k-mer-based GWAS enhances the discovery of causal variants and candidate genes in soybean

Genome-wide association studies (GWAS) are powerful statistical methods that detect associations between genotype and phenotype at genome scale. Despite their power, GWAS frequently fail to pinpoint the causal variant or the gene controlling a given trait in crop species. Assessing genetic variants other than single-nucleotide polymorphisms (SNPs) could alleviate this problem. In this study, we tested the potential of structural variant (SV)- and k-mer-based GWAS in soybean by applying these methods as well as conventional SNP/indel-based GWAS to 13 traits. We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover, k-mer-based analyses identified promising candidate genes for loci related to pod color, pubescence form, and resistance to Phytophthora sojae. In our dataset, SV-based GWAS did not add value compared to k-mer-based GWAS and may not be worth the time and computational resources invested. Despite promising results, significant challenges remain regarding the downstream analysis of k-mer-based GWAS. Notably, better methods are needed to associate significant k-mers with sequence variation. Our results suggest that coupling k-mer- and SNP/indel-based GWAS is a powerful approach for discovering candidate genes in crop species.

k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives

Genome-wide association studies (GWAS) have allowed the discovery of marker-trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only one type of genetic variation and are usually derived from alignment to a single genome assembly that may be poorly representative of the population under study. To overcome this, k-mer-based GWAS approaches have recently been developed. k-mer-based GWAS provide a universal way to assess variation due to SNPs, insertions/deletions, and structural variations without having to specifically detect and genotype these variants. In addition, k-mer-based analyses can be used in species that lack a reference genome. However, the use of k-mers for GWAS presents challenges such as data size and complexity, lack of standard tools, and potential detection of false associations. Nevertheless, efforts are being made to overcome these challenges and a general analysis workflow has started to emerge. We identify the priorities for k-mer-based GWAS in years to come, notably in the development of user-friendly programs for their analysis and approaches for linking significant k-mers to sequence variation.

The SoyaGen Project: Putting Genomics to Work for Soybean Breeders

The SoyaGen project was a collaborative endeavor involving Canadian soybean researchers and breeders from academia and the private sector as well as international collaborators. Its aims were to develop genomics-derived solutions to real-world challenges faced by breeders. Based on the needs expressed by the stakeholders, the research efforts were focused on maximizing realized yield through optimization of maturity and improved disease resistance. The main deliverables related to molecular breeding in soybean will be reviewed here. These include: (1) SNP datasets capturing the genetic diversity within cultivated soybean (both within a worldwide collection of > 1,000 soybean accessions and a subset of 102 short-season accessions (MG0 and earlier) directly relevant to this group); (2) SNP markers for selecting favorable alleles at key maturity genes as well as loci associated with increased resistance to key pathogens and pests (Phytophthora sojae, Heterodera glycines, Sclerotinia sclerotiorum); (3) diagnostic tools to facilitate the identification and mapping of specific pathotypes of P. sojae; and (4) a genomic prediction approach to identify the most promising combinations of parents. As a result of this fruitful collaboration, breeders have gained new tools and approaches to implement molecular, genomics-informed breeding strategies. We believe these tools and approaches are broadly applicable to soybean breeding efforts around the world.

Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology

BACKGROUND

Structural variants (SVs), including deletions, insertions, duplications, and inversions, are relatively long genomic variations implicated in a diverse range of processes from human disease to ecology and evolution. Given their complex signatures, tendency to occur in repeated regions, and large size, discovering SVs based on short reads is challenging compared to single-nucleotide variants. The increasing availability of long-read technologies has greatly facilitated SV discovery; however, these technologies remain too costly to apply routinely to population-level studies. Here, we combined short-read and long-read sequencing technologies to provide a comprehensive population-scale assessment of structural variation in a panel of Canadian soybean cultivars.

RESULTS

We used Oxford Nanopore long-read sequencing data (~12× mean coverage) for 17 samples to both benchmark SV calls made from Illumina short-read data and predict SVs that were subsequently genotyped in a population of 102 samples using Illumina data. Benchmarking results show that variants discovered using Oxford Nanopore can be accurately genotyped from the Illumina data. We first use the genotyped deletions and insertions for population genetics analyses and show that results are comparable to those based on single-nucleotide variants. We observe that the population frequency and distribution within the genome of deletions and insertions are constrained by the location of genes. Gene Ontology and PFAM domain enrichment analyses also confirm previous reports that genes harboring high-frequency deletions and insertions are enriched for functions in defense response. Finally, we discover polymorphic transposable elements from the deletions and insertions and report evidence of the recent activity of a Stowaway MITE.

CONCLUSIONS

We show that structural variants discovered using Oxford Nanopore data can be genotyped with high accuracy from Illumina data. Our results demonstrate that long-read and short-read sequencing technologies can be efficiently combined to enhance SV analysis in large populations, providing a reusable framework for their study in a wider range of samples and non-model species.

A Practical Guide to Using Structural Variants for Genome-Wide Association Studies

Structural variants (SVs) are known to have large functional impacts on phenotypes of agricultural interest, but they have yet to be routinely used for GWAS. Apart from the difficulty in obtaining high-quality SV genotype data for large populations, one of the main hurdles to using SVs for GWAS lies in formatting of genotype data for use with popular GWAS programs. This protocol describes how typical SV genotype data can be formatted for input to three GWAS programs commonly used by the plant genetics community: TASSEL, GAPIT, and mrMLM.

A Systematic Gene-Centric Approach to Define Haplotypes and Identify Alleles on the Basis of Dense Single Nucleotide Polymorphism Datasets

A gene-centric approach for haplotype definition was developed and implemented in R. The tool allows for allelic characterization at given loci in germplasm collections. Allelic status at four maturity genes is predicted on the basis of marker genotyping data. Assessing the allelic diversity within a germplasm collection and identifying individuals carrying favorable alleles is challenging. Advances in high-throughput technologies allow the genotyping of many individuals for thousands of markers but bridging the gap between single nucleotide polymorphisms (SNPs) and relevant alleles remains difficult. We developed a systematic approach that defines haplotypes from large SNP catalogs that aims to identify haplotypes that can be equated to alleles at given genes. Unlike haplotype visualization tools, our approach selects SNP markers that flank a gene and define haplotypes that correspond to this gene's alleles. We tested this approach on four known soybean [Glycine max (L.) Merr.] maturity genes (E1, GmGia, GmPhyA3, and GmPhyA2) in a collection of 67 lines and two genotypic datasets [a SNP array and genotyping-by-sequencing (GBS)]. For E1, GmGia, and GmPhyA3, we identified SNP haplotypes such that the allele found at these genes could be accurately predicted from the haplotype in 97.3% of the cases. For these genes, of the 12 known alleles in the collection, 10 and 8 could be correctly predicted from the haplotypes found with the SNP array and GBS datasets, with success rates of 98 and 97% for all allele-line combinations, respectively. The approach proved equally successful for data derived from a SNP array and GBS. However, in the case of GmPhyA2, a lack of markers in the genomic region prevented the identification of alleles, regardless of the dataset. We demonstrate the feasibility and reproducibility of our approach and identify limits to its applicability.

Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants

BACKGROUND

The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found in fast neutron populations has been hindered, however, by the wide range of mutations generated and the lack of affordable technologies to detect DNA sequence changes. In this study, we therefore aimed to test whether genotyping-by-sequencing (GBS) technology could be used to characterize copy number variation (CNV) induced by fast neutrons in a soybean mutant population.

RESULTS

We called CNVs from GBS data in 79 soybean mutants and assessed the sensitivity and precision of this approach by validating our results against array comparative genomic hybridization (aCGH) data for 19 of these mutants as well as targeted PCR and ddPCR assays for a representative subset of the smallest events detected by GBS. Our GBS pipeline detected 55 of the 96 events found by aCGH, with approximate detection thresholds of 60 kb, 500 kb and 1 Mb for homozygous deletions, hemizygous deletions and duplications, respectively. Among the whole set of 79 mutants, the GBS data revealed 105 homozygous deletions, 32 hemizygous deletions and 19 duplications. This included several extremely large events, exhibiting maximum sizes of ~ 11.2 Mb for a homozygous deletion, ~ 11.6 Mb for a hemizygous deletion, and ~ 50 Mb for a duplication.

CONCLUSIONS

This study provides a proof of concept that GBS can be used as an affordable high-throughput method for assessing CNVs in fast neutron mutants. The modularity of this GBS approach allows combining as many different libraries or sequencing runs as is necessary for reaching the goals of a particular study. This method should enable the low-cost genome-wide characterization of hundreds to thousands of individuals in fast neutron mutant populations or any population with large genomic deletions and duplications.

Ex situ germination as a method for seed viability assessment in a peatland orchid, Platanthera blephariglottis

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PREMISE OF THE STUDY

Assessing seed quality in orchids has been hindered by stringent germination requirements. Seed quality has traditionally been assessed in orchids using in vitro or in situ germination protocols or viability staining. However, these methods are not always well suited for rapid assessment of viability in the context of ecological studies.•

METHODS

The potential of an ex situ protocol for seed viability assessment of orchids in ecological studies was investigated by sowing seeds of Platanthera blephariglottis on Sphagnum moss collected in the orchid's natural habitat. Ex situ germination results were compared with those obtained by viability staining using triphenyltetrazolium chloride (TTC), and the effect of seed testa color on staining and germination results was investigated.•

KEY RESULTS

The ex situ protocol yielded high germination rates, with 66% of the seeds germinating after 9 wk. Depending on the seed testa color class, ex situ germination rates were about 1.4 to 2.5 times higher than viability rates determined using TTC, indicating that the TTC technique underestimated viability compared with the method using ex situ germination. The TTC estimates of viability rates were higher for seeds with dark-colored testae than for pale ones, whereas seed testa color had no effect on germination.•

CONCLUSIONS

Our study showed promising results for the use of ex situ germination as an alternative to previously developed protocols for seed viability assessment of orchids in ecological studies. Staining using TTC might not be well suited for this purpose, since it introduced a bias with respect to seed testa color.

Modulation and vectorial summation of the spinalized frog's hindlimb end-point force produced by intraspinal electrical stimulation of the cord

The ability to produce various force patterns at the ankle by microstimulation of the gray matter of the spinal cord was investigated in spinalized frogs. We evaluated the recruitment properties of individual spinal sites and found that forces increase linearly with activation level in the low-force range studied, while the structure of the force pattern remains invariant. We also measured the responses produced by coactivation of two spinal sites activated at two pairs of stimulation levels. Responses were measured at the mechanical level by recording forces at the ankle; and, at the muscular level by recording the electromyographic (EMG) activity of 11 hindlimb muscles. We found that for both pairs of activation, the forces under coactivation were the scaled vectorial summation of the individual responses. At the muscular level, rectified and integrated EMGs also summated during coactivation. Numerous force patterns could, thus, be created by the activation of a few individual sites. These results suggest that microstimulation of the circuitry of the spinal cord (higher order neurons than the motoneurons) holds promise as a new functional neuromuscular stimulation (FNS) technique for the restoration of multi-joint movements.

Tapping into spinal circuits to restore motor function

Motivated by the challenge of improving neuroprosthetic devices, the authors review current knowledge relating to harnessing the potential of spinal neural circuits, such as reflexes and pattern generators. If such spinal interneuronal circuits could be activated, they could provide the coordinated control of many muscles that is so complex to implement with a device that aims to address each participating muscle individually. The authors' goal is to identify candidate spinal circuits and areas of research that might open opportunities to effect control of human limbs through electrical activation of such circuits. David McCrea's discussion of the ways in which hindlimb reflexes in the cat modify motor activity may help in developing optimal strategies for functional neuromuscular stimulation (FNS), by using knowledge of how reflex actions can adapt to different conditions. Michael O'Donovan's discussion of the development of rhythmogenic networks in the chick embryo may provide clues to methods of generating rhythmic activity in the adult spinal cord. Serge Rossignol examines the spinal pattern generator for locomotion in cats, its trigger mechanisms, modulation and adaptation, and suggests how this knowledge can help guide therapeutic approaches in humans. Hugues Barbeau applies the work of Rossignol and others to locomotor training in human subjects who have suffered spinal cord injury (SCI) with incomplete motor function loss (IMFL). Michel Lemay and Warren Grill discuss some of the technical challenges that must be addressed by engineers to implement a neuroprosthesis using electrical stimulation of the spinal cord, particularly the control issues that would have to be resolved.

The contribution of attentional mechanisms to an irregularity effect at the graphemic buffer level

This study analyzes acquired dysgraphia observed in a French-speaking woman. The results point to an impairment of the graphemic buffer, i.e., the processing stage where abstract orthographic representations are temporarily stored while planning the written production. However, the spelling errors were more frequent in the irregular than in the regular words. A qualitative analysis of the errors in the irregular misspelled words showed that, in general, these were not "regularization" errors, but rather the same characteristics as the phonologically implausible errors found in the regular words, such as letters substitutions, deletions, additions, and transpositions. Furthermore, in a list of regular and irregular words of same length and graphemic structure, the errors not only tended to concentrate on the irregularity itself but also tended to be more frequent elsewhere in the irregular words compared to the regular words. These finding are discussed in terms of a post-lexical sensitivity to irregular spelling. It is also shown that when focusing attention on the irregularity becomes necessary, this can cause a detriment to the surrounding graphemic constituents. Interaction between attentional resources and processing of orthographic representations at the graphemic buffer level is considered.

Issues in impedance selection and input devices for multijoint powered orthotics

We investigated the applicability of impedance controllers to robotic orthoses for arm movements. We had tetraplegics turn a crank using their paralyzed arm propelled by a planar robot manipulandum. The robot was under impedance control, and chin motion served as command source. Stiffness varied between 50, 100, or 200 N/m and damping varied between 5 or 15 N/m/s. Results indicated that a low stiffness and high viscosity provided better directional control of the tangential force exerted on the crank.

In vitro microbiological characterization of novel macrolide CP-163,505 for animal health specific use

A novel 16-membered-ring macrolide agent (CP-163,505, a reductive amination derivative of repromicin) was identified as an antibacterial against Pasteurella haemolytica, P. multocida and Actinobacillus pleuropneumoniae, important etiological agents of livestock respiratory disease. In vitro MIC50/90 analysis revealed that CP-163,505 was more potent (4x) than tilmicosin against P. multocida, and equivalent to tilmicosin against P. haemolytica and A. pleuropneumoniae. In time kill kinetic studies, CP-163,505 showed bactericidal activity against P. haemolytica, P. multocida and A. pleuropneumoniae and bacteriostatic activity against E. coli at 8 times its MIC. In vitro, CP-163,505 was more potent in alkaline pH (16 approximately 32 x ) and less potent in the presence of excess cations (Mg+2 and Ca+2, 4x). EDTA and PMBN increased CP-163,505 potency against E. coli (4x) but not against the other species. Similar results were obtained with erythromycin A and tilmicosin, which were used as controls. From our data, we hypothesize that Pasteurella and Actinobacillus have an outer membrane significantly different from that of the typical enteric Gram-negative bacterium E. coli.

Closed-loop wrist stabilization in C4 and C5 tetraplegia

We investigated the feasibility of using functional neuromuscular stimulation (FNS) to stabilize wrist flexion/ extension angle in individuals with tetraplegia at C4 and C5. Three wrist position controllers were evaluated experimentally and in simulation. Closed-loop feedback regulation increased wrist stability in the presence of wrist moment disturbances, using less wrist muscle activation than an open-loop cocontraction system. However, if the disturbances were large compared to the available wrist muscle moment, controller saturation made the open-loop system more economical, even though the feedback controllers still performed better. The simulations also showed that stimulating the finger flexors can induce a negative stiffness load at the wrist, which destabilizes wrist position. The destabilizing effects of the negative stiffness were reduced if the passive wrist moment model included nonlinear damping instead of linear damping.

A dynamic model for simulating movements of the elbow, forearm, an wrist

We developed a dynamic model of the upper extremity to simulate forearm and wrist movements. The model is based on the skeletal structure of the arm and is capable of elbow flexion/extension, forearm pronosupination, and wrist flexion/extension and radial/ulnar deviation movements. Movements are produced by activation of a Hill-type model of muscle, and limits on joint motion are imposed by passive moments modeled after experimental results. We investigated the muscle output force sensitivity, as well as wrist flexion/extension motion sensitivity to parameter variations. The tendon slack length and muscle fiber length were found to have the greatest influence on muscle output and flexion/extension wrist motion. The model captured the direction of the moment vectors at the wrist well, but predicted much higher moments than were measured by stimulating the paralyzed muscles of one tetraplegic subject.

Restoration of pronosupination control by FNS in tetraplegia--experimental and biomechanical evaluation of feasibility

Individuals with C5/C6 tetraplegia lack voluntary control of the forearm pronators. We evaluated the feasibility of restoring forearm pronation/supination control using an electrically activated pronator opposed by voluntary supination. To this end, we measured the electrically produced pronation moments of subjects with tetraplegia. The maximal pronation moment achieved by stimulating the pronator quadratus ranged from 30 to 100 N cm in three forearms of two subjects. These moments were sufficient to produce forearm pronation in all three forearms. Voluntary control of pronosupination during constant pronator stimulation was achieved by having the subject voluntarily supinate or relax to change the balance of rotational torques acting on the forearm. In all cases, the subjects were able to supinate voluntarily against the continuously stimulated pronator, producing intermediate angles between full pronation and full supination. We also observed under some conditions that subjects could voluntarily pronate and supinate even without pronator stimulation. Using a biomechanical model, we show how pronation can be initiated from a supinated position using the brachioradialis, with gravity completing the pronation. This method of pronation without stimulation is extremely sensitive to the orientation of the forearm in the gravitational field, and thus is not a widely applicable technique. We conclude that forearm pronosupination via Functional Neuromuscular Stimulation is feasible, and would provide subjects the ability to pronate without the assistance of gravity.

Automated tuning of a closed-loop hand grasp neuroprosthesis

An automated tuning algorithm was developed to reduce the time and skill required to tune a closed-loop hand grasp neuroprosthesis. The time reduction results from simultaneous tuning of four gain parameters controlling the dynamic response of the system, and from automation of the calculation and decision processes. The new tuning method is therefore an automated parallel tuning method, replacing a manual sequential method in which only one parameter at a time was tuned. RMS error between the step input and the grasp output is minimized, with absence of oscillation as a constraint. The difference between the system's RMS ramp tracking errors for the two tuning methods was less than 1% of the ramp size regardless of the initial values of the parameters, implying that the tuning methods were equivalent. However, the parallel tuning method was faster and required fewer trials than the sequential method. The capability of the closed-loop system to regulate grasp output in the presence of disturbances was compared with the capability without feedback. Patients were instructed to either grasp an object at a certain force level or to match a certain grasp opening. They would then lock their command at a fixed value, and either remain immobile to test time dependence or pronate and supinate their forearm to test postural disturbances. With closed-loop control, the grasp output was better regulated in the presence of disturbances, with an average output variance 60% lower than without feedback control.