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...

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 evolution. Given their complex signatures, tendency occur repeated regions, large size, discovering SVs based on short reads is challenging compared single-nucleotide variants. The increasing availability long-read technologies has greatly facilitated SV discovery; however, these remain too...

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 gene controlling a given trait in crop species. Assessing genetic variants other than single-nucleotide polymorphisms (SNPs) could alleviate this problem. In study, we tested potential of structural (SV)- k-mer-based soybean by applying these as well conventional...

Abstract A circumpolar increase in shrub growth and cover has been underway Arctic subarctic ecosystems for the last few decades, but there is considerable spatial heterogeneity this shrubification process. Although topography, hydrology, edaphic factors are known to influence patterns, a better understanding of landscape‐scale driving phenomenon needed accurately predict its impacts on ecosystem function. In study, we generated land change models order identify variables near Umiujaq...

A gene-centric approach for haplotype definition was developed and implemented in R. The tool allows allelic characterization at given loci germplasm collections. Allelic status four maturity genes is predicted on the basis of marker genotyping data. Assessing diversity within a collection identifying individuals carrying favorable alleles challenging. Advances high-throughput technologies allow many thousands markers but bridging gap between single nucleotide polymorphisms (SNPs) relevant...

• Premise of the study: Assessing seed quality in orchids has been hindered by stringent germination requirements. Seed traditionally assessed using vitro or situ protocols viability staining. However, these methods are not always well suited for rapid assessment context ecological studies. Methods: The potential an ex protocol studies was investigated sowing seeds Platanthera blephariglottis on Sphagnum moss collected orchid's natural habitat. Ex results were compared with those obtained...

Habitat connectivity is important in conservation since isolation can diminish the potential of a population for adaptation and increase its risk extinction. However, naturally patchy ecosystems such as peatlands has mainly focused on preserving specific sites with exceptional characteristics, neglecting interconnectivity between patches. In order to better understand plant dynamics within peatland network, we assessed effect genetic distinctiveness, phenotypic variations germination rates...

Abstract 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 gene controlling a trait given locus in crop species. Assessing genetic variants beyond single-nucleotide polymorphisms (SNPs) could alleviate this problem, for example by including structural (SVs). In study, we tested potential of SV-and k -mer-based soybean...

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

Abstract Microspore embryogenesis is a model for developmental plasticity and cell fate decisions. To investigate the role of miRNAs in this development, we sequenced sRNAs degradome barley microspores collected prior to (day 0) after (days 2 5) application stress treatment known induce embryogenesis. Microspores isolated at these timepoints were uniform both appearance their complements sRNAs. We detected 68 microspores. The abundance 51 differed significantly during microspore development....

Abstract Background Structural variant (SV) discovery based on short reads is challenging due to their complex signatures and tendency occur in repeated regions. The increasing availability of long-read technologies has greatly facilitated SV discovery, however these remain too costly apply routinely population-level studies. Here, we combined short-read sequencing provide a comprehensive population-scale assessment structural variation panel Canadian soybean cultivars. Results We used...

SUMMARY Microspore embryogenesis is a model for developmental plasticity and cell fate decisions. To investigate the role of miRNAs in this development, we sequenced sRNAs degradome barley microspores collected prior to (day 0) after (days 2 5) application stress treatment known induce embryogenesis. Microspores isolated at these timepoints were uniform both appearance their complements sRNAs. We detected 68 microspores. The abundance 51 differed significantly during microspore development....