Bacteria living within eukaryotic cells can be essential for the survival or reproduction of the host but in other cases are among the most successful pathogens. Environmental Chlamydiae, including strain UWE25, thrive as obligate intracellular symbionts within protozoa; are recently discovered relatives of major bacterial pathogens of humans; and also infect human cells. Genome analysis of UWE25 predicted that this symbiont is unable to synthesize the universal electron carrier nicotinamide adenine dinucleotide (NAD+). Compensation of limited biosynthetic capacity in intracellular bacteria is usually achieved by import of primary metabolites. Here, we report the identification of a candidate transporter protein from UWE25 that is highly specific for import of NAD+ when synthesized heterologously in Escherichia coli. The discovery of this candidate NAD+/ADP exchanger demonstrates that intact NAD+ molecules can be transported through cytoplasmic membranes. This protein acts together with a newly discovered nucleotide transporter and an ATP/ADP translocase, and allows UWE25 to exploit its host cell by means of a sophisticated metabolic parasitism.

BackgroundIron (Fe) deficiency in plants is the result of low Fe soil availability affecting 30% of cultivated soils worldwide. To improve our understanding on Fe-efficiency this study aimed to (i) evaluate the influence of two different Fe regimes on morphological and physiological trait formation, (ii) identify polymorphisms statistically associated with morphological and physiological traits, and (iii) dissect the correlation between morphological and physiological traits using an association mapping population.ResultsThe fine-mapping analyses on quantitative trait loci (QTL) confidence intervals of the intermated B73 × Mo17 (IBM) population provided a total of 13 and 2 single nucleotide polymorphisms (SNPs) under limited and adequate Fe regimes, respectively, which were significantly (FDR = 0.05) associated with cytochrome P450 94A1, invertase beta-fructofuranosidase insoluble isoenzyme 6, and a low-temperature-induced 65 kDa protein. The genome-wide association (GWA) analyses under limited and adequate Fe regimes provided in total 18 and 17 significant SNPs, respectively.ConclusionsSignificantly associated SNPs on a genome-wide level under both Fe regimes for the traits leaf necrosis (NEC), root weight (RW), shoot dry weight (SDW), water (H 2O), and SPAD value of leaf 3 (SP3) were located in genes or recognition sites of transcriptional regulators, which indicates a direct impact on the phenotype. SNPs which were significantly associated on a genome-wide level under both Fe regimes with the traits NEC, RW, SDW, H 2O, and SP3 might be attractive targets for marker assisted selection as well as interesting objects for future functional analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0153-0) contains supplementary material, which is available to authorized users.

BackgroundMost agronomic plant traits result from complex molecular networks involving multiple genes and from environmental factors. One such trait is the enzymatic discoloration of fruit and tuber tissues initiated by mechanical impact (bruising). Tuber susceptibility to bruising is a complex trait of the cultivated potato (Solanum tuberosum) that is crucial for crop quality. As phenotypic evaluation of bruising is cumbersome, the application of diagnostic molecular markers would empower the selection of low bruising potato varieties. The genetic factors and molecular networks underlying enzymatic tissue discoloration are sparsely known. Hitherto there is no association study dealing with tuber bruising and diagnostic markers for enzymatic discoloration are rare.ResultsThe natural genetic diversity for bruising susceptibility was evaluated in elite middle European potato germplasm in order to elucidate its molecular basis. Association genetics using a candidate gene approach identified allelic variants in genes that function in tuber bruising and enzymatic browning. Two hundred and five tetraploid potato varieties and breeding clones related by descent were evaluated for two years in six environments for tuber bruising susceptibility, specific gravity, yield, shape and plant maturity. Correlations were found between different traits. In total 362 polymorphic DNA fragments, derived from 33 candidate genes and 29 SSR loci, were scored in the population and tested for association with the traits using a mixed model approach, which takes into account population structure and kinship. Twenty one highly significant (p < 0.001) and robust marker-trait associations were identified.ConclusionsThe observed trait correlations and associated marker fragments provide new insight in the molecular basis of bruising susceptibility and its natural variation. The markers diagnostic for increased or decreased bruising susceptibility will facilitate the combination of superior alleles in breeding programs. In addition, this study presents novel candidates that might control enzymatic tissue discoloration and tuber bruising. Their validation and characterization will increase the knowledge about the underlying biological processes.

BackgroundClimate change will lead in the future to an occurrence of heat waves with a higher frequency and duration than observed today, which has the potential to cause severe damage to seedlings of temperate maize genotypes. In this study, we aimed to (I) assess phenotypic variation for heat tolerance of temperate European Flint and Dent maize inbred lines, (II) investigate the transcriptomic response of temperate maize to linearly increasing heat levels and, (III) identify genes associated with heat tolerance in a set of genotypes with contrasting heat tolerance behaviour.ResultsStrong phenotypic differences with respect to heat tolerance were observed between the examined maize inbred lines on a multi-trait level. We identified 607 heat responsive genes as well as 39 heat tolerance genes.ConclusionOur findings indicate that individual inbred lines developed different genetic mechanisms in response to heat stress. We applied a novel statistical approach enabling the integration of multiple genotypes and stress levels in the analysis of abiotic stress expression studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1282-1) contains supplementary material, which is available to authorized users.

The diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today's highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.

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Genome-wide association (GWA) mapping in potato requires high-density genotyping. With the Illumina SolCAP potato single-nucleotide polymorphism (SNP) array, a first tool for GWA mapping in potato became available. Thirty-six tetraploid varieties and eight diploid breeding clones were genotyped for 8303 SNPs using this array. The objectives of our study were to examine in this set of germplasm: (i) the degree of polymorphism of the SolCAP SNPs in European germplasm, (ii) the population structure, (iii) temporal trends of genetic diversity and (iv) the genome-wide extent of linkage disequilibrium (LD). Three-quarters of the SNPs were polymorphic. In the principal coordinate analysis, a clear separation of tetraploid from diploid genotypes was observed, whereas no distinct subgroups among the tetraploid varieties were detected. The nonlinear trendline of the LD measure r 2 vs. the physical map distance decayed within 275 bp to an r 2 value of 0.10, indicating that theoretically, about 3 million equally distributed SNPs are required for GWA mapping in this diverse set of germplasm. As the LD decay changes with the population selected for GWA mapping, the number of required markers might be different in other germplasm.

BackgroundIron (Fe) deficiency symptoms in maize (Zea mays subsp. mays) express as leaf chlorosis, growth retardation, as well as yield reduction and are typically observed when plants grow in calcareous soils at alkaline pH. To improve our understanding of genotypical variability in the tolerance to Fe deficiency-induced chlorosis, the objectives of this study were to (i) determine the natural genetic variation of traits related to Fe homeostasis in the maize intermated B73 × Mo17 (IBM) population, (ii) to identify quantitative trait loci (QTLs) for these traits, and (iii) to analyze expression levels of genes known to be involved in Fe homeostasis as well as of candidate genes obtained from the QTL analysis.ResultsIn hydroponically-grown maize, a total of 47 and 39 QTLs were detected for the traits recorded under limited and adequate supply of Fe, respectively.ConclusionsFrom the QTL results, we were able to identify new putative candidate genes involved in Fe homeostasis under a deficient or adequate Fe nutritional status, like Ferredoxin class gene, putative ferredoxin PETF, metal tolerance protein MTP4, and MTP8. Furthermore, our expression analysis of candidate genes suggested the importance of trans-acting regulation for 2’-deoxymugineic acid synthase 1 (DMAS1), nicotianamine synthase (NAS3, NAS1), formate dehydrogenase 1 (FDH1), methylthioribose-1-phosphate isomerase (IDI2), aspartate/tyrosine/aromatic aminotransferase (IDI4), and methylthioribose kinase (MTK).