Centromere Locations inBrassicaA 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 centromerespecific 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.

Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata

“…The A genome presented a much more rapid LD decay rate and shorter LD decay distance than the C genome (Figure a), and apparent reconstruction of LD was found in the new‐type B. napus population on some chromosomes, such as C02, C03 and C08 (Figures b and S1). Large LD blocks were consistently located in the B. napus centromere regions (Mason et al ., ), particularly in C01, C04 and C07 (Figure S1), with similar results in both the BnN and BnT populations.…”

Homoeologous exchanges cause extensive dosage‐dependent gene expression changes in an allopolyploid crop

“…Gene density was the proportion of sequence annotated 'gene' in the Darmor-bzh genome annotation file (Chalhoub et al, 2014). Centromere positions used were those reported by Mason et al (2015).…”

The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate

“…Active centromeres are indicated in dark grey using the positions established by Mason et al . (). In the third outer circle, the distribution of the 2290 polymorphic SNP s, which allowed the identification of homozygous ( A n /A n and A r /A r ) and heterozygous (A n /A r ) states of blocks, is shown.…”

“…Different scales were applied to represent these densities according to the highest number of genes identified within a 250 kb window frame (see values indicated on y-axis in red for A n genes and in blue for A n À genes). Active centromeres are indicated in dark grey using the positions established by Mason et al (2016). In the third outer circle, the distribution of the 2290 polymorphic SNPs, which allowed the identification of homozygous (A n /A n and A r /A r ) and heterozygous (A n /A r ) states of blocks, is shown.…”