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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.

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Fig. 1: Development of reciprocal set of advanced-backcross populations.
Fig. 2: Retention of donor alleles in reciprocal interspecific populations.
Fig. 3: Genomic composition of 190 BC5F1 lines in G. barbadense background.
Fig. 4: Genomic composition of 179 BC5F1 lines in G. hirsutum background.

Data availability

The raw data supporting the conclusions of this article has been included in the supplementary information (Dataset 1 and Dataset 2) and has also been deposited in the Dryad repository (


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We are thankful to the members of Plant Genome Mapping Laboratory for their help in DNA extractions and SSR genotyping.


Financial support is acknowledged from the US National Science Foundation (DBI 0817707, AIR 1127755), Cotton Incorporated (14–460), and a Regents Professorship to AHP.

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Authors and Affiliations



JA conceived, designed, and performed experiments, developed populations, conducted data analysis and interpretation, and drafted and revised the manuscript. RC performed initial crosses. DV and WP helped in DNA extraction and SSR genotyping, SK performed data analysis and revised manuscript. AHP conceived the project, acquired the funds, supervised the project, and revised the manuscript. All authors contributed to the article and approved the submitted version.

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Correspondence to Andrew H. Paterson.

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Associate editor: Lindsey Compton

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Adhikari, J., Chandnani, R., Vitrakoti, D. et al. Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids. Heredity 130, 209–222 (2023).

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