Single nucleotide polymorphism genotyping and its application on mapping and marker-assisted plant breeding

The nucleotide diversity across a genome is the source of most phenotypic variation. Such DNA polymorphism is the basis for the development of molecular markers, an indispensable tool in geneticmapping studies. In general, the high resolution fine mapping of genes is often limited by lack of sufficient number of polymorphic molecular markers. This problem is compounded with traits controlled by multi-genes because in several such studies, QTL cannot be resolved to a workable resolution that could be feasible for predicting the candidate gene(s) associated with traits of interests. The availability of abundant, high-throughput sequence-based markers is the key for detailed genomewide trait analysis. Single-nucleotide polymorphisms (SNP) are the most common sequence variation and a significant amount of effort has been invested in re-sequencing alleles to discover SNPs. In fully sequenced small-genome model organisms, SNP discovery is relatively straight forward, although highthroughputSNP discovery in natural populations remains both expensive and time-consuming. Here five central biochemical reaction principles that underlie SNP-genotyping methods specifically for large panel sizes and an intermediate number of SNPs are reviewed

Integral and Rxte/Asm Observations on Igr J17098-3628

To probe further the possible nature of the unidentified source IGR J17098-3628, we have carried out a detailed analysis of its long-term time variability as monitored by RXTE/ASM, and of its hard X-ray properties as observed by INTEGRAL. INTEGRAL has monitored this sky region over years and significantly detected IGR J17098-3628 only when the source was in this dubbed active state. In particular, at $\ge$ 20 keV, IBIS/ISGRI caught an outburst in March 2005, lasting for $\sim$5 days with detection significance of 73$\sigma$ (20-40 keV) and with the emission at $<$200 keV. The ASM observations reveal that the soft X-ray lightcurve shows a similar outburst to that detected by INTEGRAL, however the peak of the soft X-ray lightcurve either lags, or is preceded by, the hard X-ray ($>$20 keV) outburst by $\sim$2 days. This resembles the behavior of X-ray novae like XN 1124-683, hence it further suggests a LMXB nature for IGR J17098-3628. While the quality of the ASM data prevents us from drawing any definite conclusions, these discoveries are important clues that, coupled with future observations, will help to resolve the as yet unknown nature of IGR J17098-3628.Comment: 15 pages, 7 figure, accepted in PAS

CpG Island Mapping by Epigenome Prediction

CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1) reliance on arbitrary threshold parameters that bear little biological justification, (2) failure to account for widespread heterogeneity among CpG islands, and (3) apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of “CpG island strength” that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted “bona fide” CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to their characteristic epigenetic and functional states. And it is superior to purely experimental epigenome mapping for CpG island detection since it abstracts from specific properties that are limited to a single cell type or tissue. In addition, using computational epigenetics methods we could identify high correlation between the epigenome and characteristics of the DNA sequence, a finding which emphasizes the need for a better understanding of the mechanistic links between genome and epigenome

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules

Assembly and Compositional Analysis of Human Genomic DNA - Doctoral Dissertation, August 2002

In 1990, the United States Human Genome Project was initiated as a fifteen-year endeavor to sequence the approximately three billion bases making up the human genome (Vaughan, 1996).As of December 31, 2001, the public sequencing efforts have sequenced a total of 2.01 billion finished bases representing 63.0% of the human genome (http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsProgress.shtml&&ORG=Hs) to a Bermuda quality error rate of 1/10000 (Smith and Carrano, 1996). In addition, 1.11 billion bases representing 34.8% of the human genome has been sequenced to a rough-draft level. Efforts such as UCSC\u27s GoldenPath (Kent and Haussler, 2001) and NCBI\u27s contig assembly (Jang et al., 1999) attempt to assemble the human genome by incorporating both finished and rough-draft sequence. The availability of the human genome data allows us to ask questions concerning the maintenance of specific regions of the human genome. We consider two hypotheses for maintenance of high G+C regions: the presence of specific repetitive elements and compositional mutation biases. Our results rule out the possibility of the G+C content of repetitive elements determining regions of high and low G+C regions in the human genome. We determine that there is a compositional bias for mutation rates. However, these biases are not responsible for the maintenance of high G+C regions. In addition, we show that regions of the human under less selective pressure will mutate towards a higher A+T composition, regardless of the surrounding G+C composition. We also analyze sequence organization and show that previous studies of isochore regions (Bernardi,1993) cannot be generalized within the human genome. In addition, we propose a method to assemble only those parts of the human genome that are finished into larger contigs. Analysis of the contigs can lead to the mining of meaningful biological data that can give insights into genetic variation and evolution. I suggest a method to help aid in single nucleotide polymorphism (SNP)detection, which can help to determine differences within a population. I also discuss a dynamic-programming based approach to sequence assembly validation and detection of large-scale polymorphisms within a population that is made possible through the availability of large human sequence contigs

Coherent network analysis technique for discriminating gravitational-wave bursts from instrumental noise

Existing coherent network analysis techniques for detecting gravitational-wave bursts simultaneously test data from multiple observatories for consistency with the expected properties of the signals. These techniques assume the output of the detector network to be the sum of a stationary Gaussian noise process and a gravitational-wave signal, and they may fail in the presence of transient non-stationarities, which are common in real detectors. In order to address this problem we introduce a consistency test that is robust against noise non-stationarities and allows one to distinguish between gravitational-wave bursts and noise transients. This technique does not require any a priori knowledge of the putative burst waveform.Comment: 18 pages, 11 figures; corrected corrupted figur

The effects of ecology and climate change on the conservation of eastern Himalayan avifauna

The existence of biodiversity is central to all biological sciences, and especially ecology. Without it, an entire branch of knowledge would cease to exist. Despite this centrality, there is considerable debate on the mechanisms that create and maintain diversity. This is especially true of high-diversity areas. There is also considerable debate on how we can best protect biodiversity, in order to allow the science of biology to flourish into the future. Here, I present an investigation of the processes that allow biodiversity to be maintained in the Eastern Himalayas, a critically understudied high-diversity region, as well as a systematic analysis of the conservation priorities there. I focus on birds as a charismatic, speciose and conspicuous set of taxa. I spent several months gathering fine-scale occurrence data for the breeding bird community in Arunachal Pradesh, a state in Northeast India that is at the heart of the Eastern Himalayan ecoregion. Using this data, I first show that bird species on the steep elevational gradient present in the region segregate into narrow elevational bands. I also show that this segregation can best be explained by evolutionary processes resulting from interspecies competition in the long term, and by continued interspecies competition in the short term. I then go on to demonstrate that these narrow ranges of climate tolerance will be greatly affected by climate change, with species’ ranges shifting and contracting over the next 50 years. Moreover, when interspecies competition is taken to account, these extent of these predicted changes is intensified. Finally, I use these predicted distributions to create a spatially explicit map of conservation priorities. I present alternatives based on different conservation goals, as well as different projections of the extent of global climate change. I also present an idealized map of areas most in need of protection, and compare that to the existing set of formally protected areas. Taken in their entirety, these studies present a cogent explanation for the existence of high biodiversity in one of the most special regions of the planet, as well as a roadmap toward protecting that diversity for future generations.Ecology, Evolution and Behavio