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2022 Speakers

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

Chao Shen

Chao Shen, Speaker at  Plant Science Conferences 2022
Guangdong University of Petrochemical Technology, China
Title : 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


Chao Shen obtained a PhD in Plant Genetics & Breeding from Huazhong Agricultural University where he studied the genetics, genomics and molecular biology in cotton. During his postgraduate, he used genome sequencing to address the cotton introgression lines, the cotton polyploidy genomics and domestication population genetics project. In 2019, he joined Guangdong University of Petrochemical Technology. At present, 25 academic papers have been published in high-level SCI journals at home and abroad, serving as editorial board member of International Journal of Genetics and Genomics, Journal of Modern Agriculture and Biotechnology and Annals of Genetics.

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