G. tomentosum genome and interspecific ultra-dense genetic maps reveal genomic structures and flowering depression in cotton

The high-quality reference-grade genome for Gossupium tomentosum can greatly promote the progress in biological research and introgression breeding for the mainly cultivated species, G. hirsutum. Here, we report a high-quality genome assembly for G. tomentosum by integrating PacBio and Hi-C technologies. Comparative genomic analysis revealed a large number of genetic variations. Two re-sequencing-based ultra-dense genetic maps were constructed which comprised 4,047,199 and 6,009,681 SNPs, 4,120 and 4,599 bins and covering 4,126.36 cM and 4,966.72 cM in the EMF2 (F2 from G. hirsutum × G. tomentosum) and GHF2 (F2 from G. hirsutum × G. barbadense). The EMF2 exhibited lower recombination rate at the whole-genome level as compared with GHF2. We mapped 22 and 33 QTL associated with crossover frequency and predicted Gh_MRE11 and Gh_FIGL1 as the candidate genes governing crossover in the EMF2 and GHF2, respectively. We identified 13 significant QTL that regulate the floral transition, and revealed that Gh_AGL18 was associated with the floral transition. Therefore, our study provides a valuable genomic resource to support a better understanding of cotton interspecific cross and recombination landscape for genetic improvement and breeding in cotton.

Audience Take Away Notes:

• The high quality G. tomentosum genome revealed massive interspecific structure variations
• Differences of interspecific genetic variation between EMF₂ and GHF₂
• A higher collinearity between the genetic and physical maps in G. hirsutum × G. tomentosum population?
• Less recombination rate and crossovers discovered in G. hirsutum × G. tomentosum population
• Genomic regions and candidate gene uncovered flowering hybrid breakdown in G. hirsutum × G. tomentosum