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

Chan, Ariel W / Villwock, Seren S / Williams, Amy L / Jannink, Jean-Luc

2021 Volume 12, Issue 1

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Alleles ; Manihot/genetics ; Plant Breeding ; Recombination, Genetic ; Sex Characteristics
Language	English
Publishing date	2021-11-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkab372
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Article ; Online: Corrigendum to: Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices.

Wolfe, Marnin D / Chan, Ariel W / Kulakow, Peter / Rabbi, Ismail / Jannink, Jean-Luc

Genetics

2022 Volume 220, Issue 2

Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyab225
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Article ; Online: Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices.

Wolfe, Marnin D / Chan, Ariel W / Kulakow, Peter / Rabbi, Ismail / Jannink, Jean-Luc

Genetics

2021 Volume 219, Issue 3

Abstract: 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 ... ...

Abstract	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).
MeSH term(s)	Crops, Agricultural/genetics ; Crosses, Genetic ; Genetic Variation ; Genome, Plant ; Manihot/genetics ; Models, Genetic ; Plant Breeding
Language	English
Publishing date	2021-10-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyab122
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Article ; Online: A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data.

Chan, Ariel W / Williams, Amy L / Jannink, Jean-Luc

BMC bioinformatics

2018 Volume 19, Issue 1, Page(s) 478

Abstract: 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 ... ...

Abstract	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 .
MeSH term(s)	Databases, Nucleic Acid/standards ; Humans ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2018-12-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-018-2512-8
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Article ; Online: Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS) Data.

Chan, Ariel W / Hamblin, Martha T / Jannink, Jean-Luc

PloS one

2016 Volume 11, Issue 8, Page(s) e0160733

Abstract: 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 ...

Abstract	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.
MeSH term(s)	Algorithms ; Gene Frequency ; Genomics/methods ; Genotype ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Manihot/genetics ; Manihot/growth & development ; Plant Breeding ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2016-08-18
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0160733
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Article ; Online: Tuneable semi-synthetic network alginate for absorptive encapsulation and controlled release of protein therapeutics.

Chan, Ariel W / Neufeld, Ronald J

Biomaterials

2010 Volume 31, Issue 34, Page(s) 9040–9047

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Absorption/drug effects ; Alginates/chemistry ; Animals ; Biomechanical Phenomena/drug effects ; Cross-Linking Reagents/pharmacology ; Delayed-Action Preparations/chemistry ; Diffusion/drug effects ; Gels ; Hydrogen-Ion Concentration/drug effects ; Kinetics ; Molecular Weight ; Polymers/chemistry ; Porosity/drug effects ; Proteins/therapeutic use ; Solutions
Chemical Substances	Alginates ; Cross-Linking Reagents ; Delayed-Action Preparations ; Gels ; Polymers ; Proteins ; Solutions
Language	English
Publishing date	2010-12
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	603079-8
ISSN	1878-5905 ; 0142-9612
ISSN (online)	1878-5905
ISSN	0142-9612
DOI	10.1016/j.biomaterials.2010.07.111
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Article ; Online: Modeling the controllable pH-responsive swelling and pore size of networked alginate based biomaterials.

Chan, Ariel W / Neufeld, Ronald J

Biomaterials

2009 Volume 30, Issue 30, Page(s) 6119–6129

Abstract: 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 ...

Abstract	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.
MeSH term(s)	Aldehydes/chemistry ; Alginates/chemistry ; Animals ; Biocompatible Materials/chemistry ; Cattle ; Diffusion ; Drug Carriers/chemistry ; Electrolytes/chemistry ; Gels ; Hydrogels/chemistry ; Hydrogen-Ion Concentration ; Materials Testing ; Polymers/chemistry ; Rheology ; Serum Albumin/chemistry
Chemical Substances	Aldehydes ; Alginates ; Biocompatible Materials ; Drug Carriers ; Electrolytes ; Gels ; Hydrogels ; Polymers ; Serum Albumin
Language	English
Publishing date	2009-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	603079-8
ISSN	1878-5905 ; 0142-9612
ISSN (online)	1878-5905
ISSN	0142-9612
DOI	10.1016/j.biomaterials.2009.07.034
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Article ; Online: Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection.

Wolfe, Marnin D / Bauchet, Guillaume J / Chan, Ariel W / Lozano, Roberto / Ramu, Punna / Egesi, Chiedozie / Kawuki, Robert / Kulakow, Peter / Rabbi, Ismail / Jannink, Jean-Luc

Genetics

2019 Volume 213, Issue 4, Page(s) 1237–1253

Abstract: 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 ( ...

Abstract	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 (
MeSH term(s)	Alleles ; Genetic Linkage ; Genome, Plant ; Genome-Wide Association Study ; Haplotypes/genetics ; Homozygote ; Inbreeding ; Inheritance Patterns/genetics ; Linkage Disequilibrium/genetics ; Manihot/genetics ; Principal Component Analysis ; Quantitative Trait Loci/genetics ; Quantitative Trait, Heritable ; Selection, Genetic
Language	English
Publishing date	2019-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.119.302757
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Article ; Online: Semisynthesis of a controlled stimuli-responsive alginate hydrogel.

Chan, Ariel W / Whitney, Ralph A / Neufeld, Ronald J

Biomacromolecules

2009 Volume 10, Issue 3, Page(s) 609–616

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Alginates/chemical synthesis ; Alginates/chemistry ; Hydrogel, Polyethylene Glycol Dimethacrylate/chemical synthesis ; Hydrogel, Polyethylene Glycol Dimethacrylate/chemistry ; Hydrogen-Ion Concentration ; Macromolecular Substances/chemical synthesis ; Macromolecular Substances/chemistry ; Molecular Structure ; Particle Size ; Surface Properties
Chemical Substances	Alginates ; Macromolecular Substances ; Hydrogel, Polyethylene Glycol Dimethacrylate (25852-47-5)
Language	English
Publishing date	2009-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/bm801316z
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Article ; Online: Kinetic controlled synthesis of pH-responsive network alginate.

Chan, Ariel W / Whitney, Ralph A / Neufeld, Ronald J

Biomacromolecules

2008 Volume 9, Issue 9, Page(s) 2536–2545

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Acetylation ; Aldehydes/chemistry ; Alginates/chemical synthesis ; Alginates/chemistry ; Biocompatible Materials/chemical synthesis ; Biocompatible Materials/chemistry ; Biopolymers/chemistry ; Catalysis ; Gels/chemical synthesis ; Gels/chemistry ; Glucuronic Acid/chemical synthesis ; Glucuronic Acid/chemistry ; Hexuronic Acids/chemical synthesis ; Hexuronic Acids/chemistry ; Hydrogen-Ion Concentration ; Kinetics ; Materials Testing ; Molecular Structure ; Molecular Weight ; Particle Size ; Temperature ; Thermodynamics ; Time Factors ; Viscosity
Chemical Substances	Aldehydes ; Alginates ; Biocompatible Materials ; Biopolymers ; Gels ; Hexuronic Acids ; Glucuronic Acid (8A5D83Q4RW) ; alginic acid (8C3Z4148WZ)
Language	English
Publishing date	2008-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/bm800594f
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