Next-generation sequencing (NGS) has revolutionized plant and animal research in many ways including new methods of high throughput genotyping. Genotyping-by-sequencing (GBS) been demonstrated to be a robust cost-effective genotyping method capable producing thousands millions SNPs across wide range species. Undoubtedly, the greatest barrier its broader use is challenge data analysis. Herein we describe comprehensive comparison seven GBS bioinformatics pipelines developed process raw...

Next-generation sequencing (NGS) technologies have accelerated considerably the investigation into composition of genomes and their functions. Genotyping-by-sequencing (GBS) is a genotyping approach that makes use NGS to rapidly economically scan genome. It has been shown allow simultaneous discovery thousands millions SNPs across wide range species. For most users, main challenge in GBS bioinformatics analysis large amount sequence information derived from libraries view calling alleles at...

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 species-representative called pan-genome better capture extent both nucleotide variation. Here, we present cultivated soybean (Glycine max), termed PanSoy, constructed using de novo assembly 204 phylogenetically geographically representative improved accessions selected from larger GmHapMap collection. PanSoy uncovers 108 Mb...

Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data 1007 Glycine max accessions and yielding 14.9 million variants as well 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number SNPs plateaued beyond approximately 800 600 respectively. This suggests extensive coverage diversity within cultivated soybean. GmHapMap were imputed onto 21 618 previously genotyped with up to 96%...

A genome-wide association study (GWAS) is currently one of the most recommended approaches for discovering marker-trait associations (MTAs) complex traits in plant species. Insufficient statistical power a limiting factor, especially narrow genetic basis species, that conventional GWAS methods are suffering from. Using sophisticated mathematical such as machine learning (ML) algorithms may address this issue and advance implication valuable method applied plant-breeding programs. In study,...

In vitro and ex Agrobacterium rhizogenes -mediated hairy root transformation (HRT) assays are key components of the plant biotechnology functional genomics toolkit. this report, both in HRT were optimized soybean using RUBY reporter. Different parameters including A. strain, optical density bacterial cell culture (OD 600 ), co-cultivation media, genotype, explant age, acetosyringone addition concentration evaluated. Overall, assay was more efficient than terms percentage induction roots...

Genotyping-by-sequencing (GBS) represents a highly cost-effective high-throughput genotyping approach. By nature, however, GBS is subject to generating sizeable amounts of missing data and these will need be imputed for many downstream analyses. The extent which such can tolerated in calling SNPs has not been explored widely. In this work, we first explore the use imputation fill genotypes datasets. Importantly, whole genome resequencing assess accuracy data. Using panel 301 soybean...

Next-generation sequencing (NGS) and bioinformatics tools have greatly facilitated the characterization of nucleotide variation; nonetheless, an exhaustive description both SNP haplotype diversity structural variation remains elusive in most species. In this study, we sequenced a representative set 102 short-season soya beans achieved extensive coverage (SV). We called close to 5M sequence variants (SNPs, MNPs indels) noticed that number unique haplotypes had plateaued within germplasm (1.7M...

Sclerotinia stem rot (SSR), caused by 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 these were proved reproduce the same phenotypic impact populations.In this study, we identified a major quantitative trait (QTL) associated with resistance SSR progression on main using genome-wide association mapping (GWAM). A population 127 soybean accessions was genotyped 1.5 M SNPs...

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 represents an attractive approach cannabis, economically important industrial, recreational, and medicinal plant. However, CRISPR requires design of precise (on-target) single-guide RNA (sgRNA). Therefore, it is essential to predict off-target activity designed sgRNAs avoid unexpected...

Soybean fixes atmospheric nitrogen through the symbiotic rhizobia bacteria that inhabit root nodules. Drought stress negatively affect fixation (SNF) in soybean. The main objective of this study was to identify allelic variations associated with SNF short-season Canadian soybean varieties under drought stress. A diversity panel 103 early-maturity evaluated greenhouse conditions determine SNF-related traits imposed after three weeks plant growth, where plants were maintained at 30% field...

Despite the increased efficiency of sequencing technologies and development reduced-representation (RRS) approaches allowing high-throughput (HTS) multiplexed samples, per-sample genotyping cost remains most limiting factor in context large-scale studies. For example, genomic selection (GS), breeders need genome-wide markers to predict breeding value large cohorts progenies, requiring thousands candidates. Here, we introduce 3D-GBS, an optimized GBS procedure, provide ultra-high-throughput...

Common beans (Phaseolus vulgaris) form a relationship with nitrogen-fixing rhizobia and through process termed symbiotic nitrogen fixation (SNF) which provides them source of nitrogen. However, are considered poor fixers, modern production practices involve routine use N fertilizer, leads to the down-regulation SNF. High-yielding, conventionally-bred bean varieties developed using conventional selection criteria, typically not including SNF efficiency, may have lost this trait over decades...

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) Alberta, 2003. Genetic resistance to clubroot adapted cultivar available since 2009, breakdown detected 2013 and new pathotypes are increasing rapidly. Information genetic similarity among pathogen populations across could be useful estimating the variation populations, predicting effect...

Abstract Cannabis sativa L., previously concealed by prohibition, is now a versatile and promising plant, thanks to recent legalization, opening doors for medical research industry growth. However, years of prohibition have left the community lagging behind in understanding genetics trait inheritance compared other major crops. To address this gap, we conducted comprehensive genome-wide association study (GWAS) nine key agronomic morphological traits, using panel 176 drug-type accessions...

Advancements in sequencing technologies have dramatically transformed genomics research by enabling the analysis of genetic information with unprecedented scale and efficiency. Next-generation (NGS), renowned for its high-throughput capabilities, has significantly reduced costs expanded scope applications. Among these, synthesis (SBS) on Illumina systems is predominant, favored accuracy cost-effectiveness. However, emerging like Element Biosciences’ Avidity (AVITI) are beginning to challenge...

This study examines the conservation of ethylene response mechanisms in cannabis seedlings, expanding on evidence ethylene’s influence mature plants, particularly sexual plasticity. Using hemp and drug-type we observed a unique triple-response-like phenotype under dark conditions with ethephon treatment, characterized by hypocotyl radicle shortening alongside thickening. Employing novel ethephon-based assay, this research circumvents challenges gaseous ethylene, enabling more accessible...