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Showing papers in "Journal of Genetics in 2012"


Journal ArticleDOI
TL;DR: Structural characteristics as well as transcriptional regulation of gene expression in response to various abiotic stresses, with particular emphasis on the role of DREB1/CBF regulon in stress-responsive gene expression are focussed on.
Abstract: Drought, high salinity and low temperature are major abiotic stresses that influence survival, productivity and geographical distribution of many important crops across the globe. Plants respond to these environmental challenges via physiological, cellular and molecular processes, which results in adjusted metabolic and structural alterations. The dehydration-responsive-element-binding (DREB) protein / C-repeat binding factors (CBFs) belong to APETALA2 (AP2) family transcription factors that bind to DRE/CRT cis-element and regulate the expression of stress-responsive genes. DREB1/CBF genes, therefore, play an important role in increasing stress tolerance in plants and their deployment using transgenic technology seems to be a potential alternative in management of abiotic stresses in crop plants. This review is mainly focussed on the structural characteristics as well as transcriptional regulation of gene expression in response to various abiotic stresses, with particular emphasis on the role of DREB1/CBF regulon in stress-responsive gene expression. The recent progress related to genetic engineering of DREB1/CBF transcription factors in various crops and model plants is also summarized.

194 citations


Journal ArticleDOI
TL;DR: Rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars are tested to ascertain their genetic diversity structure to suggest their narrow adaptation in local geographical niche.
Abstract: In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination index, was used to determine subpopulation differentiation power of each marker. Phenotypic data were collected for yield and component traits. Pattern of molecular differentiation separated indica and japonica genotypes; indica genotypes had two subpopulations within. Landraces were found to have indica genome, but formed a separate subgroup with low linkage disequilibrium. The landraces further separated into distinct group in both hierarchical clustering analysis using neighbour-joining method as well as in the model based population structure analysis. Japonica and the remaining indica cultivars formed two other distinct groups. Linkage disequilibrium observed in the whole population was considerably reduced in subpopulations. Low linkage disequilibrium of landforms suggests their narrow adaptation in local geographical niche. Many population specific alleles could be identified particularly for japonica cultivars and landraces. Association analysis revealed nine marker–trait associations with three agronomic traits, of which 67% were previously reported. Although the testing landraces together with known cultivars had permitted genome-wide association mapping, the experiment offers scope to study more landraces collected from the entire geographical region for drawing more reliable information.

73 citations


Journal ArticleDOI
TL;DR: The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.
Abstract: Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n = 2x = 14), cool-season legume crop and is consumed worldwide as a rich source of protein (∼24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F2 plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.

61 citations


Journal ArticleDOI
TL;DR: A strong genetic relationship was found between protein content and grain yield, and yield-related traits and three additional QTLs with minor effects were identified in the conditional mapping.
Abstract: Grain protein content in wheat (Triticum aestivum L.) is generally considered a highly heritable character that is negatively correlated with grain yield and yield-related traits. Quantitative trait loci (QTL) for protein content was mapped using data on protein content and protein content conditioned on the putatively interrelated traits to evaluate possible genetic interrelationships between protein content and yield, as well as yield-related traits. Phenotypic data were evaluated in a recombinant inbred line population with 302 lines derived from a cross between the Chinese cultivar Weimai 8 and Luohan 2. Inclusive composite interval mapping using IciMapping 3.0 was employed for mapping unconditional and conditional QTL with additives. A strong genetic relationship was found between protein content and grain yield, and yield-related traits. Unconditional QTL mapping analysis detected seven additive QTL for protein content, with additive effects ranging in absolute size from 0.1898% to 0.3407% protein content, jointly accounting for 43.45% of the trait variance. Conditional QTL mapping analysis indicated two QTL independent from yield, which can be used in marker-assisted selection for increasing yield without affecting grain protein content. Three additional QTL with minor effects were identified in the conditional mapping. Of the three QTLs, two were identified when protein content was conditioned on yield, which had pleiotropic effects on those two traits. Conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the individual QTL level for closely correlated traits. Further, conditional QTL mapping can reveal additional QTL with minor effects that are undetectable in unconditional mapping.

54 citations


Journal ArticleDOI
TL;DR: An additional set of 607 novel SSR in 393 SSR containing sequences is reported, however, primers could be designed for only 417 potentially useful SSR, which will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.
Abstract: Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources. We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al.2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.

50 citations


Journal ArticleDOI
TL;DR: Limitations with multiparent intercross populations are that they require longer time and more resource to be generated and they are likely to show extensive segregation for developmental traits, limiting their use in the analysis of complex traits.
Abstract: Most traits of interest to medical, agricultural and animal scientists show continuous variation and complex mode of inheritance. DNA-based markers are being deployed to analyse such complex traits, that are known as quantitative trait loci (QTL). In conventional QTL analysis, F2, backcross populations, recombinant inbred lines, backcross inbred lines and double haploids from biparental crosses are commonly used. Introgression lines and near isogenic lines are also being used for QTL analysis. However, such populations have major limitations like predominantly relying on the recombination events taking place in the F1 generation and mapping of only the allelic pairs present in the two parents. The second generation mapping resources like association mapping, nested association mapping and multiparent intercross populations potentially address the major limitations of available mapping resources. The potential of multiparent intercross populations in gene mapping has been discussed here. In such populations both linkage and association analysis can be conductted without encountering the limitations of structured populations. In such populations, larger genetic variation in the germplasm is accessed and various allelic and cytoplasmic interactions are assessed. For all practical purposes, across crop species, use of eight founders and a fixed population of 1000 individuals are most appropriate. Limitations with multiparent intercross populations are that they require longer time and more resource to be generated and they are likely to show extensive segregation for developmental traits, limiting their use in the analysis of complex traits. However, multiparent intercross population resources are likely to bring a paradigm shift towards QTL analysis in plant species.

48 citations


Journal ArticleDOI
TL;DR: More details are revealed about the allocation of USSCs into the chondrocytes through identification of miRNA signature which modulates targets and pathways required for chondrogenic lineage and could provide guidelines for future clinical treatments and anti-miRNA therapies.
Abstract: Generating appropriate cartilage for clinical applications to heal skeletal tissue loss is a major health concern. In this regard, cell-based approaches offer a potential therapeutic strategy for cartilage repair, although little is known about the precise mechanism of chondrogenesis. Unrestricted somatic stem cell (USSC) is considered as a suitable candidate because of its potential for differentiating into multiple cell types. Recent studies show that microRNAs (miRNAs) are involved in several biological processes including development and differentiation. To identify the chondro-specific miRNA signature, miRNA patterns of USSCs and differentiated chondrocytes were investigated using microarrays and validation by qPCR. Prior to these analyses, chondrogenic commitment of differentiated USSCs was verified by immunocytochemistry, specific staining and evaluation of some main chondrogenic marker genes. Various in silico explorations (for both putative targets and signalling pathways) and empirical analyses (miRNA transfections followed by qPCR of some chondrogenic indicators) were carried out to support our results. Transient modulation of multiple chondro-miRs (such as mir-630, mir-624 and mir-376) with chondrocyte targets (such as TGFbR, MAP3K, collagens, SMADs and cadherins) as mediators of chondrogenic signalling pathways including cell-cell interactions, TGF-beta, and MAPK signalling suggests a mechanism for genetic induction of chondrogenic differentiation. In conclusion, this research reveals more details about the allocation of USSCs into the chondrocytes through identification of miRNA signature which modulates targets and pathways required for chondrogenic lineage and could provide guidelines for future clinical treatments and anti-miRNA therapies.

47 citations


Journal ArticleDOI
TL;DR: Introgression, inheritance and molecular mapping of a leaf rust resistance gene of Ae.
Abstract: Rusts are the most important biotic constraints limiting wheat productivity worldwide Deployment of cultivars with broad spectrum rust resistance is the only environmentally viable option to combat these diseases Identification and introgression of novel sources of resistance is a continuous process to combat the ever evolving pathogens The germplasm of nonprogenitor Aegilops species with substantial amount of variability has been exploited to a limited extent In the present investigation introgression, inheritance and molecular mapping of a leaf rust resistance gene of Ae caudata (CC) acc pau3556 in cultivated wheat were undertaken An F2 population derived from the cross of Triticum aestivum cv WL711 – Ae caudata introgression line T291-2 with wheat cultivar PBW343 segregated for a single dominant leaf rust resistance gene at the seedling and adult plant stages Progeny testing in F3 confirmed the introgression of a single gene for leaf rust resistance Bulked segregant analysis using polymorphic D-genome-specific SSR markers and the cosegregation of the 5DS anchored markers (Xcfd18, Xcfd78, Xfd81 and Xcfd189) with the rust resistance in the F2 population mapped the leaf rust resistance gene (LrAC) on the short arm of wheat chromosome 5D Genetic complementation and the linked molecular markers revealed that LrAC is a novel homoeoallele of an orthologue Lr57 already introgressed from the 5M chromosome of Ae geniculata on 5DS of wheat

46 citations


Journal ArticleDOI
TL;DR: Comparative genomics analysis of intronic miRNAs in rice and Arabidopsis provides new insight into the functions and regulatory mechanisms of intronics miRNA-carrying introns in monocots and dicots.
Abstract: MicroRNAs (miRNAs) are potent regulators of gene transcription and posttranscriptional processes. The majority of miRNAs are localized within intronic regions of protein-coding genes (host genes) and have diverse functions in regulating important cellular processes in animals. To date, few plant intronic miRNAs have been studied functionally. Here we report a comprehensive computational analysis to characterize intronic miRNAs in rice and Arabidopsis. RT-PCR analysis confirmed that the identified intronic miRNAs were derived from the real introns of host genes. Interestingly, 13 intronic miRNAs in rice and two in Arabidopsis were located within seven clusters, of which four polycistronic clusters contain miRNAs derived from different families, suggesting that these clustered intronic miRNAs might be involved in extremely complex regulation in rice. Length analysis of miRNA-carrying introns, promoter prediction and qRT-PCR analysis results indicated that intronic miRNAs are coexpressed with their host genes. Expression pattern analysis demonstrated that host genes had a very broad expression spectrum in different stages of development, suggesting the intronic miRNAs might play an important role in plant development. This comparative genomics analysis of intronic miRNAs in rice and Arabidopsis provides new insight into the functions and regulatory mechanisms of intronic miRNAs in monocots and dicots.

38 citations


Journal ArticleDOI
TL;DR: It was concluded that complementary interaction between Vrn-1 and Ppd-D1a active alleles imparted super/very-early flowering habit to spring wheats.
Abstract: Time to flowering in the winter growth habit bread wheat is dependent on vernalization (exposure to cold conditions) and exposure to long days (photoperiod). Dominant Vrn-1 (Vrn-A1, Vrn-B1 and Vrn-D1) alleles are associated with vernalizationindependent spring growth habit. The semidominant Ppd-D1a mutation confers photoperiod-insensitivity or rapid flowering in wheat under short day and long day conditions. The objective of this study was to reveal the nature of interaction between Vrn-1 and Ppd-D1a mutations (active alleles of the respective genes vrn-1 and Ppd-D1b). Twelve Indian spring wheat cultivars and the spring wheat landrace Chinese Spring were characterized for their flowering times by seeding them every month for five years under natural field conditions in New Delhi. Near isogenic Vrn-1 Ppd-D1 and Vrn-1 Ppd-D1a lines constructed in two genetic backgrounds were also phenotyped for flowering time by seeding in two different seasons. The wheat lines of Vrn-A1a Vrn-B1 Vrn-D1 Ppd-D1a, Vrn-A1a Vrn-B1 Ppd-D1a and Vrn-A1a Vrn-D1 Ppd-D1a (or Vrn-1 Ppd-D1a) genotypes flowered several weeks earlier than that of Vrn-A1a Vrn-B1 Vrn-D1 Ppd-D1b, Vrn-A1b Ppd-D1b and Vrn-D1 Ppd-D1b (or Vrn-1 Ppd-D1b) genotypes. The flowering time phenotypes of the isogenic vernalization-insensitive lines confirmed that Ppd-D1a hastened flowering by several weeks. It was concluded that complementary interaction between Vrn-1 and Ppd-D1a active alleles imparted super/very-early flowering habit to spring wheats. The early and late flowering wheat varieties showed differences in flowering time between short day and long day conditions. The flowering time in Vrn-1 Ppd-D1a genotypes was hastened by higher temperatures under long day conditions. The ambient air temperature and photoperiod parameters for flowering in spring wheat were estimated at 25 ◦ C and 12 h, respectively.

36 citations


Journal ArticleDOI
TL;DR: A novel gene delivery technique is developed, which uses magnetic nanoparticles under the influence of an oscillating magnetic array to improve transfection efficiency in hard-to-transfect cells while maintaining the inherent advantages of magnetofection.
Abstract: Cells such as mouse embryonic fibroblasts (MEFs) and human umbilical vein endothelial cells (HUVECs) used in stem cell research and endothelial cell physiology and pathology studies are difficult to transfect using ‘standard’ nonviral transfection methods. We have developed a novel gene delivery technique, which uses magnetic nanoparticles under the influence of an oscillating magnetic array. Here we report results from this technique showing significantly higher transfection efficiency in these cells compared to a static magnetic array and lipid reagents, with no effect on cell viabilities. Further in HUVECs, we report increasing gene transfection and expression with increasing oscillation frequencies and in serum-starved conditions. Many highly differentiated mammalian cells like neurons or leucocytes, are resistant to the introduction of foreign genes. Various techniques have been developed over the decades to overcome this problem, from use of the relatively cheap lipid-based reagents to the costly nucleofection methods. Magnetofection technology is an effective nonviral transfection tool for the introduction of nucleic acids into mammalian cells. This involves, first association of nucleic acids with polymer-coated superparamagnetic iron oxide nanoparticles. Next, these complexes are subjected to a proprietary novel, strong high-gradient magnet array underlying the cell culture plate that pulls the complexes onto the surface of the cells (Plank et al. 2003; Dobson 2006). In order to improve transfection efficiency in hard-to-transfect cells while maintaining the inherent advantages of magnetofection (rapid transfection and high cell viability), we have introduced a linear oscillating motion to the magnet array to

Journal ArticleDOI
Vijay Rana1, Kalpana Thakur1, Ritu Sood1, Varun Sharma1, T. Sharma 
TL;DR: Twenty-seven accessions, collected from different ecological regions and altitudes in the northwestern Himalayan region of India ranging from 400 to 1300 m above mean sea level, were grown for morphophysiological characteriza-tion and subjected to molecular diversity analysis using RAPD and ISSR markers.
Abstract: Twenty-seven accessions, collected from different ecologicalregions and altitudes in the northwestern Himalayan regionof India ranging from 400 to 1300 m above mean sea level(table 1), were grown for morphophysiological characteriza-tion Thirty-seven accessions (including 10 more accessionsof unknown origin) were subjected to molecular diversityanalysis using RAPD and ISSR markersThe field experiment was laid out in a completely ran-domized block design (CRBD) with three replications Eachreplication comprised of 50 plants per accession The dataon 15 randomly selected plants were recorded on variousmorphophysiological parameters viz plant length (cm), stemdiameter (mm), stomatal density (mm

Journal ArticleDOI
TL;DR: Molecular cytogenetic and sequence analyses of bacterial artificial chromosomes (BACs) flanking M locus indicate that the BAC contain highly repetitive sequences that localize to centromeric and pericentromeric locations on all asparagus chromosomes.
Abstract: Garden asparagus (Asparagus officinalis L.) is an economically important plant with 2n = 2x = 20 chromosomes and a haploid genome size of 1323 Mb (Bennett and Leitch 2003). The karyotype of asparagus consists of five long (L), one medium (M) and four small (S) chromosomes (Löptien 1976). Plants of this dioecious species differ in producing either male or female flowers. The sexual dimorphism in asparagus is controlled by a region located on a pair of homomorphic sex chromosomes (chromosome L5) (Löptien 1979) termed the M locus (Flory 1932; Uno et al. 2002). Maleness is dominant with males normally heterogametic (Mm) and females homogametic (mm). Supermales (MM) can be produced from anther culture or from rarely occurring andromonoecious plants. The identification of chromosome L5 is important for studying sex chromosome evolution in asparagus. However, it was observed that the sex chromosome pair is homomorphic: X and Y chromosomes do not differ in morphology. Telgmann-Rauber et al. (2007) tried to clone the region determining sex in asparagus from its position in the genome. Molecular cytogenetic and sequence analyses of bacterial artificial chromosomes (BACs) flanking M locus indicate that the BAC contain highly repetitive sequences that localize to centromeric and pericentromeric locations on all asparagus chromosomes. However, the L5 chromosome could not be distinguished by BAC-FISH (Telgmann-Rauber et al. 2007). Recently, FISH has become a powerful and useful tool for the direct detection of specific DNA in genome. In this technique, ribosomal DNA genes (45S and 5S rDNA) are commonly used as markers for the physical mapping of plant chromosomes to analyse genomic organization (Nakayama et al. 2001; Lan et al. 2006; Grabowska-Joachimiak et al.

Journal ArticleDOI
TL;DR: The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.
Abstract: Improved Catharanthus roseus cultivars are required for high yields of vinblastine, vindoline and catharanthine and/or serpentine and ajmalicine, the pharmaceutical terpenoid indole alkaloids. An approach to derive them is to map QTL for terpenoid indole alkaloids yields, identify DNA markers tightly linked to the QTL and apply marker assisted selection. Towards the end, 197 recombinant inbred lines from a cross were grown over two seasons to characterize variability for seven biomass and 23 terpenoid indole alkaloids content-traits and yield-traits. The recombinant inbred lines were genotyped for 178 DNA markers which formed a framework genetic map of eight linkage groups (LG), spanning 1786.5 cM, with 10.0 cM average intermarker distance. Estimates of correlations between traits allowed selection of seven relatively more important traits for terpenoid indole alkaloids yields. QTL analysis was performed on them using single marker (regression) analysis, simple interval mapping and composite interval mapping procedures. A total of 20 QTL were detected on five of eight LG, 10 for five traits on LG1, five for four traits on LG2, three for one trait on LG3 and one each for different traits on LG three and four. QTL for the same or different traits were found clustered on three LG. Co-location of two QTL for biomass traits was in accord of correlation between them. The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.

Journal ArticleDOI
TL;DR: The results suggest that O. paricola may be a complex of species that have been separated for some time, and are in the process of morphological and molecular differentiation as a consequence of reproductive isolation at the geographic and chromosomal levels.
Abstract: The rodent genus Oecomys (Sigmodontinae) comprises ~16 species that inhabit tropical and subtropical forests in Central America and South America. In this study specimens of Oecomys paricola Thomas, 1904 from Belem and Marajo island, northern Brazil, were investigated using cytogenetic, molecular and morphological analyses. Three karyotypes were found, two from Belem (2n = 68, fundamental number (FN) = 72 and 2n = 70, FN = 76) and a third from Marajo island (2n = 70, FN = 72). No molecular or morphological differences were found between the individuals with differing cytotypes from Belem, but differences were evident between the individuals from Belem and Marajo island. Specimens from Belem city region may represent two cryptic species because two different karyotypes are present in the absence of significant differences in morphology and molecular characteristics. The Marajo island and Belem populations may represent distinct species that have been separated for some time, and are in the process of morphological and molecular differentiation as a consequence of reproductive isolation at the geographic and chromosomal levels. Thus, the results suggest that O. paricola may be a complex of species.

Journal ArticleDOI
TL;DR: It is shown that fluorescence in situ hybridization (FISH) physical mapping of rDNA sites is a valuable method to gain insight into the genome in Chrysanthemum and related genera of the Anthemideae and the overlapping of 5S and 45S rDNA loci is found.
Abstract: The present study has shown that fluorescence in situ hybridization (FISH) physical mapping of rDNA sites is a valuable method to gain insight into the genome in Chrysanthemum and related genera of the Anthemideae. FISH signals revealed that 45S rDNA sites were localized on the terminal regions of the sat-chromosomes, except in one case where the signals were detected on the subterminal region. However, 5S rDNA was distributed among the terminal, subterminal and / or interstitial regions. The results show the colocalization of the 5S and 45S rDNA in case of Argyranthemum, Artemisia, Leucanthemmilla, Nipponanthemum and Tanacetum. The interesting outcome of this study is the overlapping of 5S and 45S rDNA loci. Therefore, the species were meaningfully distinctive and divided into four groups from the perspective of molecular cytogenetics, which could be a valuable tool for generic genome identification. Chrysanthemum and 26 other genera, has been taxonomically placed in the subtribe Chrysantheminae O. Hoffm. (Shih and Fu 1983) or distributed in different subtribes in the tribe Anthemideae Cass (family Asteraceae, subfamily Asteroideae) (Bremer and Humphries 1993). The principal taxonomic problems within the tribe are entirely of relationships and circumscription among the genera (Bremer and Humphries 1993). In plant evolutionary studies and breeding there is often a need to discriminate between the genomes of closely related genera or species and to find the ancestors, especially polyploids (Abd El-Twab and Kondo 2003a). In land plants studied so far, ribosomal genes are organized into two highly repeated gene families that occur in tandemly

Journal ArticleDOI
TL;DR: Embryo additive and dominant effects from the tetraploid embryo genome, as well as maternal additive effects fromThe tetraspecific recombinant inbred lines which were derived from the hybrid of two parents were found to be significant contributors to genetic variation in cottonseed oil content.
Abstract: Oil content in cottonseed is a major quality trait which when improved through breeding could enhance the competitiveness of cottonseed oil among other vegetable oils. Cottonseed oil content is a quantitative trait controlled by genes in the tetraploid embryo and tetraploid maternal plant genomes, and the knowledge of quantitative trait loci (QTLs) and the genetic effects related to oil content in both genomes could facilitate the improvement in its quality and quantity. However, till date, QTL mapping and genetic analysis related to this trait in cotton have only been conducted in the tetraploid embryo genome. In the current experiment, an IF(2) population of cottonseed kernels from the random crossing of 188 intraspecific recombinant inbred lines which were derived from the hybrid of two parents, HS46 and MARCABUCAG8US-1-88, were used to simultaneously locate QTLs for oil content in the embryo and maternal plant genomes. The four QTLs found to be associated with oil content in cottonseed were: qOC-18-1 on chromosome 18; qOC-LG-11 on linkage group 11; qOC-18-2 on chromosome 18; and qOC-22 on chromosome 22. At a high selection threshold of 0.05, there was strong evidence linking the QTLs above the oil content in cottonseed. Embryo additive and dominant effects from the tetraploid embryo genome, as well as maternal additive effects from the tetraploid maternal plant genome were found to be significant contributors to genetic variation in cottonseed oil content.

Journal ArticleDOI
TL;DR: A set of microsatellites (SSRs) markers were developed for pomegranate (Punica granatum L.) through bioinformatic mining of GenBank public database, revealing a distinctive genetic background of the accessions from east–central China.
Abstract: A set of microsatellites (SSRs) markers were developed for pomegranate (Punica granatum L.) through bioinformatic mining of GenBank public database (http://www.ncbi. nlm.gov/genbank/). In total, 787 pomegranate expressed sequence tag (EST) sequences were downloaded from GenBank and assembled with CAP 3, producing 415 unigenes that contained 46 contigs and 369 singletons. Eighty bitype to penta-type SSRs were obtained from these unigenes, among which 59 EST-SSR primer pairs were successfully designed. Twenty-eight primer pairs were selected as representative samples for evaluating usability and 18 (64.3%) were usable markers. Fifteen of the 18 markers revealed polymorphism among 42 pomegranate accessions, detecting 2–5 alleles (mean = 2.80). The observed heterozygosity (Ho) and polymorphic information content (PIC) values ranged from 0.119 to 0.619 (mean = 0.381) and from 0.091 to 0.656 (mean = 0.402), respectively. Genetic diversity of the accession set was elucidated using the newly-developed markers, revealing a distinctive genetic background of the accessions from east–central China. The EST-SSR markers developed in this study will provide more SSR markers available for genetic studies in pomegranate. The genus Punica consists of two species, P. granatum and P. protopunica, of which P. granatum, pomegranate, is a predominant species and has been widely cultivated in various areas for thousands of years, while P. protopunica is only endemic to the Island of Socotra (Stover and Mercure 2007). Pomegranate is usually cultivated for its edible fruits and/or for decorative purposes. In the last few years, it has been found that pomegranate fruit acts as antioxidant, antidiabetic and hypolipidemic, and shows antibacterial, antiinflamma-

Journal ArticleDOI
TL;DR: This review is an attempt to compile the genetic factors reported to modify the development of Trichotillomania.
Abstract: Trichotillomania (TTM), an obsessive–compulsive spectrum disorder (OCSD), is a psychiatric condition characterized by repetitive hair pulling. Evidence from family and twin studies suggest a heritable link of TTM. Functional polymorphisms in genes involved in neuronal pathways might influence the susceptibility to TTM. This review is an attempt to compile the genetic factors reported to modify the development of TTM.

Journal ArticleDOI
TL;DR: It is concluded that large, well-designed studies of common polymorphisms in DNA repair genes are needed to establish the overall understanding of possible relationships between DNA repair gene polymorphisms and development of HNSCC.
Abstract: Genetic polymorphisms in some DNA repair proteins are associated with a number of malignant transformations like head and neck squamous cell carcinoma (HNSCC). Xeroderma pigmentosum group D (XPD) and X-ray repair cross-complementing proteins 1 (XRCC1) and 3 (XRCC3) genes are involved in DNA repair and were found to be associated with HNSCC in numerous studies. To establish our overall understanding of possible relationships between DNA repair gene polymorphisms and development of HNSCC, we surveyed the literature on epidemiological studies that assessed potential associations with HNSCC risk in terms of gene–environment interactions, genotype-induced functional defects in enzyme activity and/or protein expression, and the influence of ethnic origin on these associations. We conclude that large, well-designed studies of common polymorphisms in DNA repair genes are needed. Such studies may benefit from analysis of multiple genes or polymorphisms and from the consideration of relevant exposures that may influence the likelihood of HNSCC when DNA repair capacity is reduced.

Journal ArticleDOI
TL;DR: Investigation of the association of five variants at rs7896340, rs7901695,rs7903146, rs12255372, and rs11196205 of TCF7L2 with T2D by high resolution melting analysis found associations between SNP genotype and risk of type 2 diabetes.
Abstract: Type 2 diabetes (T2D) is a complex disorder caused by the interaction between genetic predisposition and environmental factors (Freeman and Cox 2006). Recent progress in genetic and genomic research of T2D has shown that genes involved in pancreatic beta-cell development and function are involved in pathogenesis of T2D. Identification of these genes will provide a better understanding of pathogenesis, which may lead to the improvement of diagnosis, treatment, and prevention of this increasingly prevalent and costly condition. Genomewide linkage analysis has revealed that a region on chromosome 10q contained a T2D susceptibility gene, which was later ascribed to possess intronic variations of the transcription factor 7-like 2 (TCF7L2). The variation of TCF7L2 was associated with a two-fold increase of T2D risk in the Icelandic population (Grant et al. 2006). This association has been replicated in cohorts of European, Asian and African descent. The precise mechanism by which variations of TCF7L2 predispose to T2D is not clear. It has been suggested that TCF7L2 encodes a transcription factor that is expressed in foetal pancreas and involved in Wnt signalling pathway through the regulation of glucagon-like peptide (GLP-1), which has a primary role in glucose homeostasis (Cauchi et al. 2006). Since there is no previous genetic study describing the TCF7L2 variation on T2D risk in Thais, we therefore investigated the association of five variants at rs7896340, rs7901695, rs7903146, rs12255372, and rs11196205 of TCF7L2 with T2D by high resolution melting analysis. The associations between SNP genotype,

Journal ArticleDOI
TL;DR: The aim of this study was to investigate the association of these four polymorphisms and haplotypes with significant coronary stenosis, coronary artery disease (CAD) and lipid parameters in a Tunisian population.
Abstract: Numerous studies have shown that apolipoprotein B (APOB) is a better predictor of cardiovascular disease (CVD) risk than low-density lipoprotein C (LDL-C). We studied the following four polymorphisms in APOB gene: 5′ins/del polymorphism (rs17240441), 3′VNTR polymorphism, XbaI polymorphism (rs693) and the EcoRI polymorphism (rs1042031). The association of these four polymorphisms with lipid variation and CVD risk have been controversial (Bøhn et al. 1994; Pan et al. 1998; Duman et al. 2005; Kallel et al. 2007; Rebhi et al. 2008). The aim of this study was to investigate the association of these four polymorphisms and haplotypes with significant coronary stenosis (SCS), coronary artery disease (CAD) and lipid parameters in a Tunisian population.

Journal ArticleDOI
TL;DR: The results indicate that an evolutionary trade-off often exists between any functional change under either positive or relaxed selection and the need to compensate for failures due to degenerative mutations, thereby guaranteeing the reliability of protein production.
Abstract: Gene duplicates have the inherent property of initially being functionally redundant. This means that they can compensate for the effect of deleterious variation occurring at one or more sister sites. Here, I present data bearing on evolutionary theory that illustrates the manner in which any functional adaptation in duplicate genes is markedly constrained because of the compensatory utility provided by a sustained genetic redundancy. Specifically, a two-locus epistatic model of paralogous genes was simulated to investigate the degree of purifying selection imposed, and whether this would serve to impede any possible biochemical innovation. Three population sizes were considered to see if, as expected, there was a significant difference in any selection for robustness. Interestingly, physical linkage between tandem duplicates was actually found to increase the probability of any neofunctionalization and the efficacy of selection, contrary to what is expected in the case of singleton genes. The results indicate that an evolutionary trade-off often exists between any functional change under either positive or relaxed selection and the need to compensate for failures due to degenerative mutations, thereby guaranteeing the reliability of protein production.

Journal ArticleDOI
TL;DR: The mitochondrial genome (mitogenome) of the quiet-calling katydids, Xizicus fascipes, was sequenced and Phylogenetic analysis found the monophyly of Conocephalinae was interrupted by Elimaea cheni from Phaneropterinae; and Meconematinee was the most basal group among these five subfamilies.
Abstract: To help determine whether the typical arthropod arrangement was a synapomorphy for the whole Tettigoniidae, we sequenced the mitochondrial genome (mitogenome) of the quiet-calling katydids, Xizicus fascipes (Orthoptera: Tettigoniidae: Meconematinae). The 16,166-bp nucleotide sequences of X. fascipes mitogenome contains the typical gene content, gene order, base composition, and codon usage found in arthropod mitogenomes. As a whole, the X. fascipes mitogenome contains a lower A+T content (70.2%) found in the complete orthopteran mitogenomes determined to date. All protein-coding genes started with a typical ATN codon. Ten of the 13 protein-coding genes have a complete termination codon, but the remaining three genes (COIII, ND5 and ND4) terminate with incomplete T. All tRNAs have the typical clover-leaf structure of mitogenome tRNA, except for tRNA Ser(AGN), in which lengthened anticodon stem (9 bp) with a bulged nuleotide in the middle, an unusual T-stem (6 bp in constrast to the normal 5 bp), a mini DHU arm (2 bp) and no connector nucleotides. In the A+T-rich region, two (TA)n conserved blocks that were previously described in Ensifera and two 150-bp tandem repeats plus a partial copy of the composed at 61 bp of the beginning were present. Phylogenetic analysis found: i) the monophyly of Conocephalinae was interrupted by Elimaea cheni from Phaneropterinae; and ii) Meconematinae was the most basal group among these five subfamilies.

Journal ArticleDOI
TL;DR: Giant binucleate oocytes may be responsible for the development of digynic triploidy whereas the currently available data do not support a role of conjoined oocytes in producing dizygotic twins, mosaicism, chimaeras or tetraploidies, but more information on the maturity and fertilizability of oocytes from binovular follicles is needed.
Abstract: Normal development of a fertilizable female gamete emanates from a follicle containing only one oocyte that becomes haploid after first meiotic division. Binovular follicles including two oocytes and binucleate giant oocytes that are diploid after first meiosis constitute notable exceptions from this rule. Data provided by programmes of human-assisted reproduction on the occurrence of both phenomena have been reviewed to evaluate possible implications for the formation of genetic abnormalities. To exclude confusion with oocytes aspirated from two adjacent individual follicles, true binovularity has been defined as inclusion of two oocytes within a common zona pellucida or their fusion in the zonal region. A total of 18 conjoined oocytes have been reported and one of the oocyte was normally fertilized in seven cases. Simultaneous fertilization of both female gametes occurred only once. No pregnancy was achieved after transfer of an embryo from a binovular follicle. Binucleate giant oocytes have been observed sporadically but a few reports suggest an incidence of up to 0.3% of all gametes retrieved. Extensive studies performed by two independent centres demonstrated that giant oocytes are diploid at metaphase II, can undergo fertilization in vitro with formation of two or three pronuclei and develop into triploid zygotes and triploid or triploid/mosaic embryos. In summary, giant binucleate oocytes may be responsible for the development of digynic triploidy whereas the currently available data do not support a role of conjoined oocytes in producing dizygotic twins, mosaicism, chimaeras or tetraploidy. However, more information on the maturity and fertilizability of oocytes from binovular follicles is needed. Future studies should also evaluate a possible impact of pharmaceutical and environmental oestrogens on the formation of multiovular follicles.

Journal ArticleDOI
TL;DR: Reanalysed the ITS sequences used by different research teams to reveal the underlying patterns of their different results, and the risk of incorporating ITS paralogues in plant evolutionary studies that can distort the phylogenetic signal should caution molecular systematists.
Abstract: Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evolution. Concerted evolution leads to intragenomic uniformity of repeats even between loci on nonhomologous chromosomes. However, a number of studies have shown that the ITS polymorphism within individuals is quite common. The molecular systematics of Bambusinae and related species were recently assessed by different teams using independently generated ITS sequences, and the results disagreed in some remarkable features. Here we compared the ITS sequences of the members of Bambusa s. l., the genera Dendrocalamus, Dinochloa, Gigantochloa, Guadua, Melocalamus, Monocladus, Oxytenanthera, Thyrsostachys, Pleioblastus, Pseudosasa and Schizostachyum. We have reanalysed the ITS sequences used by different research teams to reveal the underlying patterns of their different results. After excluding the sequences suspected to represent paralogous loci, a phylogenetic analysis of the subtribe Bambusinae species were performed using maximum parsimony and maximum-likelihood methods. The implications of the findings are discussed. The risk of incorporating ITS paralogues in plant evolutionary studies that can distort the phylogenetic signal should caution molecular systematists.

Journal ArticleDOI
TL;DR: Risk factors were calculated by mean ± SD, percentage and power calculation, and only male patients were considered.
Abstract: Samples 150 150 100% Age (years) 57.75±11.59 56.21±14.93 100% Blood pressure-systolic (mmHg) 134±26.63 123±4.75 100% Blood pressure-diastolic (mmHg) 85±15.78 80.73±2.61 98% Body mass index (BMI) (kg/m2) 25.33±3.2 23.83±3.10 95% Diabetes (%) 84/150 (56%) nil 100% Smoking∗ (%) 84/98 (85%) nil 100% Nonvegetarian diet (%) 87/150 (58%) 64/150 (42%) 78% ∗Only male patients. Risk factors were calculated by mean ± SD, percentage and power calculation.

Journal ArticleDOI
TL;DR: The common C282Y mutation in hereditary haemochromatosis (HH) patients of European origin is absent in Indians and the haplotypes associated with H63D mutation in north Indians are investigated.
Abstract: The common C282Y mutation (HFE gene) in hereditary haemochromatosis (HH) patients of European origin is absent in Indians. The frequency of the second common missense H63D (187C→G) mutation of HFE gene ranges from 9.1–13.9% in the general population. In this study we investigated the haplotypes associated with H63D mutation in north Indians. Allele and haplotype frequencies were counted, and haplotypes were generated based on expectation– maximization (EM) algorithm using Haploview software (http://www.broad.mit.edu/mpg/haploview/). HH affects predominantly people of northern European origin and is often described as a ‘Celtic mutation’ that originated in a Celtic population in central Europe and spread west and north by population movement. There are suggestions that Viking migrations were largely responsible for the distribution of the disease (Lucotte 1998). The common form of HH is caused by the Cys282Tyr mutation (C282Y; 845G-A) of the HFE gene which occurred in mainland Europe before 4000 BC (Distante et al. 2004). The second common missense mutation in the HFE gene is a C to G transversion (187C-G) which causes a histidine to aspartic acid substitution at amino acid position 63 in the unprocessed protein (H63D) (Feder et al. 1996). Coinheritance of H63D mutation with the C282Y mutation is a known risk factor for iron overload (Pointon et al. 2000) The H63D mutation is widely distributed in nearly all populations examined with a variable allele frequency and is believed to have occurred earlier than the C282Y mutation (Merryweather-Clarke et al. 1997; Rochette et al. 1999). The allele frequency for H63D in most European countries varies between 10 and 20%, with

Journal ArticleDOI
TL;DR: B ligand (RANKL), its receptor RANK and osteo-protegerin (OPG) system is involved in plaque instability and rupture by inducing plaquecalcification (Panizo 2016).
Abstract: B ligand (RANKL), its receptor RANK and osteo-protegerin (OPG) are members of tumour necrosis fac-tor (TNF) superfamily and they form a key cytokine triadinvolved in bone metabolism, specifically osteoclastogen-esis (Khosla 2001; Boyce and Xing 2008). Recent stud-ies have demonstrated that OPG/RANK/RANKL system isinvolved in plaque instability and rupture by inducing plaquecalcification (Panizo

Journal ArticleDOI
TL;DR: The affected child typically presents in the first year of life with failure to thrive, rickets, a protuberantabdomen due to hepatomegaly secondary to glucose accumu-lation and nephromegaly, glucose and galactose intolerance, fasting hypoglycemia, and characteristic tubular nephropathy.
Abstract: . 2012). The disease was firstdescribed by G. Fanconi and Horst Bickel (Fanconi andBickel 1949). The affected child typically presents in the1st year of life with failure to thrive, rickets, a protuberantabdomen due to hepatomegaly secondary to glucose accumu-lation and nephromegaly, glucose and galactose intolerance,fasting hypoglycemia, and characteristic tubular nephropathy(Yoo