Applying a Reference Genome to Cotton Breeding.

A reference genome for cotton based on the compact genome of Gossypium raimondii, together with draft genomes for G. hirsutum, G. herbaceum, and G. longicalyx and others, and their subsequent analyses, have provided new insights into key events in cotton evolutionary history. These events include a 5x multiplication of the entire genome about 60 million years ago, followed by the merger of the A and D subgenomes about 1-2 million years ago, and a rich history of intergenomic exchange that has doubled the dosage of many cotton alleles in striking patterns across time and across the genome.  The reference genome provides new insights into fiber evolution including many candidate genes that warrant further investigation, as well as a valuable resource for mitigating many long-standing challenges in cotton improvement.