Evolutionary Genomics of Peach and Almond Domestication

G3 : Genes - Genomes - Genetics
Dianne VelascoJeffrey Ross-Ibarra

Abstract

The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological 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 around seven times the genetic diversity of peach, and high genome-wide [Formula: see text] values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a 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 f...Continue Reading

References

Mar 13, 2018·The New Phytologist·Artem PankinMaria von Korff
Feb 8, 2019·The New Phytologist·Emily J Warschefsky, Eric J B von Wettberg
Jan 18, 2019·Molecular Ecology·Krystyna Nadachowska-BrzyskaHans Ellegren
Aug 1, 2018·Nature Plants·Brandon S GautYongfeng Zhou
Jul 1, 2020·Frontiers in Plant Science·Thomas M Gradziel
Oct 19, 2017·Proceedings of the National Academy of Sciences of the United States of America·Yongfeng ZhouBrandon S Gaut
Jun 15, 2019·Science·R Sánchez-PérezBirger L Møller
Jan 29, 2020·Ecology and Evolution·Ting ShiZhihong Gao

Citations

Oct 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·M Nei, W H Li
Jul 2, 2003·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Deborah Charlesworth
Oct 4, 2006·Proceedings. Biological Sciences·Sylvain GléminDeborah Charlesworth
Dec 28, 2006·Cell·John F DoebleyBruce D Smith
May 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey Ross-IbarraBrandon S Gaut
Feb 22, 2008·Genetics Research·Jorge VieiraCristina P Vieira
Aug 19, 2009·Nature Reviews. Genetics·Kent E Holsinger, Bruce S Weir
Mar 6, 2010·The New Phytologist·Doyle McKeyAnne Duputié
Jan 20, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sean MylesEdward S Buckler
Aug 26, 2011·American Journal of Botany·Allison J Miller, Briana L Gross
Nov 30, 2012·Molecular Ecology·Malou DelplanckeN Arrigo
Apr 19, 2013·Proceedings. Biological Sciences·Stephen I WrightTanja Slotte
Jun 15, 2013·Plant Biotechnology Journal·Tyson KoepkeAmit Dhingra
Jun 21, 2013·Plant Molecular Biology·Lu WangYuepeng Han
Sep 18, 2013·BMC Genetics·Xiong-Wei LiMaria José Aranzana
Jan 25, 2014·Bioinformatics·Matteo FumagalliRasmus Nielsen
Jun 24, 2014·Nature Genetics·Stephan Schiffels, Richard Durbin
Oct 19, 2014·American Journal of Botany·Briana L GrossGayle M Volk
Nov 26, 2014·BMC Bioinformatics·Thorfinn KorneliussenRasmus Nielsen
Jun 1, 2012·Evolutionary Applications·Malou DelplanckeNils Arrigo
Sep 10, 2015·PloS One·Diego MichelettiMaria José Aranzana
Nov 26, 2015·Trends in Genetics : TIG·Brandon S GautPeter L Morrell
Nov 27, 2015·Scientific Reports·Tao SuZhekun Zhou
Dec 24, 2015·Genomics Data·Yeonhwa JoWon Kyong Cho
Apr 5, 2016·Nature Biotechnology·Nicolas L BrayLior Pachter
Apr 17, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Takashi AkagiRyutaro Tao
Jun 15, 2016·Nature Plants·Timothy M BeissingerJeffrey Ross-Ibarra

Related Concepts

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