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Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.)

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Abstract

Comparative proteomic analyses were performed to detail the evolutionary consequences of strong directional selection for enhanced fiber traits in modern upland cotton (Gossypium hirsutum L.). Using two complementary proteomic approaches, 2-DE and iTRAQ LC–MS/MS, fiber proteomes were examined for four representative stages of fiber development. Approximately 1,000 protein features were characterized using each strategy, collectively resulting in the identification and functional categorization of 1,223 proteins. Unequal contributions of homoeologous proteins were detected for over a third of the fiber proteome, but overall expression was balanced with respect to the genome-of-origin in the allopolyploid G. hirsutum. About 30 % of the proteins were differentially expressed during fiber development within wild and domesticated cotton. Notably, domestication was accompanied by a doubling of protein developmental dynamics for the period between 10 and 20 days following pollination. Expression levels of 240 iTRAQ proteins and 293 2-DE spots were altered by domestication, collectively representing multiple cellular and metabolic processes, including metabolism, energy, protein synthesis and destination, defense and stress response. Analyses of homoeolog-specific expression indicate that duplicated gene products in cotton fibers can be differently regulated in response to selection. These results demonstrate the power of proteomics for the analysis of crop domestication and phenotypic evolution.

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Abbreviations

2-DE:

Two-dimensional gel electrophoresis

iTRAQ:

Isobaric tag for relative and absolute quantification

LC:

Liquid chromatography

MS:

Mass spectrometry

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Acknowledgments

We thank Kara Grupp and Anna Tuchin for help in tissue collection. We acknowledge the Protein and Proteomics Facility of the Iowa State University for technical assistance in 2-DE analysis. We acknowledge the Proteomics and Mass Spectrometry Facility of the University of Florida’s Interdisciplinary Center for Biotechnology Research for assistance in LC–MS/MS analysis. DP was supported by a training grant from Punjab Agricultural University, Ludhiana, India. The LC–MS/MS system was funded by National Institute of Health grant 1S10RR025418-01 to SC. This work was funded by Cotton Incorporated grant 09-558 and by the NSF Plant Genome Research Program, both to JFW.

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  1. Dharminder Pathak

    Present address: Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India

Authors and Affiliations

  1. Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA

    Guanjing Hu, Dharminder Pathak & Jonathan F. Wendel

  2. Department of Biology, University of Florida, Gainesville, FL, 32610, USA

    Jin Koh, Mi-Jeong Yoo & Sixue Chen

  3. Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA

    Jin Koh & Sixue Chen

  4. Genetics Institute, University of Florida, Gainesville, FL, 32610, USA

    Sixue Chen

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Correspondence to Jonathan F. Wendel.

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Hu, G., Koh, J., Yoo, MJ. et al. Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.). Planta 240, 1237–1251 (2014). https://doi.org/10.1007/s00425-014-2146-7

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