Davoud Torkamaneh

Davoud Torkamaneh
Laval University | ULAVAL · Department of Phytology

Computational Biology

About

74
Publications
19,030
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711
Citations
Introduction
I’m using multidisciplinary approaches that combine computational analysis, modeling, and prediction with experimental verification to visualize plant genome evolution over time and their implications for agricultural improvement.
Additional affiliations
September 2013 - October 2017
Laval University
Position
  • PhD
April 2008 - August 2013
Seed and Plant Improvement Institute
Position
  • Research Assistant
April 2008 - August 2013
Seed and Plant Improvement Institute
Position
  • Research Assistant

Publications

Publications (74)
Article
Full-text available
Key Message Identifying QTL associated with soybean seed quality traits from a diverse GWAS panel cultivated in Canadian and Ukrainian mega-environments may facilitate future cultivar development for foreign markets. Abstract Understanding the complex genetic basis of seed quality traits for soybean in the mega-environments (MEs) is critical for d...
Chapter
In this introductory chapter, we seek to provide the reader with a high-level overview of what goes into designing a genome-wide association study (GWAS) in the context of crop plants. After introducing some general concepts regarding GWAS, we divide the contents of this overview into four main sections that reflect the key components of a GWAS: as...
Article
Full-text available
A genome-wide association study (GWAS) is currently one of the most recommended approaches for discovering marker-trait associations (MTAs) for complex traits in plant species. Insufficient statistical power is a limiting factor, especially in narrow genetic basis species, that conventional GWAS methods are suffering from. Using sophisticated mathe...
Article
Full-text available
Sequencing technologies are evolving at a rapid pace, enabling the generation of massive amounts of data in multiple dimensions (e.g., genomics, epigenomics, transcriptomic, metabolomics, proteomics, and single-cell omics) in plants. To provide comprehensive insights into the complexity of plant biological systems, it is important to integrate diff...
Article
Full-text available
Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods often allow the identification of candidate causal genes. To provide true experimental evidence of a gene's function, reverse genetics techniques are highly valuable. Site-directed mutagenesis through transfer DNA (T-DNA) delivery is an efficien...
Article
Full-text available
Key message Significant QTL for sucrose concentration have been identified using a historical soybean genomic panel, which could aid in the development of food-grade soybean cultivars. Abstract Soybean (Glycine max (L.) Merr) is a crop of global importance for both human and animal consumption, which was domesticated in China more than 6000 years...
Article
Full-text available
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...
Article
Full-text available
Genome-wide association study (GWAS) has emerged in the past decade as a viable tool for identifying beneficial alleles from a genomic diversity panel. In an ongoing effort to improve soybean [Glycine max (L.) Merr.], which is the third largest field crop in Canada, a GWAS was conducted to identify novel alleles underlying seed yield and seed quali...
Article
Full-text available
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 read...
Chapter
Statistical models are at the core of the genome-wide association study (GWAS). In this chapter, we provide an overview of single- and multilocus statistical models, Bayesian, and machine learning approaches for association studies in plants. These models are discussed based on their basic methodology, cofactors adjustment accounted for, statistica...
Article
Full-text available
Cannabis (Cannabis sativa L.) is typically propagated using stem cuttings taken from mother plants to produce genetically uniform propagules. However, producers anecdotally report that clonal lines deteriorate over time and eventually produce clones with less vigor and lower cannabinoid levels than the original mother plant. While the cause of this...
Article
Full-text available
Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 157 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-d...
Preprint
Genome-wide association study (GWAS) is currently one of the most recommended approaches for discovering quantitative trait loci (QTL) associated with complex traits in plant species. Insufficient statistical power is a limiting factor that current conventional GWAS methods are suffering from, especially in narrow genetic bases plants such as soybe...
Article
Full-text available
Soybean [ Glycine max (L.) Merr.] is the world's leading legume crop and the largest oilseed crop. It forms a symbiotic relationship with rhizobia bacteria residing in root nodules that provide fixed nitrogen to host plants through symbiotic nitrogen fixation (SNF). In soybean, it has been widely reported that the highest SNF occurs at the pod-fill...
Article
Full-text available
Plant-derived folates (Vitamin B 9 ) are essential components of the human diet. They provide one-carbon units that are required for the synthesis of nucleic acids and proteins, and folate deficiency is associated with numerous adverse health conditions. The development of high-folate cultivars of common bean ( Phaseolus vulgaris L.) and other stap...
Preprint
Full-text available
Background Structural variant (SV) discovery based on short reads is challenging due to their complex signatures and tendency to occur in repeated regions. 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...
Article
Full-text available
Apples (Malus domestica Borkh) are prone to preharvest fruit drop, which is more pronounced in ‘Honeycrisp’. Hexanal is known to improve fruit retention in several economically important crops. The effects of hexanal on the fruit retention of ‘Honeycrisp’ apples were assessed using physiological, biochemical, and transcriptomic approaches. Fruit re...
Article
Although cannabis is legalized and accepted as an agricultural commodity in many places around the world, a significant lack of public germplasm repositories remains an unresolved problem in the cannabis industry. The acquisition, preservation and evaluation of germplasm including landraces and ancestral populations is key to unleash the full poten...
Preprint
Genome-wide association study (GWAS) is currently one of the important approaches for discovering quantitative trait loci (QTL) associated with traits of interest. However, insufficient statistical power is the limiting factor in current conventional GWAS methods for characterizing quantitative traits, especially in narrow genetic bases plants such...
Article
Full-text available
For a long time, Cannabis sativa has been used for therapeutic and industrial purposes. Due to its increasing demand in medicine, recreation, and industry, there is a dire need to apply new biotechnological tools to introduce new genotypes with desirable traits and enhanced secondary metabolite production. Micropropagation, conservation, cell suspe...
Preprint
Full-text available
Apples ( Malus domestica Borkh) are prone to pre-harvest fruit drop which is more pronounced in ‘Honeycrisp’. Using a transcriptomic approach, we analyzed the molecular mechanisms of fruit retention in ‘Honeycrisp’. A total of 726 differentially expressed genes (DEGs) were identified in the abscission zone of hexanal-treated and untreated fruit (FA...
Article
Full-text available
Studies on structural variation in plants have revealed the inadequacy of a single reference genome for an entire species and suggest that it is necessary to build a species‐representative genome, called a pan‐genome to better capture the extent of both structural and nucleotide variation. Here, we present a pan‐genome of cultivated soybean (Glycin...
Article
Full-text available
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing system has recently been used for haploid production in plants. Haploid induction using the CRISPR/Cas system represents an attractive approach in cannabis, an economically important industrial, recreational, and medicinal plant. However, the CRISPR s...
Chapter
The quality, statistical power, and resolution of genome-wide association studies (GWAS) are largely dependent on the comprehensiveness of genotypic data. Over the last few years, despite the constant decrease in the price of sequencing, whole-genome sequencing (WGS) of association panels comprising a large number of samples remains cost-prohibitiv...
Article
Lodging resistance is an important objective for soybean [Glycine max (L.) Merr.] breeding, but selection for this trait has been difficult since the resistance is controlled by multiple genes and these genes interact with the environment. One hundred thirty of 139 lines constituting a soybean GWAS panel were phenotyped for stem pushing resistance,...
Preprint
Full-text available
Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 159 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-d...
Preprint
Full-text available
Cannabis is typically propagated using stem cuttings taken from mother plants to produce 1 genetically uniform propagules. However, producers anecdotally report that clonal lines 2 deteriorate over time and eventually produce clones with less vigour and lower cannabinoid levels 3 than the original mother plant. While the cause of this deterioration...
Preprint
Full-text available
Soybean ( Glycine max (L.) Merr) is a crop of global importance for both human and animal consumption, which was domesticated in China more than 6000 years ago. A concern about losing genetic diversity as a result of decades of breeding has been expressed by soybean researchers. In order to develop new cultivars, it is critical for breeders to unde...
Article
Full-text available
Genome‐wide association studies (GWAS) have revolutionized the investigation of complex traits over the past decade and have unveiled numerous useful genotype–phenotype associations. To be comprehensive, GWAS can require identifying and genotyping hundreds of thousands to millions of genome‐wide genetic markers in large panels of accessions (Gupta...
Article
Full-text available
It is now well-documented that gene knockout (loss-of-function) alleles have played a prominent role in crop evolution during domestication, diversification, and improvement. This includes dramatic examples from the very origins of agriculture to the monumental yield increases of the Green Revolution. Recent advances in the generation of whole geno...
Article
Full-text available
Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-r...
Article
Full-text available
Background Appropriate information about genetic diversity and population structure of germplasm improves the efficiency of plant breeding. The low productivity of Nepali bread wheat (Triticum aestivum L.) is a major concern particularly since Nepal is ranked the 4th most vulnerable nation globally to climate change. The genetic diversity and popul...
Article
Genotyping-by-sequencing (GBS) is a rapid, flexible, low-cost, and robust genotyping method that simultaneously discovers variants and calls genotypes within a broad range of samples. These characteristics make GBS an excellent tool for many applications and research questions from conservation biology to functional genomics in both model and non-m...
Article
Full-text available
Common bean (Phaseolus vulgaris L.) provides critical nutrition and a livelihood for millions of smallholder farmers worldwide. Beans engage in symbiotic nitrogen fixation (SNF) with Rhizobia. Honduran hillside farmers farm marginal land and utilize few production inputs; therefore, bean varieties with high SNF capacity and environmental resiliency...
Article
Full-text available
Here we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole‐genome sequence data for 1,007 Glycine max accessions and yielding 14.9 million variants as well as 4.3M tag single nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approxim...
Article
Full-text available
Key message: Identification of marker-trait associations and trait-associated haplotypes in breeding germplasm identifies regions under selection and highlights changes in haplotype diversity over decades of soybean improvement in Canada. Understanding marker-trait associations using genome-wide association in soybean is typically carried out in d...
Article
Full-text available
Background: Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. Results: In this study, we iden...
Article
Full-text available
The soybean cyst nematode (SCN) generates more damage to soybean than any other parasite in most soybean‐producing countries. The use of SCN‐resistant cultivars remains the most effective method to limit losses caused by SCN. The SCN‐resistant accession PI 88788 has been used almost exclusively to control SCN over the past decades, inducing a shift...
Article
Full-text available
High-throughput reduced-representation sequencing (RRS)-based genotyping methods, such as genotyping-by-sequencing (GBS), have provided attractive genotyping solutions in numerous species. Here, we present NanoGBS, a miniaturized and eco-friendly method for GBS library construction. Using acoustic droplet ejection (ADE) technology, NanoGBS librarie...
Article
Full-text available
Key message We explored the genetic basis of SNF-related traits through GWAS and identified 40 candidate genes. This study provides fundamental insights into SNF-related traits and will accelerate efforts for SNF breeding. Abstract Symbiotic nitrogen fixation (SNF) increases sustainability by supplying biological nitrogen for crops to enhance yiel...
Preprint
Full-text available
Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitat...
Article
For all major crops, sizeable genebanks are maintained across the world and serve as repositories of genetic diversity and key sources of novel traits used in breeding. Although molecular markers have been used to characterize diversity in a broad sense, the most common approach to exploring these resources has been through phenotypic characterizat...
Preprint
Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitat...
Article
Full-text available
Key message Genetic diversity in Canadian soybean is maintained over decades of selection in two public breeding programs. Breeders have used a portion of the genetic diversity available in germplasm collections. Abstract Both public and private breeding efforts have been critical for the development of soybean cultivars grown around the world. Gl...
Article
Full-text available
Core ideas: 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 identifyin...
Article
Full-text available
Background: Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SS...
Article
Full-text available
Background Clubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Alberta, Canada in 2003. Genetic resistance to clubroot in an adapted canola cultivar has been available since 2009, but resistanc...
Preprint
Full-text available
Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC....
Preprint
Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitat...
Preprint
Full-text available
Background: Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. Results: In this study, we identif...
Preprint
Full-text available
Background: Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. Results: In this study, we identif...
Article
Full-text available
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 tech...
Preprint
Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous) is an important soybean disease, which has been responsible for severe losses in the past. The main strategy to control this fungus is through the introgression of resistance genes. So far, five main loci have been associated with resistance to Southern...
Article
Full-text available
Common beans (Phaseolus vulgaris) form a relationship with nitrogen-fixing rhizobia and through a process termed symbiotic nitrogen fixation (SNF) which provides them with a source of nitrogen. However, beans are considered poor nitrogen fixers, and modern production practices involve routine use of N fertilizer, which leads to the down-regulation...
Article
Motivation: Identification of DNA sequence variations such as single nucleotide polymorphisms (SNPs) is a fundamental step towards genetic studies. Reduced-representation sequencing methods have been developed as alternatives to whole genome sequencing to reduce costs and enable the analysis of many more individual. Amongst these methods, restrict...
Preprint
Full-text available
Here we describe the first worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1,007 Glycine max accessions and yielding 15 million variants. The number of unique haplotypes plateaued within this collection (4.3 million tag SNPs) suggesting extensive coverage of diversity within the cultivated germplasm....
Article
Motivation Reduced-representation sequencing is a genome-wide scanning method for simultaneous discovery and genotyping of thousands to millions of single nucleotide polymorphisms that is used across a wide range of species. However, in this method a reproducible but very small fraction of the genome is captured for sequencing, while the resulting...
Article
Domestication is an important key co‐evolutionary process through which humans have extensively altered the genomic make‐up and appearance of both plants and animals. The identification of domestication‐related genes remains very arduous. In this study, we present a systematic analytical approach that harnesses two recent advances in genomics, whol...
Article
Full-text available
Key message: Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequen...