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

Abstract

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.

Fig. 1. Development of reciprocal set of advanced-backcross populations.

GH and GB denote G. hirsutum and G. barbadense respectively. Each backcross lineage was advanced by single-seed descent.

Fig. 2. Retention of donor alleles in reciprocal interspecific populations.

X-axis shows markers across the genome separated by chromosomes and y-axis shows the frequency of donor alleles. Rectangular blocks show the tentative location of centromeres across chromosomes. Dotted lines show expected donor frequency (3.125%) for BC₅F₁ generation. Blue lines show donor allele retention in G. hirsutum background and red lines show donor allele retention in G. barbadense background.

Fig. 3. Genomic composition of 190 BC5F1 lines in G. barbadense background.

Gray areas represent G. barbadense homozygotes (BB), black areas represent heterozygotes (BH) and while areas represent missing genotypes. Chromosomes are shown in the x-axis and individuals are shown in the y-axis.

Fig. 4. Genomic composition of 179 BC5F1 lines in G. hirsutum background.

Gray areas represent G. hirsutum homozygotes (HH), black areas represent heterozygotes (HB) and while areas represent missing genotypes. Chromosomes are shown in the x-axis and individuals are shown in the y-axis.