Research Article

Table of Contents | Genet. Mol. Res. 2016 (3)

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Retraction

The GMR editorial staff was alerted about some manuscripts that were found to be substantially equal. The Publisher and Editor decided to retract these articles in accordance with the recommendations of the Committee on Publication Ethics (COPE). After a thorough investigation, we have strong reason to believe that the peer review process was failure and, after review and contacting the authors, the editors of Genetics and Molecular Research decided to retract these articles. The authors and their institutions were advised of this serious breach of ethics.

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Genet. Mol. Res. 15(3): gmr007_retraction
DOI: 10.4238/gmr.1503007
Research Article

Maize (Zea mays L.) is one of the most important food crops throughout the world, and provides oil and proteins to humans and livestock. Kernel oil and protein content in maize are two complex quantitative traits. In order to identify quantitative trait loci (QTL) controlling oil and protein concentration in maize kernels, and to evaluate their genetic effects, QTL analysis was conducted on an F3:4 population derived from a cross between an inbred line with a low oil and protein concentration (Zheng58) and an inbred line with a higher oil and protein concentration (B73). A total of 189 polymorphic simple sequence repeat markers were used to construct a linkage map. Eleven QTLs for kernel oil concentration were detected on nine chromosomes, except for chromosome 9. A single QTL explained 4.6 to 11.1% of the phenotypic variance. Ten QTLs for kernel protein concentration were also detected on nine chromosomes, except for chromosome 9. A single QTL explained 4.2 to 11.4% of the phenotypic variance. Interestingly, novel QTLs for oil concentration (qOIL08-01 and qOIL10-01) and QTLs for protein concentration (qPRO01-01 and qPRO05-01) were specific to the population studied, which could explain 7.1 to 11.1% of the phenotypic variance. These results will provide better understanding of the genetic basis of oil and protein concentrations in maize. The markers closely linked with the QTLs will facilitate breeding of maize varieties with high oil and protein concentrations through molecular marker-assisted selection.

Genet. Mol. Res. 15(3): gmr8951
DOI: 10.4238/gmr.15038951
Research Article

The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae), is an economically important pest that causes major losses in some main crop-producing areas of China. To control this pest effectively, it is necessary to investigate its population genetic diversity and genetic structure around the Bohai Gulf area of China. In this study, we used two mitochondrial genes, COI (578 bp) and Cytb (724 bp), to investigate its genetic diversity. We obtained 622 COI sequences and 462 Cytb sequences from 23 populations, and 28 and 73 haplotypes, respectively, were identified. Low to moderate levels of genetic diversity (COI: Hd = 0.267 ± 0.023, Pi = 0.00082 ± 0.00010; Cytb: Hd = 0.689 ± 0.018, Pi = 0.00255 ± 0.00029) for the total populations were observed. Phylogenetic and median-joining network analyses indicated no distinct geographical distribution pattern among the haplotypes. Overall, this study revealed that there was significant differentiation among the populations (COI: FST = 0.158, P Cytb: FST = 0.148, P FST values for Shenyang, Baoding, and Funing were significantly different to those for most of the other populations. Finally, unimodal mismatch distribution analysis, combined with negative neutrality test results, showed a recent population expansion of the beet armyworm around the Bohai Gulf area of China.

Genet. Mol. Res. 15(3): gmr9032
DOI: 10.4238/gmr.15039032
Research Article

Currently, one of the acclaimed alternatives for increasing maize yield is accomplished through utilization of heterosis in hybrid cultivars. However, upon performing crosses between related pairs, there are losses due to inbreeding depression. Thus, the aim of this study was to estimate inbreeding depression and the contribution of loci in heterozygosity in different types of maize hybrids. Eight treatments were evaluated, considering the F1 and S0 generations of four commercial hybrids. A randomized block experimental design was used, with three replications, and plots consisting of two three-meter long rows at a spacing of 0.50 m. The traits evaluated were plant height, first ear height and husked ear weight. For ear weight trait, there was a significant difference, where the treatments could be classified into three distinct groups. In this case, the single-cross hybrids AG7088 and 30F90Y exhibited greater depression through inbreeding due to the greater contribution of loci in heterozygosity and consequent predominance of deviations due to dominance.

Genet. Mol. Res. 15(3): gmr5497
DOI: 10.4238/gmr.15035497
Research Article

This study aimed to determine whether abnormal apoptosis is present in acetabular cartilage in early developmental dislocations of the hip (DDH), and if so, whether it is correlated with the expression of caspase-3 and Bcl-2. DDH was induced in 24 4-week-old New Zealand white rabbits. Acetabular cartilage specimens from the experimental and control groups were stained with hematoxylin and eosin (H&E). Animals from the experimental group developed acetabular dysplasia. Apoptotic chondrocytes were observed by ultrastructural electron microscopy and H&E. TUNEL assays revealed significantly greater acetabular chondrocyte apoptosis in the treated samples as compared to the control. Significantly higher caspase-3 expression and lower Bcl-2 expression were also measured in the DDH group compared with the control. We conclude that excessive apoptosis does occur in acetabular cartilage with DDH, and is positively correlated with high caspase-3 expression as well as low Bcl-2 expression.

Genet. Mol. Res. 15(3): gmr6809
DOI: 10.4238/gmr.15036809
Research Article

The complete genomic RNA of the Chinese sacbrood virus (CSBV) strain, which infects the honeybees in the Loess plateau, was sequenced and analyzed. The CSBV-SX strain contains 8705 nucleotides, which includes a single large open reading frame (99-8681 nucleotides) encoding 2860 amino acids. A novel efficient identification method was used to investigate the samples infected by CSBV. The putative amino acid sequence alignment analysis showed that, except for some normal well characterized domains such as RNA helicase, RNA protease, and RNA-dependent RNA polymerase domains, a calicivirus coat protein domain was identified at amino acids 493-564. Phylogenetic analysis indicated that CSBV-SX was closely related to CSBV-BJ, and this result was supported by nucleotide multiple sequence alignment and protein multiple sequence alignment analysis results. These differences in the CSBV-SX strain may be related to virus adaptation to the xerothermic, low relative humidity, and strong ultraviolet radiation conditions in the Loess Plateau.

Genet. Mol. Res. 15(3): gmr6928
DOI: 10.4238/gmr.15036928
Research Article

We evaluated the association between GSTM1, GSTT1, and GSTP1 IIe105Val gene polymorphisms and treatment outcomes of advanced non-small cell lung carcinoma. Between January 2010 and December 2012, a total of 244 patients with non-small cell lung carcinoma were recruited from Yiwu Central Hospital. The GSTM1, GSTT1, and GSTP1 IIe105Val gene polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism and the results were statistically analyzed. Conditional regression analysis, showed that individuals carrying the null GSTM1 were associated with an increased risk of response to chemotherapy when compared to the present GSTM1 (odds ratio = 1.88, 95% confidence interval (CI) = 1.01-3.47). Moreover, the GG genotype of GSTP1 IIe105Val was associated with a better response to chemotherapy compared to the AA genotype (odds ratio = 2.77, 95%CI = 1.14-6.64). The null GSTM1 genotype was associated with a lower risk of death from all causes when compared with the present GSTM1 genotype (hazard ratio = 2.16, 95%CI = 1.10-4.38). Moreover, the GG genotype of GSTP1 IIe105Val was correlated with a reduced risk of death from all causes compared with the AA genotype (hazard ratio = 2.94, 95%CI = 1.11-8.68). In conclusion, we found that the null GSTM1 and the GG genotype of GSTP1 IIe105Val were correlated with a good response to chemotherapy and improved overall survival of advanced non-small cell lung carcinoma patients.

Genet. Mol. Res. 15(3): gmr7668
DOI: 10.4238/gmr.15037668
Research Article

The conservation of plants in germplasm banks ensures the characterization and availability of these resources for future generations. The present study used DNA markers to obtain genetic information about germplasm collections of Lippia sidoides and L. gracilis, which are maintained in an Active Germplasm Bank (AGB). Genetic variability of samples in the AGB was assessed using 12 combinations of amplified fragment length polymorphism (AFLP) primers (EcoRI/MseI). Twenty simple sequence repeat primers designed for L. alba were tested to determine their transferability in L. sidoides and L. gracilis. The AFLP markers generated 789 markers. The assessed loci exhibited a moderate Shannon diversity index (I = 0.42) in both species, suggesting that the conserved accessions possess an intermediate level of genetic diversity. Twelve microsatellite loci amplified satisfactorily, and nine loci were polymorphic in each species. A total of 23, 22, and 36 alleles, with an average of 2.5, 2.4, and 3.27 alleles per locus were identified for L. sidoides and L. gracilis accessions in the AGB, and Lippia sp sampled plants, respectively. Analyses of genetic structure permitted the identification of three different groups using both sets of markers, of which two were representative of L. sidoides. The information generated in this study may help to create, expand, and maintain collections of these species and may assist in genetic-breeding programs.

Genet. Mol. Res. 15(3): gmr7781
DOI: 10.4238/gmr.15037781
Research Article

Mycobacterium tuberculosis (Mtb) is known to be responsible for tuberculosis (TB), but the pathogenesis of this disease and the host defense mechanisms involved are, for the most part, poorly understood. In this study, we divided 30 male C57BL/6 mice into control and infection groups, and following injection with physiological saline or Mtb, respectively, euthanized five mice from each group on days 1, 3, and 7. TNF-α and IL-10 levels were measured by enzyme-linked immunosorbent assay and flow cytometry, with the latter also being performed to assess apoptosis rates. Protein expression of STAT3 and its phosphorylated form (p-STAT3) was analyzed by western blotting. After Mtb infection, TNF-α and IL-10 levels, alveolar macrophage apoptosis, and STAT3 and p-STAT3 expression increased significantly on days 1, 3, and 7 (P Mtb. This provides a theoretical mechanism behind TB pathogenesis and host defense against Mtb, and contributes towards development of an effective treatment.

Genet. Mol. Res. 15(3): gmr7819
DOI: 10.4238/gmr.15037819
Research Article

The aim of the present study was to develop a transformation system that may be useful for introducing agronomically and biotechnologically relevant traits into melon. The production of transplanted melon with maternal inheritance of the transgene could solve problems related to outcrossing between genetically modified crops and conventional crops or their wild relatives. By analyzing the main influencing factors systematically, the pollination time was ascertained and the pollen-tube pathway genetic transformation system was optimized. A screening system for resistant seeds from the T1 generation was established. The transformed seedlings were grown under standard field conditions and selected using a polymerase chain reaction-based analysis. The resistant plants were detected at a rate of 5%. These results indicate that enhanced production hastens the initiation of bisexual flowers, development of mature bisexual flowers, and fruit set in melon. We have established a melon transformation system based on the pollen-tube method.

Genet. Mol. Res. 15(3): gmr8067
DOI: 10.4238/gmr.15038067
Research Article

The transcriptomes of salt-stressed and unstressed Betula kirghisorum plants were analyzed using high throughput sequencing technology. A total of 52,239,804 and 51,772,998 clean reads were obtained from the two libraries, respectively, and de novo assembled into 60,545 all-unigenes. A total of 39,997 unigenes were annotated using public databases. Overall, 7206 genes were differentially expressed in unigenes and were involved in 127 pathways. Thirteen transcription factor families were identified in B. kirghisorum, including GRAS proteins, which are plant-specific transcription factors. By using bioinformatic methods to predict and analyze physicochemical properties, structural data were obtained on the 19 potential GRAS proteins. The results revealed that these proteins are hydrophilic, with significant differences in their length and molecular weight. The main secondary structures were alpha helices and random coils. BkGRAS proteins possess typical GRAS domains: LHR I; VHIID motif; LHR II; PFYRE motif; and SAW motif. In the majority of BkGRAS proteins, AGG, AGA, UCU, GCU, GGG, CCA, GUU, GUG, AUU, GAU, and AAG codons were used preferentially. Aside from the BkGRAS17 gene (relative synonymous codon usage (RSCU) = 1.20), usage of the UUA codon by other BkGRAS genes was low (RSCU BkGRAS genes have low codon bias. Subcellular localization analysis that predicted these proteins are found in the nucleus, cytoplasm, or chloroplast. BkGRAS proteins were divided into six subfamilies: SCR, LISCL, SCL3, DELLA, HAM, and PAT1. These results provide important information for the further functional study of GRAS genes in B. kirghisorum.

Genet. Mol. Res. 15(3): gmr8321
DOI: 10.4238/gmr.15038321
Research Article

Sacral nerve stimulation (SNS) is an alternative surgical approach to alleviate fecal incontinence and constipation. This study aimed to explore the effects and underlying mechanisms of SNS with acupuncture on gut transit time and colon c-kit protein expression in rats with slow transit constipation (STC). Fifty Sprague-Dawley rats were randomly divided into five groups: blank control, SNS, Mosapride, sham SNS, and STC model control group. The STC model was established by subcutaneous injection of morphine. Each group was treated over a 15-day period. Gut transit time was measured 1 day before the treatment started and after 5, 10, and 15 days of treatment. After the 15-day treatment, animals were sacrificed and colonic tissues were collected for analysis of c-kit protein expression, using western blot analysis. We found significant differences in gut transit time in the SNS group compared with the Mosapride group after 5 (P = 0.001) and 10 (P = 0.004) days of treatment. After 15 days of treatment, there were no differences in gut transit time among the SNS, Mosapride, and blank control groups. However, significant differences were observed when comparing the SNS and Mosapride groups with the STC model and sham SNS groups. A decreased c-kit protein expression was observed in the STC model control, sham SNS, and Mosapride groups, compared with the SNS group (P = 0.001). Our data indicate that SNS can decrease gut transit time and increase the expression of c-kit protein in rats with STC to improve colon transit function.

Genet. Mol. Res. 15(3): gmr8362
DOI: 10.4238/gmr.15038362
Research Article

Glucosinolates (GSLs) are important secondary metabolites in Brassicaceae plants. Previous studies have mainly focused on GSL contents, types, and biosynthesis-related genes, but the molecular characterization patterns of GSL biosynthesis-related transcription factors remain largely unexplored in radish (Raphanus sativus L.). To isolate transcription factor genes regulating the GSL biosynthesis, genomic DNA and cDNA sequences of RsMYB28 and RsMYB29 genes were isolated in radish. Two R2R3-MYB domains were identified in the deduced amino acid sequences. Subcellular localization and yeast-one hybrid assays indicated that both the RsMYB28 and RsMYB29 genes were located in the nucleus and possessed transactivation activity. Reverse transcription quantitative analysis showed that the RsMYB28 and RsMYB29 genes were expressed in seeds, leaves, stems, and roots at the seedling, taproot thickening, and mature stages. Both genes were highly expressed during the seedling and taproot thickening stages. The expression level of RsMYB28 was found to be up-regulated following wounding, glucose, and abscisic acid treatments, whereas RsMYB29 was up-regulated following wounding and methyl jasmonate treatments. These results provide insights into the biological function and characterization of the RsMYB28 and RsMYB29 genes, and facilitate further dissection of the molecular regulatory mechanism underlying the GSL biosynthesis in radish.

Genet. Mol. Res. 15(3): gmr8381
DOI: 10.4238/gmr.15038381
Research Article

Inflammation plays an important role in cerebral ischemia reperfusion, which can cause severe damage to the brain and may lead to cerebral hemorrhage transformation. p38-mitogen-activated protein kinase (p38mapk) has been implicated in the etiology of a number of diseases because it is a cause of inflammation, but comparatively little research has been carried out into its role in the etiology of ischemia reperfusion. We investigated the expression of p38mapk in cerebral ischemia reperfusion to gain a better understanding of its potential role in hemorrhagic transformation (HT). One hundred rats were randomly divided into three groups: an ischemia reperfusion group, an ischemia group, and a sham-operated group. We carried out neurological deficit assessments, infarct volume measurements, histopathological examinations, and immunohistochemistry analyses. p38mapk was overexpressed in the ischemia reperfusion group, which exhibited severe tissue damage and greater edema than the other two groups. These results suggest that p38mapk plays an important role in cerebral ischemia reperfusion, and may be one of the causes of HT.

Genet. Mol. Res. 15(3): gmr8492
DOI: 10.4238/gmr.15038492
Research Article

Approximately 10-15% of all pregnancies end in spontaneous abortions. Many factors can lead to embryonic loss; however, it has been well established that over 50% of all miscarriages result from chromosomal abnormalities, primarily aneuploidies (>96%). Identifying the cause of miscarriage can significantly reduce the psychological stress in women, and enable better genetic counseling for a future pregnancy. Quantitative fluorescent polymerase chain reaction (QF-PCR) has been previously used in the study of chromosomal abnormalities. In this retrospective study, the frequency of aneuploidy in samples of 130 miscarriages undergone by patients (age average: 34.1 ± 4.6 years) at our institution was determined by QF-PCR using short tandem repeat markers. The gender of the miscarriage cases was determined by amplifying the amelogenin locus (70 males and 60 females). Seventy-one of these cases (54.6%) presented aneuploidies such as trisomy, monosomy, triploidy, and double trisomy. Trisomy 22 was the most common aneuploidy (present in 14 cases), followed by trisomy 15, trisomy 16, and monosomy X. We also observed monosomy at chromosomes X and 21 and a case with multiple aneuploidies at chromosomes 16 and 22. The most common aneuploidies associated with miscarriages were detected by QF-PCR; therefore, we concluded that QF-PCR is a rapid and reliable method for the detection of aneuploidy, and can be used as an accessory to the widely used karyotype analysis.

Genet. Mol. Res. 15(3): gmr8617
DOI: 10.4238/gmr.15038617

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