Toward Cotton Molecular Breeding: Challenges and Opportunities

Cotton (Gossypium spp) is the leading natural fiber in the global textile market, but progress in the development and applications of molecular tools to improve cotton lags behind other major crop plants. The slow progress is in part due to cotton’s large complex allotetraploid genome of 26 partially homoeologous chromosomes. Recently we have made significant progress in understanding the allotetraploid genome by: 1) mapping it with SSR and SNP markers, 2) sequencing its two diploid progenitor genomes, and 3) analyzing the genetic variation within and between the Gossypium genomes. Currently, the simultaneous discovery and mapping of genes/loci via genotyping by sequencing (GBS) and other new technologies are accelerating the development of genetic tools and associated knowledge essential for cotton molecular breeding. One example of the potential exploitation of abundant but underutilized genetic diversity in the Gossypium germplasm lies within the floral regulatory gene network in cotton. Various orthologous and paralogous loci in the cotton genomes can be identified using long-read next-generation sequencing (NGS). A number of chromosomal segments in the genomes also contain desirable genes for enhanced performance of cotton yield and quality. Innovative designs for cotton genetic improvement through genomics-assisted techniques are necessary and will be discussed, especially in light of the forthcoming reference sequence of whole allotetraploid cotton genome (G. hirsutum).