Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

A.S. Mason, M. Rousseau-Gueutin, J. Morice, Philipp Bayer, Nagmeh Besharat, Anouska Cousin, Aneeta Pradhan, I.A. Parkin, A.M. Chevre, Jacqueline Batley, Matthew Nelson

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)513-523
JournalGenetics
Volume202
Issue number2
Early online date27 Nov 2015
DOIs
Publication statusPublished - Feb 2016

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Centromere
Brassica
Genome
Brassica napus
Chromatids
Germ Cells
Physical Chromosome Mapping
DNA Transposable Elements
Homologous Recombination
Telomere
Meiosis
Genetic Markers
Population
Single Nucleotide Polymorphism
Sequence Analysis
Chromosomes
Technology
Genes

Cite this

Mason, A.S. ; Rousseau-Gueutin, M. ; Morice, J. ; Bayer, Philipp ; Besharat, Nagmeh ; Cousin, Anouska ; Pradhan, Aneeta ; Parkin, I.A. ; Chevre, A.M. ; Batley, Jacqueline ; Nelson, Matthew. / Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis. In: Genetics. 2016 ; Vol. 202, No. 2. pp. 513-523.
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Mason, AS, Rousseau-Gueutin, M, Morice, J, Bayer, P, Besharat, N, Cousin, A, Pradhan, A, Parkin, IA, Chevre, AM, Batley, J & Nelson, M 2016, 'Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis' Genetics, vol. 202, no. 2, pp. 513-523. https://doi.org/10.1534/genetics.115.183210

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis. / Mason, A.S.; Rousseau-Gueutin, M.; Morice, J.; Bayer, Philipp; Besharat, Nagmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, I.A.; Chevre, A.M.; Batley, Jacqueline; Nelson, Matthew.

In: Genetics, Vol. 202, No. 2, 02.2016, p. 513-523.

Research output: Contribution to journalArticle

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T1 - Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

AU - Mason, A.S.

AU - Rousseau-Gueutin, M.

AU - Morice, J.

AU - Bayer, Philipp

AU - Besharat, Nagmeh

AU - Cousin, Anouska

AU - Pradhan, Aneeta

AU - Parkin, I.A.

AU - Chevre, A.M.

AU - Batley, Jacqueline

AU - Nelson, Matthew

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N2 - 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.

AB - 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.

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DO - 10.1534/genetics.115.183210

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