Genetics

Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity Abstract Being an economical and nutritional crop, Capsicum appeases people's peppery taste and is found to be widely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of C. frutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.

Meta-analysis of genomic variants and gene expression data in schizophrenia suggests the potential need for adjunctive therapeutic interventions for neuropsychiatric disorders Abstract Schizophrenia (SZ) is a debilitating mental illness with a multigenic aetiology and significant heritability. Despite extensive genetic studies, the molecular aetiology has remained enigmatic. A recent systems biology study suggested a protein–protein interaction network for SZ with 504 novel interactions. The onset of psychiatric disorders is predominant during adolescence, often accompanied by subtle structural abnormalities in multiple regions of the brain. The availability of BrainSpan Atlas data allowed us to re-examine the genes present in the SZ interactome as a function of space and time. The availability of genomes of healthy centenarians and nonpsychiatric Exome Aggregation Consortium database allowed us to identify the variants of criticality. The expression of the SZ candidate genes responsible for cognition and disease onset was studied in different brain regions during particular developmental stages. A subset of novel interactors detected in the network was further validated using gene expression data of post-mortem brains of patients with psychiatric illness. We have narrowed down the list of drug targets proposed by the previous interactome study to 10 proteins. These proteins belonging to 81 biological pathways are targeted by 34 known Food and Drug Administration-approved drugs that have distinct potential for the treatment of neuropsychiatric disorders. We also report the possibility of targeting key genes belonging to celecoxib pharmacodynamics, \(\hbox {G}\upalpha \) signalling and cGMP-PKG signalling pathways that are not known to be specific to SZ aetiology.

Genetic variant rs10937405 of TP63 and susceptibility to lung cancer risk in north Indian population Abstract Several studies including genomewide association studies (GWASs) in diverse ethnic populations have reported a significant association of genetic variant rs10937405 of TP63 with nonsmall cell lung cancer (NSCLC). However, no data are available from any Indian population on the association of this variant with NSCLC. Using TaqMan genotyping chemistry, we conducted a case–control study involving 190 NSCLC cases and 400 ethnic, age-matched controls to explore the association of rs10937405 genetic variant with NSCLC in patients from north India. Our data support that the rs10937405 variant is also significantly associated with the NSCLC and is a risk factor in the north Indian populations to develop NSCLC. However, unlike most other studies, the wild-type allele T appears to be the risk allele, as its frequency was significantly higher in the cases than controls (0.439 in cases versus 0.383 in controls. OR = 1.95 (1.23–3.09 at 95% CI); P value (adjusted) = 0.004). Genetic association was also observed by applying different genetic models. The present study provides important information of the genetic aetiology of NSCLC and strengthens GWAS findings, highlighting the role of TP63 in lung cancer risk.

Correlation analysis of mandarin fish ( Siniperca chuatsi ) growth hormone gene polymorphisms and growth traits Abstract Screening of trait-associated molecular markers can be used to enhance the efficiency of selective breeding. Previously, we produced the first high-density genetic linkage map for the mandarin fish (Siniperca chuatsi) and identified 11 quantitative-trait loci significantly associated with growth, of which one is located within the growth hormone (GH) gene. To investigate the GH gene polymorphisms and their correlation with growth, the complete sequence was cloned and 32 single-nucleotide polymorphisms (SNPs) and one simple-sequence repeat (SSR) were identified. Of which, eight SNPs (G1–G8) and the SSR (GH-AG) were selected for genotyping and correlation analysis with growth traits in a random population. The results showed that the four novel polymorphic loci (G1, G2, G3 and GH-AG) were significantly correlated with growth traits of mandarin fish ( \(P<~0.05\) ). Of these, G1, G3 and GH-AG showed highly significant correlations with multiple growth traits ( \(P <~0.01\) ) and the combined SNP analysis showed that G1–G3 formed four effective diplotypes (D1–D4), among which D1 was highly significantly greater than D4 ( \(P<~0.01\) ) for some important growth traits. In conclusion, our results show that the four polymorphic loci G1–G3 and GH-AG within the mandarin fish GH gene are significantly correlated with growth traits and could be used as candidate molecular markers for selective breeding of superior varieties of mandarin fish.

'Distal 16p12.2 microdeletion' in a patient with autosomal recessive deafness-22 Abstract The 16p12.2 chromosome band contains three large segmental duplications: BP1, BP2 and BP3, providing a substrate for recombination and recurrent chromosomal rearrangements. The '16p12.2 microdeletion' is a recurrent deletion comprised between BP2 and BP3, associated with variable clinical findings. We identified a heterozygous 16p12.2 microdeletion spanning between BP1 and BP2 in a child evaluated for short stature and mild dyslexia. Unexpectedly, the mother carried the same deletion in the homozygous state and suffered from severe hearing loss. Detailed family history revealed consanguinity of the maternal grandparents. The 16p12.2 microdeletion is a rare condition and contains only three genes: METTL9, IGSF6 and OTOA of which the OTOA is considered responsible for DFNB22 hearing loss (MIM: 607039) under its homozygous condition. A number of OTOA mutations have been described, whereas very few cases of a 16p12.2 microdeletion similar to that observed in our family have been reported. In conclusion, we describe a rare 'distal 16p12.2 microdeletion' widening the phenotypic spectrum associated with the recurrent 16p12.2 microdeletion and support the causative role of OTOA microdeletion in hearing impairment.

Development of a drought stress-resistant rice restorer line through Oryza sativa–rufipogon hybridization Abstract Restorer line F6 (Oryza sativa L. ssp. indica) has been widely used in hybrid rice breeding systems in southern China. However, line F6 is susceptible to drought stress, which restricts its utilization in many areas. Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) has strong drought stress resistance, but the molecular factors responsible for drought resistance in DXWR remain unknown. In this study, we used the combination of phenotypic selection and molecular marker-assisted selection (MAS) to improve the drought stress resistance of line F6 by introgression of qSDT12-2, a large effect drought stress-related quantitative trait locus identified in DXWR. Molecular MAS was carried out using linked marker RM1226, which is associated with qSDT12-2. Genomic background assessment was performed using 112 polymorphic markers. Finally, a stable drought stress-resistant backcross inbred line (BIL) was developed from a \(\hbox {BC}_{{5}} \hbox {F}_{{5}}\) population, termed BIL627. Genetic constitution analysis revealed that the genome of BIL627 is almost identical (99.1%) to that of the restorer line F6. Further, BIL627 showed no yield penalty and no decrease in restoration ability under normal conditions. Taken together, our findings reveal the intrinsic value of using genetic resources present in wild species of Oryza to improve undesirable traits found in cultivated rice.

Genetic structure of Mediterranean fruit fly (Diptera: Tephritidae) populations from Turkey revealed by mitochondrial DNA markers Abstract Ceratitis capitata is one among the most destructive and economically important agricultural pests worldwide. Despite its economic significance, the population structures of this pest have remained relatively unexplored in the eastern Mediterranean basin. Using two mitochondrial markers, the present study aimed to examining the population genetic structure and diversity of C. capitata populations in Turkey, the region that covers a large part of the eastern Mediterranean area. Our results revealed that the Turkish Mediterranean fruit fly populations are characterized by low levels of genetic diversity and limited population differentiation. For comparison purposes, we merged the sequences identified in the present study with the previously reported sequences from across the world into the data matrix. The haplotype network showed that, unlike the African samples the Mediterranean samples and samples from the new world (America, Pacific region and Australia) did not show any clear pattern of geographical structuring, which indicates that the Mediterranean basin, particularly the eastern Mediterranean region populations, may have played a more important role in the colonization of C. capitata populations to the new world. The results also revealed a close genetic relationship between the Turkish and Iranian populations, suggesting that the Iranian C. capitata populations probably originated from Turkey.

SCN2A mutation in an infant with Ohtahara syndrome and neuroimaging findings: expanding the phenotype of neuronal migration disorders Abstract Neuronal migration disorders (NMDs) are a heterogeneous group of conditions caused by the abnormal migration of neuroblasts in the developing brain and nervous system, resulting in severe developmental impairment, intractable epilepsy and intellectual disability (Spalice et al. 2009). To date, many genes have been identified as the leading cause of migration defects, i.e. agyria/pachygyria, polymicrogyria, heterotopias, agenesis of the corpus callosum and agenesis of the cranial nerves (Spalice et al. 2009). Here, we present a patient with early infantile epileptic encephalopathy (Ohtahara syndrome) with seizure onset on the first day of life, severe developmental delay and an abnormal brain MRI with excessive folding of small, fused gyri and bilateral perisylvian polymicrogyria, suggestive of neuronal migration disorder. To clarify the unknown aetiology, we conducted whole-exome sequencing, which detected a de novo missense variant (c.5308A>T; p.(Met1770Leu)) in the SCN2A gene. This is a report of SCN2A gene variant identified in a patient with neuronal migration disorder which could further expand the phenotypic spectrum of these genetic disorders.

Variability of the EG95 antigen-coding gene of Echinococcus granulosus in animal and human origin: implications for vaccine development Abstract In the present study, the genetic variability of the EG95 protein-coding gene in several animal and human isolates of Echinococcus granulosus was investigated. A total of 24 isolates collected from cattle, buffalo, sheep, goat, dog and man were amplified by Eg95-coding gene-specific primers. From the generated sequence information, a conceptual amino acid sequence was deduced. Phylogenetically, the Eg95 coding gene belongs to the Eg95-1/Eg95-2/Eg95-3/Eg95-4 cluster. Further confirmation on the maximum composite likelihood analysis revealed that the overall transition/transversion bias was 2.913. This finding indicated that there is bias towards transitional and transversional substitution. Using artificial neural networks, a B-cell epitope was predicted on primary sequence information. Stretches of amino acid residues varied between animal and human isolates when hydrophobicity was considered. Flexibility also varied between larval and adult stages of the organism. This observation is important to develop vaccines. However, cytotoxic T-lymphocyte epitopes on primary sequence data remained constant in all isolates. In this study, agretope identification started with hydrophobic amino acids. Amino acids with the same physico-chemical properties were present in the middle. The conformational propensity of the Eg95-coding gene of 156 amino acid residues had \(\upalpha \) -turns and \(\upbeta \) -turns, and \(\upalpha \) -amphipathic regions up to 129, 138–156 and 151–155 residues, respectively. The results indicated potential T-cell antigenic sites. The overall Tajima's D value was negative (−2.404165), indicative of negative selection pressure.

Molecular characterization and expression pattern analysis of a novel stress-responsive gene ' BeSNAC1 ' in Bambusa emeiensis Abstract NAC transcription factors (TFs) are master regulators of environmental stresses exerting a crucial role in plant growth and development. However, the studies on NAC TFs from Bambusa emeiensis are scarce. In this investigation, a novel gene from B. emeiensis encoding NAC protein was cloned and characterized. The gene was isolated based on the amino acid sequence data of stress-responsive SNAC1 of rice, named 'BeSNAC1 (accession no. MG763922)'. The full-length sequence of 1681 bp was found to contain an open-reading frame of 912 bp that encode a protein of 303 amino-acid residues. The multiple protein sequence alignments unveiled that BeSNAC1 contains a typical NAC domain. Additionally, the phylogenetic analysis showed that the corresponding protein belonged to the SNAC group, as it cladded with SNAC1, HvSNAC1, TaNAC2, SbSNAC1 and ZmSNAC1 proteins. Transactivation and subcellular localization assay disclosed that BeSNAC1 is a transcriptional activator localized in the cell nucleus. Moreover, the time-dependent expression pattern of BeSNAC1 was profiled under abscisic acid (ABA), polyethylene glycol 6000 (PEG-6000), NaCl, \(\hbox {H}_{2}\hbox {O}_{2}\) and \(\hbox {Na}_{2}\hbox {SO}_{4}\) treatments via a quantitative real-time polymerase chain reaction. The results revealed that the expression of BeSNAC1 was significantly upregulated in all treatments, a significant difference was observed under \(\hbox {H}_{2}\hbox {O}_{2}\) , NaCl and ABA ( \(P < 0.001\) ) and PEG and \(\hbox {Na}_{2}\hbox {SO}_{4}\) ( \(P < 0.01\) ) treatments, respectively. Conclusively, our findings provide evidence that 'BeSNAC1' is a nuclear protein that might act as part of the transcription regulation complex and is involved in the ABA signalling pathway and abiotic stress tolerance mechanisms in B. emeiensis.

Alexandros Sfakianakis
Anapafseos 5 . Agios Nikolaos
Crete.Greece.72100
2841026182

6948891480

alsfakia@gmail.com