Genomic confirmation of Gossypium barbadense introgression into G. hirsutum and a subsequent MAGIC population

Authors: Fang, David; Thyssen, Gregory; WANG, MAOJUN - Huazhong Agricultural University; Jenkins, Johnie; McCarty, Jack; JONES, DON - Cotton, Inc

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2022
Publication Date: 11/8/2022
Citation: Fang, D.D., Thyssen, G.N., Wang, M.C., Jenkins, J.N., Mccarty Jr, J.C., Jones, D.C. 2022. Genomic confirmation of Gossypium barbadense introgression into G. hirsutum and a subsequent MAGIC population. Molecular Genetics and Genomics. 298:143-152. https://doi.org/10.1007/s00438-022-01974-3.
DOI: https://doi.org/10.1007/s00438-022-01974-3

Interpretive Summary: Transfer of superior quality fiber traits from Pima cotton into high yield Upland cotton has been a breeding goal for many years in cotton breeding programs around the world. However, progress has been very slow due to introgression barriers resulting from whole genome hybridization between the two species. To minimize such barriers, substitution of one Upland cotton chromosome or chromosome segment using Pima cotton chromosome was proposed, and 18 such chromosome substitution lines termed CS-B lines were developed. A multiparent advanced generation inter-cross (MAGIC) population consisting of 180 recombinant inbred lines (RILs) was subsequently made using the 18 CS-B lines and three Upland cotton cultivars as parents. In this research, we sequenced the whole genomes of the 21 parents and 180 RILs to examine the Pime cotton chromosome introgression. Of the 18 CS-B lines, 11 contained the target chromosome or chromosome segment, two contained more than two chromosomes, and five did not have the expected introgression. Residual introgression in non-target chromosomes was prevalent in all CS-B lines. A clear structure existed in the MAGIC population and the 180 RILs were distributed into three groups, i.e., high, moderate, and low introgression. Large blocks of Pima cotton chromosome introgression were still present in some RILs after five cycles of random mating, an indication of recombination suppression or genome incompatibility present in the population. Identity by descent analysis revealed that the MAGIC RILs contained less introgression than expected. This research presents an insight on understanding the complex problems of introgression between species.

Technical Abstract: Introgression of superior fiber traits from Pima cotton (Gossypium barbadense, GB) into high yield Upland cotton (G. hirsutum) has been a breeding objective for many years in a few breeding programs in the world. However, progress has been very slow due to introgression barriers resulting from whole genome hybridization between the two species. To minimize such barriers, chromosome substitution lines (CS-B) from Pima cotton 3-79 in an Upland cotton cultivar TM-1 were developed. A multiparent advanced generation inter-cross (MAGIC) population consisting of 180 recombinant inbred lines (RILs) was subsequently made using the 18 CS-B lines and three Upland cotton cultivars as parents. In this research, we sequenced the whole genomes of the 21 parents and 180 RILs to examine the G. barbadense introgression. Of the 18 CS-B lines, 11 contained the target GB chromosome or chromosome segment, two contained more than two GB chromosomes, and five did not have the expected introgression. Residual introgression in non-target chromosomes was prevalent in all CS-B lines. A clear structure existed in the MAGIC population and the 180 RILs were distributed into three groups, i.e., high, moderate, and low GB introgression. Large blocks of GB chromosome introgression were still present in some RILs after five cycles of random mating, an indication of recombination suppression or genome incompatibility present in the population. Identity by descent analysis revealed that the MAGIC RILs contained less introgression than expected. This research presents an insight on understanding the complex problems of introgression between species.