Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids

Introgression is a potential source of valuable genetic variation and
interspecific introgression lines are important resources for plant
breeders to access novel alleles. Experimental advanced-generation
backcross populations contain individuals with genomic compositions
similar to those resulting from natural interspecific hybridization and
provide opportunities to study the nature and transmission pattern of
donor chromatin in recipient genomes. Here, we analyze transmission of
donor chromatin in reciprocal backcrosses between G. hirsutum and G.
barbadense. Across the genome, recurrent backcrossing in both backgrounds
yielded donor chromatin at slightly higher frequencies than the Mendelian
expectation in BC5F1 plants, while the average frequency of donor alleles
in BC5F2 segregating families was less than expected. In the two
subgenomes of polyploid cotton, the rate of donor chromatin introgression
was similar. Although donor chromatin was tolerated over much of the
recipient genomes, 21 regions recalcitrant to donor alleles were
identified. Only limited correspondence is observed between the
recalcitrant regions in the two backgrounds, suggesting the effect of
species background on introgression of donor segments. Genetic breakdown
was progressive, with floral abscission and seed inviability ongoing
during backcrossing cycles. Regions of either high or low introgression
tended to be in terminal chromosomal regions that are generally rich in
both genes and crossover events, with long stretches around the centromere
having limited crossover activity resulting in relatively constant low
introgression frequencies. Constraints on fixation and selection of donor
alleles highlights the challenges of utilizing introgression breeding in
crop improvement.