Pair Of Alleles Research Articles

Conversion and determination of sex in Vitis vinifera L. ( sylvestris )

Sex conversion in the male V. vinifera ( sylvestris ) clone 030-44 could not be attributed to germinal mutation of the major gene for sex. The differences in sex expression among male seedling vines can best be explained on the basis of an undetermined number of minor modifying genes able to shift a very sensitive threshold. The frequency of sex conversion within a given seedling vine was greatly influenced by environmental, both local and seasonal, conditions. The following facts were established in Vitis vinifera L. ( sylvestris ): (1) the male sex is heterogametic and is inherited as a simple Mendelian factor, maleness being completely dominant; (2) homozygous males are as viable as heterozygous males, they are phenotypically alike and can only be identified by breeding tests; (3) pure and hermaphroditic males are genetically alike as far as the major gene for sex is concerned; (4) sex chromosomes are not differentiated, either morphologically or physiologically. A pair of alleles, SuF and Sum, were used to explain the results obtained on selfing the hermaphroditic male clone 030-44. The gene Su F determines maleness and its allele Su m in homozygous condition determines femaleness. The gene Su F is completely dominant over its allele Sum. The genotypes of the homozygous and heterozygous males are Su F Su F and Su F Su m respectively, and that of the female is Su m Su m . The evolution of cultivated V. vinifera hermaphrodites in the light of present results is discussed.

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci.

Three members of the Puccinia genus, Puccinia triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt. Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.

Variability of issr markers and estimation of inheritance of diagnostic characters among StY-genome species of Elymus pendulinus, E. brachypodioides and E. vernicosus (Poaceae: Triticeae)

Currently three species are recognized in Russia within the genus Elymus subsection Pendulini, namely, E. pendulinus, E. brachypodioides and E. vernicosus. The degree and quality of lemma and stem node vestitures and ecology are considered important characters for species delineation. In Primorsky krai and Altai Republic we have found a number of mixed populations in which there is visually continuous variation in lemmas vestitures from being completely glabrous to densely puberulent or pilose. Additionally, there are a number of populations in Primorsky krai in which individuals having either smooth or pilous stem nodes grow together. A study of polymorphism of ISSR markers among selective accessions of three species from different locations was carried out together with the reference species E. ciliaris and E. gmelinii. The consensus dendrogramm constructed by results of ISSR markers has shown no taxon specific patterns in accessions of the subsection Pendulini. Hybrids between the individuals of different species of the subsection in six cross combinations have been created. All F1 plants had normally developed open anthers, seed fertility (SF) ranged from 8 % to 89 % in different combinations. In F2 populations no sterile individuals or increase of SF up to normal values were observed. Hence, three taxa form a unified recombination gene pool. The diagnostic characters were found to be controlled by one pair of alternative alleles for glabrous vs. hairy stem nodes, and by one or two pairs of alleles in different cross combinations for glabrous vs. hairy lemmas. These characters can be considered as normal inter- and/or intra-population variation. Therefore, E. brachypodioides and E. vernicosus need to be relegated to infraspecific rank within Elymus pendulinus s. l. as varieties.

Cell Biology of Cheating-Transmission of Centromeres and Other Selfish Elements Through Asymmetric Meiosis.

Mendel's First Law of Genetics states that a pair of alleles segregates randomly during meiosis so that one copy of each is represented equally in gametes. Whereas male meiosis produces four equal sperm, in female meiosis only one cell, the egg, survives, and the others degenerate. Meiotic drive is a process in which a selfish DNA element exploits female meiotic asymmetry and segregates preferentially to the egg in violation of Mendel's First Law, thereby increasing its transmission to the offspring and frequency in a population. In principle, the selfish element can consist either of a centromere that increases its transmission via an altered kinetochore connection to the meiotic spindle or a centromere-like element that somehow bypasses the kinetochore altogether in doing so. There are now examples from eukaryotic model systems for both types of meiotic drive. Although meiotic drive has profound evolutionary consequences across many species, relatively little is known about the underlying mechanisms. We discuss examples in various systems and open questions about the underlying cell biology, and propose a mechanism to explain biased segregation in mammalian female meiosis.

Limited HLA sequence variation outside of antigen recognition domain exons of 360 10 of 10 matched unrelated hematopoietic stem cell transplant donor-recipient pairs.

Traditional DNA-based typing focuses primarily on interrogating the exons of human leukocyte antigen (HLA) genes that form the antigen recognition domain (ARD). The relevance of mismatching donor and recipient for HLA variation outside the ARD on hematopoietic stem cell transplantation (HSCT) outcomes is unknown. This study was designed to evaluate the frequency of variation outside the ARD in 10 of 10 (HLA-A, -B, -C, -DRB1, -DQB1) matched unrelated donor transplant pairs (n = 360). Next-generation DNA sequencing was used to characterize both HLA exons and introns for HLA-A, -B, -C alleles; exons 2, 3 and the intervening intron for HLA-DRB1 and exons only for HLA-DQA1 and -DQB1. Over 97% of alleles at each locus were matched for their nucleotide sequence outside of the ARD exons. Of the 4320 allele comparisons overall, only 17 allele pairs were mismatched for non-ARD exons, 41 for noncoding regions and 9 for ARD exons. The observed variation between donor and recipient usually involved a single nucleotide difference (88% of mismatches); 88% of the non-ARD exon variants impacted the amino acid sequence. The impact of amino acid sequence variation caused by substitutions in exons outside ARD regions in D-R pairs will be difficult to assess in HSCT outcome studies because these mismatches do not occur very frequently.

Inheritance of leaf and flower morphologies in Kalanchoe spp.

Members of the genus Kalanchoe are morphologically diverse; this increases their commercial value. Understanding the genetic mechanism of development of morphological characters could contribute to parent screening and offspring selection in future breeding programs. In this study, we investigated the inheritance of leaf color, leaf shape, anther color, and flower orientation of Kalanchoe species or varieties. Kalanchoe garambiensis, K. garambiensis G., K. gracilis, K. spathulata, and K. manginii ‘Wendy’ were used as experimental parents to establish self and interspecific crosses. The separation ratios of the leaf and flower traits were analyzed using Chi square tests. The results showed that all progenies produced by selfing of K. garambiensis (purple leaf phenotype) had purple leaves, whereas those from selfing of K. garambiensis G. (green leaf phenotype) exhibited green and purple leaves at a ratio of approximately 3:1. The S1 and S2 populations of K. garambiensis G. exhibited an expected 3:1 ratio of leaf color, whereas the S3 populations produced all green leaf inbred lines. Reciprocal hybridization of the progenies of K. gracilis (deeply lobed leaf) with K. garambiensis G. (shallowly lobed leaf) resulted in a 1:1 ratio of shallowly lobed leaves to deeply lobed leaves. The progenies of the two cross combinations (K. garambiensis G. × K. manginii ‘Wendy’ and K. garambiensis × K. manginii ‘Wendy’) produced upright-type flowers and anthers having purplish red color. These findings suggested that leaf color, leaf shape, anther color, and flower orientation of Kalanchoe are controlled by a single pair of alleles. Green leaf, deeply loped leaves, purplish red anthers, and upright-type flowers were found to be dominant traits.

Association of HLA-A and Non-Classical HLA Class I Alleles.

The HLA-A locus is surrounded by HLA class Ib genes: HLA-E, HLA-H, HLA-G and HLA-F. HLA class Ib molecules are involved in immuno-modulation with a central role for HLA-G and HLA-E, an emerging role for HLA-F and a yet unknown function for HLA-H. Thus, the principal objective of this study was to describe the main allelic associations between HLA-A and HLA-H, -G, -F and -E. Therefore, HLA-A, -E, -G, -H and -F coding polymorphisms, as well as HLA-G UnTranslated Region haplotypes (referred to as HLA-G UTRs), were explored in 191 voluntary blood donors. Allelic frequencies, Global Linkage Disequilibrium (GLD), Linkage Disequilibrium (LD) for specific pairs of alleles and two-loci haplotype frequencies were estimated. We showed that HLA-A, HLA-H, HLA-F, HLA-G and HLA-G UTRs were all in highly significant pairwise GLD, in contrast to HLA-E. Moreover, HLA-A displayed restricted associations with HLA-G UTR and HLA-H. We also confirmed several associations that were previously found to have a negative impact on transplantation outcome. In summary, our results suggest complex functional and clinical implications of the HLA-A genetic region.

Fine mapping of a fertility restoring gene for a new CMS hybrid rice system

The Fujian Abortion cytoplasmic male sterility (CMS-FA) system, a new type of sporophytic CMS system in indica rice (Oryza sativa L.), was developed using the cytoplasm and the corresponding fertility-restoring gene from a wild rice (O. rufipogon L.), which originated from Fujian Province, China. Previous studies in combination with several years of production practice demonstrated that CMS-FA hybrid rice was superior to CMS-WA hybrid rice, a prevailing hybrid rice worldwide, and that the male fertility restoration was controlled by a pair of dominant alleles. We tentatively designated the fertility restoration gene as Rf(fa). The analysis of the polymorphism between the fertile and sterile pool DNAs from a mapping segregation population (BC1F1) indicated that Rf(fa) was located on rice chromosome 10. We further delimited the Rf(fa) locus to a 121.1-kb region flanked by RM6100 and MM2023, which were approximately 0.26 cM and 0.18 cM away from Rf(fa), respectively, by simple sequence repeat molecular marker linkage genetic analysis. These results would facilitate the map-based cloning of Rf(fa), the elucidation of a novel molecular mechanism underlying cytoplasm–nucleus interaction in the CMS-FA system, and the production application of this hybrid rice.

OR18 Full gene sequencing reveals very limited variation in the regions outside of the antigen recognition domains (ARD) of 360 unrelated hematopoietic stem cell transplant donor-recipient pairs matched for 10/10 at high resolution

Aim Traditional DNA-based typing focuses primarily on interrogating the exons of HLA genes that form the ARD (peptide-binding region that interacts with T cell and killer immunoglobulin-like receptors). The relevance of mismatching outside the ARD on hematopoietic stem cell transplantation (HCT) outcomes is unknown. This study was designed to evaluate the frequency of variation outside the ARD in well matched transplant pairs. Methods 360 HLA-A, B, C, DRB1, and DQB1 high resolution matched donor (D)-recipient (R) pairs were selected based on availability of retrospective Sanger-based sequencing and DNA from the CIBMTR Repository. The majority of the population was self-identified Caucasian (80%). Next generation DNA sequencing was performed on the Illumina MiSeq platform and interpreted with Connexio Assign MPS. Class I gene sequences covered 5 ′ UTR-3 ′ UTR; DRB1, intron 1-intron 3; DQA1 5 ′ UTR-exon 4; DQB1, intron 1-3 ′ UTR. DQ noncoding regions were not evaluated. Results The majority (98.1%) of the HLA-A, B, C, DRB1 D-R allele pairs are matched for sequences outside the ARD exons: 0.5% differ in non-ARD exons, 1.9% differ in noncoding regions. A small number (0.2%) differ within ARD exons. Mismatches in non-ARD exons varies from 0.7% for HLA-C and DQA1 to 0% DQB1; noncoding variation ranges from 2.8% for HLA-C to 1.3%, HLA-B and DRB1. Within non-ARD exons, both nonsynonymous (16 allele pairs) and silent (2) variation is present. Intron variation is minor, usually a single nucleotide. Conclusions This is the first study to evaluate the genetic variation and characterize mismatching outside of the ARD in a cohort of HLA-matched donor-recipient pairs. The paucity of exonic mismatches outside of the ARD is striking. Intronic variation is more common but would not contribute to an alloreactive mismatch. At present, it does not appear to be necessary to increase the resolution of HLA typing beyond the ARD in selecting a matched donor except in cases of common non-expressed variants within G-group assignments. The impact of amino acid sequence variation caused by substitutions in exons outside ARD regions in D–R pairs will be difficult to assess in HCT outcome studies since it does not occur very frequently. Further study is warranted to confirm these findings in larger and more diverse cohorts.

P057 Measuring linkage disequilibrium with next-generation sequencing HLA typing data

Aim To show how HLA typing data from next-generation sequencing (NGS) can dramatically improve our estimates of linkage disequilibrium associations between different loci. Method Given a set of haplotypes in which loci have been placed in phase, for each pair of alleles (Xi, Yi) in two loci X and Y, a 2 × 2 contingency table (a, b, c, d) is built with the following counts: a = CARD(Xi and Yi); b = CARD(X that is not Xi and Yi); c = CARD(Xi and Y that is not Yi), and d = CARD(Xi that is not Xi and Y that is not Yi), where CARD() is a function that returns the cardinality of a set. From these 2 × 2 contingency tables several measures can be calculated, like the classical measure of linkage disequilibrium delta prime, or ‘mutual information’ from information theory, or the ‘ Ochiai semidistance’ from geometry, or chi square from statistical theory, or the likelihood ratio, as well as various useful conditional probabilities. Several testing sets with loci in phase were used. Linkage disequilibrium calculations were made at the classical high-resolution level (4-digit resolution) and at the full resolution level (4-field resolution). NGS typing was done with the Mia Fora technology from Immucor. Results A set of 755 DRB1-DQB1 blocks was used to calculate linkage disequilibrium between Xi = DQA1 ∗ 01:02 and Yi = DRB1 ∗ 13:02 (4-digit res.) and also between Xi = DQA1 ∗ 01:02:01:04 and Yi = DRB1 ∗ 13:02:01 (4-field res.). The results for the first comparison (4-digit res.) were (a, b, c, d) = (70, 0, 196, 489); and for the second comparison (4-field res.) were (a, b, c, d) = (70, 0, 0, 685). While the conditional probability of having DRB1 ∗ 13:02 in the presence of DQA1 ∗ 01:02 (4-digit res.) is 26%, the conditional probability of having DRB1 ∗ 13:02:01 in the presence of DQA1 ∗ 01:02:01:04 (4-field res.) is 100%. The chi square went from 141 for 4-digit res. to 755 for 4-field res. This is just an example of many such findings which will be presented at ASHI 2016. Conclusions Using 4-field resolution data from NGS often brings linkage disequilibrium to a much stronger level, sometime to a total certainty. The most efficient way to present linkage disequilibrium data is, as detailed here, in the form of the cardinality of the logical possibilities as a 2 × 2 contingency table.

Aneuploidy and asynchronous replication in non-alcholic fatty liver disease and cryptogenic cirrhosis

Background/aimsNon-alcoholic fatty liver disease (NAFLD) and cryptogenic cirrhosis (CC), which is largely a late sequela of NAFLD, are considered pre-neoplastic conditions that might progress to hepatocellular carcinoma. Aneuploidy, telomere aggregates and synchronization of replication were evaluated as markers of genetic instability in these patients. MethodologyPeripheral blood lymphocytes from 22 patients with NAFLD, 20 patients with CC and 20 age-matched healthy controls were analyzed. To determine random aneuploidy, we used the fluorescence in situ hybridization (FISH) with probes for chromosomes 9 and 18. The rate of aneuploidy was inferred from the fraction of cells revealing one, three or more hybridization signals per cell. Aggregate size was divided into three fusion groups of 2–5, 6–10 and 11–15 telomeres, relative to the size of a single telomere. The replication pattern was determined by FISH in two pairs of alleles, 15qter and 13qter. Asynchrony was determined by the presence of one single and one set of double dots in the same cell. ResultsSignificantly higher random aneuploidy rate was found in the CC patients than in the control group, and to a lesser degree in NAFLD patients. Telomere aggregates were insignificantly higher in both groups. Only patients with CC showed significantly higher rate of asynchronous replication with proportionately more cells with two single dots among the normal cells (p<0.001). ConclusionsThese results likely reflect changes in gene replication and cell cycle progression in these conditions, possibly correlating with their malignant potential.

Application of a library of near isogenic lines to understand context dependent expression of QTL for grain yield and adaptive traits in bread wheat.

BackgroundPrevious quantitative trait loci (QTLs) studies using the Avalon × Cadenza doubled haploid (DH) population identified eleven QTLs determining plant height, heading date and grain yield. The objectives of this study were: (i) to provide insight into the effects of these QTLs using reciprocal multiple near isogenic lines (NILs) with each pair of alleles compared in both parental backgrounds (Avalon or Cadenza), (ii) quantifying epistasis by looking at the background effects and (iii) predict favourable allelic combinations to develop superior genotypes adapted to a target environment.ResultsTo this aim, a library of 553 BC2 NILs and their recurrent parents were tested over two growing seasons (2012/2013 and 2013/2014). The results obtained in the present study validated the plant height, heading date and grain yield QTLs previously identified. Epistatic interactions were detected for the 6B QTL for plant height and heading date, 3A QTL for heading date and grain yield and 2A QTL for grain yield.ConclusionThe marker assisted backcrossing strategy used provided an efficient method of resolving QTL for key agronomic traits in wheat as Mendelian factors determining possible epistatic interactions. The study shows that these QTLs are amenable to marker assisted selection, fine mapping, future positional cloning, and physiological trait dissection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0849-6) contains supplementary material, which is available to authorized users.

Transvection in Drosophila: trans-interaction between yellow enhancers and promoter is strongly suppressed by a cis-promoter only in certain genomic regions

Transvection is a phenomenon of interallelic communication whereby enhancers of one allele can activate a promoter located on the homologous chromosome. It has been shown for many independent genes that enhancers preferentially act on the cis-linked promoter, but deletion of this promoter allows the enhancers to act in trans. Here, we tested whether this cis-preference in the enhancer-promoter interaction could be reconstituted outside of the natural position of a gene. The yellow gene was chosen as a model system. Transgenic flies were generated that carried the yellow gene modified by the inclusion of the strategically placed recognition sites for the Cre and Flp recombinases. To facilitate transvection, an endogenous Su(Hw) insulator (1A2) or gypsy insulator was placed behind the yellow gene. Independent action of the recombinases produced a pair of derivative alleles, one containing the promoter-driven yellow gene, and the other, the enhancers and promoter that failed to produce a functional yellow protein. As a result, we observed strong transvection in many genomic regions, suggesting that a complete cis-preference of the enhancer-promoter interactions is mainly restricted to genes in their natural loci.

Utilization of Plant Genetic Resources in Peanut Breeding Program of Bulgaria

Based on study of some morphological indices, responsible for productivity in 97 breeding lines Arachis hypogea L. with Bulgarian origin, a linear regression model of the plant, that is characterized with high seed yield, was established. The breeding program requires the identification of direct and indirect effects on productivity. By application of the Path Coefficient Analysis,it has been found that the higher yield plants must have low and extensive bush (i&gt; 2,0). The local accessions of peanuts are characterized by a lower index of the bush (i &lt;2,0). For this purpose, 399 genotypes with different geographical origin were introduced from USDA (USA) in 2008. Based on the evaluation of foreign accessions by height and width of the plant, seed yield from one plant and resistance to Fusarium, four genotypes were selected. They were included in crosses with Bulgarian varieties and lines of Valencia type. The heterosis expressions and some genetic effects of progenies were studied.The results show that heterosis effect in F1at some of the progenies in connection withyield of the fruit and seeds are inherited without epistatic effect. The inbred depression in F2is an indication of homozygosity in respect of allelic pairs defining yield.

The evolution of teaching evolution

Education Current research in evolution encompasses more than natural selection. However, evolutionary mechanisms other than natural selection are not always presented in classrooms. Price and Perez analyzed evolution education literature and high-school and college education standards to highlight the lack of concepts such as genetic drift, dominance in allelic pairs, and evolutionary developmental biology. They analyzed students' answers on concept inventories and found that students favor natural selection as the explanation for all evolution, which may ultimately impede their understanding of additional evolutionary mechanisms. The proposed solution, interleaving the teaching of natural selection with other evolutionary processes through iterative cycles of natural selection, genetic drift, dominance, etc., could result in students having a stronger understanding of all evolutionary processes. Am. Biol. Teach. 10.1525/abt.2016.78.2.101 (2016).

Assessment of genetic purity in rice (Oryza sativa L.) hybrids using microsatellite markers.

The objective of the present study is to detect genetic impurity in the seed lots of CMS lines, restorers and hybrids and to identify signature markers to differentiate parents and hybrids through DNA-based assays. Furthermore, attempts have been made to find out an alternative to Grow-Out-Test, which is very tedious, time consuming and used conventionally for seed genetic purity testing since beginning of quality seed multiplication chain. Fifty-one rice-specific sequence tagged microsatellite (STMS) primer pairs distributed throughout the rice genome were employed for fingerprinting of eight rice hybrids and their parental lines with a view to assess variation within parental lines and to test the genetic purity of the commercial seed lots. Among those, 51 markers, 28 microsatellite markers showed polymorphism (54.90 %). A total of 98 alleles were obtained with an average of 1.92 alleles per primer pair and number of alleles amplified for each primer pair ranged from 1 to 4. A set of markers were identified to differentiate parental lines of the hybrids and which emphasizes the immense scope of those molecular markers for their use in the unambiguous identification of hybrid, which would be of great benefit to farmers that depend on the hybrids.

Beyond the Adaptationist Legacy: Updating Our Teaching to Include a Diversity of Evolutionary Mechanisms

A paradigm shift away from viewing evolution primarily in terms of adaptation – the “adaptationist programme” of Gould and Lewontin – began in evolutionary research more than 35 years ago, but that shift has yet to occur within evolutionary education research or within teaching standards. We review three instruments that can help education researchers and educators undertake this paradigm shift. The instruments assess how biology undergraduates understand three evolutionary processes other than natural selection: genetic drift, dominance relationships among allelic pairs, and evolutionary developmental biology (evo-devo). Testing with these instruments reveals that students often explain a diversity of evolutionary mechanisms incorrectly by invoking misconceptions about natural selection. We propose that increasing the emphasis on teaching evolutionary processes other than natural selection could result in a better understanding of natural selection and a better understanding of all evolutionary processes. Finally, we propose two strategies for accomplishing this goal, interleaving natural selection with other evolutionary processes and the development of bridging analogies to describe evolutionary concepts.

Screening of intracerebral hemorrhage associated allele combinations at different loci using a novel association analysis

BackgroundGenetic research has progressed along with scientific and technological developments. However, it is difficult to identify frequency differences in the allele combination at cross-loci. ObjectiveThe purpose of this study was to examine the relationship between the presence of specific allele combinations of short tandem repeat (STR) loci and the onset of intracerebral hemorrhage (ICH) using a novel methodology. MethodsDNA samples were collected from patients with ICH, who were adult population. There were a total of 51 Chinese patients (102 chromosomes), comprising 30 males and 21 females. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler Plus PCR amplification kit (15 STR loci). Statistically significant differences between observed and expected frequencies of allele combinations were identified. To further determine allele combinations related to the disease, analyses of patient age at disease onset for those carrying a specific allele combination were conducted. Finally, cross-validation of the two sets of analytical results was carried out. ResultsA total of 1550 pairwise combinations were obtained by computer counting, of which eight pairs of alleles showed significant differences between the observed and expected frequencies (p<0.05, from 0.006 to 0.042). The p value for the cross-validation analysis was less than 0.05 for two pairs of alleles (D13S317-11 and vWA-17, p=0.021; D7S820-13 and D2S1338-18, p=0.023). ConclusionsThe study identified each population had a unique gene distribution and that distribution followed certain rules. ICH onset may be associated with this allele combinations (D13S317-11 and vWA-17; D7S820-13 and D2S1338-18). The new methodology used in this study could enable additional discoveries pertaining to the relationship between specific allele combinations at different loci and the onset of complex diseases.

Phylogenetic relationships among the first and second introns of selectedPrunus S-RNase genes

Rahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. and Hassani, D. 2015. Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145–1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD+EM-Pc1ConsRD and EM-Pc2ConsFD+EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap.

A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage

To provide new and expanded proteome documentation of the opportunistically pathogen Candida albicans, we have developed new protein extraction and analysis routines to provide a new, extended and enhanced version of the C. albicans PeptideAtlas. Two new datasets, resulting from experiments consisting of exhaustive subcellular fractionations and different growing conditions, plus two additional datasets from previous experiments on the surface and the secreted proteomes, have been incorporated to increase the coverage of the proteome. High resolution precursor mass spectrometry (MS) and ion trap tandem MS spectra were analyzed with three different search engines using a database containing allele-specific sequences. This approach, novel for a large-scale C. albicans proteomics project, was combined with the post-processing and filtering implemented in the Trans Proteomic Pipeline consistently used in the PeptideAtlas project and resulted in 49,372 additional peptides (3-fold increase) and 1630 more proteins (1.6-fold increase) identified in the new C. albicans PeptideAtlas with respect to the previous build. A total of 71,310 peptides and 4174 canonical (minimal non-redundant set) proteins (4115 if one protein per pair of alleles is considered) were identified representing 66% of the 6218 proteins in the predicted proteome. This makes the new PeptideAtlas build the most comprehensive C. albicans proteomics resource available and the only large-scale one with detections of individual alleles.