Showing papers in "Journal of Genetics in 2013"

Gene duplication as a major force in evolution.

Abstract: Gene duplication is an important mechanism for acquiring new genes and creating genetic novelty in organisms. Many new gene functions have evolved through gene duplication and it has contributed tremendously to the evolution of developmental programmes in various organisms. Gene duplication can result from unequal crossing over, retroposition or chromosomal (or genome) duplication. Understanding the mechanisms that generate duplicate gene copies and the subsequent dynamics among gene duplicates is vital because these investigations shed light on localized and genomewide aspects of evolutionary forces shaping intra-specific and inter-specific genome contents, evolutionary relationships, and interactions. Based on whole-genome analysis of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for creation of many important developmental and regulatory genes found in extant angiosperm genomes. Recent studies also provide strong indications that even yeast (Saccharomyces cerevisiae), with its compact genome, is in fact an ancient tetraploid. Gene duplication can provide new genetic material for mutation, drift and selection to act upon, the result of which is specialized or new gene functions. Without gene duplication the plasticity of a genome or species in adapting to changing environments would be severely limited. Whether a duplicate is retained depends upon its function, its mode of duplication, (i.e. whether it was duplicated during a whole-genome duplication event), the species in which it occurs, and its expression rate. The exaptation of preexisting secondary functions is an important feature in gene evolution, just as it is in morphological evolution.

Genetic polymorphism in FOXP3 gene: imbalance in regulatory T-cell role and development of human diseases

Abstract: The FOXP3 gene encodes a transcription factor thought to be important for the development and function of regulatory T cells (Treg cells). These cells are involved in the regulation of T cell activation and therefore are essential for normal immune homeostasis. Signals from microenvironment have a profound influence on the maintenance or progression of diseases. Thus, Tregs have an important marker protein, FOXP3, though it does not necessarily confer a Treg phenotype when expressed. FOXP3 polymorphisms that occur with high frequency in the general populations have been studied in common multifactorial human diseases. Dysfunction of FOXP3 gene product could result in lack of Treg cells and subsequently chronically activated CD4+ T cells which express increased levels of several activation markers and cytokines, resulting in some autoimmune diseases. In contrast, high Treg levels have been reported in peripheral blood, lymph nodes, and tumour specimens from patients with different types of cancer. The present study discusses the polymorphisms located in intron, exon and promoter regions of FOXP3 which have already been investigated by many researchers. FOXP3 has received considerable attention in attempts to understand the molecular aspect of Treg cells. Therefore, in the present study, the relationship between genetic polymorphism of FOXP3 in Treg-cell role and in disease development are reviewed considering the interactive effect of genetic factors.

Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.)

Abstract: Salinity tolerance in rice is critical at reproductive stage because it ultimately determines grain yield. An F2 mapping population derived from a Sadri/FL478 cross was exposed to saline field conditions (6–8 dS m − 1) after the active tillering stage to identify reproductive stage specific QTLs for salinity tolerance. Genetic linkage map was constructed using 123 microsatellite markers on 232 F2 progenies. Totally 35 QTLs for 11 traits under salinity stress were detected with LOD > 3, out of which 28 QTLs that explained from 5.9 to 30.0% phenotypic variation were found to be significant based on permutation test. Three major QTL clusters were found on chromosomes 2 (RM423–RM174), 4 (RM551–RM518) and 6 (RM20224–RM528) for multiple traits under salinity stress. Both parental lines contributed additively for QTLs identified for the yield components. A majority of the QTLs detected in our study are reported for the first time for reproductive stage salinity stress. Fine-mapping of selected putative QTLs will be the next step to facilitate marker-assisted backcrossing and to detect useful genes for salinity tolerance at the reproductive stage in rice.

Assessment of genetic diversity in Indian rice germplasm ( Oryza sativa L.): use of random versus trait-linked microsatellite markers

Abstract: Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-a-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer’s varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI’s Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm.

Two P5CS genes from common bean exhibiting different tolerance to salt stress in transgenic Arabidopsis

Abstract: Many plants accumulate proline in response to salt stress. Δ-pyrroline-5-carboxylate synthetase (P5CS) is the rate-limiting enzyme in proline biosynthesis in plants. Plasmid DNA (pCHF3-PvP5CS1 and pCHF3-PvP5CS2) containing the selectable neomycin phosphotransferase gene for kanamycin resistance and Phaseolus vulgaris P5CS (PvP5CS1 and PvP5CS2) cDNA was introduced into Arabidopsis plants using Agrobacterium-mediated gene transfer. Southern blot, northern blot and RT-PCR analyses demonstrated that the foreign genes were integrated into Arabidopsis chromosomal DNA and expressed. Single-gene transformants were analysed in this study. Transgenic plants expressed higher levels of PvP5CS1 and PvP5CS2 transcripts under salt stress conditions than under normal conditions. When treated with 0, 100 and 200 mM NaCl, the average proline content in leaves of transgenic plants was significantly higher (P < 0.01) than control plants. The average relative electrical conductivity (REC) of transgenic lines was significantly lower (P < 0.01) than control plants under salt stress condition. Biomass production of transgenic lines was significantly higher (P < 0.05) than control plants under 200 mM NaCl stress treatment. These results indicated that introducing PvP5CS1 and PvP5CS2 cDNA into transgenic Arabidopsis caused proline overproduction, increasing salt tolerance. Although the expression of PvP5CS1 in L4 lines and PvP5CS2 in S4 lines was the same under salt stress condition, the S4 lines accumulated 1.6 and 1.9 times more proline than the L4 lines under 100 and 200 mM NaCl treatments, respectively. The REC of S4 plants was 0.5 (100 mM NaCl) and 0.6 times (200 mM NaCl) that of L4 plants. The biomass production of S4 plants was 1.6 times (200 mM NaCl) more than in L4 plants. Total P5CS enzyme activity of S4 was significantly higher than that of L4. These results implied that the PvP5CS2 protein had stronger capacity to catalyze proline synthesis than PvP5CS1 under salt stress condition.

Conditional and unconditional QTL mapping of drought-tolerance-related traits of wheat seedling using two related RIL populations

Abstract: For discovering the quantitative trait loci (QTLs) contributing to early seedling growth and drought tolerance during germination, conditional and unconditional analyses of 12 traits of wheat seedlings: coleoptile length, seedling height, longest root length, root number, seedling fresh weight, stem and leaves fresh weight, root fresh weight, seedling dry weight, stem and leaves dry weight, root dry weight, root to shoot fresh weight ratio, root-to-shoot dry weight ratio, were conducted under two water conditions using two F8:9 recombinant inbred line (RIL) populations. The results of unconditional analysis are as follows: 88 QTLs accounting for 3.33–77.01% of the phenotypic variations were detected on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B and 7D. Among these QTLs, 19 were main-effect QTLs with a contribution rate greater than 10%. The results of the conditional QTL analysis of 12 traits under osmotic stress on normal water conditions were as follows: altogether 22 QTLs concerned with drought tolerance were detected on chromosomes 1B, 2A, 2B, 3B, 4A, 5D, 6A, 6D, 7B, and 7D. Of these QTLs, six were main-effect QTLs. These 22 QTLs were all special loci directly concerned with drought tolerance and most of them could not be detected by unconditional analysis. The finding of these QTLs has an important significance for fine-mapping technique, map-based cloning, and molecular marker-assisted selection of early seedling traits, such as growth and drought tolerance.

Role of Notch signalling pathway in cancer and its association with DNA methylation

Abstract: The Notch signalling pathway is an evolutionarily conserved cell signalling pathway involved in the development of organisms as diverse as humans and fruit flies. It plays a pivotal role in cell fate determination. Dysregulated Notch signalling is oncogenic, inhibits apoptosis and promotes cell survival. Abnormal Notch signalling is seen in many cancers like T-cell acute lymphoblastic leukaemia, acute myeloid leukaemia and cancers of the breast, cervix, colon, pancreas, skin and brain. Inhibition of Notch signalling leads to growth arrest and differentiation in those cells in which Notch pathway is activated and this represents a new target for cancer therapy. Cancer develops from genome defects, including both genetic and epigenetic alterations. Epigenetics deals with heritable changes in gene function that occur without a change in the DNA sequence. Among various epigenetic alterations such as acetylation, phosphorylation, ubiquitylation and sumoylation, promoter region methylation is considered as an important component in cancer development. Epigenetic alterations can be used as biomarkers in screening, detection, diagnosis, staging and risk stratification of various cancers. DNA methylation can be therapeutically reversed and demethylating drugs have proven to be promising in cancer treatment. This review focusses on the methylation status of genes in Notch signalling pathway from various cancers and how this epigenetic alteration can be used as a biomarker for cancer diagnosis and subsequent treatment.

Genotyping of the k-casein and β-lactoglobulin genes in Chinese Holstein, Jersey and water buffalo by PCR-RFLP.

Abstract: Since the discovery of alleles A and B of β-lactoglobulin in cattle, genetic polymorphism in milk proteins has raised great interest in animal breeding and dairy industry, due to the relationship between milk proteins and milk production traits, composition, and quality (Aschaffenburg and Drewry 1955; Caroli et al. 2004; De Marchi et al. 2008). The caseins (αs1, αs2, β and κ) and whey proteins (α-lactalbumin and β-lactoglobulin) of bovine milk all exhibit genetic polymorphism. Among them, κ-casein and β-lactoglobulin are the most important and highly studied protein genes. As of the writing of this report, 11 variants have been described in cattle for the κ-casein gene: A, B, C, E, F1, F2, G1, G2, H, I and J (Farrell et al. 2004). In addition, at least 11 variants are known for β-lactoglobulin, of which, A and B variants are most common. The variants of κ-casein affect casein content, protein content and cheese yield, as well as curd firmness, and β-lactoglobulin is significantly associated with fat, protein, casein, total solid content and cheese yield (Celik 2003; Hallen et al. 2008). Studies have been conducted to determine the frequencies of genetic variants of milk proteins in different cattle breeds (Erhardt 1996; Vohra et al. 2006). However, few studies have been performed in China, particularly involving the water buffalo. More than 23 million water buffalo are raised in China, include Murrah, Nili-Ravi, hybrids of these with local buffalo and local swamp buffalo. The predominant local breed is the swamp buffalo; however, during recent years, the Murrah and Nili-Ravi water buffalo have been introduced from India and Pakistan. Over the years, the Chinese government invested heavily in cross breeding, genetic modification, and product development of the buffalo in order

Genomewide association study identifies no major founder variant in Caucasian moyamoya disease

Abstract: Moyamoya disease (MMD) is an idiopathic cerebrovascular occlusive-stenosis disorder at the terminal portion of internal carotid arteries and its main branches, accompanied by collateral vascular networks at the base of the circle of Willis (Takeuchi and Shimizu 1957; Suzuki and Takaku 1969). MMD has the highest prevalence in East Asian countries and a low prevalence in European countries (Goto and Yonekawa 1992; Kuroda and Houkin 2008). We have found that the p.R4810K variant in the ring finger protein 213 (RNF213) is a major founder susceptibility gene for East Asian MMD (Liu et al. 2010, 2011). In this study, we aimed to test whether there is a major founder susceptibility gene for Caucasian MMD using a genomewide association study (GWAS). We demonstrated that there was no major founder variant in Caucasian MMD as it is in East Asian MMD. We identified several suggestive association regions for Caucasian MMD.

Complete sequence of the mitochondrial genome of Odontamblyopus rubicundus (Perciformes: Gobiidae): genome characterization and phylogenetic analysis

Abstract: Odontamblyopus rubicundus is a species of gobiid fishes, inhabits muddy-bottomed coastal waters. In this paper, the first complete mitochondrial genome sequence of O. rubicundus is reported. The complete mitochondrial genome sequence is 17119 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a control region and an L-strand origin as in other teleosts. Most mitochondrial genes are encoded on H-strand except for ND6 and seven tRNA genes. Some overlaps occur in protein-coding genes and tRNAs ranging from 1 to 7 bp. The possibly nonfunctional L-strand origin folded into a typical stem-loop secondary structure and a conserved motif (5′-GCCGG-3′) was found at the base of the stem within the tRNACys gene. The TAS, CSB-2 and CSB-3 could be detected in the control region. However, in contrast to most of other fishes, the central conserved sequence block domain and the CSB-1 could not be recognized in O. rubicundus, which is consistent with Acanthogobius hasta (Gobiidae). In addition, phylogenetic analyses based on different sequences of species of Gobiidae and different methods showed that the classification of O. rubicundus into Odontamblyopus due to morphology is debatable.

Molecular diversity and phylogeny in geographical collection of chickpea (Cicer sp.) accessions.

Abstract: Chickpea (Cicer arietinum L.) is the third most important pulse crop in the world and India is the largest producer of this crop. Nevertheless, its yield in India is low (0.7 tone per hectare (t/ha)) as compared to Australia, Egypt, Israel and Italy (1 t/ha) (FAOSTAT 2008, http://faostat.fao.org/). There has been a significant change in the scenario of chickpea cultivation in India during the past three decades. The expansion of irrigated agriculture in northern India has led to displacement of chickpea with wheat in large area. As a result, the area under chickpea reduced from 3.2 million ha to 1.0 million ha in northern and northwestern India (Punjab, Haryana and Uttar Pradesh), while it increased from 2.6 million ha to 4.3 million ha in central and southern India (Madhya Pradesh, Maharashtra, Andhra Pradesh and Karnataka) from 1985 to 1990. Because of relatively warm environments in central and southern India, the crop is challenged by Fusarium wilt, a major yield reducing disease, while in northwestern India, due to cooler environments, the crop is exposed to a severe foliar disease Ascochyta blight. The narrow genetic base among cultivated chickpea accessions is limiting genetic improvement of chickpea through breeding efforts. Understanding the extent of natural variation among cultivated chickpea and wild accessions at molecular level is essential to develop prebreeding and breeding strategies for chickpea. Until recently, the low intraspecific and inter-specific polymorphism in chickpea accessions detected by molecular markers and the scarcity of codominant DNA-based markers were serious constraints that hindered the preparation of dense molecular genetic maps or tagging of important traits in chickpea. However, recent studies using STMS markers reveal fairly high levels of

Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants

Abstract: Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T or C) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations. Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and transgenerational memory in plants.

Preliminary genetic linkage maps of Chinese herb Dendrobium nobile and D. moniliforme.

Abstract: Dendrobium is an endangered genus in the orchid family with medicinal and horticultural value. Two preliminary genetic linkage maps were constructed using 90 F1 progeny individuals derived from an interspecific cross between D. nobile and D. moniliforme (both, 2n = 38), using random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR). A total of 286 RAPD loci and 68 ISSR loci were identified and used for genetic linkage analysis. Maps were constructed by double pseudo-testcross mapping strategy using the software Mapmaker/EXP ver. 3.0, and Kosambi map distances were constructed using a LOD score ≥ 4 and a recombination threshold of 0.4. The resulting frame map of D. nobile was 1474 cM in total length with 116 loci distributed in 15 linkage groups; and the D. moniliforme linkage map had 117 loci placed in 16 linkage groups spanning 1326.5 cM. Both maps showed 76.91% and 73.59% genome coverage for D. nobile and D. moniliforme, respectively. These primary maps provide an important basis for genetic studies and further medicinal and horticultural traits mapping and marker-assisted selection in Dendrobium breeding programmes.

Human genetics of diabetic vascular complications.

Abstract: Diabetic vascular complications (DVC) affecting several important organ systems of human body such as the cardiovascular system constitute a major public health problem. There is evidence demonstrating that genetic factors contribute to the risk of DVC genetic variants, structural variants, and epigenetic changes play important roles in the development of DVC. Genetic linkage studies have uncovered a number of genetic loci that may shape the risk of DVC. Genetic association studies have identified many common genetic variants for susceptibility to DVC. Structural variants such as copy number variation and interactions of gene x environment have also been detected by association analysis. Apart from the nuclear genome, mitochondrial DNA plays a critical role in regulation of development of DVC. Epigenetic studies have indicated epigenetic changes in chromatin affecting gene transcription in response to environmental stimuli, which provided a large body of evidence of regulating development of diabetes mellitus. Recently, a new window has opened on identifying rare and common genetic loci through next generation sequencing technologies. This review focusses on the current knowledge of the genetic and epigenetic basis of DVC. Ultimately, identification of genes or genetic loci, structural variants and epigenetic changes contributing to risk of or protection from DVC will help uncover the complex mechanism(s) underlying DVC, with crucial implications for the development of personalized medicine for diabetes mellitus and its complications.

Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan)

Abstract: Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened across these genotypes, and amplified a total of 59 alleles with an average high polymorphic information content value of 0.52. Cluster analysis, done by UPGMA and PCA, grouped the 36 pigeonpea genotypes into two main clusters according to their Fusarium wilt reaction. Based on the Kruskal–Wallis ANOVA and simple regression analysis, six simple sequence repeat markers were found to be significantly associated with Fusarium wilt resistance. The phenotypic variation explained by these markers ranged from 23.7 to 56.4%. The present study helps in finding out feasibility of prescreened SSR markers to be used in genetic diversity analysis and their potential association with disease resistance.

Identification and expression analysis of primary auxin-responsive Aux/IAA gene family in cucumber (Cucumis sativus)

Abstract: Aux/IAA is an important gene family involved in many aspects of growth and development. Aux/IAA proteins are short-lived nuclear proteins that are induced primarily by various phytohormones. In this study, 29 Aux/IAA family genes (CsIAA01–CsIAA29) were identified and characterized in cucumber, including gene structures, phylogenetic relationships, conserved protein motifs and chromosomal locations. These genes show distinct organizational patterns of their putative motifs. The distributions of the genes vary: except for five CsIAA genes in cucumber that were not located, seven CsIAA genes were found on scaffold, while the other 17 CsIAA genes were distributed on seven other chromosomes. Based on a phylogenetic analysis of the Aux/IAA protein sequences from cucumber, Arabidopsis and other plants, the Aux/IAA genes in cucumber were categorized into seven subfamilies. To investigate whether the expression of CsIAA genes is associated with auxin induction, their transcript levels were monitored in seedlings treated with IAA (indole-3-acetic acid), and their expression patterns were analysed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). The results showed that 11/29 CsIAA genes were expressed in leaves whether treated with IAA or not and the time course of processing and compared with the control, five CsIAA genes showed low expression only after 60 min treatment with IAA, while 11 genes showed no expression. These results provide useful information for further functional analysis of Aux/IAA gene family in cucumber.

The first complete mitochondrial genome from Bostrychus genus (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotridae fish phylogeny

Abstract: To understand the phylogenetic position of Bostrychus sinensis in Eleotridae and the phylogenetic relationships of the family, we determined the nucleotide sequence of the mitochondrial (mt) genome of Bostrychus sinensis. It is the first complete mitochondrial genome sequence of Bostrychus genus. The entire mtDNA sequence was 16508 bp in length with a standard set of 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a noncoding control region. The mitochondrial genome of B. sinensis had common features with those of other bony fishes with respect to gene arrangement, base composition, and tRNA structures. Phylogenetic hypotheses within Eleotridae fish have been controversial at the genus level. We used the mitochondrial cytochrome b (cytb) gene sequence to examine phylogenetic relationships of Eleotridae by using partitioned Bayesian method. When the specific models and parameter estimates were presumed for partitioning the total data, the harmonic mean –lnL was improved. The phylogenetic analysis supported the monophyly of Hypseleotris and Gobiomorphs. In addition, the Bostrychus were most closely related to Ophiocara, and the Philypnodon is also the sister to Microphlypnus, based on the current datasets. Further, extensive taxonomic sampling and more molecular information are needed to confirm the phylogenetic relationships in Eleotridae.

Expression profile of genes coding for carotenoid biosynthetic pathway during ripening and their association with accumulation of lycopene in tomato fruits

Abstract: Fruit ripening process is associated with change in carotenoid profile and accumulation of lycopene in tomato (Solanum lycopersicum L.). In this study, we quantified the beta-carotene and lycopene content at green, breaker and red-ripe stages of fruit ripening in eight tomato genotypes by using high-performance liquid chromatography. Among the genotypes, lycopene content was found highest in Pusa Rohini and lowest in VRT-32-1. To gain further insight into the regulation of lycopene biosynthesis and accumulation during fruit ripening, expression analysis of nine carotenoid pathway-related genes was carried out in the fruits of high lycopene genotype-Pusa Rohini. We found that expression of phytoene synthase and beta-carotene hydroxylase-1 was four and thirty-fold higher, respectively, at breaker stage as compared to red-ripe stage of fruit ripening. Changes in the expression level of these genes were associated with a 40% increase in lycopene content at red-ripe stage as compared with breaker stage. Thus, the results from our study suggest the role of specific carotenoid pathway-related genes in accumulation of high lycopene during the fruit ripening processes.

A single recessive gene controls fragrance in cucumber (Cucumis sativus L.)

Abstract: . Cucumber fruits are consumed as a vegetable freshor cooked or in pickled form. Over 95% of the cucumberproduction is in Asia (FAO 2011 FAOSTAT, available athttp://faostat3.fao.org/home/index.html). Fruit quality traitsof cucumber include fruit colour, spine colour, stripes, fruitsize and firmness. Thailand is part of the centre of diversityof cucumber, where

Genomewide analysis of the chitinase gene family in Populus trichocarpa.

Abstract: The chitinase gene family is a large gene family in plants. As the first report of chitinase genes research on genome level in woody plants, here we report the identification of 37 Populus trichocarpa chitinase genes through a genomewide search. We divided these genes into five classes, based on sequence similarity and typical domain conservation. A strong correlation existed between gene structure and phylogeny, providing additional criteria to support classification. The distribution of chitinase genes on chromosomes was related to segmental duplications and tandem duplications revealing the expansion patterns of P. trichocarpa chitinase genes. As ubiquitous enzymes, chitinases are widely present in bacteria, fungi, animals and plants. They catalyse the hydrolytic cleavage of the β-1,4-glycosidic bonds between biopolymers N-acetyl-glucosamine residues from the chitin molecule which is a major structural component of fungal cell wall, exoskeleton of insects and crustacean shells (Cohen-Kupiec and Chet 1998). Plant chitinases act as defense proteins responding to pathogenic attack (Santos et al. 2008). They can play two different roles in defense mechanism against fungal pathogens. One is to degrade the fungal cell wall and inhibit fungal growth, the other is to let the fungal pathogens release small fragments that act as elicitors (Roldan Serrano et al. 2007). Besides, a lot of events in the growth and development processes such as pollination, seed germination and somatic embryogenesis cannot be completed without the participation of chitinases (Passarinho and de Vries 2002). So far, chitinase genes have been cloned and characterized from more than 20 plant species. It has been demonstrated that plant chitinase genes can be induced by various sources of stress such as elicitors, wounding, salicylic acid, plant hormones and fungal pathogens (Graham and Sticklen 1994).

Fast evolutionary genetic differentiation during experimental colonizations

Abstract: Founder effects during colonization of a novel environment are expected to change the genetic composition of populations, leading to differentiation between the colonizer population and its source population. Another expected outcome is differentiation among populations derived from repeated independent colonizations starting from the same source. We have previously detected significant founder effects affecting rate of laboratory adaptation among Drosophila subobscura laboratory populations derived from the wild. We also showed that during the first generations in the laboratory, considerable genetic differentiation occurs between foundations. The present study deepens that analysis, taking into account the natural sampling hierarchy of six foundations, derived from different locations, different years and from two samples in one of the years. We show that striking stochastic effects occur in the first two generations of laboratory culture, effects that produce immediate differentiation between foundations, independent of the source of origin and despite similarity among all founders. This divergence is probably due to powerful genetic sampling effects during the first few generations of culture in the novel laboratory environment, as a result of a significant drop in Ne. Changes in demography as well as high variance in reproductive success in the novel environment may contribute to the low values of Ne. This study shows that estimates of genetic differentiation between natural populations may be accurate when based on the initial samples collected in the wild, though considerable genetic differentiation may occur in the very first generations of evolution in a new, confined environment. Rapid and significant evolutionary changes can thus occur during the early generations of a founding event, both in the wild and under domestication, effects of interest for both scientific and conservation purposes.

K121Q ENPP1/PC-1 gene polymorphism is associated with insulin resistance in a north Indian population.

Abstract: Obesity is commonly associated with insulin resistance and hyperinsulinaemia and is often associated with various metabolic abnormalities, such as dyslipidaemia and elevated plasma glucose. A total of 642 study participants, 309 obese and 333 nonobese individuals were included in this study. Insulin, glucose and lipid levels were estimated using standard protocols. The degree of insulin resistance was calculated according to the homeostasis model assessment. All study participants were genotyped by PCR restriction fragment length polymorphism method. The K121Q polymorphism of ENPP1/PC-1 gene showed no association with obesity. The K121Q polymorphism showed association with different obesity associated phenotypes like percentage body fat, fat mass, insulin and HOMA-IR (homeostasis model assessment for insulin resistance). The strongest associations were observed in percentage body fat, fat mass, insulin and HOMA-IR under recessive and dominant models. The genetic association of ENPP1/PC-1 K121Q polymorphism with insulin resistance has been established in other population (Bacci et al. 2005). We have replicated the genetic association of ENPP1/PC-1 K121Q polymorphism with obesity and its association with plasma insulin, insulin resistance, per cent body fat and fat mass in a north Indian population. Obesity is related with significantly increased morbidity (Eckel and Krauss 1998) and mortality (Calle et al. 1999). Obesity is commonly associated with insulin resistance and hyperinsulinaemia and is often associated with high blood pressure and various metabolic abnormalities, such as dyslipidaemia and elevated plasma glucose (Thomas et al. 2004).

Genetic relationship of a cucumber germplasm collection revealed by newly developed EST-SSR markers.

Abstract: Cucumber (Cucumis sativus L.) is one of the most widely cultivated vegetables, ranked fourth after tomato, onion and cabbage (Pitrat et al. 1999). It originates from India, and China is widely regarded as its secondary origin centre (Staub et al. 1997). There are a large number of cucumber germplasms spread around China and they are generally classified into six ecotypes based on the geographical distribution and ecological characters, i.e. south China ecotype, north China ecotype, Europe greenhouse ecotype, Europe openfield ecotype, occident processing ecotype and wild ecotype (Xu 1994). Although various ecotypes have been identified in cucumber, the fact that cucumber has a narrow genetic base is widely acknowledged (Staub et al. 2005), and this limits the possibilities for trait improvement using cross breeding. Genetic diversity is desirable for long-term crop improvement and reduction of vulnerability to important crop stresses. Many cucumber cultivars have been developed from closely related parents, but limited improvement in certain agricultural traits in recent years demands a more diverse range of germplasms. Molecular markers have extensively been used for studying genetic diversity and genetic relationship in cucumber, especially PCR-based markers, such as random amplified polymorphic DNA (RAPD) (Horejsi and Staub 1999), amplification fragment length polymorphism (AFLP) (Li et al. 2004), inter-simple sequence repeat (ISSR) (Wang et al. 2007) and simple sequence repeat (SSR) (Danin-Poleg et al. 2001). From all these studies, different estimates for the degree of genetic variation were obtained, reflecting the differences in the selected sets of genotypes or marker systems.

Consistent effects of single and combined SNP(s) within bovine paired box 7 gene (Pax7) on growth traits.

Abstract: 1College of Animal Science and Technology, Northwest A & F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, People’s Republic of China 2Institute of Cellular and Molecular Biology, Xuzhou Normal University, Xuzhou, Jiangsu 221116, People’s Republic of China 3Department of Biology, Dezhou University, Dezhou, Shandong 253023, People’s Republic of China

Genetic diversity and population structure of the marbled rockfish, Sebastiscus marmoratus, revealed by SSR markers.

Abstract: The marbled rockfish, Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae, Sebastinae), is commercially important near-shore species, which is widely distributed in the East Sea and the South Sea of China, and from southern Japan to eastern Korea (Shen 1993). Generally, the rockfish attains a length of 15–20 cm, while some individuals can grow up to 30–40 cm. S. marmoratus inhabits littoral rocky bottoms and migrates within oceans typically between different spawning and feeding areas, as tunas do. The rockfish is viviparous wherein eggs are fertilized internally, retained, and undergo development in the maternal reproductive system (Wourms et al. 1988). Sebastiscus marmoratus is an important commercial species in Japan and China (Kita et al. 1996). Considerable research has been carried out on S. marmoratus in Japan, but most of these studies are related to physiological and ecological aspects (Mizue 1959; Shiokawa 1962; Watanabe 2003; Yoko et al. 2006; Wang et al. 2005, 2009). Till date, not much has been reported about genetic variation in the marbled rockfish. Lack of appropriate polymorphic markers have limited the phylogenetic and population genetic work on this species. Among the various molecular makers, microsatellite DNA markers have been successfully used in revealing population genetic diversity, because they are co-dominant and highly polymorphic (Sekino and Hara 2001; Selkoe and Toonen 2006). To investigate the genetic characteristic of S. marmoratus, we developed 11 polymorphic microsatellite loci using the fast isolation by amplified fragment length polymorphism of sequences containing repeats (FIASCO) method (Xu et al. 2010). For successful conservation and effective management of a species, including develop strategies for maintaining

Neurospora crassa ncs-1 , mid-1 and nca-2 double-mutant phenotypes suggest diverse interaction among three Ca 2 + -regulating gene products

Abstract: The calcium (Ca2+) signalling system in the filamentous fungus Neurospora crassa is unique and significantly different from that in plants and animals, mainly with regard to the second messenger systems involved in Ca2+-release from internal stores (Galagan et al. 2003). The complex Ca2+ signalling system in N. crassa contains 48 Ca2+ signalling proteins including a Ca2+ and/or CaM binding protein called neuronal calcium sensor-1 (NCS-1), a Ca2+-permeable channel MID-1 and a PMCA-type Ca2+-ATPase NCA-2 (Zelter et al. 2004; Tamuli et al. 2013). Here, we show that ncs-1, mid-1 and nca-2 interactions affect growth, carotenoid accumulation, Ca2+ stress tolerance, ultraviolet (UV) survival and circadian-regulated conidiation in N. crassa. The N. crassa homologue of NCS-1 has a role in growth, Ca2+ stress tolerance and UV survival (Deka et al. 2011; Tamuli et al. 2011). MID-1 is necessary for Ca2+homeostasis in N. crassa (Lew et al. 2008). Mid-1 in Gibberella zeae has a role in growth, development and ascospore discharge (Cavinder et al. 2011). NCA-2 is responsible for adaptation to stress conditions and functions to pump Ca2+ out of the cell in N. crassa (Benito et al. 2000; Bowman et al. 2011). In Schizosaccharomyces pombe, Ncs1p, the homologue of NCS-1, promotes Ca2+-induced closure of Yam8p Ca2+ channel, a homologue of the MID1 (Hamasaki-Katagiri and Ames 2010). The Ca2+-sensitive phenotype of the ncs1 deletion mutant is rescued by a yam8 deletion, indicating that Ncs1p negatively regulates Yam8p in S. pombe

Effective population size and evolutionary dynamics in outbred laboratory populations of Drosophila

Abstract: Census population size, sex-ratio and female reproductive success were monitored in 10 laboratory populations of Drosophila melanogaster selected for different ages of reproduction. With this demographic information, we estimated eigenvalue, variance and probability of allele loss effective population sizes. We conclude that estimates of effective size based on genefrequency change at a few loci are biased downwards. We analysed the relative roles of selection and genetic drift in maintaining genetic variation in laboratory populations of Drosophila. We suggest that rare, favourable genetic variants in our laboratory populations have a high chance of being lost if their fitness effect is weak, e.g. 1% or less. However, if the fitness effect of this variation is 10% or greater, these rare variants are likely to increase to high frequency. The demographic information developed in this study suggests that some of our laboratory populations harbour more genetic variation than expected. One explanation for this finding is that part of the genetic variation in these outbred laboratory Drosophila populations may be maintained by some form of balancing selection. We suggest that, unlike bacteria, medium-term adaptation of laboratory populations of fruit flies is not primarily driven by new mutations, but rather by changes in the frequency of preexisting alleles.

Tumour necrosis factor alpha (TNF-α) genetic polymorphisms and the risk of autoimmune liver disease: a meta-analysis

Abstract: Epidemiological studies have evaluated the association between tumour necrosis factor alpha (TNF-α)-308G/A and (TNF-α)-238G/A polymorphisms, and the risk of autoimmune liver disease (AILD), yet the results are conflicting. To derive a more precise estimation of the relationship, we performed this meta-analysis. A systematic review was conducted to identify all eligible studies of TNF-α polymorphisms and AILD risk. We used odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of the association between the two TNF-α polymorphisms and AILD risk. A total of 15 eligible studies were identified. Overall, positive associations of -308G/A polymorphism with AILD risk were found (A vs G allele: OR = 1.45, 95%CI = 1.13–1.86; AA vs GG: OR = 2.74, 95%CI = 1.51–4.96; GA vs GG: OR = 1.46, 95%CI = 1.11–1.92; dominant model: OR = 1.57, 95%CI = 1.18–2.10; recessive model: OR = 2.22, 95%CI = 1.31–3.76). In subgroup analysis by ethnicity, a significantly higher risk was found in Caucasians. In subgroup analysis by AILD category, significant association was observed in autoimmune hepatitis and primary sclerosing cholangitis, especially in Caucasians. Patients carrying TNF-α-238A allele had a slightly decreased risk of developing AILD (OR = 0.65, 95%CI = 0.48–0.87). However, we found both TNF-α polymorphisms were not associated with primary biliary cirrhosis risk, even in subgroup analysis. Our meta-analysis suggests that the TNF-α-308G/A and -238G/A polymorphisms may contribute to AILD susceptibility in Caucasians, especially for autoimmune hepatitis and primary sclerosing cholangitis. Nevertheless, we found both TNF-α polymorphisms were unlikely to be associated with the risk of primary biliary cirrhosis.

New microsatellite markers classifying nontoxic and toxic Jatropha curcas.

Abstract: Jatropha curcas (jatropha) (2n = 2x = 22) is a shrub originated from Central America and spread to Africa and Asia by Portuguese traders during 18th century. This species belongs to the family Euphorbiaceae. Jatropha seed is high in oil content and considered promising as an alternative renewable and eco-friendly energy source, especially for biodiesel. Most jatropha accessions are high in seed phorbol ester (PE), a tumour inducing substance and thus called toxic accessions. There are some low PE (nontoxic) accessions in Mexico that are locally consumed as snack foods or sweets. The toxic and nontoxic accessions cannot be distinguished morphologically (Ghosh et al. 2007; Makkar et al. 2008), thus the villagers vegetatively propagate them to avoid contamination of high PE character. Currently, the only way to identify the high and low PE seeds is by seed analysis with high performance liquid chromatography (HPLC). Jatropha breeders are looking for a cheaper and quicker way to distinguish them such as through molecular markers, provided that the location(s) of gene(s) controlling high PE content is known. To achieve this, a number of markers are required to cover all the 11 linkage groups. Basha and Sujatha (2007) reported that among 400 RAPD primers tested, 339 produced bands and 267 were polymorphic. They also tested a set of 207 ISSR primers and found that 100 of them produced bands, giving 29 polymorphic primers. They used this information to investigate genetic variation among 42 accessions of jatropha from India and a nontoxic accession from Mexico. Basha and Sujatha (2009) reported genetic variation and interspecific hybrids of Jatropha species using RAPD and ISSR as nuclear specific markers, and chloroplast microsatellite markers as organelle specific markers. Ganesh et al. (2008) studied genetic diversity of eight Jatropha species collected in India. Eighteen of 26 RAPD primers classified them into a group of J. curcas versus a group of other seven Jatropha spp. Gupta et al. (2008)

Physical mapping of (GATA) n and (TTAGGG) n sequences in species of Hypostomus (Siluriformes, Loricariidae)

Abstract: Hypostomus, a genus of Loricariidae, is one of the most diversified and widely distributed genera among fishes of South America (Weber 2003). It is the dominant genus of armoured catfish in Brazilian rivers (Weber 2003). Chromosomally, this group is highly diversified and studies of repetitive DNAs in these species are still in preliminary stages. Hypostomus karyotypes range from 54 chromosomes in H. plecostomus (Muramoto et al. 1968) to 84 chromosomes in Hypostomus sp. 2 (Cereali et al. 2008). Artoni and Bertollo (2001) consider the diploid number of 54 chromosomes as basal for Hypostominae, using Trichomycteridae as outgroup, suggesting that the chromosome evolution of Hypostomus occurred through centric fissions. Recently, Bueno et al. (2012) showed that other chromosomal rearrangements, such as inversions, deletions, duplications and heterochromatinization, could contribute to the chromosomal differentiation within the genus. Repetitive DNAs arranged in tandem are important tools in studies of taxonomic and evolutionary problems. These sequences could be associated with chromosomal rearrangement events (Wichman et al. 1991; Rosa et al. 2012; and others). According to Wichman et al. (1991), satellite DNAs rapidly diverge during evolution. Thereby, they are important for solving the taxonomic and evolutionary problems among related species.