Showing papers in "Journal of Genetics in 2007"

Mutations in the S gene region of hepatitis B virus genotype D in Turkish patients

Abstract: The S gene region of the hepatitis B virus (HBV) is responsible for the expression of surface antigens and includes the ‘a’-determinant region. Thus, mutation(s) in this region would afford HBV variants a distinct survival advantage, permitting the mutant virus to escape from the immune system. The aim of this study was to search for mutations of the S gene region in different patient groups infected with genotype D variants of HBV, and to analyse the biological significance of these mutations. Moreover, we investigated S gene mutation inductance among family members. Forty HBV-DNA-positive patients were determined among 132 hepatitis B surface antigen (HbsAg) carriers by the first stage of seminested PCR. Genotypes and subtypes were established by sequencing of the amplified S gene regions. Variants were compared with original sequences of these serotypes, and mutations were identified. All variants were designated as genotype D and subtype ayw3. Ten kinds of point mutations were identified within the S region. The highest rates of mutation were found in chronic hepatitis patients and their family members. The amino acid mutations 125 (M → T) and 127 (T → P) were found on the first loop of ‘a’-determinant. The other consequence was mutation inductance in a family member. We found some mutations in the S gene region known to be stable and observed that some of these mutations affected S gene expression.

Population genetic structure based on SSR markers in alfalfa (Medicago sativa L.) from various regions contiguous to the centres of origin of the species.

Abstract: differentiated using mosphological descriptors, and although such descriptions are indeed useful from a breeding perspective, they are inadequate for analysis of population genetic structure. Because alfalfa is native to northwestern Iran, a high level of genetic diversity may be expected among individual plants within and between populations. Thus, the objectives of the present study were to (a) identify polymorphic SSR markers with high informative value for the Iranian alfalfa in terms of population differentiation and identification, (b) estimate the genetic population structure, and (c) compare the genetic diversity between different geographical regions, especially across different latitudes. The average within-population genetic diversity evaluated using eight simple sequence repeat (SSR) markers ranged from 0.82 in the Kerman population (low latitudes) to 0.93 in the Ghareyonjeh population (higher latitudes). The genetic relationships among populations were analysed using cluster analysis by UPGMA algorithm based on the coancestry coefficient matrix. The higher distance between Ghareyonjeh population and others was due to the presence of a specific allele in all plants within this population. The trend of changes in genetic diversity across populations was concordant with latitude changes. The obtained results suggest that SSR markers are useful for identification of alfalfa populations, for assessing interpopulation and intrapopulation genetic diversity, and for estimation of genetic differentiation.

Construction of genetic linkage map of the medicinal and ornamental plant Catharanthus roseus

Abstract: An integrated genetic linkage map of the medicinal and ornamental plant Catharanthus roseus, based on different types of molecular and morphological markers was constructed, using a F2 population of 144 plants. The map defines 14 linkage groups (LGs) and consists of 131 marker loci, including 125 molecular DNA markers (76 RAPD, 3 RAPD combinations; 7 ISSR; 2 EST-SSR from Medicago truncatula and 37 other PCR based DNA markers), selected from a total of 472 primers or primer pairs, and six morphological markers (stem pigmentation, leaf lamina pigmentation and shape, leaf petiole and pod size, and petal colour). The total map length is 1131.9 cM (centiMorgans), giving an average map length and distance between two markers equal to 80.9 cM and 8.6 cM, respectively. The morphological markers/genes were found linked with nearest molecular or morphological markers at distances varying from 0.7 to 11.4 cM. Linkage was observed between the morphological markers concerned with lamina shape and petiole size of leaf on LG1 and leaf, stem and petiole pigmentation and pod size on LG8. This is the first genetic linkage map of C. roseus.

Association study of the oestrogen signalling pathway genes in relation to age at natural menopause.

Abstract: Genetic factors play a significant role in influencing the variation of age at natural menopause (AANM). Estrogen receptor beta (ESR2), is an important factor in the mechanism of action of estrogen, while the aromatase gene (CYP19) and the 17-alpha-hydroxylase gene (CYP17) are involved in the biosynthesis of estrogen. We tested whether polymorphisms of ESR2, CYP19 and CYP17 genes are associated with AANM in Caucasian females. A total of 52 SNPs (17 for ESR2, 28 for CYP19, and 7 for CYP17) were successfully genotyped for 229 Caucasian women having experienced natural menopause. Comprehensive statistical analyses focusing on the association of these genes with AANM were conducted. The effects of age, height and age at menarche on AANM were adjusted when conducting association analyses. We found that six SNPs (2, 6-7, 9, 13 and 16) within ESR2 were not significantly associated with AANM after Bonferroni correction. However, two blocks of ESR2 were associated with AANM. For CYP19, two SNPs (24 and 27) were nominally associated with AANM. No significant association was observed between CYP17 and AANM. Our results suggest that genetic variation in the ESR2 and CYP19 genes may influence the variation in AANM in Caucasian women.

Cloning and study of adult-tissue-specific expression of Sox9 in Cyprinus carpio.

Abstract: The Sox9 gene is one of the important transcription factors in the development of many tissues and organs, particularly in sex determination and chondrogenesis. We amplified the genomic DNA of Cyprinus carpio using degenerate primers, and found that there were two versions of Sox9 in this species: Sox9a and Sox9b, that differ in having an intron of different length (704 bp and 616 bp, respectively) in the conserved HMG box region that codes for identical amino acid sequences. We used a two-phase rapid amplification of cDNA ends (RACE) for the isolation of full-length cDNA of Sox9b. Sequence analyses revealed a 2447-bp cDNA containing 233-bp 5′ untranslated region, a 927-bp 3′ untranslated region, including poly(A), and a 1287 bp open reading frame (ORF) encoding a protein of 428 amino acids. The HMG box of 79 amino acid motif was confirmed from positions 96–174. Sequence alignment showed that the identity of amino acids of Sox9 among ten animal species, including C. carpio, is 75%, indicating that the Sox9 gene is evolutionarily quite conserved. The expression level of Sox9b gene varied among several organs of adult C. carpio, with the level of expression being highest in the brain and testis.

Drosophila simulans Lethal hybrid rescue mutation (Lhr) rescues inviable hybrids by restoring X chromosomal dosage compensation and causes fluctuating asymmetry of development.

Abstract: The Drosophila simulans Lhr rescues lethal hybrids from the cross of D. melanogaster and D. simulans. We describe here, the phenotypes of Lhr dependent rescue hybrids and demonstrate the effects of Lhr on functional morphology of the salivary chromosomes in the hybrids. Our results reveal that the phenotypes of the ‘Lhr dependent rescued’ hybrids were largely dependent on the genetic background and the dominance in species and hybrids, and not on Lhr. Cytological examination reveal that while the salivary chromosome of ‘larval lethal’ male carrying melanogaster X chromosome was unusually thin and contracted, in ‘rescued’ hybrid males (C mel X mel Y sim ; A mel A sim ) the X chromosome showed typical pale staining, enlarged diameter and incorporated higher rate of 3H-uridine in presence of one dose Lhr in the genome. In hybrid males carrying simulans X chromosome (C mel X sim Y mel ; A mel A sim ), enlarged width of the polytene X chromosome was noted in most of the nuclei, in Lhr background, and transcribed at higher rate than that of the single X chromosome of male. In hybrid females (both viable, e.g., C mel X mel X sim ; A mel A sim and rescued, e.g., C mel X mel X mel ; A mel A sim ), the functional morphology of the X chromosomes were comparable to that of diploid autosomes in presence of one dose of Lhr. In hybrid metafemales, (C mel X mel X mel X sim ; A mel A sim ), two dose of melanogaster X chromosomes and one dose of simulans X chromosome were transcribed almost at ‘female’ rate in hybrid genetic background in presence of one dose of Lhr. In rescued hybrid males, the melanogaster-derived X chromosome appeared to complete its replication faster than autosomes. These results together have been interpreted to have suggested that Lhr suppresses the lethality of hybrids by regulating functional activities of the X chromosome(s) for dosage compensation.

Genetic structure of the rattan Calamus thwaitesii in core, buffer and peripheral regions of three protected areas in central Western Ghats, India: do protected areas serve as refugia for genetic resources of economically important plants?

Abstract: Given the increasing anthropogenic pressures on forests, the various protected areas—national parks, sanctuaries, and biosphere reserves—serve as the last footholds for conserving biological diversity. However, because protected areas are often targeted for the conservation of selected species, particularly charismatic animals, concerns have been raised about their effectiveness in conserving nontarget taxa and their genetic resources. In this paper, we evaluate whether protected areas can serve as refugia for genetic resources of economically important plants that are threatened due to extraction pressures. We examine the population structure and genetic diversity of an economically important rattan, Calamus thwaitesii, in the core, buffer and peripheral regions of three protected areas in the central Western Ghats, southern India. Our results indicate that in all the three protected areas, the core and buffer regions maintain a better population structure, as well as higher genetic diversity, than the peripheral regions of the protected area. Thus, despite the escalating pressures of extraction, the protected areas are effective in conserving the genetic resources of rattan. These results underscore the importance of protected areas in conservation of nontarget species and emphasize the need to further strengthen the protected-area network to offer refugia for economically important plant species.

Chromosomal changes in ageing.

Abstract: Ageing as a phenomenon, and the possibilities of postpon-ing, reversing or abolishing it, have fascinated humans for avery long time as both mythology and history testify (Joshi2005). In the past couple of centuries, scientists proposed anumber of ageing theories, but none of them was completelysatisfactory. Current theories regarding proximal causes ofageing can be classified into two major categories: theo-ries invoking a program directing ageing and stochastic the-ories. Programmed ageing theories assume the existence of apurposeful genetic program that determines the ageing pro-cess. In contrast, stochastic or error-based theories suggestthat ageing is driven by random, accidental events that causemutations and/or deregulation of cellular processes, and fi-nally lead to cellular dysfunction and senescence (Hayflick2000, 2007; Semsei 2000). Considerable progress in iden-tifying genes involved in the ageing process has been madein genetically tractable model organisms such as, yeast, thenematode

A duplicated coxI gene is associated with cytoplasmic male sterility in an alloplasmic Brassica juncea line derived from somatic hybridization with Diplotaxis catholica.

Abstract: A cytoplasmic male sterile (CMS) line of Brassica juncea was derived by repeated backcrossing of the somatic hybrid (Diplotaxis catholica + B. juncea) to B. juncea. The new CMS line is comparable to euplasmic lines for almost all characters, except for flowers which bear slender, needle-like anthers with aborted pollen. Detailed Southern analysis revealed two copies of coxI gene in the CMS line. One copy, coxI-1 is similar to the coxI gene of B. juncea, whereas the second copy, coxI-2 is present in a novel rearranged region. Northern analysis with eight mitochondrial gene probes showed altered transcript pattern only for the coxI gene. Two transcripts of 2.0 and 2.4 kb, respectively, were detected in the CMS line. The novel 2.4 kb transcript was present in floral bud tissue but absent in the leaf tissue. In plants where male sterility broke down under high temperature during the later part of the growing season, the 2.4 kb coxI transcript was absent, which suggested its association with the CMS. The two coxI genes from the CMS line showed two amino acid changes in the coding region. The novel coxI gene showed unique repeats in the 5′ region suggesting recombination of mitochondrial genomes of the two species. The possible role of the duplicated coxI gene in causing male sterility is discussed.

Chromosomal evolution and phylogenetic analyses in Tayassu pecari and Pecari tajacu (Tayassuidae): tales from constitutive heterochromatin.

Abstract: The mammalian family Tayassuidae (peccaries) is confined to the New World and comprises three recognized extant species, white-lipped (Tayassu pecari), collared (Pecari tajacu) and chacoan (Catagonus wagneri) peccaries, which exhibit distinct morphological and chromosomal features. The phylogenetic relationships among the tayassuids are unclear and have instigated debate over the palaeontological, cytogenetic and molecular aspects. Constitutive heterochromatin analysis can be used in understanding the phylogenetic relationships between related species. Here we describe, for the first time, the constitutive heterochromatin (C-positive heterochromatin) of two tayassuid species, Tayassu pecari and Pecari tajacu. We demonstrate that in situ restriction endonuclease digestion with sequential C-banding could be a complementary tool in the study of constitutive heterochromatin heterogeneity in chromosomes of the Tayassuidae. Our characterization of peccary chromosomes suggests that the Pecari tajacu autosomal karyotype is more primitive and has accumulated great diversity in its constitutive heterochromatin. This idea is supported by several other studies that analysed nuclear and mitochondrial sequences of the living peccary species. Finally, the tayassuid X chromosome primitive form seems to be the one of Tayassu pecari.

Isolation, characterization and genetic analysis of canine GATA4 gene in a family of Doberman Pinschers with an atrial septal defect.

Abstract: GATA4 is expressed early in the developing heart where it plays a key role in regulating the expression of genes encoding myocardial contractile proteins. Gene mutations in the human GATA4 have been implicated in various congenital heart defects (CHD), including atrial septal defect (ASD). Although ASD is the third most common CHD in humans, it is generally rare in dogs and cats. There is also no obvious predilection for ASD in dogs and cats, based on sex or breed. However, among dogs, the incidence rate of ASD is relatively high in Samoyeds and Doberman Pinschers, where its inheritance and genetic aetiology are not well understood. In this study, we identified and investigated the genetic aetiology of an ASD affected family in a pure breed dog population. Although the GATA4 gene was screened, we did not find any mutations that would result in the alteration of the coding sequence and hence, the predicted GATA4 structure and function. Although the aetiology of ASD is multifactorial, our findings indicate that GATA4 may not be responsible for the ASD in the dogs used in this study. However, this does not eliminate GATA4 as a candidate for ASD in other dog breeds.

Unique nucleotide polymorphism of ankyrin gene cluster in Arabidopsis

Abstract: The ankyrin (ANK) gene cluster is a part of a multigene family encoding ANK transmembrane proteins in Arabidopsis thaliana, and plays an important role in protein-protein interactions and in signal pathways. In contrast to other regions of a genome, the ANK gene cluster exhibits an extremely high level of DNA polymorphism in an ∼5-kb region, without apparent decay. Phylogenetic analysis detects two clear, deeply differentiated haplotypes (dimorphism). The divergence between haplotypes of accession Col-0 and Ler-0 (Hap-C and Hap-L) is estimated to be 10.7%, approximately equal to the 10.5% average divergence between A. thaliana and A. lyrata. Sequence comparisons for the ANK gene cluster homologues in Col-0 indicate that the members evolve independently, and that the similarity among paralogues is lower than between alleles. Very little intralocus recombination or gene conversion is detected in ANK regions. All these characteristics of the ANK gene cluster are consistent with a tandem gene duplication and birth-and-death process. The possible mechanisms for and implications of this elevated nucleotide variation are also discussed, including the suggestion of balancing selection.

Genetic variation and population structure of interleukin genes among seven ethnic populations from Karnataka, India.

Abstract: The extent of genetic variation and the degree of genetic differentiation among seven ethnic populations from Karnataka, India (Bunt, Havyak, Iyengar, Lingayath, Smartha, Vaishya, Vokkaliga), was investigated using four single nucleotide polymorphisms (SNPs: IL-1A 4845, IL-1B 3954, IL-1B 511 and IL-1RA 2018) of the interleukin gene cluster. Allele frequencies varied by threefold among these populations, which also differed for gene diversity and heterozygosity levels. The average degree of population subdivision among these castes was low (FST = 0.02). However, pair-wise interpopulation differentiation ranged from 0–7%, indicating no detectable differentiation to moderate differentiation between specific populations. The results of phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data on these ethnic groups. Variation in the allele frequencies, as well as differentiation, may be attributed to differential selection and demographic factors including consanguinity among the ethnic groups. Information on the distribution of functionally relevant polymorphisms among ethnic populations may be important towards developing community medicine and public health policies.

Comparative characteristics and gene action in three petal-spotted mutants of Gossypium hirsutum.

Abstract: Of the four Gossypium species under commercial cultivation in India, G. hirsutum (upland cotton) occupies around 70% of the area as straight varieties and intra-hirsutum hybrids. Even if a variety was developed through hybridization between cultivars having a narrow genetic base, identification becomes difficult unless the new genotype has a marker gene. Marker genes with prominent morphological differences are not easily available and often have undesirable effects. Breeding for induction of a prominent morphological character, or to avoid the undesirable effect of a marker gene, is not recommended because of the time involved in this process. Nevertheless, for purposes of maintaining purity of a new variety in the seed production process, prominent morphological differences among varieties have to be found. Morphological features are indicative of the genetic makeup of the plant, and it is usually not difficult for breeders to identify their own varieties even with minor differences from other varieties. Seed production systems all over the world are still based on visual differences. Off types — deviations from the variety norm — are eliminated, and it is assumed that the rest of the population is pure (ICAC 1996). Morphological mutants ofG. hirsutum have been extensively used in genetic mapping studies and varietal identification, and in several instances have proven useful in agronomic improvement efforts. For developing high-yielding, high fibre quality varieties with marker characteristics of G. hirsutum cotton, it is also essential to study the gene action of these traits. G. hirsutum typically lacks a petal spot. Petal-spotted spontaneous mutants of the species were identified from the populations of three genotypes, CSH-2501, AKH-0308 and AKH-9618. These mutants resemble the respective parent genotypes for majority of the morphological traits but

Familial hypercholesterolemia associated with severe hypoalphalipoproteinemia in a Moroccan family.

Abstract: 1Laboratoire de Biochimie et Biologie Molecularie, Groupe de Gene tique et Biologie Moleculaire, Faculte des Sciences Ain chock. B. P. 5366, Casablanca, Morocco 2Laboratoire de Recherche sur les Lipoproteines et l’Atherosc-lerose, Faculte des Sciences Ben M’Sik. B. P. 7955, Casablanca, Morocco 3Laboratorio de Investigacion Molecular, Hospital Universitario Miguel Servet. Po Isbel la catolica, 1–3, Zaragaza, Spain 4Unitat de Recerca de Lipids i Anteriosclerosi, Facultat de Medicina, Universitat Rovira i virgili, Sant Lloren 21. 43201 Reus, Spain

Highly expressed genes are associated with inverse antisense transcription in mouse

Abstract: There is a growing evidence, that antisense transcription might have a key role in a range of human diseases. Although predefined sense-antisense pairs were extensively studied, the antisense expression of the known sense genes is rarely investigated. We retrieved and correlated the expression of sense and antisense sequences of 1182 mouse transcripts to assess the prevalence and to find the characteristic pattern of antisense transcription. We contrasted three Affymetrix MGU74A version 1 mouse genome chips to six MGU74A version 2 chips. For these 1182 transcripts, the version 1 chips contain the antisense sequences of the transcripts presented on the version 2 chips. The original data was taken from the GEO database (GDS431 and GDS432). As the Affymetrix data are semiquantitative, the relative expression levels of antisense partners were analysed. We detected antisense transcription, although the average antisense expression is shifted towards smaller expression values (MGU74A version 1, 516; version 2, 1688). An inverse direct correlation between sense and antisense expression values could be observed at high expression values. At a very high relative expression—above 40,000—the Pearson correlation coefficient is getting closer to −1. Transcripts with high inverse expression ratio may be correlated to the investigated gene (major histocompatibility complex class II trans activator). The ratio of sense to antisense transcripts varied among different chromosomes; on chromosomes 14 and 1 the level of antisense expression was higher than that of sense. We conclude that antisense transcription is a common phenomenon in the mouse genome. The hypothesis of regulatory role of antisense transcripts is supported by the inverse antisense gene expression of highly expressed genes.

FOXL2 mutations in Indian families with blepharophimosis-ptosis-epicanthus inversus syndrome.

Abstract: Blepharophimosis–ptosis–epicanthus inversus syndrome(BPES) (MIM#110100) is an autosomal dominant geneticcondition characterized by a complex eyelid malformation.The main features of BPES are shortening of the horizon-tal palpebral fissures (blepharophimosis), congenital ptosis,telecanthus and epicanthus inversus, and variable expressiv-ity of female infertility (premature ovarian failure) (POF) intype I BPES while absent in type II (Zlotogora

High frequency of BRCA1/2 and p53 somatic inactivation in sporadic ovarian cancer

Abstract: Faculty of Medicine, Charles University, Prague, and theGeneral Teaching Hospital in Prague. All analysed tumourswere sporadic i.e. no other tumours were referred to in thefamily history and all the patients were more than 40 yearsold at the time of diagnosis. All participants gave their writ-ten informed consent.All freshly frozen samples were examined by a pathol-ogist to evaluate the proportion of tumourous and nontu-mourous tissue. Only samples with over 50% tumouroustissue were used for our study. The histopathological char-acteristics of analysed tumours are given in table 1. Majorityof patients (21/30 : 70%) were diagnosed in stage III Inter-national Federation of Gynocology and Obstetrics (FIGO).Stages I and IV were similarly represented (4/30 and 5/30:13.3% and 16.7%, respectively), and none of the analysedtumours belong to stage II patient.

Prevalence of the exon 2 deletion of the COMMD1 gene in Australian Bedlington terriers.

Abstract: Inherited copper toxicosis in Bedlington terriers is a chronic progressive hepatic disease caused by an abnormal accumulation of copper due to genetic derangement in the biliary copper excretion pathway. In this study, we screened a group of Australian Bedlington terriers for a previously identified mutation, an exon 2 deletion in the COMMD1 gene. The DNA samples used in this study were collected from 149 Bedlington terriers (60 males and 89 females), aged between four weeks to 13 years from eight different pedigrees obtained over a period of three years. We found 60 dogs (40%) were homozygous wild type, 42 dogs (28%) were homozygous mutant, and 47 dogs (32%) were heterozygous for the deletion of exon 2 in the COMMD1 gene. Not only this reports the first large scale genetic screening of the known COMMD1 mutation in Bedlington terriers, but our results also indicate a high prevalence of the COMMD1 mutation in Bedlington terriers that might also be useful as a marker of copper toxicosis. Inherited copper toxicosis was first identified in Bedlington terrier in USA, in 1975 (Hardy et al. 1975) and has since been reported in other countries including Australia (Eriksson 1983; Robertson et al. 1983; Kelly et al. 1984). This disease is an inherited autosomal recessive disorder characterized by a progressive accumulation of copper, predominantly in the liver (Hardy 1984; Johnson et al. 1980). The main pathogenesis of the copper toxicosis in Bedlington terrier appears to be related to the reduced biliary excretion of stored copper resulting from a genetic derangement in copper metabolism (Hardy 1984; Hyun and Filippich 2004). A mutation resulting in the deletion of exon 2 in the COMMD1 (formerly known asMurr1) gene was found to be responsible for copper toxicosis in a subpopulation of Bedlington terriers (Van de Sluis et al. 2002)

Transposon display supports transpositional activity of P elements in species of the saltans group of Drosophila

Abstract: Mobilization of two P element subfamilies (canonical and O-type) from Drosophila sturtevanti and D. saltans was evaluated for copy number and transposition activity using the transposon display (TD) technique. Pairwise distances between strains regarding the insertion polymorphism profile were estimated. Amplification of the P element based on copy number estimates was highly variable among the strains (D. sturtevanti, canonical 20.11, O-type 9.00; D. saltans, canonical 16.4, O-type 12.60 insertions, on average). The larger values obtained by TD compared to our previous data by Southern blotting support the higher sensitivity of TD over Southern analysis for estimating transposable element copy numbers. The higher numbers of the canonical P element and the greater divergence in its distribution within the genome of D. sturtevanti (24.8%) compared to the O-type (16.7%), as well as the greater divergence in the distribution of the canonical P element, between the D. sturtevanti (24.8%) and the D. saltans (18.3%) strains, suggest that the canonical element occupies more sites within the D. sturtevanti genome, most probably due to recent transposition activity. These data corroborate the hypothesis that the O-type is the oldest subfamily of P elements in the saltans group and suggest that the canonical P element is or has been transpositionally active until more recently in D. sturtevanti.

Origin of new Brassica types from a single intergeneric hybrid between B. rapa and Orychophragmus violaceus by rapid chromosome evolution and introgression.

Abstract: Many novel lines were established from an intergeneric mixoploid between Brassica rapa (2n = 20) and Orychophragmus violaceus (2n = 24) through successive selections for fertility and viability. Pedigrees of individual F2 plants were advanced to the 10th generation by selfing. Their breeding habit was self-compatible and different from the self-incompatibility of their female parent B. rapa, and these lines were reproductively isolated to different degrees from B. rapa and B. napus. The lines with high productivity showed not only a wide spectrum of phenotypes but also obvious variations in fatty acid profiles of seed oil and glucosinolate contents in seed meal. These lines had 2n = 36, 37, 38, 39 and 40, with 2n = 38 being most frequent (64.56%), and no intact O. violaceus chromosomes were detected by genomic in situ hybridization (GISH) analysis. Amplified fragment length polymorphism (AFLP) analyses revealed a high extent of variation in genomic compositions across all the lines. O. violaceus-specific bands, deleted bands in B. rapa and novel bands for two parents were detected in these lines, with novel bands being the most frequent. The morphological and genetic divergence of these novel types derived from a single hybrid is probably due to rapid chromosomal evolution and introgression, and provides new genetic resources for rapeseed breeding.

Nucleotide variation at the dopa decarboxylase ( Ddc ) gene in natural populations of Drosophila melanogaster

Abstract: We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.

Meiosis in a triploid hybrid of Gossypium: high frequency of secondary bipolar spindles at metaphase II.

Abstract: Studies on meiosis in pollen mother cells (PMCs) of a triploid interspecific hybrid (3x = 39 chromosomes, AAD) between tetraploid Gossypium hirsutum (4n = 2x = 52,AADD) and diploid G. arboreum (2n = 2x = 26,AA) are reported. During meiotic metaphase I, 13 AA bivalents and 13 D univalents are expected in the hybrid. However, only 28% of the PMCs had this expected configuration. The rest of the PMCs had between 8 and 12 bivalents and between 12 and 17 univalents. Univalents lagged at anaphase I, and at metaphase II one or a group of univalents remained scattered in the cytoplasm and failed to assemble at a single metaphase plate. Primary bipolar spindles organized around the bivalents and multivalents. In addition to the primary spindle, several secondary and smaller bipolar spindles organized themselves around individual univalents and groups of univalents. Almost all (97%) of the PMCs showed secondary spindles. Each spindle functioned independently and despite their multiple numbers in a cell, meiosis I proceeded normally, with polyad formation. These observations strongly support the view that in plant meiocytes bilateral kinetochore symmetry is not required for establishing a bipolar spindle and that single unpaired chromosomes can initiate and stabilize the formation of a functional bipolar spindle.

Mesosternal bristle number in a cosmopolitan drosophilid: an X-linked variable trait independent of sternopleural bristles

Abstract: Mesosternal (MS) bristles in Drosophila are a pair of machrochaetae found at the sternal end of the sternopleural (STP) microchaetae, and are thought to be invariable In a closely related drosophilid genus, Zaprionus, their number is four and, in contrast to Drosophila, they show interspecific and intraspecific variability The genetic basis of MS bristle number variability was studied in Z indianus, the only cosmopolitan species of the genus The trait responded rapidly to selection and two lines were obtained, one lacking any bristles (0-0) and the other bearing the normal phenotype (2-2) Other symmetrical phenotypes, (1-1) and (3-3), could also be selected for, but with lesser success By contrast, STP bristle number did not vary significantly between the two lines (0-0) and (2-2), revealing its genetic independence from MS bristle number Reciprocal crosses between these two lines showed that MS bristle number is mainly influenced by a major gene on the X chromosome (ie F1 males always resembled their mothers) with codominant expression (ie heterozygous F1 females harboured an average phenotype of 2 bristles) However, trait penetrance was incomplete and backcrosses revealed that this variability was partly due to genetic modifiers, most likely autosomal The canalization of MS bristle number was investigated under different temperatures, and the increased appearance of abnormal phenotypes mainly occurred at extreme temperatures There was a bias, however, towards bristle loss, as shown by a liability (developmental map) analysis Finally, when ancestral and introduced populations were compared, the latter were far less stable, suggesting that genetic bottlenecks may perturb the MS bristle number canalization system MS bristle number, thus, appears to be an excellent model for investigating developmental canalization at both the quantitative and the molecular level

Male accessory gland secretory protein polymorphism in natural populations of Drosophila nasuta nasuta and Drosophila sulfurigaster neonasuta.

Abstract: Male accessory gland secretory protein polymorphism was analysed in natural populations of Drosophila nasuta nasuta and D. sulfurigaster neonasuta for the first time, using SDS-PAGE to score polymorphism of these proteins in 2788 individuals of D. n. nasuta and 2232 individuals of D. s. neonasuta from 12 different populations from southern India. A total of 25 and 18 variant protein phenotypes were identified in D. n. nasuta and D. s. neonasuta, respectively. Protein fractions of group III were more polymorphic than those from groups I and II. The results show that accessory gland secretory proteins show high levels of polymorphism, irrespective of species or habitat. Moreover, we have used the variation in the accessory gland proteins to assess the extent of divergence between the species and to infer their population structure. The study suggests that though both D. n. nasuta and D. s. neonasuta belong to the same subgroup, they differ in population structure, as far as accessory gland protein polymorphism is concerned.

A new method of testing for Hardy-Weinberg equilibrium and ordering populations.

Abstract: The assumption of Hardy-Weinberg equilibrium (HWE) among alleles in a nonevolving population is of fundamental importance in genetic studies. Deviation from HWE in a population usually indicates inbreeding, stratification and sometimes problems in genotyping. In populations of affected individuals, these deviations can also provide evidence for association. In this paper, we introduce a measure based on the Kullback-Leibler discrimination information function that quantifies the deviation from HWE in a population. We use this measure to order populations. We also propose a test for HWE based on an estimate of this measure. The test is a statistically consistent test of the null hypothesis for all alternatives and is very easy to implement. Our proposed test statistic is compared with an earlier, widely used, test. Finally, the use of the proposed new test is shown in an illustrative example.

Patterns of nucleotide sequence variation in ICAM1 and TNF genes in twelve ethnic groups of India: roles of demographic history and natural selection.

Abstract: We have studied DNA sequence variation in and around the genes ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India, with a view to investigating the relative roles of demographic history and natural selection in shaping the observed patterns of variation. The total numbers of single nucleotide polymorphisms (SNPs) detected at the ICAM1 and TNF loci were 29 and 12, respectively. Haplotype and allele frequencies differed significantly across populations. The site frequency spectra at these loci were significantly different from those expected under neutrality, and showed an excess of intermediate-frequency variants consistent with balancing selection. However, as expected under balancing selection, there was no significant reduction of F ST values compared to neutral autosomal loci. Mismatch distributions were consistent with population expansion for both loci. On the other hand, the phylogenetic network among haplotypes for the TNF locus was similar to expectations under population expansion, while that for the ICAM1 was as expected under balancing selection. Nucleotide diversity at the ICAM1 locus was an order of magnitude lower in the promoter region, compared to the introns or exons, but no such difference was noted for the TNF gene. Thus, we conclude that the pattern of nucleotide variation in these genes has been modulated by both demographic history and selection. This is not surprising in view of the known allelic associations of several polymorphisms in these genes with various diseases, both infectious and noninfectious.

Mapping autonomously replicating sequence elements in a 73-kb region of chromosome II of the fission yeast, Schizosaccharomyces pombe.

Abstract: Autonomously replicating sequence (ARS) elements are the genetic determinants of replication origin function in yeasts. They can be easily identified as the plasmids containing them transform yeast cells at a high frequency. As the first step towards identifying all potential replication origins in a 73-kb region of the long arm of fission yeast chromosome II, we have mapped five new ARS elements using systematic subcloning and transformation assay. 2D analysis of one of the ARS plasmids that showed highest transformation frequency localized the replication origin activity within the cloned genomic DNA. All the new ARS elements are localized in two clusters in centromere proximal 40 kb of the region. The presence of at least six ARS elements, including the previously reported ars727, is suggestive of a higher origin density in this region than that predicted earlier using a computer based search.

Time to death in the presence of E. coli: a mass-scale method for assaying pathogen resistance in Drosophila.

Abstract: There is now increasing realization that tradeoffs between parasite or pathogen resistance and other life-history related traits could play an important role in shaping life-history evolution (Sheldon and Verhulst 1996; Zuk and Stoehr 2002), and a few experimental studies have examined such tradeoffs in Drosophila (Hoang 2001; Kraaijeveld et al. 2001; McKean and Nunney 2001) and other insects (Moret and Schmidt-Hempel 2000; Hosken 2001; Adamo et al. 2001; Cotter et al. 2004). D. melanogaster has a well-developed innate immune system that is well characterized genetically (Rutschmann et al. 2000; De Gregorio et al. 2001; Irving et al. 2001) and involves phagocytosis, melanization and production of antimicrobial peptides (Elrod-Erickson et al. 2000; Hoffmann 2003). Given that it is also one of the best studied model systems for life-history evolution (Prasad and Joshi 2003), D. melanogaster is an attractive choice for studies on life-history related tradeoffs involving the immune system (Sharmila Bharathi et al. 2004). A potential limitation in using D. melanogaster for rigorous evolutionary experimentation on immune function tradeoffs with life-history related traits is that neither the commonly used infection technique (pricking the fly with a contaminated needle: ElrodErickson et al. 2000; Rutschmann et al. 2000; De Gregorio et al. 2001; McKean and Nunney 2001), nor the typical assays for immune competence (e.g. rate of clearing of pathogen: McKean and Nunney 2001; level of antimicrobial peptides induced: Rutschmann et al. 2000; extent of phagocytosis:

Evolutionary appearance of mononucleotide repeats in the coding sequences of four genes in primates

Abstract: The replication instability of homopolymeric nucleotide runs is associated with several human diseases and has linked with colorectal cancers (Shibata et al. 1994). Little is known, however, about the evolutionary pattern of these sequences. The aim of this study was to analyse the long homopolymeric nucleotide runs that are unstable regions subject to replication errors, present in the coding sequence of four genes, TGFBRII, BAX, MSH6 andMLH3, in six nonhuman primates encompassing 55 million years of evolution, and in humans. The results show that the (A)10 of TGFBRII and the (G)8 of BAX are already present in the ancestral ring-tailed lemur. The (C)8 of MSH6 appears during the orangutan–gorilla divergence and the (A)9 ofMLH3 coexists with a putative precursor of the homopolymeric nucleotide runs until the rhesus macaque–orangutan divergence. Variations between clones of the homopolymeric nucleotide runs in each species are probably somatic changes due to slipped mispairing. They are not observed with homopolymeric nucleotide runs of less than eight nucleotides and, with runs of eight nucleotides or more, there is a tendency toward an increase in the sequence variations with the length of the run.