs and explain both efficacy and toxicity profiles reported by patients. Case presentation. We present the case of a woman suffering from triple-positive breast cancer; she had early-stage disease at the onset and after four years developed metastatic disease. During her history, she presented different toxicities due to antineoplastic treatments. Particularly, hypertransaminasemia was found during every line of treatment. Nevertheless, we were able to guarantee the patient an excellent therapeutic adhesion thanks to the supportive treatments and the reduction of drug dosage. Moreover, we conducted a simultaneous analysis of the patient’s biochemical and genomic data thanks to Drug-PIN software, and we found several significant SNPs of the main enzymes and transporters involved in drug metabolism. Conclusion. Our case report demonstrated the relevance of DDGI in clinical practice management of a patient treated for advanced breast cancer, suggesting the role of Drug-PIN software as an easy-to-use tool to prevent adverse events during cancer treatment and to help physicians in therapeutic algorithms. However, further studies are needed to confirm these results.

Due to the important role of N6-methyladenosine (m6A) in breast cancer, single nucleotide polymorphisms (SNPs) in genes with m6A modification may also be involved in breast cancer pathogenesis. In this study, we used a public genome-wide association study dataset to identify m6A-SNPs associated with breast cancer and to further explore their potential functions. We found 113 m6A-SNPs associated with breast cancer that reached the genome-wide suggestive threshold (5.0E-05), and 86 m6A-SNPs had eQTL signals. Only six genes were differentially expressed between controls and breast cancer cases in GEO datasets (GSE15852, GSE115144, and GSE109169), and the SNPs rs4829 and rs9610915 were located next to the m6A modification sites in the 3ʹUTRs of TOM1L1 and MAFF, respectively. In addition, we found that polyadenylate-binding protein cytoplasmic 1 might have a potential interaction with rs4829 (TOM1L1) and rs9610915 (MAFF). In summary, these findings indicated that the SNPs rs4829 and rs9610915 are potentially associated with breast cancer because they had eQTL signals, altered gene expression, and were located next to the m6A modification sites in the 3ʹUTRs of their coding genes. However, further studies are still needed to clarify how genetic variation affects the epigenetic modification, m6A, and its subsequent functions in the pathogenesis of breast cancer.

Expression of cytokines and growth factors have been shown to be highly correlated with the prognosis of esophageal squamous cell carcinoma (ESCC), a deadly disease with poor prognosis. The suppressor of cytokine signaling (SOCS) family of proteins are key factors in regulating cytokines and growth factors. Yet the role of the SOCS proteins in ESCC is hardly investigated. We currently investigated the prognostic role of SOCS5 in ESCC. We analyzed the prognostic effects of 16 single nucleotide polymorphisms (SNPs) within the SOCS genes in 632 ESCC patients. We repeatedly observed that the 3 SNPs in SOCS5, SOCS5:rs3814039, SOCS5:rs3738890, and SOCS5: rs3768720, were significantly correlated with both overall (OS) and progression-free survival (PFS) of ESCC patients (rs3814039, p=0.032 for OS and p=0.009 for PFS; rs3738890, p=0.016 for OS, and p=0.008 for PFS; rs3768720, p=0.005 for OS and p=0.002 for PFS). SOCS5: rs3768720 was also significantly associated with distant metastasis (Ptrend=0.028). The luciferase assay revealed that SOCS5:rs3814039 and SOCS5: rs3768720 might influence the prognosis by regulating SOCS5 expression. Functional analysis demonstrated SOCS5 was able to regulate epidermal growth factor receptor (EGFR) expression and migration activity of ESCC cells. Furthermore, Patients with strong SOCS5 in normal tissues exhibited significantly better PFS (P=0.049) and reduced risk of distant metastasis (P=0.004) compared to those with weak SOCS5 expression. Overall, our study demonstrates the novel function of SOCS5 in ESCC prognosis. The genetic polymorphisms and expression of SOCS5 could serve as a novel therapeutic biomarker for improving the prognosis of ESCC.

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.

Plant breeders and geneticists use molecular marker-assisted selection also called as MAS as a useful approach for breeding of plant to make selection more efficient and speed up the breeding cycle. MAS can be more efficient, effective, and reliable than phenotypic selection. Molecular markers are useful to identify the economically important traits in the breeding population for further manipulation in a short time. Due to the applicability of markers at the seedling stage ensuring high precision at the reduced level of cost, marker-assisted selection offer the chances to improve responses from selection. The MAS using DNA level polymorphism accelerate the pace of selection. The main marker technologies applied are chiefly co-dominant markers i.e. microsatellite markers/SSR (Simple Sequence Repeats) marker, RFLP (Restriction Fragment Length Polymorphism) marker and SNPs (Single nucleotide polymorphisms). This review overviews the various MAS technologies and their applications in crop improvement programs.

Background: In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism. Methods: A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes. Results: Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus. Conclusion: The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.

Yunfan Ma, Yinxi Zhou, Huixin Zhang, Xiaoan Su Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, People’s Republic of ChinaCorrespondence: Yunfan MaDepartment of Thoracic Surgery, General Hospital of Ningxia Medical University, #804 Shengli South Road, Xingqing Region, Yinchuan, Ningxia 750004, People’s Republic of ChinaTel/Fax +86 951-6743244Email mayunfan2020@163.comPurpose: This study aimed to evaluate the associations between immune response-related genes – STAT4, IL8RA and CCR7 polymorphisms and risk of lung cancer.Methods: Seven polymorphisms of STAT4, IL8RA and CCR7 were genotyped in 350 cases and 350 controls using a MassARRAY platform.Results: The STAT4 rs1400656-G and rs7574865-T alleles may decrease the susceptibility to lung cancer (prs1400656= 0.020; prs7574865= 0.014); while IL8RA rs1008562-C and CCR7 rs3136685-T alleles may increase the risk of disease (prs1008562< 0.001; prs3136685= 0.018). The STAT4 rs1400656-GA and rs7574865-GT genotypes were determined as protective genotypes against lung cancer risk (prs1400656= 0.048; prs7574865= 0.042). However, IL8RA rs1008562-CG/GG and CCR7 rs3136685-TT genotypes were significantly associated with an elevated risk of disease (prs1008562< 0.0001; prs3136685= 0.020). Genetic model analysis revealed that STAT4 rs1400656 and rs7574865 were relate to a declining risk of disease under dominant and log-additive models (rs1400656: p dominant = 0.014, p log-additive= 0.016; rs7574865: p dominant = 0.013, p log-additive= 0.013). In contrast, IL8RA rs1008562 exhibited a strong correlation with an elevated risk of lung cancer under all three models (p dominant < 0.0001, p recessive = 0.011, p log-additive< 0.0001). Moreover, CCR7 rs3136685 was correlated with an increased risk of disease under recessive and log-additive models (p recessive = 0.007, p log-additive= 0.019); and CCR7 rs17708087 was also identified as a risk factor in the dominant model (p = 0.038).Conclusion: These results widen the scope of knowledge about the association between STAT4, IL8RA and CCR7 polymorphisms and risk of lung cancer.Keywords: lung cancer, signal transducers and activators of transcription 4, STAT4, interleukin 8-receptor alpha, IL8RA, Chemokine (C-C motif) receptor 7, CCR7, single nucleotide polymorphisms, SNPs

Hirschsprung disease (HSCR) is complex genetic disorder of the enteric nervous system (ENS) characterized by an absence of ganglion cells in various parts of the intestine. The disease has a strong genetic association with RET-protooncogene (RET) and various genes involved in neural crest development. SOX10 is a transcriptional regulator whose expression is essential in the development of the ENS. The association between single-nucleotide polymorphisms (SNPs) in SOX10, rs139883 and rs139884, and sporadic HSCR has not been reported. We evaluated the genetic associations between two SNPs in SOX10 and Thai sporadic HSCR, using a case-control design. The study included 120 HSCR and 242 sex-matched controls whose DNA was genotyped using the RFLP (rs139883) and Taqman SNP genotyping (rs139884) methods. The study found minor allele frequencies (MAF) at 0.25 and 0.24 for rs139883 (allele C) and rs139884 (allele A), respectively. Both SNPs complied with the Hardy-Weinberg equilibrium and were further examined through disease association. The association analysis found that the risk-genotype of rs139883 (CC) was associated with HSCR (odds ratio [OR] 2.09; 95% confidence interval [CI] 1.07-4.08; P=0.03). When a subgroup analysis was performed, CC genotype of the rs139883 was significantly associated with HSCR only in females (OR 5.6; 95% CI 1.1-19.5; P=0.01). Moreover, the long segment disease group significantly harbored the risk genotype at a higher frequency (28.6%) compared to the short HSCR (12.0%, P=0.02). In conclusion, the study suggests a genetic association between rs139883 in SOX10 and Thai-female HSCR.

Background: Cytokines are the key regulator molecules that modulate immune response. Tumor necrosis factor (TNF- α-308 G/A and TNF-β +252 A/G ) are inflammatory cytokine that control the progression of several types of cancer. They play a vital role in both tumor progression and destruction based on their concentrations. The role of TNF-α-308 G/A and TNF-β +252 A/G gene polymorphism in the etiology of breast cancer (BC) is not clearly understood. Therefore, present study investigates the association of TNF-α -308 G/A and TNF-β +252 A/G and the clinical features with Breast cancer patients. Methods: In a case- control study, we have investigated 150 breast cancer patients and 300 age and ethnically matched healthy controls for duration of 3 years from North India. Promoter polymorphisms of tumor necrosis factor gene (TNF-α -308 G/A and TNF-β +252 A/G) were genotyped using allele specific oligonucleotide polymerase chain reaction ASO and restriction fragment length polymorphism (PCR-RFLP). The associations were evaluated by calculating the pooled odds ratio (OR) with 95% confidence interval (95% CI) using SPSS. Results: Patients with different clinico-pathological variables and healthy controls were analyzed. Significant association was observed in A allele of TNF-α -308 G/A in breast cancer patients as compared to healthy controls (p

Background Chronic inflammation with sustained unregulated immune stimulation in autoimmune rheumatic diseases (ARD) may be a risk factor for developing lymphoproliferative disorders (LPD). Markers of ARD activity as high erythrocyte sedimentation rate or erosive joint diseases and the development of B-symptoms were accounted as risk factors for LPD development. We investigated the association of five inflammatory cytokine genes single nucleotide polymorphisms (SNPs): TNF-α -308G>A; TGF-β1 gene codon 10 T>C and 25 G>C; IL-10 promoter SNPs -1082 A>G, -819T>C, and -592A>C; IL-6 -174G>C; and IFN-γ 874 T>A with the risk of LPD development in ARD patients. The study was conducted on 70 patients divided into group I, 25 ARD patients diagnosed as RA (n = 15) and SLE (n = 10) and with no history of malignancy; group II, 25 patients diagnosed with LPD and had no ARD; and group III, 20 patients diagnosed with both diseases: ARD and LPD. Cytokine genotyping was analyzed by PCR-sequence-specific primer (PCR-SSP). Results ARD+LPD patients had significantly higher frequency of TNF-α -308A allele and AA+AG genotype (high TNF-α producers) and IL-10 -1082A allele and AA genotype (low IL-10 producers) than ARD patients (p = 0.003, p = 0.024, p = 0.003, p = 0.03, respectively) with a significantly increased risk of LPD development in ARD patients expressing the corresponding alleles and genotypes. No significant differences were detected in the distribution frequency of either TGF-β1, IL-6, or IFN-γ SNPs between groups I and III or any of the studied SNPs between groups II and III. The distribution frequency of IL-10 ATA haplotype was significantly increased in group III as compared to group I (p = 0.037). Conclusion The significantly increased frequency of the high-TNF-α- and low-IL-10-producing alleles and genotypes in ARD patients may participate in the provision of a proinflammatory milieu that eventually increases the risk of LPD development.

Ascomycetous fungi are found associated with a wide variety of substrates which range from fresh water to marine ecosystems, tropical to temperate forest soils and deserts, throughout the world over. These demystifying fungi exist as endophytes, pathogens and saprobes. They have been studied due to their ability to contaminate foods and feedstuffs, causing an elaboration of mycotoxins. The objectives of the study included extensive analyses of the morphological features of fungi, especially Aspergilli, which have been presented while studying them on specific mycological media. It is also an elaborate compilation of substantive macro- and micro-morphological characterization of different Aspergilli isolated from the spice Foeniculum vulgare used in India and other countries in the world. Further, a first of its kind attempt has been made to study their relative abundance and frequency of occurrence, molecular phylogeny and genetic relatedness to characterize the Aspergilli into specific sections, groups and clades. Single nucleotide polymorphism (SNP) analysis was carried out to evaluate the functional consequences of nucleotide variations, synonymous and non-synonymous mutations in the protein structure. The study resulted in a total of 3,506 Aspergillus isolates, which were obtained from seventy (70) fennel samples, representing 14 Aspergillus species. The two most frequently found species were A. niger and A. flavus with a relative abundance of 32.24 and 11.63%, respectively. The taxonomy and current placements have been reappraised with suggestions and prospects for future research from six sections namely Terrei, Flavi, Fumigati, Nidulantes, Nigri, and Versicolores. In addition, a total number of 27 isolates were studied and deposited at the National Centre for Biotechnology Information (NCBI) and five Aspergillus species have been identified and are being reported for the first time from the fennel seeds, based on partial sequence analysis of the official fungal barcode namely, Internal Transcribed Spacer (ITS) and a functional gene, beta tubulin gene locus, coupled with phenotypic characterization. SNPs for specific DNA regions have been used to identify variants in Aspergilli obtained from Indian fennel seeds for the first time. The need for a polyphasic approach of morphological identification and genetic characterization of Aspergilli from Foeniculum vulgare is addressed and presented here in adequate detail. Our current work makes extensive use of partial beta-tubulin gene sequences analyses to evaluate the association between SNPs in five Aspergillus species sections.

Purpose The objective of this study is to validate the existence of dual cores within the typical phosphotyrosine binding (PTB) domain and to identify potentially damaging and pathogenic nonsynonymous coding single nuclear polymorphisms (nsSNPs) in the canonical PTB domain of the CCM2 gene that causes cerebral cavernous malformations (CCMs). Methods The nsSNPs within the coding sequence for PTB domain of human CCM2 gene, retrieved from exclusive database searches, were analyzed for their functional and structural impact using a series of bioinformatic tools. The effects of mutations on the tertiary structure of the PTB domain in human CCM2 protein were predicted to examine the effect of nsSNPs on the tertiary structure of PTB Cores. Results Our mutation analysis, through alignment of protein structures between wildtype CCM2 and mutant, predicted that the structural impacts of pathogenic nsSNPs is biophysically limited to only the spatially adjacent substituted amino acid site with minimal structural influence on the adjacent core of the PTB domain, suggesting both cores are independently functional and essential for proper CCM2 PTB function. Conclusion Utilizing a combination of protein conservation and structure-based analysis, we analyzed the structural effects of inherited pathogenic mutations within the CCM2 PTB domain. Our results predicted that the pathogenic amino acid substitutions lead to only subtle changes locally, confined to the surrounding tertiary structure of the PTB core within which it resides, while no structural disturbance to the neighboring PTB core was observed, reaffirming the presence of independently functional dual cores in the CCM2 typical PTB domain., Highlights • The pathogenic amino acid mutants lead to subtle structural changes in the PTB core. • No structural disturbance to the neighboring PTB core was observed. • Data reaffirm the presence of dual functional cores in the CCM2 PTB domain. • More new genetic variants leading to CCM pathogenesis were suggested.

[ES] El virus de la hoja rizada del tomate de Nueva Delhi (ToLCNDV) constituye una de las principales amenazas para el cultivo de cucurbitáceas en la cuenca del Mediterráneo. Dentro de esta familia hortícola, la producción de pepino (Cucumis sativus) se ha visto mermada por la incidencia de esta virosis. El uso de resistencias genéticas es la estrategia de control más eficiente para hacer frente a patógenos virales. Los grupos de Virología y Mejora Genética de Cucurbitáceas del COMAV-UPV identificaron accesiones de pepino resistentes a ToLCNDV y mapearon un QTL ligado a la resistencia en el cromosoma 2. Sin embargo, para la obtención de variedades comerciales con resistencia completa y durable a la infección es necesario el desarrollo de herramientas moléculares y la caracterización de nuevas fuentes de resistencia que permitan transferir y piramidalizar genes complementarios de resistencia a fondos genéticos de interés agronómico. El objetivo de este Trabajo Final de Máster consiste en profundizar en la caracterización genética de la resistencia a ToLCNDV. Para ello, se ha llevado a cabo la secuenciación mediante GBS de accesiones resistentes y susceptibles al virus, así como de plantas con diferente respuesta a la infección de una población segregante F2. Tras el análisis de los datos, se han identificado polimorfismos de tipo SNP localizados en la región del QTL ligado a la resistencia en pepino. Se han desarrollado marcadores SNPs para genotipar mediante tecnología ¿High Resolution Melting¿ (HRM) las poblaciones segregantes F2 y de retrocruce, lo que permitirá acotar la región candidata e identificar genes y marcadores moleculares estrechamente ligados a la resistencia. Por otra parte, se han obtenido semillas de tipo híbrido F1 derivadas de una accesión de pepino con resistencia a ToLCNDV de la que aún no se desconoce el tipo de herencia que la regula. Plantas F1 han sido cultivadas en invernadero y autofecundadas y retrocruzadas para generar poblaciones segregantes. Las plantas de las familias obtenidas se han inoculado con un clon infeccioso del virus y se han fenotipado según evaluación visual de su sintomatología. Para llevar a cabo un diagnóstico preciso de la enfermedad, la carga viral de cada planta ha sido evaluada mediante hibridación molecular con sondas de RNA y PCR cuantitativa. Los SNPs desarrollados a partir de la secuenciación por GBS se utilizarán para genotipar las nuevas poblaciones desarrolladas y validar si el locus del cromosoma 2 también controla la resistencia a ToLCNDV en esta accesión., [EN] Tomato leaf curl virus New Delhi (ToLCNDV) is one of the main threats to cucurbit crops in the Mediterranean basin. Within this vegetable family, cucumber (Cucumis sativus) production has been reduced by the incidence of this virus. The use of genetic resistance is the most effective control strategy to deal with viral pathogens. The Cucurbit Virology and Breeding groups of COMAV-UPV identified cucumber accessions resistant to ToLCNDV and mapped a QTL linked to the resistance on chromosome 2. However, to obtain commercial varieties with complete and durable resistance to infection, the development of molecular tools and the characterization of new sources of resistance that allow the transfer and pyramiding of complementary resistance genes to genetic backgrounds of agronomic interest is necessary. The objective of this Final Master's Thesis is to deepen in the genetic characterization of resistance to ToLCNDV. For this purpose, GBS sequencing of resistant and susceptible accessions to the virus, as well as plants with different response to infection of a segregating F2 population has been carried out. After data analysis, SNP polymorphisms located in the region of the QTL linked to resistance in cucumber have been identified. SNP markers have been developed to genotype by High Resolution Melting (HRM) technology the F2 segregating and backcross populations, which will allow to narrow down the candidate region and identify genes and molecular markers closely linked to the resistance. On the other hand, F1 hybrid seeds have been obtained from a cucumber accession with resistance to ToLCNDV of which the type of inheritance that regulates it is not yet known. F1 plants have been grown in greenhouse and self- fertilized and backcrossed to generate segregating populations. Plants from the families obtained were inoculated with an infectious clone of the virus and phenotyped according to visual assessment of their symptomatology. To carry out an accurate diagnosis of the disease, the viral load of each plant was evaluated by molecular hybridization with RNA probes and quantitative PCR. The SNPs developed from GBS sequencing have been used to genotype the newly developed populations and validate whether the chromosome 2 locus also controls resistance to ToLCNDV in this accession., Este trabajo ha sido cofinanciado por el Ministerio de Ciencia e Innovación (Proyecto número PID2021-125787OR-C33) a través de la Agencia Estatal de Investigación y fondos FEDER y por el proyecto PROMETEO para grupos de excelencia (proyecto 2021/072) de la Conselleria d’Educació, Investigació, Cultura i Esports (Generalitat Valenciana).

Background: Suicide is a preventable but escalating global health crisis. Genome-wide association studies (GWAS) studies to date have been limited, and some are underpowered. In this study, we aimed to perform the PsychArray-based GWAS study to identify single nucleotide variations associated with suicide in the Indian population. Methods: We recruited unrelated subjects who died by suicide as cases (N = 313) and the non-suicidal deaths as controls (N = 294). The 607 samples were genotyped, including cases and controls using the Illumina Infinium PsychArray-24 BeadChip v1.3 Results: In our study, four single nucleotide polymorphisms (SNPs) crossed the threshold of significance level

Most studies in the field of CHRNA5-A3 and CHRNB3-A6 have only focused on lung cancer risk; however, the associations with chronic obstructive pulmonary disease (COPD) risk and smoking cessation is less understood, particularly in the Chinese male population. In this study, samples from 823 male patients with COPD (non smokers: 416; still smoking: 407) and 435 smoking male healthy control subjects were performed with DNA extraction and single nucleotide polymorphism (SNP) genotyping. We studied three SNPS in two genes, namely rs667282 and rs3743073 in CHRNA5-A3 and rs4950 in CHRNB3-A6, and their distributions in the three groups are not statistically different (p >0.05). We grouped COPD patients according to whether they had successfully quit smoking, the CT genotype of rs667282 demonstrated association with an increased rate of successful smoking cessation compared with the TT genotype [adjusted odds ratio (OR) = 0.54, 95% confidence interval (95% CI) = 0.37-0.7, p p p p >0.05). Our findings confirmed the hypothesis that CHRNA5-A3 and CHRNB3-A6 variation are not associated with the risk of COPD. We found CHRNA5-A3 and CHRNB3-A6 were significantly associated with successful smoking cessation in smoking COPD patients.

Minor histocompatibility antigens (mHAg) composed of peptides presented by HLA molecules can cause immune responses involved in graft-versus-host disease (GVHD) and graft-versus-leukemia effects after allogeneic hematopoietic cell transplantation (HCT). The current study was designed to identify individual graft-versus-host genomic mismatches associated with altered risks of acute or chronic GVHD or relapse after HCT between HLA-genotypically identical siblings. Our results demonstrate that in allogeneic HCT between a pair of HLA-identical siblings, a mHAg manifests as a set of peptides originating from annotated proteins and non-annotated open reading frames, which i) are encoded by a group of highly associated recipient genomic mismatches, ii) bind to HLA allotypes in the recipient, and iii) evoke a donor immune response. Attribution of the immune response and consequent clinical outcomes to individual peptide components within this set will likely differ from patient to patient according to their HLA types.

BackgroundA Delphi consensus was conducted to evaluate the influence of single nucleotide polymorphisms (SNPs) in genes encoding gonadotropin and gonadotropin receptors on clinical ovarian stimulation outcomes following assisted reproductive technology (ART) treatment.MethodsNine experts plus two Scientific Coordinators discussed and amended statements plus supporting references proposed by the Scientific Coordinators. The statements were distributed via an online survey to 36 experts, who voted on their level of agreement or disagreement with each statement. Consensus was reached if the proportion of participants agreeing or disagreeing with a statement was >66%.ResultsEleven statements were developed, of which two statements were merged. Overall, eight statements achieved consensus and two statements did not achieve consensus. The statements reaching consensus are summarized here. (1) SNP in the follicle stimulating hormone receptor (FSHR), rs6166 (c.2039A>G, p.Asn680Ser) (N=5 statements): Ser/Ser carriers have higher basal FSH levels than Asn/Asn carriers. Ser/Ser carriers require higher amounts of gonadotropin during ovarian stimulation than Asn/Asn carriers. Ser/Ser carriers produce fewer oocytes during ovarian stimulation than Asn/Asn or Asn/Ser carriers. There is mixed evidence supporting an association between this variant and ovarian hyperstimulation syndrome. (2) SNP of FSHR, rs6165 (c.919G>A, p.Thr307Ala) (N=1 statement): Few studies suggest Thr/Thr carriers require a shorter duration of gonadotropin stimulation than Thr/Ala or Ala/Ala carriers. (3) SNP of FSHR, rs1394205 (−29G>A) (N=1 statement): Limited data in specific ethnic groups suggest that A/A allele carriers may require higher amounts of gonadotropin during ovarian stimulation and produce fewer oocytes than G/G carriers. (4) SNP of FSH β-chain (FSHB), rs10835638 (−211G>T) (N=1 statement): There is contradictory evidence supporting an association between this variant and basal FSH levels or oocyte number. (5) SNPs of luteinizing hormone β-chain (LHB) and LH/choriogonadotropin receptor (LHCGR) genes (N=1 statement): these may influence ovarian stimulation outcomes and could represent potential future targets for pharmacogenomic research in ART, although data are still very limited.ConclusionsThis Delphi consensus provides clinical perspectives from a diverse international group of experts. The consensus supports a link between some variants in gonadotropin/gonadotropin receptor genes and ovarian stimulation outcomes; however, further research is needed to clarify these findings.

Leucine aminopeptidase 3 (LAP3) is a metallopeptidase that cleaves N-terminal residues and is involved in protein maturation and degradation. In this study, we characterized the leucine aminopeptidase 3 (LAP3) gene from Tegillarca granosa (Tg-LAP3 for short), which appeared to consist of 15,731 nucleotides encoding 530 amino acids. We identified 12 introns and 13 exons in the Tg-LAP3 gene, suggesting a highly conserved genomic structure. The proximal promoter sequence consists of 1922 bps with a typical TATA box structure, which is the general structural characteristic of core promoters in eukaryotes. We found two functional domains in the Tg-LAP3 protein, including an N-terminal domain (41–174aa) and a peptidase_M17 catalytic domain (209–522aa). Multiple alignment showed that Tg-LAP3 shares 73.4% identity with LAP3 of Mizuhopecten&nbsp, yessoensis and 55.2–70.7% identity with LAP3 of other species. Quantitative analysis of Tg-LAP3 in embryos/larvae and adult tissues indicated that the highest expression occurred in eyebot larva, with limited expression in other stages, among tissues, the highest expression was found in the liver (p &lt, 0.05). Association analysis found that three single-nucleotide polymorphisms (SNPs) (g.-488A &gt, G, g.-1123C &gt, T, and g.-1304C &gt, A) in the proximal promoter were successfully typed, but there was no significant difference in growth traits (body weight, shell length, shell width, and shell height) among these genotypes. The results of our study demonstrate the functional roles of the Tg-LAP3 gene and provide valuable information for molecular marker-assisted selection (MAS) of the blood clam.

Healthcare associated infections caused by vancomycin-resistant Enterococcus faecium (VREfm) have a major impact on health outcomes. VREfm is difficult to treat because of intrinsic and acquired resistance to many clinically used antimicrobials, with daptomycin being one of the few last line therapeutic options for treating multidrug-resistant VREfm. The emergence of daptomycin-resistant VREfm is therefore of serious clinical concern. Despite this, the impact that daptomycin-resistant VREfm have on patient health outcomes is not clearly defined and knowledge on the mechanisms and genetic signatures linked with daptomycin resistance in VREfm remains incomplete. To address these knowledge gaps, phenotypic daptomycin susceptibility testing was undertaken on 324 E. faecium isolates from Australia and New Zealand. Approximately 15% of study isolates were phenotypically resistant to daptomycin. Whole genome sequencing revealed a strong association between vanA-VREfm and daptomycin resistance, with 95% of daptomycin-resistant study isolates harbouring vanA. Genomic analyses showed that daptomycin-resistant VREfm isolates were polyclonal and carried several previously characterised mutations in the liaR and liaS genes as well as several novel mutations within the rpoB, rpoC, and dltC genes. Overall, 70% of daptomycin-resistant study isolates were found to carry mutations within the liaR, rpoB, rpoC, or dltC genes. Finally, in a mouse model of VREfm bacteraemia, infection with the locally dominant daptomycin-resistant clone led to reduced daptomycin treatment efficacy in comparison to daptomycin-susceptible E. faecium. These findings have important implications for ongoing VREfm surveillance activities and the treatment of VREfm infections.

PurposeAlthough MYBL2 had been validated to participate in multiple cancers including leukemia, the role of MYBL2 polymorphisms in acute lymphoblastic leukemia (ALL) was still not clear. In this study, we aimed to evaluate the association between MYBL2 single nucleotide polymorphisms (SNPs) and ALL risk in children.MethodsA total of 687 pediatric ALL cases and 971 cancer-free controls from two hospitals in South China were recruited. A case-control study by genotyping three SNPs in the MYBL2 gene (rs285162 C>T, rs285207 A>C, and rs2070235 A>G) was conducted. The associations were assessed by odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Subgroup and stratification analyses were conducted to explore the association of rs285207 with ALL risk in terms of age, sex, immunophenotype, risk level, and other clinical characteristics. The false-positive report probability (FPRP) analysis was performed to verify each significant finding. Functional analysis in silico was used to evaluate the probability that rs285207 might influence the regulation of MYBL2.ResultsOur study demonstrated that rs285207 was related to a decreased ALL risk (adjusted OR = 0.78; 95% CI = 0.63-0.97, P = 0.022) in the dominant model. The associations of rs285207 with ALL risk appeared stronger in patients with pre B ALL (adjusted OR=0.56; 95% CI=0.38-0.84, P=0.004), with normal diploid (adjusted OR=0.73; 95% CI=0.57-0.95, P=0.017), with low risk (adjusted OR=0.68; 95% CI=0.49-0.94, P=0.021), with lower WBC (adjusted OR=0.62; 95% CI=0.43-0.87, P=0.007) or lower platelet level (adjusted OR=0.76; 95% CI=0.59-0.96, P=0.023). With FPRP analysis, the significant association between the rs285207 polymorphism and decreased ALL risk was still noteworthy (FPRP=0.128). Functional analysis showed that IKZF1 bound to DNA motif overlapping rs285207 and had a higher preference for the risk allele A. As for rs285162 C>T and rs2070235 A>G, no significant was found between them and ALL risk.ConclusionIn this study, we revealed that rs285207 polymorphism decreased the ALL risk in children, and rs285207 might alter the binding to IKZF1, which indicated that the MYBL2 gene polymorphism might be a potential biomarker of childhood ALL.

Cowpea aphids (Aphis craccivora Koch) double as a direct damaging pest and a virus vector to cowpea, threatening the economic yield of the crop. Given the multiple ecotypes, different alleles have been implicated in aphid resistance, necessitating the identification of key genes involved. The present study implemented a genome-wide scan using 365 cowpea mini-core accessions to decipher loci involved in resistance to aphid ecotype from Kano, Nigeria. Accessions were artificially inoculated with A. craccivora in insect-proof cages and damage severity assessed at 21 days after infestation. Significant phenotypic differences based on aphid damage severity were registered among the accessions. Skewed phenotypic distributions were depicted in the population, suggesting the involvement of major genes in the control of resistance. A genome-wide scan identified three major regions on chromosomes Vu10, Vu08 and Vu02, and two minor ones on chromosomes Vu01 and Vu06, that were significantly associated with aphid resistance. These regions harbored several genes, out of which, five viz Vigun01g233100.1, Vigun02g088900.1, Vigun06g224900.1, Vigun08g030200.1 and Vigun10g031100.1 were the most proximal to the peak single nucleotide polymorphisms (SNPs) positions. These genes are expressed under stress signaling, mechanical wounding and insect feeding. The uncovered loci contribute towards establishing a marker-assisted breeding platform and building durable resistance against aphids in cowpea.

Rapeseed is a globally cultivated commercial crop, primarily grown for its oil. High-density single nucleotide polymorphism (SNP) arrays are widely used as a standard genotyping tool for rapeseed research, including for gene mapping, genome-wide association studies, germplasm resource analysis, and cluster analysis. Although considerable rapeseed genome sequencing data have been released, DNA arrays are still an attractive choice for providing additional genetic data in an era of high-throughput whole-genome sequencing. Here, we integrated re-sequencing DNA array data (32,216, 304 SNPs) from 505 inbred rapeseed lines, allowing us to develop a sensitive and efficient genotyping DNA array, Bnapus50K, with a more consistent genetic and physical distribution of probes. A total of 42,090 high-quality probes were filtered and synthesized, with an average distance between adjacent SNPs of 8 kb. To improve the practical application potential of this array in rapeseed breeding, we also added 1,618 functional probes related to important agronomic traits such as oil content, disease resistance, male sterility, and flowering time. The additional probes also included those specifically for detecting genetically modified material. These probes show a good detection efficiency and are therefore useful for gene mapping, along with crop variety improvement and identification. The novel Bnapus50K DNA array developed in this study could prove to be a quick and versatile genotyping tool for B. napus genomic breeding and research.

Simple Summary The purpose of the study was to identify SNPs in genes encoding TLR7 and TLR8 in goats of Carpathian breed and analyze their association with the SRLVs provirus concentration. A total of 14 SNPs were detected, 6 SNPs in the TLR7 gene locus and 8 SNPs in the TLR8 gene. These SNPs were located in intron, 3′UTR and 5′UTR regions and within the coding sequences leading to the synonymous mutations. Our results revealed that 9 out 14 identified polymorphisms were associated with the SRLVs proviral concentration. This finding supports a role for genetic variations of TLR7 and TLR8 in SRLVs infection. Abstract Toll-like receptors (TLRs) 7 and 8 are important in single-stranded viral RNA recognition, so genetic variation of these genes may play a role in SRLVs infection and disease progression. Present study aimed to identify SNPs in genes encoding TLR7 and TLR8 in goats of Carpathian breed and analyze their association with the SRLVs provirus concentration as index of disease progression. A total of 14 SNPs were detected, 6 SNPs in the TLR7 gene locus and 8 SNPs in the TLR8 gene. Nine of the 14 identified polymorphisms, 4 in the TLR7 gene and 5 in TLR8 gene, were significantly associated with the SRLVs proviral concentration. These SNPs were located in 3′UTR, 5′UTR and intron sequences as well as in the coding sequences, but they led to silent changes. Homozygous genotypes of three TLR7 SNPs (synonymous variant 1:50703293, 3′UTR variant 1:50701297 and 5′UTR variant 1:50718645) were observed in goats with lower provirus copy number as well as in seronegative animals. The results obtained in this study suggest that SNPs of TLR7/TLR8 genes may induce differential innate immune response towards SRLVs affecting proviral concentration and thereby disease pathogenesis and progression. These findings support a role for genetic variations of TLR7 and TLR8 in SRLVs infection and warrants further studies on the effect of TLR7/TLR8 polymorphisms on SRLVs infection in different populations.

Due to the important role of N6-methyladenosine (m6A) in breast cancer, single nucleotide polymorphisms (SNPs) in genes with m6A modification may also be involved in breast cancer pathogenesis. In this study, we used a public genome-wide association study dataset to identify m6A-SNPs associated with breast cancer and to further explore their potential functions. We found 113 m6A-SNPs associated with breast cancer that reached the genome-wide suggestive threshold (5.0E-05), and 86 m6A-SNPs had eQTL signals. Only six genes were differentially expressed between controls and breast cancer cases in GEO datasets (GSE15852, GSE115144, and GSE109169), and the SNPs rs4829 and rs9610915 were located next to the m6A modification sites in the 3ʹUTRs of TOM1L1 and MAFF, respectively. In addition, we found that polyadenylate-binding protein cytoplasmic 1 might have a potential interaction with rs4829 (TOM1L1) and rs9610915 (MAFF). In summary, these findings indicated that the SNPs rs4829 and rs9610915 are potentially associated with breast cancer because they had eQTL signals, altered gene expression, and were located next to the m6A modification sites in the 3ʹUTRs of their coding genes. However, further studies are still needed to clarify how genetic variation affects the epigenetic modification, m6A, and its subsequent functions in the pathogenesis of breast cancer.

Background A chronic inflammatory state is a prominent feature in patients with end-stage renal disease (ESRD). Nuclear factor-kappa B (NF-κB) is a transcription factor that regulates the expression of genes involved in inflammation. Some genetic studies have demonstrated that the NF-κB genetic mutation could cause kidney injury and kidney disease progression. However, the association of a gene polymorphism in the transcription factor binding site of NF-κB with kidney disease is not clear. Methods We used the Taiwan Biobank database, the University of California, Santa Cruz, reference genome, and a chromatin immunoprecipitation sequencing database to find single nucleotide polymorphisms (SNPs) at potential binding sites of NF-κB. In addition, we performed a case–control study and genotyped 847 patients with ESRD and 846 healthy controls at Tri-Service General Hospital from 2015 to 2016. Furthermore, we used the ChIP assay to identify the binding activity of different genotypes and used Luciferase reporter assay to examine the function of the rs9395890 polymorphism. Result The results of biometric screening in the databases revealed 15 SNPs with the potential binding site of NF-κB. Genotype distributions of rs9395890 were significantly different in ESRD cases and healthy controls (P = 0.049). The ChIP assay revealed an approximately 1.49-fold enrichment of NF-κB of the variant type TT when compared to that of the wild-type GG in rs9395890 (P = 0.027; TT = 3.20 ± 0.16, GT = 2.81 ± 0.20, GG = 1.71 ± 0.18). The luciferase reporter assay showed that the NF-κB binding site activity in T allele was slightly higher than that in G allele, though it is not significant. Conclusions Our findings indicate that rs9395890 is associated with susceptibility to ESRD in Taiwan population. Electronic supplementary material The online version of this article (10.1186/s12882-019-1471-2) contains supplementary material, which is available to authorized users.

Background The aim of this study was to screen for noise-induced hearing loss (NIHL)-associated single nucleotide polymorphisms (SNPs) and to construct genetic risk prediction models for NIHL in a Chinese population. Methods Four hundred seventy-six subjects with NIHL and 476 matched controls were recruited from a cross-sectional survey on NIHL in China. A total of 83 candidate SNPs were genotyped using nanofluidic dynamic arrays on a Fluidigm platform. NIHL-associated SNPs were screened with a multiple logistic model, and a genetic risk model was constructed based on the genetic risk score (GRS). The results were validated using a prospective cohort population. Results Seven SNPs in the CDH23, PCDH15, EYA4, MYO1A, KCNMA1, and OTOG genes were significantly (P 0.05 and P

Crop-wild introgressions have long been exploited without knowing the favorable recombination points. Synthetic hexaploid wheats are one of the most exploited genetic resources for bread wheat improvement. However, despite some QTL with major effects, much less is known about genome-wide patterns of introgressions and their effects on phenotypes. We used two genome-wide association approaches: SNP-GWAS and haplotype-GWAS to identify SNPs and haplotypes associated with productivity under water-limited conditions in a synthetic-derived wheat (SYN-DER) population. Haplotype-GWAS further enriched and identified 20 more genomic regions associated with drought adaptability that did not overlap with SNP-GWAS. Since GWAS is biased to the phenotypes in the study and may fail to detect important genetic diversity during breeding, we used five complementary analytical approaches (t-test, Tajima’s D, nucleotide diversity (π), Fst, and EigenGWAS) to identify divergent selections in SYN-DER compared to modern bread wheat. These approaches consistently pinpointed 89 ‘selective sweeps’, out of which 30 selection loci were identified on D-genome. These key selections co-localized with important functional genes of adaptive traits such as TaElf3-D1 (1D) for earliness per se (Eps), TaCKX-D1 (3D), TaGS1a (6D) and TaGS-D1 (7D) for grain size, weight and morphology, TaCwi-D1 (5D) influencing drought tolerance, and Vrn-D3 (7D) for vernalization. Furthermore, 55 SNPs and 23 haplotypes of agronomic and physiological importance such as grain yield, relative water content and thousand grain weight in SYN-DER, were among the top 5% of divergent selections contributed by synthetic hexaploid wheats. These divergent selections associated with improved agronomic performance carry new alleles that have been introduced to wheat. Our results demonstrated that GWAS and selection sweep analyses are powerful approaches for investigating favorable introgressions under strong selection pressure and the use of crop-wild hybridization to assist the improvement of wheat yield and productivity under moisture limiting environments.

Objective To investigate the association between single nucleotide polymorphisms (SNPs) in six candidate genes (enamelin [ ENAM]; tuftelin 1 [ TUFT1]; matrix metallopeptidase 13 [ MMP13]; interleukin 1 beta [ IL1B]; interleukin 10 [ IL10]; interleukin 1 receptor antagonist [ IL1RN]) and dental caries in children from northwest China. Methods This case–control study enrolled children (12–15 years) who underwent routine dental examinations. The children were divided into two groups based on the presence of dental caries. A saliva sample was collected and seven SNPs (rs3806804A/G in ENAM, rs3811411T/G in TUFT1, rs2252070A/G and rs597315A/T in MMP13, rs1143627C/T in IL1B, rs1800872A/C in IL10 and rs956730G/A in IL1RN) were genotyped. Results A total of 357 children were enrolled in the study: 161 with dental caries and 196 without dental caries. No significant difference was found in the alleles and genotypes of five genes ( ENAM, TUFT1, MMP13, IL10 and IL1RN) between those with and without dental caries. A significant relationship was found between the IL1B rs1143627C/T polymorphism and dental caries susceptibility with those carrying the rs1143627CT genotype having a lower risk of dental caries compared with those carrying the CC genotype (odds ratio 0.557; 95% confidence interval 0.326, 0.952). Conclusion The IL1B rs1143627C/T polymorphism may be associated with dental caries susceptibility in children from northwest China.

Detection of epistatic interactions, which are referred to as nonlinear interactive effects of single nucleotide polymorphisms (SNPs), is increasingly being recognized as an important route in capturing the underlying genetic causes of complex diseases. Its methodological and computational challenges have been well understood, and many methods also have been proposed from different perspectives. Among them ant colony optimization (ACO)-based methods are promising due to their controllable time complexities, heuristic positive feedback search, and high detection power. Nevertheless, there is no comprehensive overview of them so far. This paper, therefore, provides a systematic review of 25 ACO-based epistasis detection methods. First, the generic ACO algorithm, as well as how it is applied to detect epistatic interactions, is briefly described. Then, an in-depth review of ACO-based methods for detecting epistatic interactions is discussed from four aspects, including path selection strategies, pheromone updating rules, fitness functions, and two-stage designs. Finally, this paper analyzes the strengths and limitations of involved methods, provides guidelines for applying them, and gives several views on the future directions of epistasis detection methods.

Background: The basal core promoter (BCP) double mutations (A1762T and G1764A) of hepatitis B virus (HBV) have been reported to be an aetiological factor of hepatocellular carcinoma (HCC). What distinguishes the subset of HBV carriers in whom these mutations are selected? Methods: A genome-wide association study (GWAS) was carried out on 218 asymptomatic HBsAg carriers infected with HBV with BCP double mutations and 191 controls infected with HBV with the wild type BCP. The highest ranking nucleotide polymorphisms (SNPs) were validated with other study subjects, 203 cases and 181 controls. The expression of the gene nearest a SNP found to be significant was examined using RT-PCR. Results: Forty-five candidate SNPs were identified in the GWAS. Three SNPs were found to be associated with the selection of HBV BCP double mutations in the replication stage, including rs7717457 at 5p13.1, rs670011 at 17q21.2, rs2071611 at 6p22.2. Especially, rs7717457 (P= 4.57×10-5 combined P) reached the potential GWAS significance level. The expression of gene complement component 7 (C7), nearest to SNP rs7717457, differed significantly between the case and control groups (t=2.045, P=0.04), suggesting that SNP rs7717457 was associated with the expression of its nearest gene. Conclusions: SNP rs7717457 is associated with the selection of HBV BCP double mutations, providing an important clue to understanding the mechanisms of oncogenesis of HBV BCP double mutations.

Common bean (Phaseolus vulgaris L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines (RILs) from a bi-parental population were evaluated for marsh spot resistance during five years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The RILs were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphisms (SNPs) were identified and filtered to generate a high-quality set of 2066 SNPs for QTL mapping. A genetic map based on 1273 SNP markers distributed on 11 chromosomes and covering 1599 cm was constructed. A total of 12 stable and 4 environment-specific QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport-related candidate genes co-locating within six QTL regions. In particular, two QTL (QTL.3.1 and QTL.3.2) with the highest R2 values (21.8% and 24.5%, respectively) harbored several metal transport genes Phvul.003G086300, Phvul.003G092500, Phvul.003G104900, Phvul.003G099700, and Phvul.003G108900 in a large genomic region of 16.8–27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization.

Objective The purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs. Methods The traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records. Results The outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL. Conclusion The genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.

PurposeTo investigate the impact of genetic variants of DNA repair and pro-fibrotic pathway genes on the severity of radiation-induced subcutaneous fibrosis in patients of oropharyngeal carcinoma treated with radical radiotherapy.Materials and MethodsPatients of newly diagnosed squamous cell carcinoma of oropharynx being treated with two-dimensional radical radiotherapy were enrolled in the study. Patients who had undergone surgery or were receiving concurrent chemotherapy were excluded. Patients were followed up at 6 weeks post completion of radiotherapy and every 3 months thereafter for a median of 16 months. Subcutaneous fibrosis was graded according to the Radiation Therapy Oncology Group (RTOG) and the European Organization for Research and Treatment of Cancer (EORTC) grading system and the maximum grade was recorded over the length of the patient’s follow-up. Patients with severe fibrosis (≥G3), were compared to patients with minor (≤G2) fibrotic reactions. Eight single nucleotide polymorphisms of 7 DNA repair genes and 2 polymorphisms of a single pro-fibrotic pathway gene were analyzed by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism and were correlated with the severity of subcutaneous fibrosis.Results179 patients were included in the analysis. Subcutaneous fibrosis was seen in 168 (93.9%) patients. 36 (20.1%) patients had severe (grade 3) fibrosis. On multivariate logistic regression analysis, Homozygous CC genotype of XRCC3 (722C>T, rs861539) (p=0.013*, OR 2.350, 95% CI 1.089-5.382), Homozygous AA genotype of ERCC4 Ex8 (1244G>A, rs1800067) (p=0.001**, OR 11.626, 95% CI 2.490-275.901) and Homozygous TT genotype of XRCC5 (1401G>T, rs828907) (p=0.020*, OR 2.188, 95% CI 1.652-7.334) were found to be predictive of severe subcutaneous fibrosis. On haplotype analysis, the cumulative risk of developing severe fibrosis was observed in patients carrying both haplotypes of variant Homozygous AA genotype of ERCC4 Ex8 (1244G>A, rs1800067) and Homozygous TT genotype of XRCC5 (1401 G>T, rs828907) (p=0.010*, OR 26.340, 95% CI 4.014-76.568).ConclusionWe demonstrated significant associations between single nucleotide polymorphisms of DNA repair genes and radiation-induced subcutaneous fibrosis in patients of oropharyngeal carcinoma treated with radiotherapy. We propose to incorporate these genetic markers into predictive models for identifying patients genetically predisposed to the development of radiation-induced fibrosis, thus guiding personalized treatment protocols.

BackgroundThe tumor necrosis factor superfamily (TNFSF) and TNF receptor superfamily (TNFRSF) play important roles in the immune responses to infections. The aim of this study was to determine the impact of single nucleotide polymorphisms (SNPs) of several TNFSF/TNFRSF genes on the risk of hepatitis C virus (HCV) infection in the Chinese high-risk population.MethodsThe TNFSF4-rs1234313, TNFSF4-rs7514229, TNFSF8-rs3181366, TNFSF8-rs2295800, TNFRSF8-rs2298209, and TNFRSF8-rs2230625 SNPs were genotyped in 2309 uninfected controls, 597 subjects with spontaneous HCV clearance and 784 patients with persistent HCV infection using the TaqMan-MGB assay. The putative functions of the positive SNPs were determined using online bioinformatics tools.ResultsAfter adjusting for gender, age, high-risk population, alanine transaminase (ALT), aspartate aminotransferase (AST), IL28B-rs12979860 and rs8099917 genotypes, the non-conditional logistic regression showed that rs7514229-T, rs3181366-T, and rs2295800-C were associated with an increased risk of HCV infection (all PFDR < 0.05). Combined analysis of rs7514229-T and rs3181366-T risk alleles showed that the subjects carrying 2–4 risk alleles were more susceptible to HCV infection compared with those lacking any risk allele (all P < 0.001). Furthermore, the risk of HCV infection increased with the number of risk alleles (Ptrend < 0.001). In silico analysis showed that rs7514229, rs3181366, and rs2295800 polymorphisms may affect the transcription of mRNA by regulating miRNA binding, TF binding, and promoter activation, respectively, which may have biological consequences.ConclusionTNFSF4-rs7514229, TNFSF8-rs3181366, and TNFSF8-rs2295800 are associated with increased risk of HCV infection in the Chinese high-risk population.

Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.

The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillussporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxiasporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans. In addition, the genomes of the H.sporothermodurans type strain (DSM 10599T) and the closest phylogenetic neighbors Heyndrickxiaoleronia (DSM 9356T) and Heyndrickxia vini (JCM 19841T) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans. When examining the genome sequences of all H.sporothermodurans strains from this study, together with 4 H. sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.

Based on experimental results, this chapter describes applications of SAR polarimetry to extract relevant information on agriculture and wetland scenarios by exploiting differences in the polarimetric signature of different scatterers, crop types and their development stage depending on their physical properties. Concerning agriculture, crop type mapping, soil moisture estimation and phenology estimation are reviewed, as they are ones with a clear benefit of full polarimetry over dual or single polarimetry. For crop type mapping, supervised or partially unsupervised classification schemes are used. Phenology estimation is treated as a classification problem as well, by regarding the different stages as different classes. Soil moisture estimation makes intensive use of scattering models, in order to separate soil and vegetation scattering and to invert for soil moisture from the isolated ground component. Then, applications of SAR polarimetry to wetland monitoring are considered that include the delineation of their extent and their characterisation by means of polarimetric decompositions. In the last section of the chapter, the use of a SAR polarimetric decomposition is shown for the assessment of the damages consequential to earthquakes and tsunamis.

The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillus sporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxia sporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans. In addition, the genomes of the H. sporothermodurans type strain (DSM 10599T) and the closest phylogenetic neighbors Heyndrickxia oleronia (DSM 9356T) and Heyndrickxia vini (JCM 19841T) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans. When examining the genome sequences of all H. sporothermodurans strains from this study, together with 4 H. sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.

Background: In 2013, the group of Cicero Coimbra, Brazil, reported the clinical efficacy of high doses of vitamin D3 in patients suffering from autoimmune skin disorders (“Coimbra protocol”, CP). However, hypercalcemia and the subsequent impaired renal function may be major concerns raised against this protocol. Methods: We report for the first time for a broad spectrum of autoimmune diseases in 319 patients (mean age (±SD) 43.3 ± 14.6 years, 65.5% female, 34.5% male) safety data for high doses of orally applied vitamin D3 (treatment period: up to 3.5 years) accompanied by a strict low-calcium diet and regular daily fluid intake of at least 2.5 L. Results: Mean vitamin D3 dose was 35,291 ± 21,791 IU per day. The measurement of more than 6100 single relevant laboratory parameters showed all mean values (±SD) within the normal range for total serum calcium (2.4 ± 0.1 mmol/L), serum creatinine (0.8 ± 0.2 mg/dL), serum creatinine associated estimated GFR (92.5 ± 17.3 mL/min), serum cystatin C (0.88 ± 0.19 mg/L), serum TSH (1.8 ± 1 mIU/L), and for 24 h urinary calcium secretion (6.9 ± 3.3 mmol/24 h). We found a very weak relationship between the dosage of oral vitamin D3 and the subsequent calcium levels, both in serum and in urinary excretion over 24 h, respectively. Conclusions: Our data show the reliable safety of the CP in autoimmune patients under appropriate supervision by experienced physicians.

The goal of this project is to study the relationship between the genotype (SNPs) and phenotype (feed efficiency, FE) of a cow population of size n = 608. In order to achieve this goal, a descriptive analysis of the genetic data has been done as a first step. Data has also been filtered, by the deletion and imputation of missing data, as well as through a genetic exploration process, performing a minor allele frequency (MAF) histogram and the Hardy Weinberg Equilibrium (HWE) test. After the data has been cleaned, genetic relatedness research has been carried out through PCA and MDS, and by the study of the number of alleles shared by each pair of cattle individuals. Once all the above-mentioned analyses have been concluded, the GWAS has been conducted. Linear models (LM) and linear mixed models (LMM) have been created to study the relationship between cow feed efficiencies and genetic data. GWASs have also been performed for milk, protein and fat traits. One polymorphism has been found to be significantly associated with all these variables.

Since its introduction to North America in the early 1900s, white pine blister rust (WPBR) caused by the fungal pathogen Cronartium ribicola has resulted in substantial economic losses and ecological damage to native North American five-needle pine species. The high susceptibility and mortality of these species, including limber pine (Pinus flexilis), creates an urgent need for the development and deployment of resistant germplasm to support recovery of impacted populations. Extensive screening for genetic resistance to WPBR has been underway for decades in some species but has only started recently in limber pine using seed families collected from wild parental trees in the USA and Canada. This study was conducted to characterize Alberta limber pine seed families for WPBR resistance and to develop reliable molecular tools for marker-assisted selection (MAS). Open-pollinated seed families were evaluated for host reaction following controlled infection using C. ribicola basidiospores. Phenotypic segregation for presence/absence of stem symptoms was observed in four seed families. The segregation ratios of these families were consistent with expression of major gene resistance (MGR) controlled by a dominant R locus. Based on linkage disequilibrium (LD)-based association mapping used to detect single nucleotide polymorphism (SNP) markers associated with MGR against C. ribicola, MGR in these seed families appears to be controlled by Cr4 or other R genes in very close proximity to Cr4. These associated SNPs were located in genes involved in multiple molecular mechanisms potentially underlying limber pine MGR to C. ribicola, including NBS-LRR genes for recognition of C. ribicola effectors, signaling components, and a large set of defense-responsive genes with potential functions in plant effector-triggered immunity (ETI). Interactions of associated loci were identified for MGR selection in trees with complex genetic backgrounds. SNPs with tight Cr4-linkage were further converted to TaqMan assays to confirm their effectiveness as MAS tools. This work demonstrates the successful translation and deployment of molecular genetic knowledge into specific MAS tools that can be easily applied in a selection or breeding program to efficiently screen MGR against WPBR in Alberta limber pine populations.

This article outlines recent findings on genetics of juvenile myoclonic epilepsy (JME), where JME occurrence is associated with polymorphic allelic variants in BRD2 gene (locus EJM3) and GJD2 gene (locus EJM2).Objective: To establish risk factors for development of JME in the context of genetic predisposition; specifically, polymorphic allelic variants rs206787 and rs516535 in the BRD2 gene and rs3743123 in the GJD2 gene.Materials and Methods: Using RT-PCR, we identified carriers of single nucleotide polymorphisms (SNPs) rs206787 and rs516535 in gene BRD2 and rs3743123 in gene GJD2, from samples of 79 JME patients and 150 healthy volunteers of European descent residing in the Siberian Federal District.Results: We found complete linkage disequilibrium between studied loci in patients with JME and healthy controls, however there was no association between SNPs rs206787 and rs516535 and JME development in our study population (р > 0,05). Haplotype TT/TT for SNPs rs206787 and rs516535 in the BRD2 gene associated with photoparoxysmal response (OR = 3,6; 95% CI 1,37 – 9,48; p = 0,02) in JME patients. Homozygosity of allele T (rs3743123) in the GJD2 gene was associated with risk of JME development in our study population (OR = 2,66; 95% CI 1,24 – 5,74; р = 0,04).Conclusion: These results strongly suggest that genotyping JME patients of European descent living in Siberia to identify carriers of haplotype TT/TT in BRD2 SNPs (locus EJM3) and T allele (rs3743123) in the GJD2 gene will enable personalised approach to JME diagnosis and management, as well as identification of high-risk individuals in affected families.