De Santiago, Luis Miguel (2020-07). Identifying, Mapping and Overcoming Genomic Impediments to Intraspecific Genetic Improvement of Upland Cotton Through Interspecific Hybridization and Introgression. Doctoral Dissertation.
Thesis
Cotton, the leading natural textile fiber, develops as modified seed trichomes, produced in copious amounts by genetically elite cultivars of two domesticated New World Upland tetraploid (2n=4x=52) species, Upland cotton (Gossypium hirsutum L.) and Pima cotton (G. barbadense L.). Future cultivars must improve production sustainability, economic yield, and address the many challenges caused by global climate change. Their creation will require beneficial genetic diversity, relevant recombination, breeding, and selection. This work was undertaken [1] to better understand available diversity and natural constraints on its use, especially recombination, [2] to increase genetic diversity, and [3] to improve recombination as a tool for extracting value from diversity. Aside from transgenes and occasional mutations, induced or created, new cotton cultivars are created from fast-track breeding programs that rely exclusively on genetic variation among cultivars and elite breeding germplasm, not on wild intraspecific or interspecific accessions; cyclic re-use of elite germplasm is implicit. Using CottonSNP63K data and a long-read genomic assembly, I characterized the genomic distribution of genetic diversity by identifying, mapping, and comparing haplotypic structures and their diversity among 257 elite Upland lines and 71 non-elite G. hirsutum accessions. Independent analyses using comparable types of data for 9 at intra- and interspecific linkage mapping populations revealed their recombination patterns. Comparisons showed strong relationships between static haplotypic blocks and low experimental recombination rates. Genomic characterization of highly and lowly recombinant regions revealed significant associations and correlations between recombination and transposable element densities and biological pathways between three allotetraploid cotton species and G. hirsutum. An intriguing observation during linkage analyses was that hybridization with wild allotetraploid cotton species led to novel recombination events that disrupted long-standing haplotypic blocks. Such disruption and the recovery of novel genetic variation suggests potential for a new era in Upland cotton improvement involving extensive use interspecific hybridization to disrupt haplotypic blocks, as well as diversify genes. Indeed, this was demonstrated through recombination modeling and through the development of a chromosome segment substitution lines consisting of introgressed G. tomentosum chromatin. These findings indicate potentially major if not revolutionary ramifications for breeding Upland cotton, and likely Pima, as well.
