High‐resolution molecular karyotyping uncovers pairing between ancestrally related Brassica chromosomes

Abstract

SummaryHow do chromosomal regions with differing degrees of homology and homeology interact at meiosis? We provide a novel analytical method based on simple genetics principles which can help to answer this important question. This method interrogates high-throughput molecular marker data in order to infer chromosome behavior at meiosis in interspecific hybrids.We validated this method using high-resolution molecular marker karyotyping in two experimental Brassica populations derived from interspecific crosses among B. juncea, B. napus and B. carinata, using a single nucleotide polymorphism chip.This method of analysis successfully identified meiotic interactions between chromosomes sharing different degrees of similarity: full-length homologs; full-length homeologs; large sections of primary homeologs; and small sections of secondary homeologs.This analytical method can be applied to any allopolyploid species or fertile interspecific hybrid in order to detect meiotic associations. This genetic information can then be used to identify which genomic regions share functional homeology (i.e., retain enough similarity to allow pairing and segregation at meiosis). When applied to interspecific hybrids for which reference genome sequences are available, the question of how differing degrees of homology and homeology affect meiotic interactions may finally be resolved.

Centromere Locations inBrassicaA and C Genomes Revealed Through Half-Tetrad Analysis

“…The Brassica 60K Infinium array (Illumina, San Diego) was used to generate SNP marker data for the experimental populations, parental species, and B. napus 3 B. carinata and B. juncea 3 B. napus interspecific hybrid controls (Mason et al 2014a). Data were visualized in Genome Studio (Illumina).…”

“…This resulted in an average SNP density of one SNP every 42 kbp in the A genome and one SNP every 36 kbp in the C genome. Putatively multilocus SNP markers (as evidenced by heterozygosity in the homozygous parent lines or by multiple genotype clusters in Genome Studio) and SNPs with haplotype patterns not matching the chromosome on which they were putatively located were removed from the analysis [see Mason et al (2014a) for a detailed description of this method]. SNP markers that were monomorphic between parent genotypes within a progeny set were set as missing values.…”

The Fate of Chromosomes and Alleles in an AllohexaploidBrassicaPopulation

“…A SNP chip with 52,157 SNPs designed for B. napus (Illumina Infinium 60K bead array) was used to assess allele inheritance in SP_051 to SP_115, as well as parental controls [see Mason et al (2014) for details of SNP data analysis]. Chip hybridization was carried out according to the manufacturer's instructions at The University of Queensland, Brisbane, Australia, and chips were scanned using a HiScanSQ (Illumina).…”

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

“…Recent marker genotyping of populations derived from various interspecific hybrids has revealed frequencies of homologous and non-homologous recombination between each of the A, B and C genomes (Szadkowski et al 2010;Mason et al 2014aMason et al , 2015a, as well as the effects of genotype , ploidy level (Nicolas et al 2009), genetic factors (Cifuentes et al 2010;Grandont et al 2014) and additional chromosomes (Suay et al 2014) on meiotic behaviour. Earlier studies also identified chromosome rearrangements within the established B. napus gene pool using molecular markers: genotype-specific translocations were detected through assessment of marker segregation patterns (Sharpe et al 1995;Osborn et al 2003).…”

“…Dalton-Morgan et al 2014). These arrays comprise an extremely valuable resource for the genetics and breeding communities in Brassica, and have already been used for applications such as linkage mapping of agricultural traits for flowering time, plant height, seed yield, germination, seedling emergence and disease resistance Schiessl et al 2015), tracking allele inheritance in interspecific hybrid populations (Mason et al 2014a(Mason et al ,b, 2015a and species identification in germplasm collections (Mason et al 2015b). SNP arrays are fast, highly reproducible and produce easy-to-analyse data (Hayward et al 2012).…”