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Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

View ORCID ProfileRoberto Lozano, Elodie Gazave, Jhonathan P.R. dos Santos, View ORCID ProfileMarkus Stetter, View ORCID ProfileRavi Valluru, View ORCID ProfileNonoy Bandillo, View ORCID ProfileSamuel B. Fernandes, Patrick J. Brown, View ORCID ProfileNadia Shakoor, View ORCID ProfileTodd C. Mockler, View ORCID ProfileJeffrey Ross-Ibarra, View ORCID ProfileEdward S. Buckler, View ORCID ProfileMichael A. Gore
doi: https://doi.org/10.1101/777623
Roberto Lozano
1Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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  • ORCID record for Roberto Lozano
Elodie Gazave
1Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Jhonathan P.R. dos Santos
1Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
2Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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Markus Stetter
3Botanical Institute, Biozentrum, University of Cologne, Cologne, Germany
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Ravi Valluru
4Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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  • ORCID record for Ravi Valluru
Nonoy Bandillo
4Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
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  • ORCID record for Nonoy Bandillo
Samuel B. Fernandes
5Department of Crop Sciences, University of Illinois at Urbana-Champaign, IL 61820, USA
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Patrick J. Brown
6Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
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Nadia Shakoor
7Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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Todd C. Mockler
7Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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Jeffrey Ross-Ibarra
8Center for Population Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
9Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
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Edward S. Buckler
1Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
4Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
10United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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Michael A. Gore
1Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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  • ORCID record for Michael A. Gore
  • For correspondence: mag87@cornell.edu
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Abstract

Sorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analyzed 13 million variants identified from whole genome resequencing of 468 sorghum lines together with 25 million variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes, and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the “domestication cost” hypothesis that predicts a higher deleterious burden among domesticates compared to wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy higher than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing them for removal through genome editing and breeding.

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Posted September 23, 2019.
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Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize
Roberto Lozano, Elodie Gazave, Jhonathan P.R. dos Santos, Markus Stetter, Ravi Valluru, Nonoy Bandillo, Samuel B. Fernandes, Patrick J. Brown, Nadia Shakoor, Todd C. Mockler, Jeffrey Ross-Ibarra, Edward S. Buckler, Michael A. Gore
bioRxiv 777623; doi: https://doi.org/10.1101/777623
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Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize
Roberto Lozano, Elodie Gazave, Jhonathan P.R. dos Santos, Markus Stetter, Ravi Valluru, Nonoy Bandillo, Samuel B. Fernandes, Patrick J. Brown, Nadia Shakoor, Todd C. Mockler, Jeffrey Ross-Ibarra, Edward S. Buckler, Michael A. Gore
bioRxiv 777623; doi: https://doi.org/10.1101/777623

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