Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

MOTIVATION: Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although the method is expected to be useful in SNP/indel callers and bisulfite mapping, because accurate estimation of aligned columns or gaps is important in those analyses. RESULTS: In this study, we propose methods of probabilistic alignment that consider quality scores of (one of) the sequences as well as a usual score matrix. The method is based on posterior decoding techniques in which various marginal probabilities are computed from a probabilistic model of alignments with quality scores, and can arbitrarily trade-off sensitivity and positive predictive value (PPV) of prediction (aligned columns and gaps). The method is directly applicable to read mapping (alignment) toward accurate detection of SNPs and indels. Several computational experiments indicated that probabilistic alignments can estimate aligned columns and gaps accurately, compared with other mapping algorithms e.g. SHRiMP2, Stampy, BWA and Novoalign. The study also suggested that our approach yields favorable precision for SNP/indel calling.     

Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers

The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.PEDIGREE-BASED prediction of genetic values based on the additive infinitesimal model (Fisher 1918) has played a central role in genetic improvement of complex traits in plants and animals. Animal breeders have used this model for predicting breeding values either in a mixed model (best linear unbiased prediction, BLUP) (Henderson 1984) or in a Bayesian framework (Gianola and Fernando 1986). More recently, plant breeders have incorporated pedigree information into linear mixed models for predicting breeding values (Crossa et al. 2006, 2007; Oakey et al. 2006; Burgueño et al. 2007; Piepho et al. 2007).The availability of thousands of genome-wide molecular markers has made possible the use of genomic selection (GS) for prediction of genetic values (Meuwissen et al. 2001) in plants (e.g., Bernardo and Yu 2007; Piepho 2009; Jannink et al. 2010) and animals (Gonzalez-Recio et al. 2008; VanRaden et al. 2008; Hayes et al. 2009; de los Campos et al. 2009a). Implementing GS poses several statistical and computational challenges, such as how models can cope with the curse of dimensionality, colinearity between markers, or the complexity of quantitative traits. Parametric (e.g., Meuwissen et al. 2001) and semiparametric (e.g., Gianola et al. 2006; Gianola and van Kaam 2008) methods address these problems differently.In standard genetic models, phenotypic outcomes, , are viewed as the sum of a genetic value, , and a model residual, ; that is, . In parametric models for GS, is described as a regression on marker covariates (j = 1,  …  , p molecular markers) of the form , such that(or , in matrix notation), where is the regression of on the jth marker covariate .Estimation of via multiple regression by ordinary least squares (OLS) is not feasible when p > n. A commonly used alternative is to estimate marker effects jointly using penalized methods such as ridge regression (Hoerl and Kennard 1970) or the Least Absolute Shrinkage and Selection Operator (LASSO) (Tibshirani 1996) or their Bayesian counterpart. This approach yields greater accuracy of estimated genetic values and can be coupled with geostatistical techniques commonly used in plant breeding to model multienvironments trials (Piepho 2009).In ridge regression (or its Bayesian counterpart) the extent of shrinkage is homogeneous across markers, which may not be appropriate if some markers are located in regions that are not associated with genetic variance, while markers in other regions may be linked to QTL (Goddard and Hayes 2007). To overcome this limitation, many authors have proposed methods that use marker-specific shrinkage. In a Bayesian setting, this can be implemented using priors of marker effects that are mixtures of scaled-normal densities. Examples of this are methods Bayes A and Bayes B of Meuwissen et al. (2001) and the Bayesian LASSO of Park and Casella (2008).An alternative to parametric regressions is to use semiparametric methods such as reproducing kernel Hilbert spaces (RKHS) regression (Gianola and van Kaam 2008). The Bayesian RKHS regression regards genetic values as random variables coming from a Gaussian process centered at zero and with a (co)variance structure that is proportional to a kernel matrix K (de los Campos et al. 2009b); that is, , where , are vectors of marker genotypes for the ith and jth individuals, respectively, and is a positive definite function evaluated in marker genotypes. In a finite-dimensional setting this amounts to modeling the vector of genetic values, , as multivariate normal; that is, where is a variance parameter. One of the most attractive features of RKHS regression is that the methodology can be used with almost any information set (e.g., covariates, strings, images, graphs). A second advantage is that with RKHS the model is represented in terms of n unknowns, which gives RKHS a great computational advantage relative to some parametric methods, especially when p ≫ n.This study presents an evaluation of several methods for GS, using two extensive data sets. One contains phenotypic records of a series of wheat trials and recently generated genomic data. The other data set pertains to international maize trials in which different traits were measured in maize lines evaluated under severe drought and well-watered conditions.     

Enhancement of carbon dioxide fixation by alteration of illumination duringChlorella vulgaris-Buitenzorg's growth

Alteration of illumination with optimum carbon dioxide fixation-based curve in this research successfully enhanced the CO₂-fixation (q_co2) capability ofChlorella vulgaris Buitenzorg cultivated in a bubble column photo bioreactor. The level of CO₂ fixation was up to 1.91 times that observed from cultivation with intensification of illumination on an optimum growth-based curve. During 144 h of cultivation, alteration of light intensity on an optimum CO₂-fixation-based curve produced a q_CO2 of 6.68 h^?1. Increases in light intensity based on a curve of optimum CO₂-fixation produced a final cell concentration of about 5.78 g/L. Both cultivation methods were carried out under ambient pressure at a temperature of 29°C with a superficial gas velocity of 2.4 m/h (U_G). Cells were grown on Beneck medium in a 1.0 L Bubble Column Photo bioreactor illuminated by aPhillips Halogen Lamp (20 W/12 V/50 Hz). The inlet gas had a carbon dioxide content of 10%.     

Multidimensional local false discovery rate for microarray studies

MOTIVATION: The false discovery rate (fdr) is a key tool for statistical assessment of differential expression (DE) in microarray studies. Overall control of the fdr alone, however, is not sufficient to address the problem of genes with small variance, which generally suffer from a disproportionally high rate of false positives. It is desirable to have an fdr-controlling procedure that automatically accounts for gene variability. METHODS: We generalize the local fdr as a function of multiple statistics, combining a common test statistic for assessing DE with its standard error information. We use a non-parametric mixture model for DE and non-DE genes to describe the observed multi-dimensional statistics, and estimate the distribution for non-DE genes via the permutation method. We demonstrate this fdr2d approach for simulated and real microarray data. RESULTS: The fdr2d allows objective assessment of DE as a function of gene variability. We also show that the fdr2d performs better than commonly used modified test statistics. AVAILABILITY: An R-package OCplus containing functions for computing fdr2d() and other operating characteristics of microarray data is available at http://www.meb.ki.se/~yudpaw.     

Genetic structures of the CIMMYT international yield trial targeted to irrigated environments

International yield trials are assembled by CIMMYT to disseminate promising wheat breeding materials worldwide. To assess the genomic structure and linkage disequilibrium (LD) within this germplasm, wheat lines disseminated during 25 years of the Elite Spring Wheat Yield Trial (ESWYT) targeted for irrigated environments of the world were genotyped with the high-throughput Diversity Arrays Technology (DArT) marker system. Analyses of population structure assigned the ESWYT germplasm into five major sub-populations that are shaped by prominent CIMMYT wheat lines and their descendants. Based on genetic distance, we concluded that a constant level of genetic diversity was maintained over the years of ESWYT dissemination. Genetic distance between the individual ESWYT lines significantly increased when the ESWYT were grouped according to the differences in years of ESWYT dissemination, suggesting a systematic change in allele frequencies over time, most probably due to breeding and directional selection. By means of multiple regression analyses, 78 markers displaying a significant change in allele frequency across years were identified and interpreted as an indicator for constant selection. The markers identified were partly associated with grain yield, leaf, stem, and yellow rust and point to key genomic regions for further investigation. Large numbers of adjacent DArT marker pairs showed significant LD across the ESWYT population and within each of the five sub-populations identified. Sub-population differentiation measured by the fixation index and average genetic distance were highly correlated with LD levels, suggesting that the sub-populations themselves explain much of the LD.     

Acoustic structure of male loud-calls support molecular phylogeny of Sumatran and Javanese leaf monkeys (genus <Emphasis Type="Italic">Presbytis</Emphasis>)

Background  

The degree to which loud-calls in nonhuman primates can be used as a reliable taxonomic tool is the subject of ongoing debate. A recent study on crested gibbons showed that these species can be well distinguished by their songs; even at the population level the authors found reliable differences. Although there are some further studies on geographic and phylogenetic differences in loud-calls of nonhuman primate species, it is unclear to what extent loud-calls of other species have a similar close relation between acoustic structure, phylogenetic relatedness and geographic distance. We therefore conducted a field survey in 19 locations on Sumatra, Java and the Mentawai islands to record male loud-calls of wild surilis (Presbytis), a genus of Asian leaf monkeys (Colobinae) with disputed taxanomy, and compared the structure of their loud-calls with a molecular genetic analysis.     

Comparison of l‐tyrosine containing dipeptides reveals maximum ATP availability for l‐prolyl‐l‐tyrosine in CHO cells

Increasing markets for biopharmaceuticals, including monoclonal antibodies, have triggered a permanent need for bioprocess optimization. Biochemical engineering approaches often include the optimization of basal and feed media to improve productivities of Chinese hamster ovary (CHO) cell cultures. Often, l ‐tyrosine is added as dipeptide to deal with its poor solubility at neutral pH. Showcasing IgG1 production with CHO cells, we investigated the supplementation of three l ‐tyrosine (TYR, Y) containing dipeptides: glycyl‐l ‐tyrosine (GY), l ‐tyrosyl‐l ‐valine (YV), and l ‐prolyl‐l ‐tyrosine (PY). While GY and YV led to almost no phenotypic and metabolic differences compared to reference samples, PY significantly amplified TYR uptake thus maximizing related catabolic activity. Consequently, ATP formation was roughly four times higher upon PY application than in reference samples.     

Combined effect of 24-epibrassinolide and salicylic acid mitigates lead (Pb) toxicity by modulating various metabolites in <Emphasis Type="BoldItalic">Brassica juncea</Emphasis> L. seedlings

The present study demonstrated the combined effect of 24-epibrassinolide and salicylic acid against lead (Pb, 0.25, 0.50, and 0.75 mM) toxicity in Brassica juncea seedlings. Various parameters including water status, metal uptake, total water- and lipid-soluble antioxidants, metal chelator content (total thiols, protein-bound thiols, and non-protein-bound thiols), phenolic compounds (flavonoids, anthocyanins, and polyphenols), and organic acids were studied in 10-day-old seedlings. Dry matter content and the heavy metal tolerance index were reduced by 42.24 and 52.3%, respectively, in response to Pb treatment. Metal uptake, metal-chelating compounds, phenolic compounds, and organic acids were increased in Pb-treated seedlings as compared to control plants. The treatment of Pb-stressed seedlings with combination of EBL and SA resulted in enhancement of heavy metal tolerance index by 40.07%, water content by 1.84%, and relative water content by 23.45%. The total water- and lipid-soluble antioxidants were enhanced by 21.01 and 2.21%, respectively. In contrast, a significant decline in dry weight, metal uptake, thiol, and polyphenol contents was observed following the application of 24-epibrassinolide and salicylic acid. These observations indicate that Pb treatment has an adverse effect on B. juncea seedlings. However, co-application of 24-epibrassinolide and salicylic acid mitigates the negative effects of Pb, by lowering Pb metal uptake and enhancing the heavy metal tolerance index, water content, relative water content, antioxidative capacities, phenolic content, and organic acid levels.     

Mitigation of sodium chloride toxicity in Solanum lycopersicum L. by supplementation of jasmonic acid and nitric oxide

We investigated the effects of exogenous application of jasmonic acid (JA) and nitric oxide (NO) on growth, antioxidant metabolism, physio-biochemical attributes and metabolite accumulation, in tomato (Solanum lycopersicum L.) plants exposed to salt stress. Treating the plants with NaCl (200 mM) resulted in considerable growth inhibition in terms of biomass, relative water content, and chlorophyll content, all of which were significantly improved upon application of JA and NO under both normal and NaCl-stress treatments. Salt treatment particularly 200 mM NaCl caused an apparent increase in electrolyte leakage, lipid peroxidation, and hydrogen peroxide production, which were reduced by exogenous application of JA and NO. Salt treatment triggered the induction of antioxidant system by enhancing the activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR). Application of JA and NO separately as well as in combination caused a significant improvement in activities of SOD, CAT, APX, and GR activities. JA and NO either applied individually or in combination boosted the flavonoid, proline and glycine betaine synthesis under NaCl treatments. In conclusion, the exogenous application of JA and NO protected tomato plants from NaCl-induced damage by up-regulating the antioxidant metabolism, osmolyte synthesis, and metabolite accumulation.     

Phylogeography of the eight-barbel loach <Emphasis Type="Italic">Lefua nikkonis</Emphasis> (Cypriniformes: Nemacheilidae): how important were straits in northern Japan as biogeographical barriers?

Many straits in the Japanese archipelago have been proposed as biogeographical boundaries, but there is disagreement regarding their importance as historic barriers against dispersal of terrestrial and freshwater taxa. Mitochondrial DNA haplotype and phylogenetic analyses of Lefua nikkonis, a primary freshwater fish inhabiting northern Japan and descendent from Siberia, revealed that the species is genetically structured within its geographic range, but that two major haplotypes are widely distributed across the Ishikari Lowland of Hokkaido Island as well as across the Tsugaru Strait between Hokkaido and Honshu Islands, two well-known biogeographical boundaries of northern Japan. The two major haplotypes were separated from each other by only one mutational step, and many other haplotypes, including those endemic to the region south of these barriers, have diverged from the major haplotypes, suggesting rapid range expansion and local differentiation. Divergence-time estimates, based on vicariance of the Honshu endemic congener L. echigonia via uplift of the Central Highlands, demonstrated that the southward dispersal of L. nikkonis from Hokkaido Island to Honshu Island occurred less than 0.08–0.19 Mya, suggesting that a land bridge emerged at the Tsugaru Strait during the Riss glaciation. Given that other freshwater taxa crossed the strait earlier (during the Middle Pleistocene), it is likely that land bridges in the strait have repeatedly emerged. The fact that L. nikkonis invaded only the northern part of Honshu, and that many other freshwater species also have the limit of their distribution ranges in this area as well, indicates that a faunal transition zone might persist even without the Tsugaru Strait. Thus, straits and lowlands in northern Japan are likely to have been less important as dispersal barriers to freshwater taxa than is currently thought.