• Volume 99, All articles

      Continuous Article Publishing mode

    • Low-penetrance susceptibility variants and postmenopausal oestrogen receptor positive breast cancer

      ASUMAN ÖZGÖZ FADİME MUTLU İÇDUYGU AYŞEGÜL YÜKSELTÜRK HALE ŞAMLI KUYAŞ HEKİMLER ÖZTÜRK ZUHAL BAŞKAN

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      The risk of breast cancer (BC) in women is high and many factors including genetic factors increase the risk for the disease. It is revealed that the variations of low-penetrance susceptibility genes are important for carcinogenesis as they interact with the environmental and hereditary factors. Recently, the list of BC-associated common single nucleotide polymorphisms (SNPs) and chromosomal loci in low-penetrance susceptibility genes have been expanded in genomewide association studies. FGFR2, LSP1, MAP3K1, TGFB1, TOX3, 2q35 and 8q loci variations are some examples for these common SNPs. These SNPs and their association with BC risk was investigated in many different populations. Therefore in this study, we aimed to evaluate low-penetrance susceptibility SNPs; namely FGFR2 rs1219648, rs2981579, rs2981582; MAP3K1 rs889312; TOX3 rs3803662; LSP1 rs909116, rs3817198 and SLC4A7 rs4973768 together, for the firsttime in Turkish postmenopausal oestrogen receptor positive BC cases. Following the DNA isolation, multiplex PCR and matrix-assisted laser desorption/ionization mass spectrometry with time of flight measurement (MALDI-TOF) based SNP analysis were performed. MAP3K1 rs889312 SNP demonstrated the strongest association with BC risk among the other low penetrant SNPs, it was also associated with BC risk in a dominant model. Only in a ressesive model, TOX3 rs3803662 was associated with BC risk. In addition, rs4973768 CC and rs909116 CC genotypes are correlated with higher tumour size which is not reported in the literature as yet; on the other hand there are no associations between any of the other SNP genotypes and clinopathological parameters. In our opinion, MAP3K1 rs889312 may be a good BC susceptibility biomarker candidate for Turkish population.

    • Single-nucleotide polymorphisms in CLEC7A, CD209 and TLR4 gene and their association with susceptibility to paratuberculosis in Indian cattle

      B. GOPI RAN VIR SINGH SATISH KUMAR SUSHIL KUMAR ANUJ CHAUHAN AMIT KUMAR SHOOR VIR SINGH

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      The aim of this study was to identify the single-nucleotide polymorphisms (SNPs) in bovine candidate genes CLEC7A, CD209 and TLR4, and explore the association between these SNPs with the occurrence of bovine paratuberculosis (PTB) disease. For this purpose, 549 animals were screened by a panel of four diagnostic tests, namely Johnin PPD test, ELISA test, faecal microscopy and IS900 blood PCR against Mycobacterium avium ssp. paratuberculosis (MAP) to develop case–control populations. SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism method. Genotypic–phenotypic associations were assessed by the PROCLOGISTIC procedure of SAS 9.3. Of the seven SNPs; rs110353594 in CLEC7A gene and rs8193046 in TLR4 gene were found to be associated with PTB. For SNP rs110353594, odds of CC and CT genotypes vs TT genotype was 1.543 (0.420–5.667; 95% CI) and 0.284 (0.104–0.774; 95% CI), respectively which means that CT genotype was more resistant than TT and CC genotypes against bovine PTB. For SNP rs8193046, odds of AA and AG genotypes versus GG genotype was 0.947 (0.296–3.034; 95% CI) and 3.947 (1.555–10.022; 95% CI), respectively, i.e. probability for getting an infection in animals with AG genotype was 3.94 times more as compared to GG genotype. Hence, a selection programme favouring CT genotype for rs110353594 and against AG genotype for rs8193046 may be beneficial for conferring resistance against bovine PTB.

    • Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis

      XI ZHA XIAOYANG WANG JINRONG LI FEI GAO YIJUN ZHOU

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      Sophora alopecuroides belongs to the genus Sophora of the family Papilionoideae. It is mainly distributed in the desert and semidesert areas of northern China, and has high medicinal value and ecological function. Previous studies have reported the chemical composition and ecological functions of S. alopecuroides. However, only a few reports are available on the genomic information of S. alopecuroides, especially the chloroplast genome, which greatly limits the study of the evolutionary relationship between other species of Papilionoideae. Here, we report the complete chloroplast genome of S. alopecuroides. The size of the chloroplast genome is 155,207 bp, and the GC content is 36.44%. The S. alopecuroides chloroplast genome consists of 132 genes, including 83 protein-coding genes, 41 transfer RNA (tRNA) genes,and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed the taxonomic position of S. alopecuroides in Papilionoideae, and the genus Sophora and the genus Ammopiptanthus were highly related. Comparative genomics analysis revealed the gene rearrangement in the evolution of S. alopecuroides. The comparison between S. alopecuroides and the species of the Papilionoideae identified a novel 23 kb inversion between the trnC-GCA and trnF-GAA which occurred before the divergence of Sophora and Ammopiptanthus of Thermopsideae. This study provided an essential data for the understanding of phylogenetic status of S. alopecuroides.

    • Drosophila ananassae: a species characterized by spontaneous male recombination in appreciable frequency

      BASHISTH N. SINGH

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      Mutation and recombination are primarily responsible for generating the genetic variability in natural populations of microorganisms, plant and animal species including humans. Upon such genetic variations, elemental forces of evolution such as natural selection, random genetic drift and migration operate to bring about micro-evolutionary changes. Recombination or crossing-over produces new combinations of genes due to interchange of corresponding segments between nonsister chromatids of homologous chromosomes, thus, it is an important evolutionary factor. Since the time of T. H. Morgan, Drosophila has been subjected to extensive investigations on crossing over while employing a number of markers, which were used for gene mapping. Interestingly, recombination occurs in females of D. melanogaster but not in males. Later on, male crossing over was investigated in various species and its occurrence was reported in D. melanogaster, D. ananassae, D. simulans, D. willistoni, D. littoralis and D. bipectinata. Recombination occurs at very low rate in all these species except for D. ananassae, which shows spontaneous male crossing over in appreciable frequency, which is meiotic in origin. This unusual phenomenon in D. ananassae is influenced by various genetic factors as well as it shows strain variation as far as frequency of male recombination is concerned. Further, the presence of chiasmata during meiosis in males at a frequency capable of accounting for the observed recombination frequency extends evidence for meiotic origin of recombination in males of D. ananassae.

    • Mining genes associated with furanocoumarin biosynthesis in an endangered medicinal plant, Glehnia littoralis

      JIEJIE SONG HONGMEI LUO ZHICHAO XU YUXI ZHANG HUA XIN DAN ZHU XUNZHI ZHU MENGMENG LIU WEIQING WANG HONGWEI REN HONGYU CHEN TING GAO

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      The endangered medicinal plant Glehnia littoralis is one of the important natural source of furanocoumarin, which has been used as mucolytic, antitussive, antitumour and antibacterial. However, the genetic information of furanocoumarin biosynthesis in G. littoralis is scarce at present. The objective of this study was to mine the putative candidate genes involved in the biosynthesis pathwayof furanocoumarin and provide references for gene identification, and functional genomics of G. littoralis. We carried out the transcriptome analysis of leaves and roots in G. littoralis, which provided a dataset for gene mining. Psoralen, imperatorin and isoimperatorin were detected in G. littoralis by high performance liquid chromatography analysis. Candidate key genes were mined based on the annotations and local BLAST with homologous sequences using BioEdit software. The relative expression of genes was analysed using quantitative real-time polymerase chain reaction. Further, the CYP450 genes were mined using phylogenetic analyses using MEGA 6.0 software. Atotal of 156,949 unigenes were generated, of which 9021 were differentially-expressed between leaves and roots. A total of 82 unigenes encoding eight enzymes in furanocoumarin biosynthetic pathway were first obtained. Seven genes that encoded key enzymes in the downstream furanocoumarin biosynthetic pathway and expressed more in roots than leaves were screened. Twenty-six candidate CYP450 unigenes expressed abundantly in roots and were chiefly concentrated in CYP71, CYP85 and CYP72 clans. Finally, we filtered 102 differentially expressed transcription factors (TFs) unigenes. The transcriptome of G. littoralis was characterized which would help to elucidate the furanocoumarin biosynthetic pathway in G. littoralis and provide an invaluable resource for further study of furanocoumarin.

    • Genomewide analysis of the CIII peroxidase family in sweet orange (Citrus sinensis) and expression profiles induced by Xanthomonas citri subsp. citri and hormones

      QIANG LI WANFU DOU JINGJING QI XIUJUAN QIN SHANCHUN CHEN YONGRUI HE

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      Class III peroxidase (CIII prx) is a plant-specific multigene family that regulates the physiological and stress responses. This research aimed to exhaustively annotate and analyse the CIII prx family in sweet orange and to explore the regulated expression profiles by Xanthomonas citri subsp. citri (Xcc) and plant hormones. We further assessed the relationship between CIII prxs and citrus bacterial canker. The phylogeny, gene structure, conserved motifs, gene duplications and microsynteny of the CIII prx family were analysed. Expression profiles of specific CsPrxs induced by Xanthomonas citri subsp. citri and plant hormones were detected by quantitative reverse transcription-polymerase chain reaction. Subcellular localization was analysed through transient expression assessments. A total of 72 CIII prx members were identified from the genomes of sweet orange. In all chromosomes of sweet orange, the CsPrxs could be detected except in chromosome 8. In addition, three segmental duplications, four tandem duplications and 11 whole-genome duplications occurred among the CsPrxs, contributing to the family size expansion. From the Ka/Ks ratios, 15 of 18 duplicated CsPrxs pairs have experienced purifying selection process. A total of 15 conserved motifs were detected in CsPrxs, four of which were detected in all complete CsPrxs. A total of 12 expressed genes were identified from the EST database. The expression trends of 12 CsPrxs were differently expressed at different stages of infection by Xcc, five of which were potential candidate genes involved in Xcc resistance. These genes could be induced by salicylic acidand methyl jasmonate, and were extracellular proteins. These results further support our understanding of CIII prxs in citrus, particularly incitrus bacterial canker studies.

    • Two-phase SSU and SKAT in genetic association studies

      YUAN XUE JUAN DING JINJUAN WANG SANGUO ZHANG DONGDONG PAN

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      The sum of squared score (SSU) and sequence kernel association test (SKAT) are the two good alternative tests for genetic association studies in case–control data. Both SSU and SKAT are derived through assuming a dose-response model between the risk of disease and genotypes. However, in practice, the real genetic mode of inheritance is impossible to know. Thus, these two tests might losepower substantially as shown in simulation results when the genetic model is misspecified. Here, to make both the tests suitable in broad situations, we propose two-phase SSU (tpSSU) and two-phase SKAT (tpSKAT), where the Hardy–Weinberg equilibrium test is adopted to choose the genetic model in the first phase and the SSU and SKAT are constructed corresponding to the selected genetic model in the second phase. We found that both tpSSU and tpSKAT outperformed the original SSU and SKAT in most of our simulation scenarios. Byapplying tpSSU and tpSKAT to the study of type 2 diabetes data, we successfully identified some genes that have direct effects on obesity. Besides, we also detected the significant chromosomal region 10q21.22 in GAW16 rheumatoid arthritis dataset, with P<10-6. These findings suggest that tpSSU and tpSKAT can be effective in identifying genetic variants for complex diseases in case–control association studies.

    • Codon usage by chloroplast gene is bias in Hemiptelea davidii

      HUABO LIU YIZENG LU BAOLIANG LAN JICHEN XU

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      The base composition of the chloroplast genes is of great interest because they play a highly significant role in the evolutionary development of the plants. Evaluation of the 48 chloroplast protein-coding genes of Hemiptelea davidii showed that the average GC content was about 37.32%, while at the third codon base position alone the average GC content was only 27.80%. The 48 genes were classified into five groups based on the gene function and each group displayed specific codon characteristics. Based on the relative synonymous codon usage analysis, a total of 30 high-frequency codons and 11 optimal codons were identified, most of them ended with A or T. Neutrality plot, ENC-plot and PR2-plot analyses showed that the codon usage bias of the chloroplast genes of H. davidii was greatly influenced by natural selection pressures. Meanwhile, the frequency of codon usage of chloroplast genes among different plant species displayed similarities, with some synonymous codons were preferred to be used in H. davidii. In this study, the codon usage pattern of the chloroplast protein coding genes of H. davidii provides us with a better understanding of the expression of chloroplast genes, and may advice the future molecular breeding programmes.

    • A novel de novo mutation in the PURA gene associated with a new clinical finding: large brainstem

      MARÍA ELENA RODRÍGUEZ-GARCÍA FRANCISCO JAVIER COTRINA-VINAGRE ELENA ARRANZ-CANALES ANA MARTÍNEZ DE ARAGÓN LAURA HERNÁNDEZ-SÁNCHEZ FÁTIMA RODRÍGUEZ-FORNÉS PATRICIA CARNICERO-RODRÍGUEZ MONTSERRAT MORALES-CONEJO ELENA MARTÍN-HERNÁNDEZ FRANCISCO MARTÍNEZ-AZORÍN

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      We report the case of a Caucasian Spanish boy, who showed profound neonatal hypotonia, feeding difficulties, apnea, severe developmental delay, epilepsy, bilateral convergent strabismus, poor verbal language development and a large brainstem. Whole-exome sequence uncovered a novel de novo mutation in the purine-rich element binding protein A gene (PURA; NM_005859.4:c.72del:p.(-Gly25AlafsTer53)) that encodes the transcriptional activator protein Pur-alpha (PURA). Mutations in this gene have been identified in patients with PURA syndrome, a rare disorder characterized by an early hypotonia, developmental delay, severe intellectual disability with or without epilepsy, and disability in expressive language development. Although, up to 75 cases have been identified worldwide, to the best of our knowledge, this is the first patient described with a brainstem larger than normal. In conclusion, our data expand both geneticand phenotypic spectrum associated with PURA gene mutations.

    • Assessment of FMR1 triplet repeats in patients affected with mental retardation, fragile X syndrome and primary ovarian insufficiency

      ZEINAB SALIMY MOHAMMAD TAGHI AKBARI FARAVAREH KHORDADPOOR DEILAMANI

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      The CGG repeats in the FMR1 gene expand in patients with fragile X syndrome, fragile X-associated tremour/ataxia syndrome and fragile X-associated primary ovarian failure. In this study, the CGG repeats in the FMR1 gene were studied in 449 males and 207 females using traditional polymerase chain reaction and triplet repeat primed PCR methods, also 18 CVS samples (six males and 12 females) were tested for prenatal diagnosis. Further, methylation sensitive multiplexed ligation dependent probe amplification was performed on some samples to confirm the results. Regarding the male patients, 1.1% and 9.7% had premutation (PM) and full mutation (FM) alleles, respectively. Also three (0.66%) male patients were mosaic for PM and FM alleles. Among females, 1.9% were GZ carriers and 5.8% were PM carriers. Prenatal diagnosis resulted in detection of two PM and one FM males as well as one FM carrier female. Our results were in concordance with the previously published results.

    • Variation of grain quality characters and marker-trait association in rice (Oryza sativa L.)

      K. SUMAN P. MADHUBABU RAMYA RATHOD D. SANJEEVA RAO A. ROJARANI S. PRASHANT L. V. SUBBARAO V. RAVINDRABABU C. N. NEERAJA

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      A set of 24 genotypes were studied for 17 grain quality characters and validated with the reported associated rice microsatellite markers with grain quality characters. Using 23 polymorphic markers distributed across 11 chromosomes marker-trait associations were studied. The percentage of polymorphism information content (PIC) of the markers ranged between 54.0 and 86.7. Eight markers with >80% and seven markers with >70% of PIC were found to be efficient in differentiating the studied grain quality characters. A total of 37 significant marker-trait associations (P ≤ 0.09) were found with R2 ranging from 4.70% to 43.80%. Eight markers a (RM246, RM11, RM241, RM16427, RM421, RM3, RM234 and RM257) showed association with more than one character suggesting their utility for the selection for grain quality characters which can be deployed in the rice crop improvement programmes.

    • A novel DNAH5 variant in a Tunisian patient with primary ciliary dyskinesia

      RAHMA MANI JIHÉNE BOUGUILA SALMA BEN AMEUR MONGIA HACHICHA ZOHRA SOUA IMED MABROUK

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      Primary ciliary dyskinesia (PCD) is a genetically heterogeneous hereditary disease caused by the structural abnormalities and dysfunction of motile cilia. The DNAH5 is the most frequently mutated gene in PCD patients and hot spot exons were reported in this gene. Here, we aim to screen mutations in a set of five hot spot exons of DNAH5 gene in a cohort of 10 clinically diagnosed Tunisian PCD patients using an optimized polymerase chain reaction-single-strand conformational polymorphism screening technique. Only one patient harboured a novel heterozygous variant in exon 63 (c.10767A[G), which was inherited from his father. This variant activates a cryptic splicing site. No deleterious mutation has been identified while screening the exons of the remaining patients. Our results show that the reported hot spot exons of DNAH5 gene are not mutated in Tunisian PCD patients. This is probably due to the differences of ethnical background of the previously reported patients. Further investigations should be performed to identify the mutations underlying PCD in this group of patients.

    • Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize (Zea mays L.)

      BING HE PIBIAO SHI YUANDA LV ZHIPING GAO GUOXIANG CHEN

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      Shi-related sequence (SRS) proteins are plant-specific transcription factors that play important roles in developmental processes, including regulating hormone biosynthesis, response or signal transduction. However, systematical analysis of the SRS gene family in maize has not yet been conducted. In this study, 11 SRS genes with 13 transcripts were identified and characterized. The characteristics of the gene family were analysed in terms of phylogenetic relationships, chromosome distribution and gene structure. RNA-sequencing data analysis showed that the expression patterns of SRS genes were quite different from each other in maize, indicating their divergence in function. Interestingly, the GRMZM2G077752 gene is highly expressed in senescent leaves. Using further coexpression network analysis, we determined that the module containing GRMZM2G077752 were over-represented by genes related to abscisic acid (ABA) stimulus and carbohydrate metabolic process. This result indicated that GRMZM2G077752 might perceive ABA signal and cause the activation of carbohydrate remobilization during leaf ageing. This study provides valuable information for understanding the functions of the SRS genes in maize.

    • Role of MMP-1, MMP-8 and MMP-9 gene polymorphisms in preterm birth

      MONIKA PANDEY SHALLY AWASTHI

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      Novel approaches to preterm births are underway building upon our prior discoveries and probing into unknown discovery pathways. The recent findings showed a high affinity of MMP-9 in serum and its polymorphisms for preterm birth. This study, which is a hospital-based case–control study, aims to investigate the association of MMP-1, MMP-8 and MMP-9 polymorphisms, and levels of MMP-9 in preterm birth. Increased level of MMP-9 was reported in cases as compared to control. The significant association of MMP-9 (-1562) CT (P = 0.001; OR = 1.44(CI = 0.97–2.14)) and TTgenotype (P = 0.05;OR = 2.6 (CI = 1.46–4.69)) were reported in preterm birth. Our findings suggest that the MMP-9 plays an important role in contributing preterm labour and this can be used as a diagnostic tool during pregnancy.

    • Signatures of positive selection on the hepatic lipase gene in human populations

      SERGIO V. FLORES CARLA F. OLIVARI LUIS FLORES PRADO

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      The hepatic lipase plays a central role in the lipid metabolism, catalyzing the hydrolysis of phospholipids, monoglycerides, diglycerides, and triglycerides, and acyl-CoA. It is also implied in the conversion of very low-density lipoprotein and intermediate density lipoprotein to low density lipoproteins. As a consequence, the gene encoding the hepatic lipase (LIPC) is associated with several diseases derived from the imbalance of lipids that are in general derived from the interaction between life styles and genetic architecture. Therefore, it is interesting to understand more about the characteristics of the microevolutionary processes affecting genes that, like LIPC, have a role in nutrition and lipid metabolism in human populations. We explored the selection signatures on LIPC in 26 populations, detecting three regions under recent positive selection.

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