Reference-Grade Genome Assemblies Facilitate Exploitation of Favorable Genetic Variations Underlying the Development of Superior Cotton Fibers

Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. Because of the superior fiber quality of G. barbasense, one of the rational approach for G. hirsutum fiber improvement is to introduce favorable chromosome segments from G. barbadense to G. hirsutum, which requires a detailed and robust understanding of genomic organization. The draft genome sequences of both species are available, but they are highly fragmented and incomplete. Here we report the reference-grade genome assemblies and annotations for G. hirsutum and G. barbadense by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes, these genome sequences show remarkable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative analyses of both genomes reveal extensive genomic variations that likely occurred post-polyploidization. To identify favorable variations, we integrated genomic data from two introgression line population between G. hirsutum and G. barbadense, allowing us to identify quantitative trait loci associated with superior fiber quality. Additionally, we also identified several causal genetic variations underlying fiber quality-related traits by using a Multiparent Advanced Generation Inter-Cross (MAGIC) population in G. hirsutum. These resources will accelerate evolutionary and functional genomic studies in cotton, and inform future breeding programs for fiber improvement.