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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #410772
Research Project: Management of Cotton Genetic Resources and Genetic Improvement of Cotton

Location: Crop Germplasm Research

Title: The assembled genome of landrace Cedex (SA-1766) reveals genetic potential for stress tolerance not represented in the current model of Gossypium hirsutum

Author
item CUSHMAN, KEVIN - Texas Tech University
item KITAZUMI, AI - Texas Tech University
item LIM, ALEXANDER - Oklahoma State University
item NAIDENOV, BRYAN - Oklahoma State University
item CHEN, CHARLES - Oklahoma State University
item Hinze, Lori
item SWEENEY, MEGAN - Basf Corporation North America
item DE LOS REYES, BENILDO - Texas Tech University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/9/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Intense selection for a few economically desirable traits has limited the genetic potential of modern cultivars to tolerate less-than-ideal environmental conditions. Fiber and cottonseed production, the main emphases of cotton domestication and breeding, has minimized the naturally evolved stress tolerance potential of Gossypium hirsutum (L.). The landrace Cedex has shown an enhanced resistance to both biotic and abiotic stresses. Here, we assembled a well-resolved genome sequence of Cedex and compared that to the reference sequence of TM-1 (CRI_v1). To this end, we have annotated the genome of Cedex for genic content by anchoring Gossypium genes from diploids (e.g. A1, A2, D5, and D10) and tetraploids (e.g. AD1, AD2, AD3, AD4, and AD5) to elucidate the conservation, diversification, and potential erosion. Additionally, we have annotated the transposable element (TE) content and estimated the age by Kimura substitution levels across all panels. The genome assembly of Cedex (2,312Mb) was comparable to TM-1 (2,333Mb) but reveals extensive gene duplication in stress response genes. Disrupted synteny was also observed due to large structural variations (e.g. inversion, translocation, inverted translocation and non-syntenic content) in the A-subgenome, particularly in chromosomes A2, A8, and A12. Cedex appears to have undergone a recent proliferation of several LTR-type elements. These trends represent genetic erosion associated with intense selection for fiber traits. The evolutionary significance of LTR-type elements in the large chromosomal rearrangements and genetic diversity is discussed.