Alleles In Genome Research Articles

Microarray analysis unmasked paternal uniparental disomy of chromosome 12 in a patient with isolated sulfite oxidase deficiency

BackgroundIn the investigation of a proband with a biochemical diagnosis of isolated sulfite oxidase deficiency, we identified a homozygous nonsense mutation of the SUOX gene in the proband. However, the mutation was only detected in the father and not the mother. Deletion of the SUOX gene of the mother and paternal disomy of chromosome 12, where the SUOX gene is located, were suspected in view that allele dropout of the mother non-amplified wild-type allele is unlikely. MethodsTo distinguish the two possible causes, we performed a genome wide microarray analysis in the patient and parents using high-density single-nucleotide microarrays. Whole genome allele sharing of the genomes of the patient and parents were performed by dChip. ResultsIn the proband, the whole genome scan showed loss of heterozygosity (LOH) of the entire chromosome 12. However, the LOH is copy neutral and deletion of the SUOX gene of the mother was thus excluded. On whole genome allele sharing analysis, the proband showed a high degree of allele sharing with the father and a very low allele sharing with the mother only in chromosome 12. The cause of the homozygosity of the mutation of the patient is UPD (12) pat. ConclusionsTo the best of our knowledge, this study is the first UPD (12) pat causing isolated sulfite oxidase deficiency in humans. Even with one parent being a carrier of an autosomal recessive disease, a fetus with the autosomal recessive disease is still possible. This will have clinical impact on genetic counseling.

A Computational Workflow to Identify Allele-specific Expression and Epigenetic Modification in Maize

Allele-specific expression refers to the preferential expression of one of the two alleles in a diploid genome, which has been thought largely attributable to the associated cis-element variation and allele-specific epigenetic modification patterns. Allele-specific expression may contribute to the heterosis (or hybrid vigor) effect in hybrid plants that are produced from crosses of closely-related species, subspecies and/or inbred lines. In this study, using Illumina high-throughput sequencing of maize transcriptomics, chromatic H3K27me3 histone modification and DNA methylation data, we developed a new computational framework to identify allele-specifically expressed genes by simultaneously tracking allele-specific gene expression patterns and the epigenetic modification landscape in the seedling tissues of hybrid maize. This approach relies on detecting nucleotide polymorphisms and any genomic structural variation between two parental genomes in order to distinguish paternally or maternally derived sequencing reads. This computational pipeline also incorporates a modified Chi-square test to statistically identify allele-specific gene expression and epigenetic modification based on the Poisson distribution.

The wheat Lr34 gene provides resistance against multiple fungal pathogens in barley

The Lr34 gene encodes an ABC transporter and has provided wheat with durable, broad-spectrum resistance against multiple fungal pathogens for over 100years. Because barley does not have an Lr34 ortholog, we expressed Lr34 in barley to investigate its potential as a broad-spectrum resistance resource in another grass species. We found that introduction of the genomic Lr34 sequence confers resistance against barley leaf rust and barley powdery mildew, two pathogens specific for barley but not virulent on wheat. In addition, the barley lines showed enhanced resistance against wheat stem rust. Transformation with the Lr34 cDNA or the genomic susceptible Lr34 allele did not result in increased resistance. Unlike wheat, where Lr34-conferred resistance is associated with adult plants, the genomic Lr34 transgenic barley lines exhibited multipathogen resistance in seedlings. These transgenic barley lines also developed leaf tip necrosis (LTN) in young seedlings, which correlated with an up-regulation of senescence marker genes and several pathogenesis-related (PR) genes. In wheat, transcriptional expression of Lr34 is highest in adult plants and correlates with increased resistance and LTN affecting the last emerging leaf. The severe phenotype of transgenic Lr34 barley resulted in reduced plant growth and total grain weight. These results demonstrate that Lr34 provides enhanced multipathogen resistance early in barley plant development and implies the conservation of the substrate and mechanism of the LR34 transporter and its molecular action between wheat and barley. With controlled gene expression, the use of Lr34 may be valuable for many cereal breeding programmes, particularly given its proven durability.

Deleterious Alleles in the Human Genome Are on Average Younger Than Neutral Alleles of the Same Frequency

Large-scale population sequencing studies provide a complete picture of human genetic variation within the studied populations. A key challenge is to identify, among the myriad alleles, those variants that have an effect on molecular function, phenotypes, and reproductive fitness. Most non-neutral variation consists of deleterious alleles segregating at low population frequency due to incessant mutation. To date, studies characterizing selection against deleterious alleles have been based on allele frequency (testing for a relative excess of rare alleles) or ratio of polymorphism to divergence (testing for a relative increase in the number of polymorphic alleles). Here, starting from Maruyama's theoretical prediction (Maruyama T (1974), Am J Hum Genet USA 6:669–673) that a (slightly) deleterious allele is, on average, younger than a neutral allele segregating at the same frequency, we devised an approach to characterize selection based on allelic age. Unlike existing methods, it compares sets of neutral and deleterious sequence variants at the same allele frequency. When applied to human sequence data from the Genome of the Netherlands Project, our approach distinguishes low-frequency coding non-synonymous variants from synonymous and non-coding variants at the same allele frequency and discriminates between sets of variants independently predicted to be benign or damaging for protein structure and function. The results confirm the abundance of slightly deleterious coding variation in humans.

Comparison of the Development Diabetic Induced Renal Disease in Strains of Goto-Kakizaki Rats

This study compared temporal changes in renal hemodynamics, proteinuria and the development of renal disease in Goto-Kakizaki (GK) type II diabetic rats that are resistant to the development of diabetic nephropathy and a genetically modified GK substrain (T2DN) carrying the mitochondrial genome and other alleles from Fawn hooded-hypertensive (FHH) rats is more susceptible to the development of renal injury. Both GK and T2DN rats were diabetic (>250 mg/ dL) and blood glucose levels were not significantly different at 3, 6 and 18 months of age. Blood pressure was also similar in both strains at all 3 ages. Renal blood flow (RBF) was 45% higher in 3 month old T2DN rats than GK rats but glomerular filtration rate (GFR) was similar. T2DN rats exhibited a progressive increase in proteinuria from 41 ± 2 to 524 ± 50 mg/day and 57% fall in GFR as they aged from 3 to 18 months of age. In contrast, proteinuria only increased to 162 ± 31 mg/day in GK rats and GFR remained unaltered. The kidneys from 18 month old T2DN rats exhibited severe glomerulosclerosis, interstitial fibrosis and tubular necrosis while kidneys from GK rats did not. Plasma creatinine levels were 2.4 fold higher in 18 month old T2DN than in GK rats. These data demonstrate that T2DN rats develop most of the features of diabetic nephropathy including progressive proteinuria and chronic kidney disease whereas the closely related GK strain does not, even though blood pressure and the level of hyperglycemia are similar.

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kühn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1Mb for the diploid status of the genome. ‘Contig-length vs. read-count’ analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7#130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214bp, whereas introns on average are 66bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories.

Genome-wide analysis of key salinity-tolerance transporter (HKT1;5) in wheat and wild wheat relatives (A and D genomes)

Exclusion of sodium ions from cells is one of the key salinity tolerance mechanisms in plants. The high-affinity cation transporter (HKT1;5) is located in the plasma membrane of the xylem, excluding Na+ from the parenchyma cells to reduce Na+ concentration. The regulatory mechanism and exact functions of HKT genes from different genotypic backgrounds are relatively obscure. In this study, the expression patterns of HKT1;5 in A and D genomes of wheat were investigated in root and leaf tissues of wild and domesticated genotypes using real-time PCR. In parallel, the K+/Na+ ratio was measured in salt-tolerant and salt-sensitive cultivars. Promoter analysis were applied to shed light on underlying regulatory mechanism of the HKT1;5 expression. Gene isolation and qPCR confirmed the expression of HKT1;5 in the A and D genomes of wheat ancestors (Triticum boeoticum, AbAb and Aegilops crassa, MMDD, respectively). Interestingly, earlier expression of HKT1;5 was detected in leaves compared with roots in response to salt stress. In addition, the salt-tolerant genotypes expressed HKT1;5 before salt-sensitive genotypes. Our results suggest that HKT1;5 expression follows a tissue- and genotype-specific pattern. The highest level of HKT1;5 expression was observed in the leaves of Aegilops, 6 h after being subjected to high salt stress (200 mM). Overall, the D genome allele (HKT1;5-D) showed higher expression than the A genome (HKT1;5-A) allele when subjected to a high NaCl level. We suggest that the D genome is more effective regarding Na+ exclusion. Furthermore, in silico promoter analysis showed that TaHKT1;5 genes harbor jasmonic acid response elements.

Polymorphisms upstream of the melanocortin‐1 receptor coding region are associated with human pigmentation variation in a Brazilian population

We describe an association of two SNPs, rs3212345:C>T and rs3212346:G>A, located approximately 2.5 kb upstream of the melanocortin-1 receptor (MC1R) translation initiation codon, with pigmentation phenotype variation in a Southeast Brazilian miscegenated population. One hundred thirty-eight genetically unrelated subjects, with multicolor phenotype, were selected from the southeast region of Brazil. Skin, hair and eye color, and tanning ability were rated. Genotypes for each SNP (rs3212345:C>T and rs3212346:G>A) were determined. A logistic regression analysis was performed with the additive model to determine which of the polymorphisms contributed to a specific phenotype. We found that the rs3212345:C>T is associated with light skin, red hair, and poor tanning ability, while the rs3212346:G>A is associated with dark skin, black hair, and strong tanning ability. The presence of rs3212345-C and rs3212346-A alleles in human, chimpanzee, gorilla, orangutan, and marmoset genomes suggests that they are the ancestral alleles. These data suggest that the rs3212345-T and rs3212346-G alleles may have contributed to lighter pigmentation phenotypes in modern humans. Genotyping for these SNPs may prove useful to the fields of molecular anthropology and forensic genetics.

Characterization of the S-RNase genomic DNA allele sequence in Prunus speciosa and P. pseudocerasus

In this study, eight S-RNase alleles were isolated from two Prunus pseudocerasus and two Prunus speciosa accessions by PCR amplification from genomic DNA. Analysis of the amino acid sequences revealed five novel and three published S-alleles. These S-RNases share typical structural features with S-RNases from other Prunus species exhibiting gametophytic self-incompatibility. The deduced amino acid identities ranged from 60.8 to 75.6% among four S-RNase alleles in Prunus speciosa and ranged from 73 to 81.4% among four S-RNase alleles in Prunus pseudocerasus. The size of the first introns ranged from 197 to 341bp, and the size of second introns ranged from 81 to 1182bp. Sequence analysis demonstrated that the deduced amino acid identities, by comparison with other Prunus species, were often higher than those of intraspecific identities. Moreover, exceptionally high identities were found between Pspe-S1 and Pd-S28; between Pspe-S31 and Pm-S6; among Pspe-S51, Pa-S29 and Pweb-S7; and among Pps-S13, Psim-S4 and Ps-Sb, indicating that the S-RNase alleles evolved before Prunus species divergence. Interestingly, the similarities of the first and second introns were also high between the two S-RNase alleles, which range from 83.63 to 100% among the first introns and from 46.13 to 100% among the second introns. These information could not increase our knowledge on the S-alleles of Prunus species, but is available for molecular breeding of fruit trees, to avoid cross-incompatibility.

Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.

Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations.

Cannabinoids: Novel Medicines for the Treatment of Huntingtons Disease

Cannabinoid pharmacology has experienced a notable increase in the last 3 decades which is allowing the development of novel cannabinoid-based medicines for the treatment of different human pathologies, for example, Cesamet® (nabilone) or Marinol® (synthetic Δ9-tetrahydrocannabinol for oral administration) that were approved in 80s for the treatment of nausea and vomiting associated with chemotherapy treatment in cancer patients and in 90s for anorexiacachexia associated with AIDS therapy. Recently, the british company GW Pharmaceuticals plc has developed an oromucosal spray called Sativex®, which is constituted by an equimolecular combination of Δ9-tetrahydrocannabinol- and cannabidiol- enriched botanical extracts. Sativex® has been approved for the treatment of specific symptoms (i.e. spasticity and pain) of multiple sclerosis patients in various countries (i.e. Canada, UK, Spain, New Zealand). However, this cannabis- based medicine has been also proposed to be useful in other neurological disorders given the analgesic, antitumoral, anti-inflammatory, and neuroprotective properties of their components demonstrated in preclinical models. Numerous clinical trials are presently being conducted to confirm this potential in patients. We are particularly interested in the case of Huntington's disease (HD), an autosomal-dominant inherited disorder caused by an excess of CAG repeats in the genomic allele resulting in a polyQ expansion in the encoded protein called huntingtin, and that affects primarily striatal and cortical neurons thus producing motor abnormalities (i.e. chorea) and dementia. Cannabinoids have been studied for alleviation of hyperkinetic symptoms, given their inhibitory effects on movement, and, in particular, as disease-modifying agents due to their anti-inflammatory, neuroprotective and neuroregenerative properties. This potential has been corroborated in different experimental models of HD and using different types of cannabinoid agonists, including the phytocannabinoids present in Sativex®, and we are close to initiate a clinical trial with this cannabis-based medicine to evaluate its capability as a disease-modifying agent in a population of HD patients. The present review will address all preclinical evidence supporting the potential of Sativex® for the treatment of disease progression in HD patients. The article presents some promising patents on the cannabinoids.

Signatures of natural selection among lineages and habitats inOncorhynchus mykiss

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

Subcutaneous mass as the primary manifestation of gestational choriocarcinoma: A case report

1. IntroductionChoriocarcinoma is a highly malignant trophoblastic tumor com-posed of two types of cells, syncytiotrophoblasts and cytotrophoblasts(Seckl et al., 2010). Its incidence is reported variously from 1 in 13,000 to 50,000 pregnancies (Alveyn and Loehry, 1988). Metastasis ismost often associated with choriocarcinomas in contrast to other vari-ants of the GTT (Berkowitz and Goldstein, 1996). Choriocarcinomacommonly metastasizes to the lungs and vagina, and less commonly,to the liver, brain, kidneys and gastrointestinal tract (Bagshawe,1992). Vaginal bleeding, abdominal swelling, amenorrhea, chest andneurologicalsymptomsarethemostcommonpresentationsdependingontheextentofthedisease,butbyfarthecommonestsymptomisvag-inal bleeding, a consequence of the tumor invading the uterus (Chamaet al., 2002).To the best of our knowledge, there was no choriocarcinoma withclinical presentation of subcutaneous metastasis reported in the liter-ature. An abdominal subcutaneous mass as the primary manifestationof choriocarcinoma is extremely rare and difficult for diagnosis. Herewe reported a case of gestational choriocarcinoma with the primarymanifestationof subcutaneousmetastasis10 yearsafterher lastpreg-nancy. No uterine or ovarian tumors were noted except subcutaneoustumor over anterior abdominal wall with bilateral multiple pulmo-nary nodules by image studies. Wide excision of the abdominal tumorrevealed that the tumor cells were positive for cytokeratin and humanchorionic gonadotropin by immunohistochemical stainings. DNA poly-morphism analysis revealed that the tumor cells possessed both geno-mic DNA alleles from the patient and her husband. Gestationalchoriocarcinoma was finally diagnosed. The serum level of β-hCG inthepatientwas 382 mIu/ml after surgery. So the EMA-COchemothera-peutic regimens (etoposide, methotrexate, and actinomycin, followedbycyclophosphamideandvincristine)weregiven.Thepatientachievedclinicalremissionfor7 monthsafterchemotherapy.Subcutaneousmasscan be the first manifestation of choriocarcinoma. Choriocarcinomashould be the differential diagnosis for special manifestation ofwomen in reproductive ages.2. Case reportA49-year-oldwomanpalpatedarapidgrowingmassoverlowerab-domen for three months. Her menstrual cycles became irregular since2 months ago. The patient had conceived 7 times with 4 miscarriagesand her three children were all delivered through cesarean section.Her last cesarean section was 20 years ago and her last pregnancy wasartificial abortion 10years ago.Pelvicexaminationrevealedasmoothcervix,andnormalsizeofuter-usandbilateraladnexae.Amultilo culatedmasswhichwasaroundbase-ball size within the abdominal wall was noted. The subcutaneous masslocated nearby the wound of the cesarean section with intact abdominalskin. Transabdominal ultrasonography revealed a multilocular tumormeasuring 8×6×5 cm located behind the cesarean scar and within thelower anterior subcutaneous layer. No abnormal finding was identifiedin the endometrial cavity, uterus and bilateral ovaries. Magnetic reso-nance imaging (MRI) study showed a large in filtrative and heteroge-neous mass, measured around 14 cm in largest dimension, and locatedwithin the anterior pelvis wall ( Fig. 1). Computed tomography (CT)study showed bilateral multiple pulmonary nodules. Subcutaneous ma-lignancy with pulmonary metastases was suspected. Biopsies of the ab-dominal wall tumor were undergone and the pathologic reportrevealed a poorly-differentiated squamous cell carcinoma. Immunohis-tochemically, the tumor cells were po sitive for cytokeratin (AE1/AE3)andp63butnegativeforvimentin,CD31,CD34,S-100 protein,calretinin

An MDR1 promoter allele with higher promoter activity is common in clinically isolated strains of Candida albicans

In the opportunistic fungal pathogen Candida albicans, up-regulation of MDR1, encoding an efflux transporter, leads to increased resistance to the antifungal drug fluconazole. Antifungal resistance has been linked to several types of genetic change in C. albicans, including changes in genome structure, genetic alteration of the drug target, and overexpression of transporters. High-level over-expression of MDR1 is commonly mediated by mutation in a trans-acting factor, Mrr1p. This report describes a second mechanism that contributes to up-regulation of MDR1 expression. By analyzing the sequence of the MDR1 promoter region in fluconazole-resistant and fluconazole-susceptible strains, we identified sequence polymorphisms that defined two linkage groups, corresponding to the two alleles in the diploid genome. One of the alleles conferred higher MDR1 expression compared with the other allele. Strains in which both alleles were of the higher activity type were common in collections of clinically isolated strains while strains carrying only the less active allele were rare. As increased expression of MDR1 confers higher resistance to drugs, strains with the more active MDR1 promoter allele may grow or survive longer when exposed to drugs or other selective pressures, providing greater opportunity for mutations that confer high-level drug resistance to arise. Through this mechanism, higher activity alleles of the MDR1 promoter could promote the development of drug resistance.

Haploid transcriptome analysis reveals allelelic gene expression variants, co-expressed gene groups, and linkages between expression and copy number variation

Background Genetic variation can cause changes in gene expression (mRNA abundance) among individuals. This so-called heritable variation in gene expression is affected by genetic variants that are co-segregating with the gene locus (local/cis effects) and/or segregating independently from it (distant/trans effects). Genetic variation in gene expression can be measured to estimate the extant of variation in gene expression within a population, and to determine to what degree expression alleles of different genes are connected within regulatory networks. Furthermore, determining whether variation in the expression of a gene is linked to local or distant effects allows us to make inferences about how heritable variation may change depending on gene function, the number of interacting partners, genetic architecture and evolutionary history [1,2]. Detecting heritable variation in gene expression can be a challenging task in diploid organisms, mainly because of tissue-specificity and dominance effects of allelic expression. For example, up to 70% of gene expression alleles in Drosophila may be masked by dominance [3]. We developed an experimental system to overcome these obstacles by utilizing the conifer seed’s maternally derived haploid tissue, the megagametophyte. Analyzing a set of sibling megagametophytes allows us to first, measure separately the expression each of the two alleles in the maternal genome in the absence of dominance and second, identify genes whose expression levels are co-segregating. In addition, the megagametophyte allows us to categorize the underlying genetic variants into local or distant with a simple co-segregation assay.

Simple Sequence Repeat Polymorphisms in Nigerian Sesame Cultivars and its Relationship with Morpho-Agronomic Traits

Sesame (Sesamum indicum L.) is an important oilseed crop of global importance. The genetic diversity of 30 Nigerian sesame cultivars was characterized using simple sequence repeat (SSR) markers, and the molecular polymorphisms were related to the divergence in morpho-agronomic traits. The cultivars varied significantly in shattering characteristics, days to germination (4–7 days), plant height (85–183 cm), flowering time (60–125 days), number of flowers/axil (1–2), maturity period (89–130 days), and seed size (6.2–8.0 mm). Significant correlations were observed among these morpho-agronomic traits, with the strongest correlation being between days to germination and shattering characteristics (r = 0.937, p < 0.0001). The potential utility of the SSR marker technology in sesame genome analysis was assessed based on the screening of 10 sesame SSR primer pairs that were highly polymorphic. Three to six alleles were observed per SSR locus, with an average of 4.6 alleles in the sesame genome and fragment size ranging from 150 to 307 bp. High genetic variability was found among the accessions, with the repeat motifs (TC12–TC25) from two selected highly informative primer pairs clearly differentiating the 30 cultivars into eight groups. The observed diversity at the molecular level closely reflected the wide variation in phenotypic traits and can serve as a useful tool for unlocking the genetic diversity in the Nigerian sesame cultivars for plant breeding purposes.

From genes to games: Cooperation and cyclic dominance in meiotic drive

Evolutionary change can be described on a genotypic level or a phenotypic level. Evolutionary game theory is typically thought of as a phenotypic approach, although it is frequently argued that it can also be used to describe population genetic evolution. Interpreting the interaction between alleles in a diploid genome as a two player game leads to interesting alternative perspectives on genetic evolution. Here we focus on the case of meiotic drive and illustrate how meiotic drive can be directly and precisely interpreted as a social dilemma, such as the prisoners dilemma or the snowdrift game, in which the drive allele takes more than its fair share. Resistance to meiotic drive can lead to the well understood cyclic dominance found in the rock–paper–scissors game. This perspective is well established for the replicator dynamics, but there is still considerable ground for mutual inspiration between the two fields. For example, evolutionary game theorists can benefit from considering the stochastic evolutionary dynamics arising from finite population size. Population geneticists can benefit from game theoretic tools and perspectives on genetic evolution.

Polymorphism of SSR alleles in pear cultivars grown in Belarus

Using SSR markers designed for Malus x domestica Borkh, genetic polymorphism of 43 pear accessions cultivated in Belarus was examined. A total of 217 alleles were identified with the mean number of 12.8 alleles per marker. The mean PIC value was 0.81; the mean number of informative alleles, 6.49. The heterozygosity level ranged from 0.30 to 0.84. Genetic diversity of SSR alleles in pear and apple genomes was compared. A method of identification of commercial pear cultivars using a set of six SSR markers was suggested.

Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

BackgroundGenetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat.ResultsBased on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry.ConclusionsThe high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.

The tendency to recreate ancestral CG dinucleotides in the human genome

BackgroundThe CG dinucleotides are known to be deficient in the human genome, due to a high mutation rate from 5-methylated CG to TG and its complementary pair CA. Meanwhile, many cellular functions rely on these CG dinucleotides, such as gene expression controlled by cytosine methylation status. Thus, CG dinucleotides that provide essential functional substrates should be retained in genomes. How these two conflicting processes regarding the fate of CG dinucleotides - i.e., high mutation rate destroying CG dinucleotides, vs. functional processes that require their preservation remains an unsolved question.ResultsBy analyzing the mutation and frequency spectrum of newly derived alleles in the human genome, a tendency towards generating more CGs was observed, which was mainly contributed by an excess number of mutations from CA/TG to CG. Simultaneously, we found a fixation preference for CGs derived from TG/CA rather than CGs generated by other dinucleotides. These tendencies were observed both in intergenic and genic regions. An analysis of Integrated Extended Haplotype Homozygosity provided no evidence of selection for newly derived CGs.ConclusionsAncestral CG dinucleotides that were subsequently lost by mutation tend to be recreated in the human genome, as indicated by a biased mutation and fixation pattern favoring new CGs that derived from TG/CA.