Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm.

Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing data and a validated multigenerational pedigree from the International Institute of Tropical Agriculture cassava breeding germplasm consisting of 7020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium. We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.

Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices.

Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection.

Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.

A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data.

BACKGROUND: Researchers typically sequence a given individual multiple times, either re-sequencing the same DNA sample (technical replication) or sequencing different DNA samples collected on the same individual (biological replication) or both. Before merging the data from these replicate sequence runs, it is important to verify that no errors, such as DNA contamination or mix-ups, occurred during the data collection pipeline. Methods to detect such errors exist but are often ad hoc, cannot handle missing data and several require phased data. Because they require some combination of genotype calling, imputation, and haplotype phasing, these methods are unsuitable for error detection in low- to moderate-depth sequence data where such tasks are difficult to perform accurately. Additionally, because most existing methods employ a pairwise-comparison approach for error detection rather than joint analysis of the putative replicates, results may be difficult to interpret. RESULTS: We introduce a new method for error detection suitable for shallow-, moderate-, and high-depth sequence data. Using Bayes Theorem, we calculate the posterior probability distribution over the set of relations describing the putative replicates and infer which of the samples originated from an identical genotypic source. CONCLUSIONS: Our method addresses key limitations of existing approaches and produced highly accurate results in simulation experiments. Our method is implemented as an R package called BIGRED (Bayes Inferred Genotype Replicate Error Detector), which is freely available for download: https://github.com/ac2278/BIGRED .

Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS) Data.

Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult. Our primary interest lies in the issue of how one can accurately infer or impute missing genotypes in HTS-derived datasets. Many of the existing genotype imputation algorithms and software packages were primarily developed by and optimized for the human genetics community, a field where a complete and accurate reference genome has been constructed and SNP arrays have, in large part, been the common genotyping platform. We set out to answer two questions: 1) can we use existing imputation methods developed by the human genetics community to impute missing genotypes in datasets derived from non-human species and 2) are these methods, which were developed and optimized to impute ascertained variants, amenable for imputation of missing genotypes at HTS-derived variants? We selected Beagle v.4, a widely used algorithm within the human genetics community with reportedly high accuracy, to serve as our imputation contender. We performed a series of cross-validation experiments, using GBS data collected from the species Manihot esculenta by the Next Generation (NEXTGEN) Cassava Breeding Project. NEXTGEN currently imputes missing genotypes in their datasets using a LASSO-penalized, linear regression method (denoted 'glmnet'). We selected glmnet to serve as a benchmark imputation method for this reason. We obtained estimates of imputation accuracy by masking a subset of observed genotypes, imputing, and calculating the sample Pearson correlation between observed and imputed genotype dosages at the site and individual level; computation time served as a second metric for comparison. We then set out to examine factors affecting imputation accuracy, such as levels of missing data, read depth, minor allele frequency (MAF), and reference panel composition.

Tuneable semi-synthetic network alginate for absorptive encapsulation and controlled release of protein therapeutics.

Stimuli-responsive hydrogels swell or contract in response to external pH, ionic strength or temperature, and are of considerable interest as pharmaceutical controlled release devices. Alginate, a mucoadhesive biopolymer, was used as building block in the semi-synthesis of a tetra-functional acetal-linked networked polymer (SNAP) with carboxylate moieties preserved as stimuli-responsive sensors and tuneable pore sizes larger than the hydrodynamic radius of model molecules ranging between 1 and 540 kDa. Based on the diffusion coefficients calculated from protein uptake experiments, the networked polymer with pre-designed pore size of 80 nm can allow vitamin B(12), lysozyme, subtilisin, insulin, albumin, and urease to diffuse freely into the hydrogel with diffusivity ratio of D(gel)/D(water) (diffusion coefficients in hydrogel to water) between 0.60 and 0.95. Drying was applied as post-fabrication modification to alter/control the diffusional properties of the gel matrix. Together with the pH-responsive swelling properties, SNAP granules containing acid-labile protein therapeutics such as insulin showed protective characteristics by retaining collapsed/compact state in gastric environment (pH˜1.2) while swelling in neutral pH to release the bioactives at near zero-order kinetics. SNAP, a new class of tuneable biomaterial, can be semi-synthesized with desired pore properties, which when applied with the absorptive encapsulation technique, can serve as a technology platform for oral delivery of biomolecules with wide range of molecular sizes.

The function of cortactin in the clustering of acetylcholine receptors at the vertebrate neuromuscular junction.

BACKGROUND: Postsynaptic enrichment of acetylcholine receptors (AChRs) at the vertebrate neuromuscular junction (NMJ) depends on the activation of the muscle receptor tyrosine MuSK by neural agrin. Agrin-stimulation of MuSK is known to initiate an intracellular signaling cascade that leads to the clustering of AChRs in an actin polymerization-dependent manner, but the molecular steps which link MuSK activation to AChR aggregation remain incompletely defined. METHODOLOGY/PRINCIPAL FINDINGS: In this study we used biochemical, cell biological and molecular assays to investigate a possible role in AChR clustering of cortactin, a protein which is a tyrosine kinase substrate and a regulator of F-actin assembly and which has also been previously localized at AChR clustering sites. We report that cortactin was co-enriched at AChR clusters in situ with its target the Arp2/3 complex, which is a key stimulator of actin polymerization in cells. Cortactin was further preferentially tyrosine phosphorylated at AChR clustering sites and treatment of myotubes with agrin significantly enhanced the tyrosine phosphorylation of cortactin. Importantly, forced expression in myotubes of a tyrosine phosphorylation-defective cortactin mutant (but not wild-type cortactin) suppressed agrin-dependent AChR clustering, as did the reduction of endogenous cortactin levels using RNA interference, and introduction of the mutant cortactin into muscle cells potently inhibited synaptic AChR aggregation in response to innervation. CONCLUSION: Our results suggest a novel function of phosphorylation-dependent cortactin signaling downstream from agrin/MuSK in facilitating AChR clustering at the developing NMJ.

Modeling the controllable pH-responsive swelling and pore size of networked alginate based biomaterials.

Semisynthetic network alginate polymer (SNAP), synthesized by acetalization of linear alginate with di-aldehyde, is a pH-responsive tetrafunctionally linked 3D gel network, and has potential application in oral delivery of protein therapeutics and active biologicals, and as tissue bioscaffold for regenerative medicine. A constitutive polyelectrolyte gel model based on non-Gaussian polymer elasticity, Flory-Huggins liquid lattice theory, and non-ideal Donnan membrane equilibria was derived, to describe SNAP gel swelling in dilute and ionic solutions containing uni-univalent, uni-bivalent, bi-univalent or bi-bi-valent electrolyte solutions. Flory-Huggins interaction parameters as a function of ionic strength and characteristic ratio of alginates of various molecular weights were determined experimentally to numerically predict SNAP hydrogel swelling. SNAP hydrogel swells pronouncedly to 1000 times in dilute solution, compared to its compact polymer volume, while behaving as a neutral polymer with limited swelling in high ionic strength or low pH solutions. The derived model accurately describes the pH-responsive swelling of SNAP hydrogel in acid and alkaline solutions of wide range of ionic strength. The pore sizes of the synthesized SNAP hydrogels of various crosslink densities were estimated from the derived model to be in the range of 30-450 nm which were comparable to that measured by thermoporometry, and diffusion of bovine serum albumin. The derived equilibrium swelling model can characterize hydrogel structure such as molecular weight between crosslinks and crosslinking density, or can be used as predictive model for swelling, pore size and mechanical properties if gel structural information is known, and can potentially be applied to other point-link network polyelectrolytes such as hyaluronic acid gel.

Semisynthesis of a controlled stimuli-responsive alginate hydrogel.

Benefits of the use of natural polymers include biodegradability, biocompatibility, natural abundance, and unique physicochemical/biological properties. Native alginate was used to semisynthesize a new class of biomaterial in which the physical properties such as swelling and pore size can be chemically tailored for desired end use. Semisynthetic network alginate polymer (SNAP) was prepared by reaction with glutaraldehyde, forming an acetal-linked network polymer gel with carboxylate moieties preserved as stimuli-responsive sensors. The molecular structure of the hydrogel was confirmed by cross-polarization magic-angle spinning (13)C solid state NMR, and reaction parameters affecting the polymer synthesis, including reactant, catalyst concentrations, and solvent composition, were characterized by gel equilibrium swelling. The acetalization reaction can be thermodynamically controlled, offering fine-tuned control of gel swelling and pore properties. In addition, SNAP demonstrated pronounced swelling at alkaline pH and contraction in acidic environment with oscillatory response to repeated pH-stimuli, yielding a potential pulsatile, oral drug delivery vehicle. Through selection of reaction conditions, gel swelling, pore size, and stimuli-responsive characteristics can be specifically tailored for applications such as a tissue scaffold in regenerative medicine, as a targeted delivery vehicle, and as a superabsorbent in environmental cleanup.

Kinetic controlled synthesis of pH-responsive network alginate.

Alginates are of considerable interest in the fields of biotechnology and biomedical engineering. To enable the control of properties generally not possible with the native polymer, we have chemically modified alginate with dialdehyde via acid-catalyzed acetalization. The kinetics of acetalization measured through equilibrium swelling of the networked polymer were found to undergo a zero- and second-order reaction with respect to alginate and dialdehyde, respectively. With the determined rate constant of 19.06 microL x mole(-1) x s(-1) at 40 degrees C and activation energy of 78.58 kJ x mol(-1), a proposed predictive reaction model may be used a priori to select reaction conditions providing specific polymer properties. Gel swelling and average pore size were then able to be controlled between 80-1000-fold and 35-840 nm, respectively, by predictive estimation of reagent concentration and formulation conditions. This semisynthetic but natural polymer is stimuli-responsive exhibiting high water absorbency and may potentially be used as drug delivery vehicle for protein therapeutics.

The function of Shp2 tyrosine phosphatase in the dispersal of acetylcholine receptor clusters.

BACKGROUND: A crucial event in the development of the vertebrate neuromuscular junction (NMJ) is the postsynaptic enrichment of muscle acetylcholine (ACh) receptors (AChRs). This process involves two distinct steps: the local clustering of AChRs at synapses, which depends on the activation of the muscle-specific receptor tyrosine kinase MuSK by neural agrin, and the global dispersal of aneural or "pre-patterned" AChR aggregates, which is triggered by ACh or by synaptogenic stimuli. We and others have previously shown that tyrosine phosphatases, such as the SH2 domain-containing phosphatase Shp2, regulate AChR cluster formation in muscle cells, and that tyrosine phosphatases also mediate the dispersal of pre-patterned AChR clusters by synaptogenic stimuli, although the specific phosphatases involved in this latter step remain unknown. RESULTS: Using an assay system that allows AChR cluster assembly and disassembly to be studied separately and quantitatively, we describe a previously unrecognized role of the tyrosine phosphatase Shp2 in AChR cluster disassembly. Shp2 was robustly expressed in embryonic Xenopus muscle in vivo and in cultured myotomal muscle cells, and treatment of the muscle cultures with an inhibitor of Shp2 (NSC-87877) blocked the dispersal of pre-patterned AChR clusters by synaptogenic stimuli. In contrast, over-expression in muscle cells of either wild-type or constitutively active Shp2 accelerated cluster dispersal. Significantly, forced expression in muscle of the Shp2-activator SIRPalpha1 (signal regulatory protein alpha1) also enhanced the disassembly of AChR clusters, whereas the expression of a truncated SIRPalpha1 mutant that suppresses Shp2 signaling inhibited cluster disassembly. CONCLUSION: Our results suggest that Shp2 activation by synaptogenic stimuli, through signaling intermediates such as SIRPalpha1, promotes the dispersal of pre-patterned AChR clusters to facilitate the selective accumulation of AChRs at developing NMJs.

Regulation of ACh receptor clustering by the tyrosine phosphatase Shp2.

At the vertebrate neuromuscular junction (NMJ), postsynaptic aggregation of muscle acetylcholine receptors (AChRs) depends on the activation of MuSK, a muscle-specific tyrosine kinase that is stimulated by neural agrin and regulated by muscle-intrinsic tyrosine kinases and phosphatases. We recently reported that Shp2, a tyrosine phosphatase containing src homology two domains, suppressed MuSK-dependent AChR clustering in cultured myotubes, but how this effect of Shp2 is controlled has remained unclear. In this study, biochemical assays showed that agrin-treatment of C2 mouse myotubes enhanced the tyrosine phosphorylation of signal regulatory protein alpha1 (SIRPalpha1), a known activator of Shp2, and promoted SIRPalpha1's interaction with Shp2. Moreover, in situ experiments revealed that treatment of myotubes with the Shp2-selective inhibitor NSC-87877 increased spontaneous and agrin-induced AChR clustering, and that AChR clustering was also enhanced in myotubes ectopically expressing inactive (dominant-negative) Shp2; in contrast, AChR clustering was reduced in myotubes expressing constitutively active Shp2. Significantly, expression of truncated (nonShp2-binding) and full-length (Shp2-binding) forms of SIRPalpha1 in myotubes also increased and decreased AChR clustering, respectively, and coexpression of truncated SIRPalpha1 with active Shp2 and full-length SIRPalpha1 with inactive Shp2 reversed the actions of the exogenous Shp2 proteins on AChR clustering. These results suggest that SIRPalpha1 is a novel downstream target of MuSK that activates Shp2, which, in turn, suppresses AChR clustering. We propose that an inhibitory loop involving both tyrosine kinases and phosphatases sets the level of agrin/MuSK signaling and constrains it spatially to help generate high-density AChR clusters selectively at NMJs.