Ingvarsson, P. | Search bioRxiv

bioRxiv2023

Haplotype differences in common bean accessions confer the capacity to flower under Scandinavian summer conditions.

The capacity to flower under long days has been a major pre-requisite for the adaptation of the common bean to European climates. The complexity of such adaptation has been studied, mostly under the optics of QTL mapping, but still the genetic basis of the trait remains elusive. In the current study we sequenced a collection of >200 accessions of P. vulgaris of Mesoamerican, Andean and European origin, for which the flowering capacity under long days during the summer season in Sweden was evaluated. Our variant calling strategy allowed us to identify 16.9e6 SNPs and 38.6e3 long structural variants. Furthermore, we observed gene-pool specific selective sweeps that correspond to the independent domestication events in the Americas. GWAS and haplotype structure tests identified single nucleotide and structural variants strongly associated to the capacity to flower under long days, particularly in chromosome 1.

plant biology↗

bioRxiv2019

An Improved Genome Assembly of the European Aspen Populus tremula

Aspen (Populus tremula L.) is a widely distributed keystone species and a model system for forest tree genomics, with extensive resources developed for population genetics and genomics. Here we present an updated resource comprising a chromosome-scale assembly of P. tremula and population genetics and genomics data integrated into the PlantGenIE.org web resource. We demonstrate use of the diverse data types included to explore the genetic basis of natural variation in leaf size and shape as examples of traits with complex genetic architecture. We present a chromosome-scale genome assembly generated using long-read sequencing, optical and high-density genetic maps containing 39,894 annotated genes with functional annotations for 73,765 transcripts from 37,184 gene loci. We conducted whole-genome resequencing of the Ume[a] Aspen (UmAsp) collection comprising 227 aspen individuals. We utilised the assembly, the UmAsp re-sequencing data and existing whole genome re-sequencing data from the Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections to perform genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq) and identified genomic regions of accessible chromatin and subset SNPs to these regions, which improved the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples and quantified their expression in an updated co-expression network (AspLeaf, available in PlantGenIE.org), which we further used to explore the functions of candidate genes identified from the GWAS. We examined synteny to the reference P. trichocarpa assembly and identified P. tremula-specific regions. Analysis of whole-genome duplication indicated differential substitution rates for the two Populus species, indicating more rapid evolution in P. tremula. A GWAS of 26 leaf physiognomy traits and all SNPs in each of the three aspen collections found significant associations for only two traits in ScotAsp collection and one in UmAsp, whereas subsetting SNPs to those in open chromatin regions revealed associations for a further four traits among all three aspen collections. The significant SNPs were associated with genes annotated for developmental and growth functions, which represent candidates for further study. Of particular interest was a 177-kbp region of chromosome 9 harbouring SNPs associated with multiple leaf phenotypes in ScotAsp, with the set of SNPs in linkage disequilibrium explaining 24 to 30 % of the phenotypic variation in leaf indent depth variation. We have incorporated the assembly, population genetics, genomics and leaf physiognomy GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version. This enables easy exploration and visualisation of the genomics data and exploration of GWAS results. We provide all raw and processed data used for the presented analyses to facilitate reuse in future studies.

genomics↗

bioRxiv2018

Design and evaluation of a large sequence-capture probe set and associated SNPs for diploid and haploid samples of Norway spruce (Picea abies)

Massively parallel sequencing has revolutionized the field of genetics by providing comparatively high-resolution insights into whole genomes for large number of species so far. However, whole-genome resequencing of many conspecific individuals remains cost-prohibitive for most species. This is especially true for species with very large genomes with extensive genomic redundancy, such as the genomes of coniferous trees. The genome assembly for the conifer Norway spruce (Picea abies) was the first published draft genome assembly for any gymnosperm. Our goal was to develop a dense set of genome-wide SNP markers for Norway spruce to be used for assembly improvement and population studies. From 80,000 initial probe candidates, we developed two partially-overlapping sets of sequence capture probes: one developed against 56 haploid megagametophytes, to aid assembly improvement; and the other developed against 6 diploid needle samples, to aid population studies. We focused probe development within genes, as delineated via the annotation of ~67,000 gene models accompanying P. abies assembly version 1.0. The 31,277 probes developed against megagametophytes covered 19,268 gene models (mean 1.62 probes/model). The 40,018 probes developed against diploid tissue covered 26,219 gene modules (mean 1.53 probes/model). Analysis of read coverage and variant quality around probe sites showed that initial alignment of captured reads should be done against the whole genome sequence, rather than a subset of probe-containing scaffolds, to overcome occasional capture of sequences outside of designed regions. All three probe sets, anchored to the P. abies 1.0 genome assembly and annotation, are available for download.

genomics↗