SNP high-throughput screening in grapevine using the SNPlex™ genotyping system

Background

Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP) discovery and genotyping in grapevine (Vitis vinifera L.). However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs) thus providing a valuable source for high-throughput genotyping methods.

Results

Herein we report the first application of the SNPlex? genotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah × Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA) methods were used for preparation of genomic DNA for the SNPlex assay.

Conclusion

Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA), is a good solution for future applications in well-equipped laboratories.     

Molecular and phenotypic diversity in Chionactis occipitalis (Western Shovel-nosed Snake), with emphasis on the status of C. o. klauberi (Tucson Shovel-nosed Snake).

Chionactis occipitalis (Western Shovel-nosed Snake) is a small colubrid snake inhabiting the arid regions of the Mojave, Sonoran, and Colorado deserts. Morphological assessments of taxonomy currently recognize four subspecies. However, these taxonomic proposals were largely based on weak morphological differentiation and inadequate geographic sampling. Our goal was to explore evolutionary relationships and boundaries among subspecies of C. occipitalis, with particular focus on individuals within the known range of C. o. klauberi (Tucson Shovel-nosed snake). Population sizes and range for C. o. klauberi have declined over the last 25 years due to habitat alteration and loss prompting a petition to list this subspecies as endangered. We examined the phylogeography, population structure, and subspecific taxonomy of C. occipitalis across its geographic range with genetic analysis of 1100 bases of mitochondrial DNA sequence and reanalysis of 14 morphological characters from 1543 museum specimens. We estimated the species gene phylogeny from 81 snakes using Bayesian inference and explored possible factors influencing genetic variation using landscape genetic analyses. Phylogenetic and population genetic analyses reveal genetic isolation and independent evolutionary trajectories for two primary clades. Our data indicate that diversification between these clades has developed as a result of both historical vicariance and environmental isolating mechanisms. Thus these two clades likely comprise ‘evolutionary significant units’ (ESUs). Neither molecular nor morphological data are concordant with the traditional C. occipitalis subspecies taxonomy. Mitochondrial sequences suggest specimens recognized as C. o. klauberi are embedded in a larger geographic clade whose range has expanded from western Arizona populations, and these data are concordant with clinal longitudinal variation in morphology.     

Limited genetic structure and evidence for dispersal among populations of the endangered Florida grasshopper sparrow, Ammodramus savannarum floridanus

The Florida grasshopper sparrow, Ammodramus savannarum floridanus, is a non-migratory, endangered subspecies endemic to the prairie region of south-central Florida. It has experienced significant population declines and is currently restricted to five locations. We found substantial levels of variation in microsatellites and mtDNA control region sequences, estimates of inbreeding genetic effective population sizes that were much larger than the estimated census size, and no evidence of inbreeding within five sampled populations (n = 105). We also found a lack of genetic structure among populations (F _ST = 0.0123 for microsatellites and θ = 0.008 for mtDNA), and evidence for dispersal between populations, with 7.6% of all individuals identified as immigrants to their population of capture. We suggest that the subspecies be managed as a single management unit on a regional scale rather than as multiple management units on a local subpopulation scale. There is still a limited opportunity to preserve much of the present genetic variation in this subspecies, if immediate measures are taken to reverse the current population decline before this variation is reduced by genetic drift.     

Sperm environment affects offspring quality in broadcast spawning marine invertebrates

The provisioning of offspring can have far-reaching consequences for later life in a wide range of organisms and generally this provisioning is thought to be under maternal influence or control. In experiments with a broadcast-spawning ascidian, we found that the size of offspring was determined by egg size and the abundance of sperm present during fertilization. Larger eggs were fertilized at low sperm concentrations, whilst smaller eggs were successfully fertilized at high sperm concentrations. These differences in fertilized egg size resulted in differences in the development rate, hatching success and mean size of the subsequent larvae. Our results suggest that, in contrast to females that reproduce by other mating systems, free-spawning mothers lack some control over the provisioning of offspring. Furthermore, because males can alter the sperm environment, they can exert paternal (non-genetic) control over key offspring characteristics.     

Sperm aggregations in female Agkistrodon piscivorus (Reptilia:Squamata): a histological and ultrastructural investigation

Upon copulation in female Agkistrodon piscivorus, sperm migrate up the oviduct to sperm storage tubules (SSTs) in the posterior infundibulum. The epithelium of the SSTs is composed of ciliated and secretory cells and differs ultrastructurally from that of the epithelium lining the lumen of the posterior infundibulum. Sperm pass through an area composed primarily of ciliated cells at the opening of each gland before aligning themselves in parallel arrays with their nuclei facing an area composed primarily of secretory cells at the base of the tubules. Sperm are also found embedded inter- and intracellularly in the SSTs. The secretory vacuoles in the SSTs become highly electron dense after the start of the fall mating season along with the synthesis of lipid droplets. Histochemical analysis reveals that the alteration in secretory material density is caused by the production of neutral carbohydrates. Some sperm remain in aggregates in the nonglandular section of the posterior uterus until the time of ovulation. However, ultrastructural evidence indicates these sperm degrade before ovulation. Therefore, sperm in posterior aggregates have no role in fertilization of ovulated ova. The data presented here support the hypothesis that infundibular sperm storage is the mode that snakes utilize to sequester viable sperm until ovulation.     

Renal sexual segment of the Cottonmouth snake, Agkistrodon piscivorous (Reptilia, Squamata, Viperidae)

The seasonal variation of the renal sexual segment (RSS) of males of the Cottonmouth snake, Agkistrodon piscivorous, is described using light and electron microscopy. This study is the first to describe the ultrastructure of the RSS of a viper (Viperidae) and only the fourth on a snake. Renal sexual segments from males collected February to May and from August to November are similar in appearance. The cells are eosinophilic and react with periodic acid/Schiff procedure (PAS) for neutral carbohydrates and bromphenol blue (BB) for proteins. At the ultrastructure level, the cells contain large (2 microm diameter), electron-dense secretory granules and smaller vesicles with a diffuse material, and these structures abut against the luminal border and upon clear vacuoles continuous with intercellular canaliculi. Evidence was found for both apocrine and merocrine processes of product release. In June and July, the RSS are significantly smaller in diameter, largely basophilic, and have only scattered granules that are PAS+ and BB+. Cytologically, the RSS from June to July lack electron-dense secretory granules and the smaller vesicles with diffuse material. Numerous condensing vacuoles and abundant rough endoplasmic reticulum, however, indicate that active product synthesis is occurring. This is the first report of significant seasonal variation in the histology and ultrastructure of the RSS of a snake, although such reports exist for lizards. The seasons when the RSS is most highly hypertrophied correspond to the fall and spring mating seasons of A. piscivorous, as determined by other studies.     

Insights into Zn2+ homeostasis in neurons from experimental and modeling studies

To understand the mechanisms of neuronal Zn2+ homeostasis better, experimental data obtained from cultured cortical neurons were used to inform a series of increasingly complex computational models. Total metals (inductively coupled plasma-mass spectrometry), resting metallothionein, (65)Zn2+ uptake and release, and intracellular free Zn2+ levels using ZnAF-2F were determined before and after neurons were exposed to increased Zn2+, either with or without the addition of a Zn2+ ionophore (pyrithione) or metal chelators [EDTA, clioquinol (CQ), and N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine]. Three models were tested for the ability to match intracellular free Zn2+ transients and total Zn2+ content observed under these conditions. Only a model that incorporated a muffler with high affinity for Zn2+, trafficking Zn2+ to intracellular storage sites, was able to reproduce the experimental results, both qualitatively and quantitatively. This "muffler model" estimated the resting intracellular free Zn2+ concentration to be 1.07 nM. If metallothionein were to function as the exclusive cytosolic Zn2+ muffler, the muffler model predicts that the cellular concentration required to match experimental data is greater than the measured resting concentration of metallothionein. Thus Zn2+ buffering in resting cultured neurons requires additional high-affinity cytosolic metal binding moieties. Added CQ, as low as 1 microM, was shown to selectively increase Zn2+ influx. Simulations reproduced these data by modeling CQ as an ionophore. We conclude that maintenance of neuronal Zn2+ homeostasis, when challenged with Zn2+ loads, relies heavily on the function of a high-affinity muffler, the characteristics of which can be effectively studied with computational models.     

Lrp4 is a receptor for Agrin and forms a complex with MuSK

Neuromuscular synapse formation requires a complex exchange of signals between motor neurons and skeletal muscle fibers, leading to the accumulation of postsynaptic proteins, including acetylcholine receptors in the muscle membrane and specialized release sites, or active zones in the presynaptic nerve terminal. MuSK, a receptor tyrosine kinase that is expressed in skeletal muscle, and Agrin, a motor neuron-derived ligand that stimulates MuSK phosphorylation, play critical roles in synaptic differentiation, as synapses do not form in their absence, and mutations in MuSK or downstream effectors are a major cause of a group of neuromuscular disorders, termed congenital myasthenic syndromes (CMS). How Agrin activates MuSK and stimulates synaptic differentiation is not known and remains a fundamental gap in our understanding of signaling at neuromuscular synapses. Here, we report that Lrp4, a member of the LDLR family, is a receptor for Agrin, forms a complex with MuSK, and mediates MuSK activation by Agrin.     

Synaptic asymmetry to go

Cell polarity is critical for T lymphocyte movement during their hunt for antigen-bearing cells and for infected target cells. In this issue of Cell, Yeh et al. (2008) now reveal a direct link between T cell polarity and the production of proinflammatory cytokines in mice lacking the class I MHC-restricted T cell-associated molecule (Crtam).     

Streptozocin Diabetes Elevates all Isoforms of TGF-β in the Rat Kidney

Transforming growth factor beta (TGF-β) is a major promoter of diabetic nephropathy. While TGF-β1 is the most abundaft renal isoform, types 2 and 3 are present as well and have identical in vitro effects. Whole kidney extracts were studied 2 weeks after induction of streptozocin diabetes and in control rats. Mean glomerular area was 25% greater in the diabetic animals. TGF-β1 showed a 2-fold increase in message with a 3-fold increase in protein. TGF-β2 mRNA increased approximately 6% while its protein doubled. TGF-β-message increased by 25%, producing a 35% increase in its protein. TGF-β- inducible gene H3 mRNA was increased 35% in the diabetic animals, consistent with increased activity of this growth factor. All isoforms of TGF-β are increased in the diabetic rat kidney. Future studies need to address the specific role that each isoform plays in diabetic nephropathy as well as the impact of therapies on each isoform.