Current issues

Table of contents: 2018

Research Article

The butterflies are one of the insect groups which undergo typical complete metamorphosis in their life history. However, up to now, little is known about the genomic mechanism that regulates the butterfly metamorphosis. In this study, using a swallowtail butterfly P. polytes as a model organism, a high-throughput sequencing platform was employed to perform the transcriptome and gene expression analyses in order to explore the P. polytes transcriptome features during different developmental stages. The results showed that approximately 398 million useful (Q20) reads were assembled into groups of 14698 (L1), 14264 (L2), 15084 (L3), 15520 (P1), 15052 (P2), 15720 (P3) and 15709 (A1), 14668 (A2), 16152 (A3) genes, respectively, with 58.19% to 67.11% of the data successfully mapped to the reference genome; the transcriptome change analysis via the DEGs Package revealed that dramatic gene expression differences were presented among the different developmental stages, that is, totally, 1162, 891 and 1723 genes were differentially expressed between adult and pupal, adult and larval, larval and pupal stages, respectively, with a number of these differentially expressed genes associated with the functions of digestion, cuticularization, chemoreception, wing formation, and so on. These differentially expressed genes and potential candidate genes required for butterfly metamorphosis by comparative transcriptomics may shed some new insights on molecular mechanisms underlying complete metamorphosis.

Genet. Mol. Res. 17(2): gmr16039902
DOI: 10.4238/gmr16039902
Research Article

Sheeppox virus (SPPV) is one of the listed and notifiable disease affect sheep production with major effect on the trade of new breed of sheep. This study was conducted to identify sheep pox by using cell culture, electron microscope (EM) and open reading frame (ORF) 103 gene during an outbreak of local breed of sheep occurred in Sharkia Governorate, Egypt in April 2017. Affected adult sheep showed typical skin pox lesion on face, the inner side of lips, inner aspect of the thigh and under the tail. The incidence rate of infection was 23.5% and the mortality rate in young lambs aged 3 to 6 months old was 8.2%. Forty-three scabs and tissue samples from clinically diseased adult sheep and dead lambs were collected and subjected to culture on Vero cell. The cytopathic effect (CPE) was observed within 3 to 7 days in 40 samples. A typical Poxvirus was a brick-like shape with round ends by negative staining of EM and ovoid like structure with dumb-bell shaped DNA core with concave bodies sides by positive staining of EM. By conventional PCR utilizing ORF103 gene and obtained bands of about 570 bp referred to SPPV. The sequence amplicon was analyzed by NCBI-BLAST and register in GeneBank under accession N. MG873537 and phylogentic tree was designed which revealed that the isolated strain of SPPV was resembled with other strains of SPPV isolated in Egypt, India, China, and USA. Finally, both EM and PCR are considered as sensitives, rapids, and powerful methods to identify SPPV from tissue and scab’s samples without the need of further culture in addition to the useful and easily use of ORF103 gene to differentiate SPPV from other Capripoxvirus.

Genet. Mol. Res. 17(2): gmr16039901
DOI: 10.4238/gmr16039901
Research Article

Pigeon Pea (Cajanus cajan), an important grain legume, is susceptible to Fusarium wilt (FW), sterility mosaic disease (SMD), and Phytophthora blight. Identification of resistance gene analogs (RGAs) is important for development of resistant varieties. In this study, degenerate primers targeting nucleotide binding sites (NBS) of known resistance (R) genes were used to amplify RGAs from two Pigeon Pea genotypes with differing disease resistance profiles. The translated cloned RGAs had high amino acid identity (68–71%) with putative disease resistance proteins in Glycine Max. Five RGA open reading frames were found in the whole Pigeon Pea genome after BLASTN analysis with the cloned sequences. Translated RGA proteins contained several characteristic features such as the NB-ARC domain (characteristic of death-related disease resistance genes) and four NBS motifs. A tryptophan residue at the kinase-2 motif was indicative of the non-TIR-NBS class of proteins. Phylogenetic analysis revealed two major clusters. The seven Pigeon Pea RGAs were in a non-TIR group alongside wilt resistance proteins from tomato. Specific primers were designed against the RGAs identified by BLASTN, and these successfully amplified sequences from all eight Pigeon Pea genotypes. The 40 resultant sequences were combined according to genotype and subjected to phylogenetic analysis. Genotypes clustered according to breeding pedigree. Multiple alignments of the 40 sequences revealed several single nucleotide polymorphisms (SNPs) that are useful in identifying candidate resistance genes associated with FW and SMD.

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Genet. Mol. Res. 17(1): gmr16039895
DOI: 10.4238/gmr16039895
Research Article

Breeding for water-deficit tolerance is fundamental to guarantee the sustainability of upland rice production, mainly due to the possibility of an increased frequency of drought episodes due to climate change. This work aimed to identify single nucleotide polymorphism (SNP) markers, derived from RNA sequencing (RNA-Seq), genome-wide association study (GWAS) and candidate genes from Arabidopsis, with potential for use in marker-assisted selection (MAS) for drought tolerance. RNA-Seq and GWAS were efficient in identifying useful SNP markers from the data obtained from three years of field experiments for 175 upland rice accessions, which were sequenced using 32 genes by Capture-Seq. Three genes were equally able to generate SNP markers that discriminated 95% of the 20 most drought susceptible accessions in the joint analysis of the experiments. The elimination of the genotypes with the unfavourable SNP allele reduced the initial number of accessions to one third, and transferring this result in a breeding routine, would enable to conduct smaller experiments per target location, increasing the precision and reducing the cost of the drought phenotyping.

Genet. Mol. Res. 17(1): gmr16039886
DOI: 10.4238/gmr10.4238/gmr16039886
Research Article

Fungus ability to respond to environmental changes allows their adaptation to a wide variety of conditions such as pH, temperature, light, nutrient availability, chemicals, and competition among species. Temperature and pH can affect fungal growth as well as their metabolism. Knowing these factors on fungus species is relevant for the development of biotechnological applications and process optimization to produce biomass and enzymes. This study aimed to evaluate Lentinus crinitus mycelial growth and laccase production at different initial pH and temperatures of the cultivation medium. L. crinitus U15-9 reduced laccase production with pH increase with maximum production at pH 6 (39 U/mL) whereas L. crinitus U9-1 increased laccase production with pH increase with maximum activity at pH 7 (25.8 U/mL). Neither of the strains had mycelial growth significantly affected by initial pH in the culture medium. The greatest laccase production occurred at 28 ºC for U15-9 (50 U/mL) and U9-1 (41.5 U/mL). An increase in U9-1 mycelial biomass occurred when the temperature went up from 25 to 28 ºC whereas for U15-9 it was from 28 to 37 ºC; at 37 ºC, U15-9 produced 225% more mycelial biomass than at 28 ºC, and 108% more mycelial biomass than U9-1 at 37 ºC. The variation of responses to environmental stimuli between the strains makes evident that intra-specific variations are common in basidiomycetes. Our findings highlighted the best conditions of pH and temperature to produce L. crinitus laccase and make evident how different strains respond distinctly to cultivation conditions.

Genet. Mol. Res. 17(1): gmr16039885
DOI: 10.4238/gmr16039885
Research Article

Objectives: The present study evaluates the effect of food intake on 90 biomarkers for cardiovascular disease (CVD) and inflammation with the Proseek Multiplex CVD II kit. Methods: Twenty-two healthy subjects (11 male and 11 females aged 25.9±4.2 years) were investigated. A total of 90 biomarkers were measured before a standardized meal, 30 and 120 minutes thereafter with the Proseek Multiplex CVD II kit. Results: The levels for 27 biomarkers changed significantly after food intake. Two biomarkers increased 120 minutes after food intake, five biomarkers decreased 30 minutes after food intake, seven biomarkers decreased 120 minutes after food intake, and 13 biomarkers decreased both 30 and 120 minutes after food intake. Fourteen biomarkers changed 10% or more after food intake, all 120 minutes after food intake: Heat shock 27 kDa protein (10%), Proto-oncogene tyrosine-protein kinase Src (13%), Growth hormone (13%), Carbonic anhydrase 5A, mitochondrial (14%), Carcinoembryonic antigen related cell adhesion molecule 8 (15%), Fatty acid-binding protein, intestinal (16%), Pentraxin-related protein PTX3 (17%), Fibroblast growth factor 21 (18%), C-C motif chemokine 3 (25%), 2,4-dienoyl-CoA reductase, mitochondrial (28%), Gastrotropin (36%), Poly [ADP-ribose] polymerase 1 (37%), Interleukin-6 (42%), and Melusin (52%). Conclusions: The present study shows that food intake affects several different biomarkers analyzed with the Proseek Multiplex CVD II kit, and the effect is at times substantial. Timing of blood sampling in relation to food intake, therefore, appears to be a major concern. Further studies are warranted in older healthy subjects and in patients with various cardiac diseases to determine whether the findings are reproducible.

Genet. Mol. Res. 17(1): gmr16039884
DOI: 10.4238/gmr16039884
Research Article

Genetic variability among pepper genotypes is essential in obtaining hybrid combinations with greater heterotic effect and in obtaining superior strains. This work’s goal was to evaluate the genetic diversity between accessions of Capsicum annuum L., indicating the selection of promising individuals for ornamental purposes. The experiment was carried out in at the Plant Biotechnology Laboratory of the Center of Agricultural Sciences, Federal University of Paraíba. The experiment was conducted in a completely randomized design with 16 treatments and eight replications. The plants were evaluated for 28 morphoagronomic traits. Data were submitted to analysis of variance and grouped according to Scott and Knott's test at 1% probability. The Tocher grouping was performed based on Mahalanobis distance and analysis of canonical variables were performed with graphical dispersion of the accessions. All variables were significant by the F test (p = 0.01) and presented high heritability and a CVg/CVe ratio higher than 1.0 for most traits, indicating genetic divergence between accessions. In keeping with the Scott-Knott's test (p = 0.01), the accessions were grouped into two to eight classes, varying according to the character. The of Tocher optimization method separated the accessions into five distinct groups. There is phenotypic divergence between the accessions of Capsicum annuum L. which can be used in ornamental peppers’ breeding programs. Only the number of stamens trait presented a heritability value (65.81%) lower than 70%. The characters that most contributed to divergence among the accessions were fresh fruit mass, stem diameter, widest fruit diameter and fruit weight. The accessions UFPB001, UFPB004, UFPB45, UFPB77.3, UFPB099, UFPB134, UFPB390 and Calypso are designated as potential accessions for ideal ornamental pepper plant with vigorous seedling, small port, large flowers and small fruits. Ornamental pepper accessions with larger anthers are indicated for selection, for facilitating the breeder’s work during flower emasculations for crossings.

Genet. Mol. Res. 17(1): gmr16039883
DOI: 10.4238/gmr16039883
Research Article

Plantains in Brazil are produced from the `Terra Maranhão’, ‘Terrinha’ and ‘D´Angola’ cultivars, which are all susceptible to black Sigatoka, weevils and nematodes. Therefore, the development of resistant plantain cultivars with agronomic characteristics aligned with market demands is the most efficient way to overcome these barriers regarding fruit production. The objectives of this work were to evaluate plantain cultivars for agronomic and physicochemical characteristics, and to estimate their genetic variability using ISSR molecular markers. The experimental design used was randomized block with ten plantain genotypes distributed in five blocks with four plants per plot. Ten agronomic and five physicochemical characteristics were measured. The agronomic, physicochemical and molecular (ISSR) characteristics were analyzed together using the Ward-MLM algorithm. Based on the agronomic and physicochemical evaluations, the ‘Red Yad’, ‘Curare Enano’ and ‘Chifre de Vaca’ genotypes could potentially be recommended to farmers, especially due to their short height and higher bunch mass and number of hands. The analysis of the combined data using the Ward-MLM algorithm identified genetic variability that, although restricted, can be used for genetic improvement strategies. To the best of our knowledge this is the first work that validates new plantains under Brazilian conditions, increasing cultivar options for farmers.

Genet. Mol. Res. 17(1): gmr16039882
DOI: 10.4238/gmr16039882
Research Article

Introduction: Sarcopenia, one of the geriatric syndromes, is defined as generalized and progressive reduction in skeletal muscle mass accompanied by loss of muscle strength and/or function. There is a paucity of research in the Turkish population about the effects of interleukin 1 (IL-1) and IL-6 gene polymorphism on sarcopenia. The aim of this study was to evaluate the relationship between IL-1 and IL-6 gene polymorphism and sarcopenia in the older Turkish population. Materials and Methods: The study included elderly residents of nursing homes who were 65 years or older had resided in a nursing home. Data regarding the patients’ demographics, anthropometric measurements, muscle strength and physical performance were retrospectively examined. Sarcopenia screening was performed as specified in the European Union Geriatric Association’s 2010 report entitled “The European Working Group on Sarcopenia in Older People”. Fat-free mass (FFM) was compared to individuals in the general population between 18 and 45 years old with no illnesses or medication use (534 men, 180 women). Nursing home residents were divided into two groups: with or without sarcopenia. A blood sample was taken from each participant. DNA was obtained from peripheral blood and Interleukin 1 and 6 Gene Polymorphism was genotyped by polymerase chain reaction and restriction fragment length polymorphism method. Results: A total of 149 elderly patients were included in the study. The overall rate of sarcopenia was determined as 42.2 %. There was no statistically significant difference in sarcopenia based on IL-6, IL-1B31, and IL-1B511 genotype distributions and allele frequencies. Conclusions: Our study demonstrates that sarcopenia in Turkish population is not influenced by IL-1 and IL-6 polymorphism

Genet. Mol. Res. 17(1): gmr16039881
DOI: 10.4238/gmr16039881
Research Article

The maize NAC gene, encoding a NAC domain transcription factor, plays vital roles in the growth process of maize under abiotic stresses. To investigate the response of ZmNAC33 to salinity stress, we analyzed the expression of the ZmNAC33 gene in roots and leaves of three-leaf stage seedlings among maize inbred lines. The result showed that the expression of ZmNAC33 was up-regulated in the salinity tolerant inbred line Ji853 and down-regulated in the salinity susceptible inbred line Chang7-2. The cDNA and the full sequence from maize inbred line Ji853 were amplified to analyze genetic structure. ZmNAC33 gene comprises three exons and two introns. We compared genetic diversity of ZmNAC33 among 69 elite maize inbred lines, a total of 144 sequence variants, including 113 SNPs and 31 Indels. Neutrality tests were negative selection by Tajima’s D and Fu and Li’s test. Analysis of polymorphism sites showed that at least 28 recombination’s have occurred. This finding provides insight into the development of breeding programs, germplasm management and association genetic studies.

Genet. Mol. Res. 17(1): gmr16039879
DOI: 10.4238/gmr16039879
Research Article

The objective of prenatal diagnosis (PD) is to provide prenatal diagnostic testing services for genetic conditions that enable families to make informed choices consistent with their individual needs and values, and to support them in deal with the outcome of such testing. This case we reported is about two fetuses with ventricular septal defect (VSD) and trisomy 7q11.23q21.3. With Karyotypic analyses, array-SNP and FISH, the trisomy 7q11.23q21.3 of two fetuses inherit from her mother. In her family pedigree, the carriers are all normal, especially heart. Because the defects with diameter is 3.1mm,2.9mm respectively without other abnormal phenotype, so surgery and catheter interventional treatment are both good methods to treat the VSD. Although we didn’t advise the woman terminal this pregnancy, the woman need take examinations to observe two fetuses regularity by ultrasound examination in the hospital.

Genet. Mol. Res. 17(1): gmr16039878
DOI: 10.4238/gmr16039878
Research Article

Prader–Willi syndrome (PWS) is a complex genetic disorder with different manifestations in infancy and childhood including obesity, type 2 diabetes mellitus, mild to moderate intellectual impairment and learning disabilities. In this syndrome, growth hormone therapy improves outcomes. For the first time, here we report a 11-year-old boy with PWS who presented with three episodes of unilateral facial palsy after starting growth hormone therapy.

Genet. Mol. Res. 17(1): gmr16039877
DOI: 10.4238/gmr16039877
Research Article

Monopterus albus is a special economic aquatic animal in China. Most of cultured M. albus are wild species captured from different areas, and this makes the wild resources of M. albus are under great threat. Microsatellite markers can help us understand the genetic resources of M. albus in different areas. In this study, using RAD-seq (restriction site associated DNA sequencing) protocol, a total of 9,897 microsatellites were identified in the genome with average frequency of 195 microsatellites per megabase of genomic sequences. Among these SSRs, the dinucleotide repeat motif was the most abundant type representing 61.77 % of the total microsatellite loci, followed by pentanucleotides (13.91 %), trinucleotides (12.08 %), tetranucleotides (9.30 %) and hexanucleotides (2.94 %). A total of 100 SSR primers were designed for PCR amplification. The polymorphism analysis showed that 28 primer pairs could successfully amplify the polymorphic fragments and the number of alleles per polymorphic locus ranged from 2 to 13, with an average of 5.70 alleles/locus. The values of observed and expected heterozygosity’s ranged from 0.0333 to 0.8000 and 0.0333 to 0.8887, respectively. This microsatellite locus will be useful to understand the structure, genetic diversity, and genetic difference of this species.

Genet. Mol. Res. 17(1): gmr16039880
DOI: 10.4238/gmr16039880
Research Article

Apricot is a staple stone fruit crop cultivated in Southern Xinjiang of China. This crop is important for the rural communities, as they generate significant employment and income. Here, seventy-eight apricot genotypes, including seventy-six common apricots (Prunus armeniaca L.) and two purple apricots (Prunus dasycarpa Ehrh.), were mainly collected from Aksu, Kashgar, Hetian and Bayingolin. Start Codon Targeted (SCoT) markers and ITS (internal transcribed spacers) sequences were used to investigate the genetic diversity and species identification respectively. Based on POPGENE showed that apricot cultivars from Aksu group exhibited the highest genetically diverse as compared with other groups, cluster analysis of SCoT markers (basede on UPGMA and PCoA method) showed that these apricot cultivars could be divided into three major clusters, which was in agreement with their geographic distribution and pedigrees. It was indicated that there were possible three primary diversity centers in the area: Aksu, Kashgar and Hetian, and also possible introgression among these populations. Furthermore, based on the complete ITS sequences, the phylogenetic analysis showed that P. dasycarpa clustered separated from other the section armeniaca of species. Therefore, it was proposed that P. dasycarpa would be a hybrid species. Our results indicated that SCoT markers are informative and could be used to evaluate genetic diversity of apricots, and ITS could be used effectively to identify P. dasycarpa. These results will provide much more useful information for the native apricots protection and utilization strategies.

Genet. Mol. Res. 17(1): gmr16039875
DOI: 10.4238/gmr16039874
Research Article

Lung cancer is the leading cause of cancer-related deaths worldwide. Despite therapeutic advances over the last several decades, the overall 5-year survival remains only 16%. (Siegel R, 2013). Molecular studies have indicated that Adenocarcinomas have distinct genomic alterations allowing classification into clinically relevant molecular subsets. Such specific molecular level alterations are sometimes important for initiation and maintenance of the tumour serving as “drivers” in lung cancer tumorigenesis. Not only is mutant KRAS difficult to restrain, its presence in some types of cancers predicts that there will be no response to other targeted drugs. For example, patients with colorectal cancer may benefit from additional treatment with an antibody drug that targets the EGFR protein (cetuximab or panitumumab). However, this benefit is seen only in patients who have a “wild-type” (not mutated) KRAS gene. The reason for this is that EGFR and other related receptor proteins rely on KRAS to transmit proliferation signals.

Genet. Mol. Res. 17(1): gmr16039874
DOI: 10.4238/gmr16039873