Specific Whole-Chromosome Identification of the A01/C1 Homoeologs Through Oligonucleotide-Based Chromosome Painting in Brassica Species.

Despite the high importance of Brassica species as crops, their complex genomic relationships and their small, poorly differentiated chromosomes are challenging for analysis. Brassica diploids have AA, BB, and CC genomes, whereas allopolyploids can occur in different subgenome combinations. During interspecific hybridization, frequently used for crop improvement, chromosome fragments are often exchanged, potentially impacting crop traits. Hence, the ability to produce chromosome karyotypes for individual plants is highly desirable. Here, we developed molecular cytogenetics probes designed from unique regions identified from genomic sequence data to differentiate each chromosome pair from A, B, and C subgenomes, generating two complementary oligo libraries, a density- and a synthesis-optimized library. Specifically, we tested the highly similar (homoeologous) A01 and C1 chromosomes, which undergo frequent exchanges and translocation events in Brassica hybrids. Unique signals for one single chromosome pair were observed for the A01 painting probe in B. rapa and B. napus species and for the C1 painting probe in B. oleracea and B. napus. In addition, one A01/C1 translocation in B. napus Surpass400_024DH and a translocation of an A01 chromosome fragment into a C1 chromosome in an allohexaploid Brassica (B. carinata × B. rapa) were identified. Our subgenome chromosome-specific probes may help to uncover rearranged fragments and nonhomologous chromosome pairing involving the Brassica A, B, and C genomes. In summary, we present a subgenome-specific and chromosome-specific cytogenetic tool to unravel the complex dynamics between the highly agronomically relevant Brassica crop genomes.