Evaluation of Cultivated and Wild Brinjal Germplasm against Bacterial Wilt Disease with Tollinterleukin-1 Receptors (TIR)-NBS-LRR Type R-gene Specific Degenerate Primer

The experiment was conducted at C-Block Farm of Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India during 2017–18 to screen eight brinjal germplasm lines against BW disease using tollinterleukin-1 receptors (TIR)-NBS-LRR type R-gene specific degenerate primer. The study showed that wild genotype S. torvum was highly resistant to bacterial wilt incidence with no wilting symptom whereas two cultivated genotypes (Utkal Anushree and Utkal Madhuri) and one wild genotype S. sisymbriifolium were found to be resistant to BW disease. Out of the 7 germplasm sequences, 2 had no match with R-genes whereas the remaining 5 sequences have 70-93% homology with R-genes of other plant species submitted in Gene Bank sequence database. Nearly 90% sequence identity of brinjal NBS-LRR RGA was found by analyzing through BLASTn with NBS-LRR RGAs of other solanaceous crops. Two cultivated resistant genotypes (Utkal Madhuri and Utkal Tarini) were similar to the wild resistant type S. sisymbriifloium, while cultivable resistant genotype Utkal Anushree was highly different at sequence level. Two cultivable susceptible genotypes (BCB-30 and Garia) showed high level of similarity among them and they were strongly associated with the wild susceptible genotype S. macrocarpum. Two cultivable genotypes Utkal Anushree and Utkal Madhuri could be utilized in future breeding programme and two wild genotypes S. torvum and S. sisymbriifolium could be used as resistant rootstocks in brinjal grafting.

Co-inheritance of G6PD deficiency and 211 G to a variation of UGT1A1 in neonates with hyperbilirubinemia in eastern Guangdong

Background Glucose-6-phosphate dehydrogenase (G6PD) deficiency, which may manifest as neonatal hyperbilirubinemia, is the most prevalent erythrocytic enzyme-related disease in the world. Objective To investigate the association between neonatal hyperbilirubinemia and co-inheritance of G6PD deficiency and 211 G to A variation of UGT1A1 in Chaozhou city of eastern Guangdong province, the effects of G6PD deficiency and UGT1A1 gene variant on the bilirubin level were determined in neonates with hyperbilirubinemia. Method The activity of G6PD was assayed by an auto-bioanalyzer. PCR and flow-through hybridization were used to detect 14 common G6PD mutations in G6PD deficient neonates. 211 G to A variation of UGT1A1 was determined by PCR and sequencing. The data of neonatal bilirubin was collected and analyzed retrospectively. Results Seventy four cases of the 882 hyperbilirubinemia neonates were G6PD deficiency (8.39%) while 12 cases of the 585 non-hyperbilirubinemia neonates (control group) were G6PD deficiency (2.05%). The rate of G6PD deficiency in the hyperbilirubinemia group was higher than that of the control group. Moreover, the peak bilirubinin of the G6PD-deficient group of hyperbilirubinemia neonates was 334.43 ± 79.27 μmol/L, higher than that of the normal G6PD group of hyperbilirubinemia neonates (300.30 ± 68.62 μmol/L). The most common genotypes of G6PD deficiency were c.1376G > T and c.1388G > A, and the peak bilirubin of neonates with these two variants were 312.60 ± 71.81 μmol/L and 367.88 ± 75.79 μmol/L, respectively. The bilirubin level of c.1388G > A was significantly higher than that of c.1376G > T. Among the 74 hyperbilirubinemia neonates with G6PD deficiency, 6 cases were 211 G to A homozygous mutation (bilirubin levels 369.55 ± 84.51 μmol/L), 27 cases were 211 G to A heterozygous mutation (bilirubin levels 341.50 ± 63.21 μmol/L), and 41 cases were wild genotypes (bilirubin levels 324.63 ± 57.52 μmol/L). Conclusion The rate of G6PD deficiency in hyperbilirubinemia neonates was significantly higher than that of the non-hyperbilirubinemia neonates in Chaozhou. For the hyperbilirubinemia group, neonates with G6PD deficiency had a higher bilirubin level compared to those with normal G6PD. For hyperbilirubinemia neonates with G6PD deficiency, there was a declining trend of bilirubin levels among 211 G to A homozygous mutation, heterozygous mutation, and wild genotype, but there was no significance statistically among the three groups.

Follicle-stimulating hormone (FSH) receptor gene polymorphisms in Iraqi patients with non-obstructive azoospermia

Background: Follicle-stimulating hormone (FSH) is a pivotal hormone for male fertility, and its action on gonads is exerted by FSH receptors (FSHRs). Objectives: To examine whether the presence of FSHR gene single nucleotide polymorphisms (SNPs), G919A and A2039G, involved in non-obstructive azoospermia (NOA) in Iraqi infertile men. Methods: Two common SNPs, A919G and A2039G, in the FSHR gene were analyzed in 104 subjects (70 infertile patients with NOO: 33 NOA patients were not receiving treatment and 37 were on infertility treatment, and 34 normozoospermic fertile men as controls). Results: The results revealed that the homozygous wild genotype (AA) of rs6165 FSHR gene SNP was more abundant than (AG) and (GG) genotypes in both groups of infertile NOA patients with a frequency of 49% in those who untreated, 81% in patients undergoing treatment and in the control group 41%. Whereas, the highest percentage of heterozygous genotype (AG) in the fertile control group was 41% when compared to NOApatients with a genotype frequency of 24% (for those who untreated) and 11% (for patients on treatment), respectively; with (A) allele frequency of 86% and the observed frequency of (G) allele was only 14% in the patients’ group as compared to that of controls that were (65 %) and (35 %), respectively. The rs6166 genotyping revealed that the homozygous wild genotype (GG) of FSHR gene was more abundant than (AG) and (AA) genotypes in NOA patients receiving infertility treatment with a frequency of (68%), in NOA patients who didn’t receive treatment 49%, while the lowest frequency was detected in the healthy fertile control group (47%). Conclusions: These results support the evidence that rs6165 and rs6166, FSHR SNPs, might be involved in the pathogenesis and protection against NOA, respectively.

A Personalized Approach to the Treatment of Primary Open-Angle Glaucoma

Aim — to study of gene polymorphisms affecting the effectiveness of timolol treatment of primary open-angle glaucoma.Patients and Methods. The study included 39 Russian patients (29 women and 10 men) aged 53 to 89 years old with a diagnosis of primary open-angle glaucoma (POAG). Intraocular pressure (IOP) was measured before the start of therapy and after 2 weeks during treatment. Сoefficient of decrease in IOP was calculated in percentage of its initial level (∆D). Patients were genotyped according to the polymorphic loci MMP1-160insG, MMP12A-82G, TIMP1C536T, ADRB1Arg389Gly, ADRB1Ser49Gly, NAT2Lys268Arg, GSTP1Ile105Val using the corresponding SNP-express reagent kits (NPF Lytech, Moscow).Results. No effect of MMP12A-82G, TIMP1C536T, ADRB1Arg389Gly, NAT2Lys268Arg polymorphisms on efficiency of reduction of IOP under action of thymolol in “best” eyes was revealed. The carriage of a homozygous genotype GSTP1Ile105Ile resulted in the best ophthalmic hypotensive effect of a timolol (∆D ≥ 20 %), which probability was 5.63 times higher in comparison with ∆D < 20 %. In the “worst” eyes, the association of carriage of a combination of wild genotypes GSTP1Ile105Ile×NAT2Lys268Lys with the best response of patients to timolol was revealed. The ophthalmic hypotensive effect of 10 ≤ ∆D < 20 % in such carriers was more than 11 times more likely than ∆D < 10 %.Conclusion. The carriage of the wild genotype GSTP1Ile105Ile determines the best ophthalmic hypotensive effect of timolol and can be a prognostic marker for the effective treatment of patients with POAG. The combination of wild genotypes GSTP1Ile105Ile×NAT2Lys268Lys can contribute to the better therapeutic effect of timolol, and mutant ones can prevent it.

Co-Inheritance of G6PD Deficiency and 211 G to A Variation of UGT1A1 in Neonates with Hyperbilirubinemia In Eastern Guangdong

Background: Glucose-6-phosphate dehydrogenase (G6PD) deficiency, which may manifest as neonatal hyperbilirubinemia, is the most prevalent erythrocytic enzyme-related disease in the world.Objective: To investigate the association between neonatal hyperbilirubinemia and co-inheritance of G6PD deficiency and 211 G to A variation of UGT1A1 in Chaozhou city of eastern Guangdong province, the effects of G6PD deficiency and UGT1A1 gene variant on the bilirubin level were determined in neonates with hyperbilirubinemia.Method: The activity of G6PD was assayed by an auto-bioanalyzer. PCR and flow-through hybridization were used to detect 14 common G6PD mutations in G6PD deficient neonates. 211 G to A variation of UGT1A1 was determined by PCR and sequencing. The data of neonatal peak bilirubin was collected and analyzed retrospectively.Results: 74 cases of the 882 hyperbilirubinemia neonates were G6PD deficiency (8.39%) while 12 cases of the 585 non-hyperbilirubinemia neonates (control group) were G6PD deficiency (2.05%). The rate of G6PD deficiency in the hyperbilirubinemia group was higher than that of the control group. Moreover, the peak bilirubin in the G6PD-deficient group of hyperbilirubinemia neonates was 334.43±79.27μmol/L, higher than that of the normal G6PD group of hyperbilirubinemia neonates (300.30±68.62 μmol/L). The most common genotypes of G6PD deficiency were c.1376G>T and c.1388G>A, and the peak bilirubin of neonates with these two variants were 312.60±71.81μmol/L and 367.88±75.79 μmol/L, respectively. The bilirubin level of c.1388G>A was significantly higher than that of c.1376G>T. Among the 74 hyperbilirubinemia neonates with G6PD deficiency, 6 cases were 211 G to A homozygous mutation (bilirubin levels 369.55±84.51 μmol/L), 27 cases were 211 G to A heterozygous mutation (bilirubin levels 341.50±63.21 μmol/L), and 41 cases were wild genotypes (bilirubin levels 324.63±57.52 μmol/L). Conclusion: The rate of G6PD deficiency in hyperbilirubinemia neonates was significantly higher than that of the non-hyperbilirubinemia neonates in Chaozhou. For the hyperbilirubinemia group, neonates with G6PD deficiency had a higher bilirubin level compared to those with normal G6PD. For hyperbilirubinemia neonates with G6PD deficiency, there was a declining trend of bilirubin levels among 211 G to A homozygous mutation, heterozygous mutation, and wild genotype, but there was no significance statistically among the three groups.

Growth and development of domesticated and wild genotypes of red clover (Trifolium pratense L.) in the Middle Urals

В данной статье представлены результаты сравнительной оценки 11 сортов клевера лугового и одного образца-дикороса, проведённой в Пермском НИИ сельского хозяйства в 2018–2019 годах. Все селекционные сорта сформировали полноценные первый и второй укосы или отаву в оба года использования. Дикорастущая форма формировала только один укос, демонстрируя особенность позднеспелого одноукосного типа. Сорта Кретуновский и Ранний 2 показали себя как типичные раннеспелые двухукосные. Другие сорта занимали промежуточное положение. Наибольший сбор сухого вещества обеспечивал образец-дикорос в оба года при крайне различных погодных условиях (1,266 и 1,259 кг/м2 соответственно). Дикорастущая форма и сорт Ранний 2 обеспечивали стабильные урожаи зелёной массы и сухого вещества независимо от возраста и погодных условий. Образец дикорастущего клевера имел более однородный фенотип по сравнению с сортом Пермский местный — стандартом для позднеспелого типа, что указывает на большую генетическую однородность. Согласно всесторонней оценке, включающей степень перезимовки, урожайность зелёной и сухой массы, характер цветения, созревания, формирования и конечный урожай семян, образец-дикорос имеет отличительные признаки позднеспелого (одноукосного) типа и может использоваться в качестве исходного генетического материала для дальнейшей селекции позднеспелых одноукосных сортов клевера лугового, характеризующихся экономически ценными свойствами: высокой устойчивостью к неблагоприятным условиям окружающей среды, высокой и стабильной урожайностью зелёной массы и семян. Исследования будут продолжены с оценкой ряда образцов дикорастущих форм клевера лугового, обнаруженных в 2019 году в природных биоценозах Пермского края. This article deals with the competitive trial of 11 varieties and 1 wild genotype of red clover conducted at the Research Institute of Agriculture in 2018–2019. All the varieties provided good yields of green mass both in the first and second cuts. Wild genotype provided only one cut as long-season one-cut type. “Kretunovskiy” and “Ranniy 2” performed as typical short-season two-cut varieties. Wild genotype produced the highest yield of dry matter (DM) under contrast weather conditions (1.266 and 1.259 kg/m2, respectively). Wild genotype and “Ranniy 2” formed stable yields of green mass and DM regardless of time period and weather. Wild genotype showed homogeneous phenotype compared to “Permskiy mestnyy” — long-season standard variety indicating high genetic uniformity. Such traits as winter hardiness, green and dry mass yields, flowering pattern, seed maturation, formation and production were evaluated. According to this evaluation wild genotype performed as long-season (one-cut) type showing high resistance to unfavorable conditions, high and stable yield of green mass and seeds. Therefore, it can be used a source of economically important traits for future breeding programs of red clover. Further investigations will focus on the evaluation of wild genotypes of red clover found in the Perm region in 2019.

The Identification of Mutation in BMP15 Gene Associated with Litter Size in Xinjiang Cele Black Sheep

The Bone Morphogenetic Protein 15 (BMP15) gene is known to have multiple single-nucleotide polymorphism sites associated with sheep fecundity. This study used gene sequence analysis and mutation detection assays for BMP15 by using 205 blood samples of ewes with known lambing records. Sequence analysis showed that mutation B1 missed the CTT base in exon 1 at positions 28–30, leading to a leucine deletion in the BMP15 protein. Litter size of ewes differed significantly between BB and B+ genotypes of B1 (p < 0.05); however, the differences between wild genotype (++) and homozygous (BB) or wild genotype (++) and heterozygous (B+) were not significant (p > 0.05). Another mutation, T755C, is a T-to-C base change at position 755 of exon 2, resulting in leucine replacement by proline at this position of the BMP15 protein (p.L252P). Two genotypes were identified in the flock: heterozygous (E+) and wild-type genotype (++). Ewes with heterozygous (E+) p.L252P had significantly larger litter sizes than those with the wild-type genotype (p < 0.05). Comprehensive analysis suggests that p.L252P is a mutation that affects fecundity in Cele black sheep.

Study the Incidence of TNF-α-induced Protein 3 Genetic Polymorphisms in Primary Immune Thrombocytopenia Patients

BackgroundImmune Thrombocytopenia (ITP) is a relatively common acquired hematological disorder, affecting 2 to 4/100000 adults. Understanding of the pathogenesis of ITP has been greatly improved with taking into consideration the important role of the genetic variants. This study aimed at investigating the incidence of TNFAIP3 SNPs (rs2230926 and rs5029939) in primary ITP Egyptian patients as well as their response to therapy in addition to the linkage between the two SNPs.Methods and Resultsthe study was conducted in 110 ITP patients diagnosed as primary ITP (PITP) selected among cases referred to the Hematology Outpatient Clinic of Kasr El Aini Hospital and 110 matched healthy controls. The polymorphisms were detected by real-time polymerase chain reaction (real-time PCR). Data indicated that there is a significant difference in the allelic distribution between PITP patients and the control group regarding rs2230926 and rs5029939 (p-value <0.05). Regarding LD analysis of the two SNPs, it has been revealed that there was a significant linkage disequilibrium between rs2230926 and rs5029939 among PITP group LD (D' = 0.966, r2 = 0.694, p-value < 0.001). On behalf of improvement by treatment, patients with rs2230926 wild genotype showed a more significant response to treatment than mutant type (p-value <0.05).ConclusionThere was a correlation between TNFAIP3 SNPs (rs2230926 and rs5029939) and the occurrence of primary ITP in the adult Egyptian populations and there was a linkage disequilibrium between them. Moreover, patients with rs2230926 wild genotype showed significant improvement than mutant type.

Transcriptomic analysis reveals key transcription factors associated to drought tolerance in a wild papaya (Carica papaya) genotype

Most of the commercial papaya genotypes show susceptibility to water deficit stress and require high volumes of irrigation water to yield properly. To tackle this problem, we have collected wild native genotypes of Carica papaya that have proved to show better physiological performance under water deficit stress than the commercial cultivar grown in Mexico. In the present study, plants from a wild Carica papaya genotype and a commercial genotype were subjected to water deficit stress (WDS), and their response was characterized in physiological and molecular terms. The physiological parameters measured (water potential, photosynthesis, Fv/Fm and electrolyte leakage) confirmed that the papaya wild genotype showed better physiological responses than the commercial one when exposed to WDS. Subsequently, RNA-Seq was performed for 4 cDNA libraries in both genotypes (susceptible and tolerant) under well-watered conditions, and when they were subjected to WDS for 14 days. Consistently, differential expression analysis revealed that after 14 days of WDS, the wild tolerant genotype had a higher number of up-regulated genes, and a higher number of transcription factors (TF) that were differentially expressed in response to WDS, than the commercial genotype. Thus, six TF genes (CpHSF, CpMYB, CpNAC, CpNFY-A, CpERF and CpWRKY) were selected for further qRT-PCR analysis as they were highly expressed in response to WDS in the wild papaya genotype. qRT-PCR results confirmed that the wild genotype had higher expression levels (REL) in all 6 TF genes than the commercial genotype. Our transcriptomic analysis should help to unravel candidate genes that may be useful in the development of new drought-tolerant cultivars of this important tropical crop.

Correlation between ZBRK1/ZNF350 gene polymorphism and breast cancer

Background This study is to explore the relationship between the ZBRK1/ZNF350 (Zinc finger and BRCA1-interacting protein with KRAB domain-1; also known as zinc-finger protein 350) gene polymorphism and early-onset breast cancer. Methods The ZBRK1/ZNF350 gene exon detection analysis was performed with the direct sequencing and Snapshot methods in 80 cases of breast cancer (aged ≤ 40 years old) and 240 healthy subjects (aged ≤ 40 years old). Results Totally 9 sequence variants were detected, including 5 missense mutations and 4 synonymous mutations, located at EXON3, EXON4 and EXON5, respectively. The rs4987241 and rs3764538 variants were published for the first time, while the remaining variants had been reported before. There were significant differences in the frequency distribution of family history between the breast cancer and control groups. Moreover, there were significant differences in the CT genotype frequency at the rs138898320 locus between the breast cancer and healthy control groups. Compared with the carriers of CC wild genotype at rs138898320, the risk of breast cancer was reduced by 88.3% in the CT mutant genotype carriers, with significant difference. In the stratification with no family history, compared with the carriers of CC wild genotype at rs138898320, significant differences were observed for the CT mutant genotype carriers. In the stratification with family history, there was no significant difference in the variation of rs138898320. Conclusion The rs138898320 CT mutation genotype of ZBRK1/ZNF350 may reduce the risk of breast cancer, and the protecting effect would be increased in the stratification with no family history. Trial registration Not applicable.