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Plant Systematics and Evolution

, Volume 303, Issue 8, pp 1021–1042 | Cite as

Nucleotide diversity in the two co-resident genomes of allopolyploid cotton

  • Corrinne E. Grover
  • Joseph P. Gallagher
  • Emmanuel P. Szadkowski
  • Justin T. Page
  • Michael A. Gore
  • Joshua A. Udall
  • Jonathan F. Wendel
Original Article
Part of the following topical collections:
  1. Polyploidy in Shallow and Deep Evolutionary Times

Abstract

Genetic diversity within and among populations lies at the heart of evolution. Unraveling the extent to which each intrinsic or extrinsic factor determines levels of diversity among genes, populations, and species is challenging, given the difficulty of isolating any single potentially important variable from all others. Allopolyploid species provide an opportunity to disentangle external and intrinsic factors, as the two (or more) homoeologous genomes co-occur in the same nucleus, often exhibiting high collinearity along homoeologous chromosomes. Here we evaluate the pace of molecular evolution and intraspecific, intragenomic diversity in two species of allopolyploid Gossypium, G. hirsutum and G. barbadense, using several hundred genes sequenced from multiple accessions of each species. Genic diversity in both species is low, having been influenced both by the polyploid bottleneck and a domestication bottleneck (for cultivated accessions), but with a directional bias in homoeolog diversity favoring the same genome in both allopolyploids. Total diversity is remarkably similar for the two homoeologous genomes overall, but the two copies of many gene pairs have accumulated statistically different diversity levels, and in a biased fashion with respect to genome. Domesticated accessions show reduced diversity in both genomes, as expected, but with a much greater reduction in one of the two homoeologous genomes. Furthermore, this biased reduction affects opposite homoeologous genomes in the two species. Interspecific introgression has played a role in shaping diversity within each species. Introgression was only detected for certain accessions, and only from G. barbadense into G. hirsutum in one of the two co-resident genomes.

Keywords

Domestication Genetic variation Gossypium Hybridization Introgression Polyploidy 

Notes

Acknowledgements

We thank Guanjing Hu and Mark A. Arick for technical assistance; Daniel Ilut, John Nason, and Matthew Hufford for analytical advice; and Richard Percy for assistance in selecting the G. barbadense accessions. The authors are supported by the USDA-ARS and grants from the National Science Foundation, Supima, and Cotton Incorporated. J. P. Gallagher is supported by National Science Foundation Graduate Research Fellowship DGE1247194.

Compliance with Ethical Standards

Conflict of interest

The authors declare no conflicts of interest.

Human and animal rights statement

The present research does not involve human or animal participants. All authors have approved the manuscript.

Supplementary material

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Copyright information

© Springer-Verlag Wien 2017

Authors and Affiliations

  • Corrinne E. Grover
    • 1
  • Joseph P. Gallagher
    • 1
  • Emmanuel P. Szadkowski
    • 2
  • Justin T. Page
    • 3
  • Michael A. Gore
    • 4
  • Joshua A. Udall
    • 3
  • Jonathan F. Wendel
    • 1
  1. 1.Iowa State UniversityAmesUSA
  2. 2.INRA UR1052 GAFLAvignonFrance
  3. 3.Brigham Young UniversityProvoUSA
  4. 4.Plant Breeding and Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaUSA

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