title: Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.
abstract: Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia annaliese.mason@agrar.uni-giessen.de m.nelson@kew.org.
authors.forename: Annaliese S
authors.initials: AS
authors.lastname: Mason
authors.affiliation: IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Rousseau-Gueutin
authors.affiliation: IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Morice
authors.affiliation: School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.
authors.forename: Philipp E
authors.initials: PE
authors.lastname: Bayer
authors.affiliation: School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.
authors.forename: Naghmeh
authors.initials: N
authors.lastname: Besharat
authors.affiliation: School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.
authors.forename: Anouska
authors.initials: A
authors.lastname: Cousin
authors.affiliation: School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.
authors.forename: Aneeta
authors.initials: A
authors.lastname: Pradhan
authors.affiliation: Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada.
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
authors.affiliation: IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Chèvre
authors.affiliation: School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom annaliese.mason@agrar.uni-giessen.de m.nelson@kew.org.
authors.forename: Matthew N
authors.initials: MN
authors.lastname: Nelson
mesh_terms: D001937:Brassica / Q000235:genetics*; D002503:Centromere / Q000235:genetics*; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D004251:DNA Transposable Elements; D017343:Genes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D060005:Genotyping Techniques; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements; D005819:Genetic Markers
keywords: Brassica; centromeres; molecular karyotyping; recombination; unreduced gametes