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Evolutionary genomics of peach and almond domestication

View ORCID ProfileDianne Velasco, Josh Hough, Mallikarjuna Aradhya, View ORCID ProfileJeffrey Ross-Ibarra
doi: https://doi.org/10.1101/060160
Dianne Velasco
*Department of Plant Sciences, University of California, Davis, California 95616,
†USDA-ARS National Clonal Germplasm Repository, Davis, California 95616, USA,
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Josh Hough
*Department of Plant Sciences, University of California, Davis, California 95616,
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Mallikarjuna Aradhya
†USDA-ARS National Clonal Germplasm Repository, Davis, California 95616, USA,
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Jeffrey Ross-Ibarra
‡Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, Davis CA 95616
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Abstract

The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originate on opposite sides of Asia and were independently domesticated approximately 5000 years ago. While interfertile, they possess alternate mating systems and differ in a number of morpholog-ical and physiological traits. Here we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has ∼7X the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of approximately 8 Mya, coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application and further the understanding of evolution in these species.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 27, 2016.
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Evolutionary genomics of peach and almond domestication
Dianne Velasco, Josh Hough, Mallikarjuna Aradhya, Jeffrey Ross-Ibarra
bioRxiv 060160; doi: https://doi.org/10.1101/060160
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Evolutionary genomics of peach and almond domestication
Dianne Velasco, Josh Hough, Mallikarjuna Aradhya, Jeffrey Ross-Ibarra
bioRxiv 060160; doi: https://doi.org/10.1101/060160

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