Genome resources for three modern cotton lines guide future breeding efforts

Avinash Sreedasyam; John T Lovell; Sujan Mamidi; Sameer Khanal; Jerry W Jenkins; Christopher Plott; Kempton B Bryan; Zhigang Li; Shengqiang Shu; Joseph Carlson; David Goodstein; Luis De Santiago; Ryan C Kirkbride; Sebastian Calleja; Todd Campbell; Jenny C Koebernick; Jane K Dever; Jodi A Scheffler; Duke Pauli; Johnie N Jenkins; Jack C McCarty; Melissa Williams; LoriBeth Boston; Jenell Webber; Joshua A Udall; Z Jeffrey Chen; Fred Bourland; Warwick N Stiller; Christopher A Saski; Jane Grimwood; Peng W Chee; Don C Jones; Jeremy Schmutz

doi:10.1038/s41477-024-01713-z

Genome resources for three modern cotton lines guide future breeding efforts

Nat Plants. 2024 Jun;10(6):1039-1051. doi: 10.1038/s41477-024-01713-z. Epub 2024 May 30.

Authors

Avinash Sreedasyam^#^{1

2}, John T Lovell^#^{3

4}, Sujan Mamidi³, Sameer Khanal⁵, Jerry W Jenkins³, Christopher Plott³, Kempton B Bryan⁶, Zhigang Li⁶, Shengqiang Shu⁴, Joseph Carlson⁴, David Goodstein⁴, Luis De Santiago⁷, Ryan C Kirkbride⁷, Sebastian Calleja⁸, Todd Campbell⁹, Jenny C Koebernick¹⁰, Jane K Dever^{11

12}, Jodi A Scheffler¹³, Duke Pauli⁸, Johnie N Jenkins¹⁴, Jack C McCarty¹⁴, Melissa Williams³, LoriBeth Boston³, Jenell Webber³, Joshua A Udall¹⁵, Z Jeffrey Chen⁷, Fred Bourland¹⁶, Warwick N Stiller¹⁷, Christopher A Saski⁶, Jane Grimwood³, Peng W Chee⁵, Don C Jones¹⁸, Jeremy Schmutz^{19

20}

Affiliations

¹ Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. asreedasyam@hudsonalpha.org.
² DOE Joint Genome Institute, Berkeley, CA, USA. asreedasyam@hudsonalpha.org.
³ Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
⁴ DOE Joint Genome Institute, Berkeley, CA, USA.
⁵ Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA.
⁶ Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA.
⁷ Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
⁸ School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
⁹ USDA-ARS, Coastal Plains Soil Water and Plant Research Center, Florence, SC, USA.
¹⁰ Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, USA.
¹¹ Texas A&M AgriLife Research, Lubbock, TX, USA.
¹² Pee Dee Research and Education Center, Clemson University, Florence, SC, USA.
¹³ USDA-ARS, Crop Genetics Research Unit, Stoneville, MS, USA.
¹⁴ USDA-ARS, Genetics and Sustainable Agriculture Research Unit, Mississippi State, MS, USA.
¹⁵ USDA-ARS, Crop Germplasm Research Unit, College Station, TX, USA.
¹⁶ Northeast Research and Extension Center (NEREC), University of Arkansas, Keiser, AR, USA.
¹⁷ CSIRO Agriculture and Food Cotton Research Unit, Narrabri, New South Wales, Australia.
¹⁸ Agriculture and Environmental Research Cotton Incorporated, Cary, NC, USA.
¹⁹ Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. jschmutz@hudsonalpha.org.
²⁰ DOE Joint Genome Institute, Berkeley, CA, USA. jschmutz@hudsonalpha.org.

^# Contributed equally.

Abstract

Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Cotton Fiber
Genetic Variation
Genome, Plant*
Gossypium* / genetics
Gossypium* / growth & development
Phenotype
Plant Breeding* / methods

Abstract

Publication types

MeSH terms

Grants and funding