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

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.

Twinned microspore-derived embryos of canola (Brassica napus L.) are genetically identical.

Microspore culture is used extensively in several crop species to generate diverse populations of homozygous, doubled haploid lines for breeding and genetic analyses. In our canola (Brassica napus L.) doubled haploid breeding programme we regularly observe conjoined microspore-derived embryos, most commonly twins, joined either at the base of the hypocotyl or along the length of the hypocotyl axis. The aim of this study was to determine if twinned embryos were genetically identical or non-identical in order to gauge their value for breeding and linkage analysis. Microsatellite marker fingerprinting of 12 pairs of twinned embryos produced by microspore culture of heterozygous F(1) lines revealed that pairs of twins were genetically identical. Based on this finding, we recommend breeders and geneticists using microspore culture technology to retain only one embryo from each pair of twinned embryos.