Unraveling the Genetic Architecture of Somatic Embryogenesis in Upland Cotton

Somatic embryogenesis is the de novo development of asexual embryos because of the plasticity of the plant cell. In tissue culture, the biochemical and genetic mechanisms of dedifferentiated callus tissues can be reprogrammed to transdifferentiate into developed, polarized embryos, which can ultimately regenerate into whole plants. Although this rarely occurs in nature, scientists have exploited this process for decades to regenerate whole plants following gene transformation or for micropropagation. While some species are amenable to in vitro regeneration, upland cotton is particularly recalcitrant, with regenerative potential being confined to only several genotypes. The lack of elite, regenerable genotypes greatly restricts our ability to broadly conduct functional genomics studies and accelerated breeding activities in cotton. A primary goal is to enable the ability to improve trait genetics, in a tailored fashion, in elite breeding and commercially cultivated germplasm with the latest genome editing and engineering technologies; in a genotype-independent manner. Progress has been made in monocots to discover genes, epigenetic factors, and other regulatory mechanisms that govern somatic embryogenesis, however, experiments with these genes in eudicots do not produce the same result, suggesting alternative genetic mechanisms. The studies presented herein provides new insights in the genetic architecture of somatic embryogenesis in upland cotton. This investigation sought to utilize both morphological and embryogenic traits paired with low-pass whole-genome sequencing to robustly map key somatic embryogenesis genetic regulatory elements in the cotton genome. The identified quantitative trait loci associated with variation in regenerative potential in a biparental mapping population were biased to the D subgenome on chromosomes D07 and D09. Several candidate genes were identified including a fatty acid omega-hydroxylase, a MYB domain containing transcription factor, an AP2 domain containing transcription factor, and several unannotated genes on the D07 chromosome, as well as a sulfite oxidase gene and another unannotated gene on the D09 chromosome