Jacob I. Marsh
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View article: Effects of rescaling forward-in-time population genetic simulations
Effects of rescaling forward-in-time population genetic simulations Open
Forward-in-time population genetic simulations enable modelling of a wide array of complex evolutionary scenarios. Simulating small genomic regions, and rescaling by reducing population size by a scaling factor while maintaining population…
View article: Comparative neurofilament light chain trajectories in CSF and plasma in autosomal dominant Alzheimer’s disease
Comparative neurofilament light chain trajectories in CSF and plasma in autosomal dominant Alzheimer’s disease Open
View article: Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean Open
The timing of flowering in soybean [ Glycine max (L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect crop yield, productivity, and geographical adaptation. Desp…
View article: Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean
Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean Open
The timing of flowering in soybean [Glycine max (L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect crop yield, productivity, and geographical adaptation. Despi…
View article: Author Correction: Adaptive gene loss in the common bean pan-genome during range expansion and domestication
Author Correction: Adaptive gene loss in the common bean pan-genome during range expansion and domestication Open
View article: Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset Open
The surge in high‐throughput technologies has empowered the acquisition of vast genomic datasets, prompting the search for genetic markers and biomarkers relevant to complex traits. However, grappling with the inherent complexities of high…
View article: Adaptive gene loss in the common bean pan-genome during range expansion and domestication
Adaptive gene loss in the common bean pan-genome during range expansion and domestication Open
View article: Generation of a gene-corrected human isogenic iPSC line from an Alzheimer’s disease iPSC line carrying the PSEN1 H163R mutation
Generation of a gene-corrected human isogenic iPSC line from an Alzheimer’s disease iPSC line carrying the PSEN1 H163R mutation Open
We report the generation of a gene-edited human induced pluripotent stem cell (iPSC) line from an Alzheimer's disease patient-derived iPSC line harbouring the PSEN1 H163R mutation. This line demonstrates pluripotent stem cell morphology, e…
View article: Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection
Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection Open
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps c…
View article: Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection
Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection Open
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps c…
View article: Biases in ARG-based inference of historical population size in populations experiencing selection
Biases in ARG-based inference of historical population size in populations experiencing selection Open
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps c…
View article: crosshap: R package for local haplotype visualization for trait association analysis
crosshap: R package for local haplotype visualization for trait association analysis Open
Summary Genome-wide association studies (GWAS) excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide…
View article: Local haplotype visualization for trait association analysis with crosshap
Local haplotype visualization for trait association analysis with crosshap Open
Summary GWAS excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local la…
View article: Diversity of fatty acid biosynthesis genes across the soybean pangenome
Diversity of fatty acid biosynthesis genes across the soybean pangenome Open
Soybean ( Glycine max ) is a major crop that contributes more than half of global oilseed production. Much research has been directed towards improvement of the fatty acid profile of soybean seeds through marker assisted breeding. Recently…
View article: Legume‐wide comparative analysis of pod shatter locus <i>PDH1</i> reveals phaseoloid specificity, high cowpea expression, and stress responsive genomic context
Legume‐wide comparative analysis of pod shatter locus <i>PDH1</i> reveals phaseoloid specificity, high cowpea expression, and stress responsive genomic context Open
SUMMARY Pod dehiscence is a major source of yield loss in legumes, which is exacerbated by aridity. Disruptive mutations in “ Pod indehiscent 1 ” ( PDH1 ), a pod sclerenchyma‐specific lignin biosynthesis gene, has been linked to significan…
View article: Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies
Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies Open
Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of…
View article: Parenchymal border macrophages regulate the flow dynamics of the cerebrospinal fluid
Parenchymal border macrophages regulate the flow dynamics of the cerebrospinal fluid Open
Macrophages are important players in the maintenance of tissue homeostasis1. Perivascular and leptomeningeal macrophages reside near the central nervous system (CNS) parenchyma2, and their role in CNS physiology has n…
View article: Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale
Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale Open
Rye (Secale cereale) is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions…
View article: Genetic and Genomic Resources for Soybean Breeding Research
Genetic and Genomic Resources for Soybean Breeding Research Open
Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced ge…
View article: Expanding Gene-Editing Potential in Crop Improvement with Pangenomes
Expanding Gene-Editing Potential in Crop Improvement with Pangenomes Open
Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data…
View article: Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003
Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003 Open
Key message The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Abstr…
View article: Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003
Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003 Open
Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A signifi…
View article: Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding Open
The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will mod…