On the application of estimation of distribution algorithms to multi-marker tagging SNP selection

This paper presents an algorithm for the automatic selection of a minimal subset of tagging single nucleotide polymorphisms (SNPs) using an estimation of distribution algorithm (EDA). The EDA stochastically searches the constrained space of possible feasible solutions and takes advantage of the underlying topological structure defined by the SNP correlations to model the problem interactions. The algorithm is evaluated across the HapMap reference panel data sets. The introduced algorithm is effective for the identification of minimal multi-marker SNP sets, which considerably reduce the dimension of the tagging SNP set in comparison with single-marker sets. New reduced tagging sets are obtained for all the HapMap SNP regions considered. We also show that the information extracted from the interaction graph representing the correlations between the SNPs can help to improve the efficiency of the optimization algorithm. keywords: SNPs, tagging SNP selection, multi-marker selection, estimation of distribution algorithms, HapMap

A natural histone H2A variant lacking the Bub1 phosphorylation site and regulated depletion of centromeric histone CENP-A foster evolvability in Candida albicans.

Eukaryotes have evolved elaborate mechanisms to ensure that chromosomes segregate with high fidelity during mitosis and meiosis, and yet specific aneuploidies can be adaptive during environmental stress. Here, we identify a chromatin-based system required for inducible aneuploidy in a human pathogen. Candida albicans utilizes chromosome missegregation to acquire tolerance to antifungal drugs and for nonmeiotic ploidy reduction after mating. We discovered that the ancestor of C. albicans and 2 related pathogens evolved a variant of histone 2A (H2A) that lacks the conserved phosphorylation site for kinetochore-associated Bub1 kinase, a key regulator of chromosome segregation. Using engineered strains, we show that the relative gene dosage of this variant versus canonical H2A controls the fidelity of chromosome segregation and the rate of acquisition of tolerance to antifungal drugs via aneuploidy. Furthermore, whole-genome chromatin precipitation analysis reveals that Centromere Protein A/ Centromeric Histone H3-like Protein (CENP-A/Cse4), a centromeric histone H3 variant that forms the platform of the eukaryotic kinetochore, is depleted from tetraploid-mating products relative to diploid parents and is virtually eliminated from cells exposed to aneuploidy-promoting cues. We conclude that genetically programmed and environmentally induced changes in chromatin can confer the capacity for enhanced evolvability via chromosome missegregation

Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

UnlabelledThe genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5' RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the D. alaskensis G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene Dde_3007 is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to O-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.ImportanceSulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in Desulfovibrio alaskensis G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria

The Challenges and Opportunities Associated with Biofortification of Pearl Millet (Pennisetum glaucum) with Elevated Levels of Grain Iron and Zinc

Deficiencies of essential micronutrients such as iron and zinc are the cause of extensive health problems in developing countries. They adversely affect performance, productivity and are a major hindrance to economic development. Since many people who suffer from micronutrient deficiencies are dependent on staple crops to meet their dietary requirements, the development of crop cultivars with increased levels of micronutrients in their edible parts is becoming increasingly recognized as a sustainable solution. This is largely facilitated by genetics and genomic platforms. The cereal crop pearl millet (Pennisetum glaucum), is an excellent candidate for genetic improvement due to its ability to thrive in dry, semi-arid regions, where farming conditions are often unfavorable. Not only does pearl millet grow in areas where other crops such as maize and wheat do not survive, it contains naturally high levels of micronutrients, proteins and a myriad of other health benefitting characteristics. This review discusses the current status of iron and zinc deficiencies and reasons why interventions such as fortification, supplementation, and soil management are neither practicable nor affordable in poverty stricken areas. We argue that the most cost effective, sustainable intervention strategy is to biofortify pearl millet with enhanced levels of bioavailable iron and zinc. We discuss how naturally occurring genetic variations present in germplasm collections can be incorporated into elite, micronutrient rich varieties and what platforms are available to drive this research. We also consider the logistics of transgenic methods that could facilitate the improvement of the pearl millet gene pool

Monitoring occupancy and abundance of New England cottontails using non-invasive genetic tools

The New England cottontail (Sylvilagus transitionalis ) is a species of conservation concern. Efficient monitoring methods are needed to guide and assess conservation decisions in an adaptive management framework. I used genetic tools and non-invasively collected fecal DNA to determine New England cottontail detection rates during presence/absence surveys and to identify the environmental and behavioral factors that influence detection. I found New England cottontail detection rates to be high (\u3e90%) when surveys were conducted under ideal conditions. Prior knowledge of cottontail activity, low snow depth, and allowing 2-4 days without high winds following a snowfall are the most important factors positively associated with cottontail detection. I also found that increased patch size reduces detection when search efforts are limited to 20 minutes. I used genetic mark-recapture methods to produce baseline abundance estimates for New England cottontail populations across their range. I used microsatellite genotyping in conjunction with single session mark-recapture models in the program CAPWIRE to estimate New England cottontail abundance on 17 occupied patches in Maine, New Hampshire, and New York. Precision of estimates was reasonable for most small sites and several large sites, but decreased with increasing subsampling distance. I also evaluated the methodology used and recommended changes to future survey efforts to improve efficiency and precision. These recommendations include allowing at least three days to pass following a snow fall before conducting a population survey, and sampling pellets intensively on sites to provide a better chance of obtaining an adequate number of recaptures. The tools developed herein will be useful in future occupancy monitoring and abundance estimation needed for the adaptive management of New England cottontail populations

Genetic analysis and molecular characterization of the W4 locus and the k2 Mdh1-n y20 chromosomal region in soybean [Glycine max (L) Merr]

The W4 locus is an important locus to the anthocyanin biosynthesis in soybean flowers and hypocotyls. Mutations at this locus would cause less-pigmented flowers and hypocotyls, such as near-white flowers conditioned by the w4 allele. Its mutable allele (w4-m) was suspected to contain an autonomous transposon. In this study, we reported a mutation with pale flowers and green hypocotyls conditioned by a new allele at the W4 locus, w4-p. The dominance of these four alleles is: W4 \u3e w4-m \u3e w4-p \u3e w4. The inbred mutant line (w4-p w4-p) was assigned Genetic Type Collection number T369. The W4 locus was positioned on the MLG D2 between Satt386 and nearby telomere with 2.3 cM genetic distance from Satt386.;The major components of anthocyanins in soybean flowers were found to be delphinidin and its derivatives, which were reduced in less pigmented flower petals caused by mutations at the W4 locus. Results in this study showed that the pigment reduction was due to low transcript level of the DFR 2 (dihydroflavonol reductase 2) gene. The results also indicated that the W4 gene very likely encoded the DFR2 protein.;Three closely linked genes k2, Mdh1-n, and y20 form an unstable chromosomal region. The Mdh1-n mutation in T261 and all the Mdh1-n y20 mutations were suggested to be due to genomic deletions. Four more new mutants in this region were reported in this study. One had tan-saddle seed coat (k2) isolated from a bulk harvest of cv. Kenwood. Three independent mutants ( k2 Mdh1-n y20) were reported in the instability experiments. The unstable region was located on MLG H near SSR markers Satt253, Satt279, and Satt314. In addition, an extra putative deletion that covered Satt253, Satt279, and Satt314 was identified in T261. Mapping results indicated the two deletions were separate.;An Mdh1 contig with size around 96 kb was constructed. Three copies of truncated Calypso5-1 like retroelements were found downstream of the Mdh1 gene (AF180335), and clustered in a ~16 kb chromosomal region. The deletions in all the Mdh1 -n or Mdh1-n y20 mutants examined were larger that ~70 kb, but the breakpoints couldn\u27t be identified