Abstract
Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.
Highlights
Cotton is an important natural fiber crop cultivated worldwide that provides an ideal model for investigating evolution and domestication of polyploids
As the less divergent long terminal repeat (LTR) were well-assembled, we found that most LTRs in the A2 genome were young and active; a similar situation was found in the At subgenome of G. hirsutum, Glossary
Wang et al combined an optical map with high-throughput chromosome conformation capture (Hi-C) and Pacific Biosciences (PacBio) long-reads to generate the reference genomes of two cultivated tetraploid species
Summary
Cotton is an important natural fiber crop cultivated worldwide that provides an ideal model for investigating evolution and domestication of polyploids. Comparative population genomics illuminated the genetic history of cotton domestication and identified the genomic variation determining fiber yield, quality, and stress resistance. The D genome (G. raimondii) together with the A genome (Gossypium arboreum or Gossypium herbaceum) is the likely ancestor of G. hirsutum and G. barbadense, two important cotton fiber-producing species [4].
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