Bilineal disease and trans-heterozygotes in autosomal dominant polycystic kidney disease

In searching for a putative third gene for autosomal dominant polycystic kidney disease (ADPKD), we studied the genetic inheritance of a large family (NFL10) previously excluded from linkage to both the PKD1 locus and the PKD2 locus. We screened 48 members of the NFL10 pedigree, by ultrasonography, and genotyped them, with informative markers, at both the PKD1 locus and the PKD2 locus. Twenty-eight of 48 individuals assessed were affected with ADPKD. Inspection of the haplotypes of these individuals suggested the possibility of bilineal disease from independently segregating PKD1 and PKD2 mutations. Using single-stranded conformational analysis, we screened for and found a PKD2 mutation (i.e., 2152delA; L736X) in 12 affected pedigree members. Additionally, when the disease status of these individuals was coded as "unknown" in linkage analysis, we also found, with markers at the PKD1 locus, significant LOD scores (i.e., >3.0). These findings strongly support the presence of a PKD1 mutation in 15 other affected pedigree members, who lack the PKD2 mutation. Two additional affected individuals had trans-heterozygous mutations involving both genes, and they had renal disease that was more severe than that in affected individuals who had either mutation alone. This is the first documentation of bilineal disease in ADPKD. In humans, trans-heterozygous mutations involving both PKD1 and PKD2 are not necessarily embryonically lethal. However, the disease associated with the presence of both mutations appears to be more severe than the disease associated with either mutation alone. The presence of bilineal disease as a confounder needs to be considered seriously in the search for the elusive PKD3 locus.     

Multiple paternity in Littorina obtusata (Gastropoda, Littorinidae) revealed by microsatellite analyses.

Parental identity for juvenile Littorina obtusata was determined from three egg masses by means of microsatellite DNA markers. Results confirm that the attendant adult female in each case was the dam of the offspring and that at least 4-6 males contributed to each brood. This correlates with our behavioral observations that indicated multiple copulations between the female and several males in each experimental aquarium. A significant number of offspring from each brood were sired by non-sampled males (males that had copulated with females before capture) whose sperm had been stored by the female. This is the first direct evidence of multiple paternity in the Littorinidae. Results are discussed in reference to current theories of sperm competition, male precedence, and cryptic female choice.     

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield

To understand the genetic basis of inbreeding depression and heterosis in rice, main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers, replicated phenotyping experiments, and the mixed model approach. The mapping populations included 254 F(10) recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers (Zhong 413 and IR64). For both BY and GY, there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations. The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements. The hybrid breakdown (part of inbreeding depression) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids, indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice. A large number of epistatic QTL pairs and a few main-effect QTL were identified, which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation. Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results. First, most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis. Second, most ( approximately 90%) QTL contributing to heterosis appeared to be overdominant. These observations tend to implicate epistasis and overdominance, rather than dominance, as the major genetic basis of heterosis in rice. The implications of our results in rice evolution and improvement are discussed.     

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon

Genome duplication is potentially a good source of new genes, but such genes take time to evolve. We have found a group of "duplication-resistant" genes, which have undergone convergent restoration to singleton status following several independent genome duplications. Restoration of duplication-resistant genes to singleton status could be important to long-term survival of a polyploid lineage. Angiosperms show more frequent polyploidization and a higher degree of duplicate gene preservation than other paleopolyploids, making them well-suited to further study of duplication-resistant genes.     

QTL analysis of cotton fiber length in advanced backcross populations derived from a cross between <Emphasis Type="Italic">Gossypium hirsutum</Emphasis> and <Emphasis Type="Italic">G. mustelinum</Emphasis>

Key message

QTLs for fiber length mapped in three generations of advanced backcross populations derived from crossing Gossypium hirsutum and Gossypium mustelinum showed opportunities to improve elite cottons by introgression from wild relatives.

Abstract

The molecular basis of cotton fiber length in crosses between Gossypium hirsutum and Gossypium mustelinum was dissected using 21 BC₃F₂ and 12 corresponding BC₃F_2:3 and BC₃F_2:4 families. Sixty-five quantitative trait loci (QTLs) were detected by one-way analysis of variance. The QTL numbers detected for upper-half mean length (UHM), fiber uniformity index (UI), and short fiber content (SFC) were 19, 20, and 26 respectively. Twenty-three of the 65 QTLs could be detected at least twice near adjacent markers in the same family or near the same markers across different families/generations, and 32 QTLs were detected in both one-way variance analyses and mixed model-based composite interval mapping. G. mustelinum alleles increased UHM and UI and decreased SFC for five, one, and one QTLs, respectively. In addition to the main-effect QTLs, 17 epistatic QTLs were detected which helped to elucidate the genetic basis of cotton fiber length. Significant among-family genotypic effects were detected at 18, 16, and 16 loci for UHM, UI, and SFC, respectively. Six, two, and two loci showed genotype?×?family interaction for UHM, UI and SFC, respectively, illustrating complexities that might be faced in introgression of exotic germplasm into cultivated cotton. Co-location of many QTLs for UHM, UI, and SFC accounted for correlations among these traits, and selection of these QTLs may improve the three traits simultaneously. The simple sequence repeat (SSR) markers associated with G. mustelinum QTLs will assist breeders in transferring and maintaining valuable traits from this exotic source during cultivar development.

     

Fine mapping and candidate gene analysis of <Emphasis Type="Italic">qFL-chr1</Emphasis>, a fiber length QTL in cotton

Key message

A fiber length QTL, qFL-chr1, was fine mapped to a 0.9 cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length.

Abstract

Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers used to genotype 1672 BC₄F₂ plants identified 432 recombinants containing breakpoints in the target region. Substitution mapping using 141 informative recombinants narrowed the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible effects of non-target introgressions on fiber length, different heterozygous BC₄F₃ plants introgressed between SSR markers NAU3384 and CGR5144 were selected to develop sub-NILs. The qFL-chr1 was further mapped at 0.9-cM interval between MUSS422 and CIR018 by comparisons of sub-NIL phenotype, and increased fiber length by ~1 mm. The 2.38-Mb region between MUSS422 and CIR018 in G. barbadense contained 19 annotated genes. Expression levels of two of these genes, GOBAR07705 (encoding 1-aminocyclopropane-1-carboxylate synthase) and GOBAR25992 (encoding amino acid permease), were positively correlated with fiber length in a small F₂ population, supporting these genes as candidates for qFL-chr1.

     

Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids

In addition to the genomes of Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa), two near-complete rosid genome sequences, grape (Vitis vinifera) and papaya (Carica papaya), have been recently released. The phylogenetic relationship among these four genomes and the placement of their three independent, fractionated tetraploidies sum to a powerful comparative genomic system. CoGe, a platform of multiple whole or near-complete genome sequences, provides an integrative Web-based system to find and align syntenic chromosomal regions and visualize the output in an intuitive and interactive manner. CoGe has been customized to specifically support comparisons among the rosids. Crucial facts and definitions are presented to clearly describe the sorts of biological questions that might be answered in part using CoGe, including patterns of DNA conservation, accuracy of annotation, transposability of individual genes, subfunctionalization and/or fractionation of syntenic gene sets, and conserved noncoding sequence content. This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically.     

Effect of sediment type on microphytobenthos vertical distribution: Modelling the productive biomass and improving ground truth measurements

Intertidal flats are frequently colonised by microphytobenthos (MPB) assemblages that form transient biofilms at the sediment surface which are responsible for large fractions of estuarine primary production. The large spatio-temporal variability in MPB biomass distribution in concert with the fact that tidal flats can cover many km² makes the use of remote sensing particularly useful in assessing MPB distribution. Water content, sediment type and MPB vertical migration are variables that affect the relationship between ground truth measurements and remote sensing of benthic chlorophyll. The effect of chlorophyll depth distribution (top 2 mm) on the relationship between benthic chlorophyll and several remote sensing indices (NDVI, PI, R562/R647, derivative indices and PAM fluorescence) was investigated over a 2 year sampling period at 6 sites (Tagus estuary, Portugal). Additionally, the effect of the dark adaptation time required to measure the minimum fluorescence parameter (F₀) was also tested. Sediment type strongly affected MPB depth distribution with muddy sites showing a strong negative exponential decay in chlorophyll with distance from the surface while sandy sites had a homogenous distribution over the same scale (2 mm). Chlorophyll content (mass per unit mass, μg g^− 1) in the top 2 mm was better correlated with remote sensing indices than concentration (mass per unit volume, mg m^− 3), both for NDVI (0.72 vs. 0.45) and for PAM fluorescence (0.70 vs. 0.55). Separating the data by transect increased the correlation values in all situations. A fitted model of chlorophyll depth distribution showed that the effect of asymmetrical chlorophyll depth distribution was stronger on the correlations between chlorophyll concentration and NDVI than on chlorophyll content and NDVI (0.46-2 mm vs. 0.74-125 μm, muddy site) the same was valid for fluorescence (0.66-2 mm vs. 0.92-125 μm, muddy site). Dark adapting the samples for more than 5 min did not result in any significant difference in the relationship between F₀ and chlorophyll a. The residuals from the regression of chlorophyll content on NDVI were positively correlated (0.7) with the mass per unit of mass of sediment < 63 μm and negatively (− 0.6) with chlorophyll concentration, this indicates that if no correction is performed to account for chlorophyll depth distribution both units will be strongly affected by the mass of < 63 μm particles. The results demonstrate that although expressing chlorophyll a as concentration is generally a better option for ground truth measurements care should be taken to account for chlorophyll depth distribution since strong asymmetries within the sampling depth can introduce large errors.     

Root exudation from Hordeum vulgare in response to localized nitrate supply

Root proliferation as a response to exploit zones of nutrient enrichment in soil has been demonstrated for a wide range of plant species. However, the effectiveness of this as a strategy to acquire nutrients is also dependent on interactions with the soil microbial community. Specifically, C-flow from roots modifies microbial activity and probably the balance between nutrient mineralization and immobilization processes in the rhizosphere. In this study, near-natural abundance 13C-labelling and gene-reporter methods were applied to determine the effects of uneven nitrate supply to roots of Hordeum vulgare on assimilate partitioning and root exudation. Plants were initially grown in uniform nitrate supply in split-root, sand microcosms after which one treatment continued to receive uniform supply, and the other received nitrate to one root compartment only. At the time of imposing the treatments, the CO2 supplied to the plants was switched to a cylinder source, providing a distinct delta13C-signature and allowing the fate of new assimilate within the plants to be determined. The labelling approach allowed quantification of the expected preferential allocation of new C-assimilate to roots in enriched nitrate, prior to any measurable effect on whole biomass or root architecture. Biosensor (lux-marked Pseudomonas fluorescens 10586 pUCD607) bioluminescence, quantified spatially by CCD imaging, demonstrated that root exudation was significantly increased for roots in enriched nitrate. This response of root exudation, being primarily associated with root apices and concurrent with enhanced assimilate supply, strongly suggests that C-flow from roots is an integral component of the proliferation response to nitrate.     

The quantitative variability and monosaccharide composition of sediment carbohydrates associated with intertidal diatom assemblages

The extracellular secretions of epipelic diatoms (Bacillariophyceae) axe an important source of carbohydrates on intertidal sediments. For analytical purposes, sediment carbohydrates have been operationally separated into colloidal and bulk fractions that are often assumed to be similar in their chemical properties. However, there has been little investigation into the nature of the two fractions. In this study, carbohydrate fractions were sampledin situ, isolated, purified and biochemically characterised using gas chromatography-mass spectrometry (GC-MS). Both carbohydrate fractions were found to contain similar sugars although in different proportions. Glucose represented more than 80% of the monosaccharides identified in the colloidal carbohydrate fraction while only 37% of monosaccharides present in the bulk carbohydrate fraction. Colloidal carbohydrate concentrations showed short-term variability and were correlated with diatom biomass (as chlorophylla) suggesting the colloidal fraction is labile and may be of recent origin, perhaps representing diatom activity. Concentrations of the bulk carbohydrate fraction did not show significant short-term variation and was therefore more refractory. This combination of biochemical and field data suggested that the bulk and colloidal carbohydrate fractions were chemically and physically different. These findings have relevance to studies of estuarine carbon cycling.Abbreviations LTSEM Low-temperature scanning electron microscopy - GC-MS Gas chromatography-mass spectroscopy - EPS Extracellular polymeric substances