Genomic characterization of a MAGIC population containing introgressions from four tetraploid Gossypium species

One strategy for increasing the genetic diversity of upland cotton (Gossypium hirsutum) involves the introgression of beneficial alleles from related and wild tetraploid species. Progress in this area has been limited due to undesirable outcomes associated with whole genome interspecific hybridization. To minimize genetic influences from other chromosomes, chromosome substitution lines (CSLs) were developed in upland cotton TM-1 using Gossypium barbadense (GB), Gossypium mustelinum (GM), and Gossypium tomentosum (GT) as donor species. A multiparent advanced generation intercross (MAGIC) population comprising 797 recombinant inbred lines (RILs) was developed by crossing 32 CSLs with five upland cotton cultivars. Whole-genome sequencing of all parental lines and MAGIC RILs was performed to assess alien genome introgressions. Of the 32 CSLs, 28 exhibited targeted chromosome substitutions, although residual alien genome introgressions were prevalent across all lines. Among the 797 MAGIC RILs, 794 displayed varying levels of introgressed segments, with each RIL containing introgressions in an average of nine chromosomes. GB-derived introgressions predominated in 356 RILs, suggesting that GB alleles outcompeted GM or GT alleles during population development. Kinship analysis revealed a clear structure within the MAGIC population, which could be categorized into four groups. Despite five cycles of random mating, large alien genome segments persisted in many RILs, highlighting a continuing challenge posed by linkage drag in interspecific hybridization. This study offers new perspectives on the complexities of utilizing wild species in cotton improvement and provides valuable genetic materials for future breeding efforts.