QTL mapping of potato chip color and tuber traits within an autotetraploid family

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid crop species, and this creates challenges for traditional line development and molecular breeding. Recent availability of a single-nucleotide polymorphism (SNP) array with 8303 features and software packages for linkage and association mapping in autotetraploid species present new opportunities for the identification of genomic regions that contribute to high-value traits in cultivated potato. A biparental tetraploid potato population was evaluated across three field seasons and storage trials in order to identify quantitative trait loci (QTL) for multiple tuber traits including fried chip color after 5.5–7.2 °C storage. Tetra-allelic dosage information was used to construct a genetic linkage map that covered 1041 cM and contained 2095 SNP markers with a median marker interval of 0.4 cM. A total of 41 QTL were identified for flower color, tuber yield, tuber number per plant, tuber weight, tuber size, and chip color after various storage regimes. Moderate effect QTL for chip color at 3 months were identified that co-localized with candidate genes vacuolar invertase (VInv), invertase inhibitor (INH2), and apoplastic invertase (Inv _ap -b). A separate QTL for chip color after 6 months of storage was identified in the short arm of chromosome 2, and this locus may contribute to variation in senescent sweetening resistance. QTL for tuber weight, length, and width co-localized with a known QTL for plant maturity on chromosome 5. Genome-wide association mapping using a polyploid model detected the tuber size QTL and identified a number of candidate SNPs, but was unable to detect markers significantly associated with chip color.     

Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum

The density and distribution of single-nucleotide polymorphisms (SNPs) across the genome has important implications for linkage disequilibrium mapping and association studies, and the level of simple-sequence microsatellite polymorphisms has important implications for the use of oligonucleotide hybridization methods to genotype SNPs. To assess the density of these types of polymorphisms in P. falciparum, we sampled introns and noncoding DNA upstream and downstream of coding regions among a variety of geographically diverse parasites. Across 36,229 base pairs of noncoding sequence representing 41 genetic loci, a total of 307 polymorphisms including 248 polymorphic microsatellites and 39 SNPs were identified. We found a significant excess of microsatellite polymorphisms having a repeat unit length of one or two, compared to those with longer repeat lengths, as well as a nonrandom distribution of SNP polymorphisms. Almost half of the SNPs localized to only three of the 41 genetic loci sampled. Furthermore, we find significant differences in the frequency of polymorphisms across the two chromosomes (2 and 3) examined most extensively, with an excess of SNPs and a surplus of polymorphic microsatellites on chromosome 3 as compared to chromosome 2 (P=0.0001). Furthermore, at some individual genetic loci we also find a nonrandom distribution of polymorphisms between coding and flanking noncoding sequences, where completely monomorphic regions may flank highly polymorphic genes. These data, combined with our previous findings of nonrandom distribution of SNPs across chromosome 2, suggest that the Plasmodium falciparum genome may be a mosaic with regard to genetic diversity, containing chromosomal regions that are highly polymorphic interspersed with regions that are much less polymorphic.     

Ontogeny of the mandarinfish <Emphasis Type="Italic">Siniperca chuatsi</Emphasis> (Perciformes: Sinipercidae) reared in aquarium

Early-stage morphologies of the mandarinfish Siniperca chuatsi are described on the basis of an ontogenetic series of reared specimens in an aquarium. Spherical eggs (diameter 1.70–1.82mm) with a single oil globule (0.40–0.48mm) were free-demersal and easily floated when agitated. Hatching occurred about 3 days after spawning at about 24°C. Newly hatched larvae (3.8–4.2mm in notochord length: NL) had many melanophores on the yolk sac. After reaching ca. 5.5mm NL (8–9+19–20=27–28 myomeres), larvae had almost completely absorbed the yolk, possessed a large mouth and sharp teeth, and were starting to prey on other fish larvae. Three large preopercle spines appeared at ca. 5.5mm NL, five spines by ca. 8.5mm NL, and eight by ca. 21mm in standard length (SL). The interopercle bore a single spine at ca. 8.5mm NL and two spines at ca. 13.5mm SL. A single spine appeared at the supracleithrum and another at the opercle at ca. 10mm SL. Dorsal fin spines and pelvic, anal, and caudal fins were completed at ca. 10mm SL. Dorsal fin rays and pectoral fins were completed at ca. 13.5mm SL. Four ontogenetic characters (free-demersal eggs, large jaws with large teeth, conspicuous head spination, and precocious completion of dorsal fin spines) are rare among freshwater percoids.     

Apoplastic synthesis of nitric oxide by plant tissues

Nitric oxide (NO) is an important signaling molecule in animals and plants. In mammals, NO is produced from Arg by the enzyme NO synthase. In plants, NO synthesis from Arg using an NO synthase-type enzyme and from nitrite using nitrate reductase has been demonstrated previously. The data presented in this report strongly support the hypothesis that plant tissues also synthesize NO via the nonenzymatic reduction of apoplastic nitrite. As measured by mass spectrometry or an NO-reactive fluorescent probe, Hordeum vulgare (barley) aleurone layers produce NO rapidly when nitrite is added to the medium in which they are incubated. NO production requires an acid apoplast and is accompanied by a loss of nitrite from the medium. Phenolic compounds in the medium can increase the rate of NO production. The possible significance of apoplastic NO production for germinating grain and for plant roots is discussed.     

Long-Tract Mitotic Gene Conversion in Yeast: Evidence for a Triparental Contribution during Spontaneous Recombination

In Saccharomyces cerevisiae, spontaneous mitotic gene conversion at one site is statistically correlated with recombination at other loci. In general, coincident conversion frequencies are highest for tightly linked markers and decline as a function of intermarker distance. Paradoxically, a significant fraction of mitotic gene convertants exhibits concomitant nonreciprocal segregation for multiple and widely spaced markers. We have undertaken a detailed genetic analysis of this class of mitotic recombinants. Our results indicate that mitotic gene conversion in yeast is frequently associated with nonreciprocal segregation of markers centromere-distal to the selected site of conversion. In addition, distal markers are often found to be mosaic within the product colonies. These observations, and others described here, suggest that a percentage of gene conversion in vegetative yeast cells is coupled to a chromosome break and repair mechanism. This hypothesis was further tested using a strain trisomic for chromosome VII which was specially marked to detect homolog-dependent repair events. An association between mitotic gene conversion events and the production of broken chromosomes which are repaired by a homologous-pairing-copy mechanism was supported.     

Egg production and survival of the citrus red mite on an artificial feeding system

An artificial feeding system was developed for the citrus red mite, Panonychus citri McGregor (Acari: Tetranychidae) to determine egg production and survival of adult female mites in response to various nutrient solutions. Egg production increased with increasing sugar concentration up to 20%, then declined. Autoclaved sodium caseinate was the most suitable nitrogen source examined, and egg production was highest on diet fractions containing 8% sodium caseinate, the highest concentration examined. Fecundity was higher when dietary nitrogen was provided entirely by protein than in whole or in part by free amino acids. Results are qualitatively similar to studies with Tetranychus urticae Koch, however optimal concentrations of major nutrients were ca. 4 to 10 times higher for P. citri than for T. urticae.

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Résumé Une méthode d'alimentation sur diète artificielle a été mise au point pour l'acarien du citrus, Panonychus citri Mc Gregor (Acari: Tetranychidae) et a été utilisée pour déterminer l'influence de différentes solutions nutritives sur la fécondité et la survie des femelles adultes. La fécondité augmente avec la teneur en sucre jusqu'à une concentration maximale de 30%, et décline ensuite pour des concentrations supérieures. Du caséinate de sodium autoclavé s'est révélé être la meilleure source d'azote et la fécondité a été la plus forte sur des milieux contenant 8% de caséinate de sodium, concentration la plus élevée testée. La fécondité est plus grande lorsque l'azote alimentaire est fourni entièrement sous forme de protéine plutôt que sous forme d'acides aminés libres, en tout ou en partie. Les résultats sont qualitativement semblables à ceux obtenus précédemment chez Tetranychus urticae Koch, cependant les concentrations optimales des nutriments majeurs sont environ 4 à 10 fois plus élevées pour P. citri que pour T. urticae.

     

Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation‐growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.