Biology subjects

Arens, P.

Publications and source records attributed to Arens, P..

6 recordsLinked to original sources

bioRxiv2025

High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination

We present the first reference genome of highly heterozygous autotetraploid Allium porrum (leek). Combining long-read sequencing with SNP-array screening of two experimental F1 populations, we generated a genetic map with 11,429 SNP markers across 8 linkage groups and a chromosome-scale assembly of Allium porrum (leek) totaling 15.2 Gbp in size. High quality of the reference genome is substantiated by 97.2% BUSCO completeness and a mapping rate of 96% for full-length transcripts. The linkage map exposes the recombination landscape of leek and confirms that crossovers are predominantly proximal located to the centromeres, contrasting with distal recombination landscapes observed in other Allium species. Comparative genomics revealing structural rearrangements between A. porrum and its relatives (A. fistulosum, A. sativum, A. cepa), suggests a closer genomic relationship to A. sativum. Our annotated high-quality reference genome delivers crucial insights into the leek genome structure, recombination landscape, and evolutionary relationships within the Allium genus, offering significant implications for breeding programs, facilitating marker-assisted selection and genetic improvement in leek.

plant biology↗

bioRxiv2022

Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data

Potato is one of the worlds major staple crops and like many important crop plants it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge, hindering the use of genomic data in breeding strategies. Here, we introduce a novel strategy for the assembly of polyploid genomes and present an assembly of the autotetraploid potato cultivar Altus. Our method uses low-depth sequencing data from an offspring population, which is available in many plant breeding settings, to achieve chromosomal clustering and haplotype phasing directly on the assembly graph. This involves a novel strategy for the analysis of k-mers unique to specific graph nodes. Our approach generates assemblies of individual chromosomes with phased haplotig N50 values of up to 13 Mb and haplotig lengths of up to 31 Mb. This major advance provides high-quality assemblies with haplotype-specific sequence resolution of whole chromosome arms and can be applied in common breeding scenarios where collections of offspring are available.

genomics↗

bioRxiv2021

De novo whole-genome assembly of Chrysanthemum makinoi, a key wild ancestor to hexaploid Chrysanthemum

Chrysanthemum is among the top ten cut, potted and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The wild diploid Chrysanthemum makinoi is thought to be one of the ancestors of the cultivated hexaploid varieties which are currently grown all around the world. Using a combination of Oxford Nanopore long reads, Pacific Biosciences long reads, Illumina short reads, Dovetail sequences and a genetic map, we assembled 3.1 Gb of its sequence into 9 pseudochromosomes, with an N50 of 330 Mb and BUSCO complete score of 92.1%. Our ab initio annotation pipeline predicted 95 074 genes and marked 80.0% of the genome as repetitive. This genome assembly of C. makinoi provides an important step forward in understanding the chrysanthemum genome, evolution and history.

genomics↗

bioRxiv2021

Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR

MotivationThe investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement. ResultsHere we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent (IBD) probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualisation tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. Availability and implementationpolyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR. Contactpeter.bourke@wur.nl or chris.maliepaard@wur.nl Supplementary informationSupplementary data are available

genetics↗

bioRxiv2018

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.\n\nWe produced a haploid rose line from R. chinensis Old Blush and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

genomics↗

bioRxiv2017

polymapR: linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

MotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the worlds most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.\n\nResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.\n\nAvailability and ImplementationpolymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/packages=polymapR.\n\nContactChris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl

genetics↗