Genome re-sequencing reveals the evolutionary history of peach fruit edibility

Abstract

Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species. Here we explore the evolutionary history of peach using a large-scale SNP data set generated from 58 high-coverage genomes of cultivated peach and closely related relatives, including 44 newly re-sequenced accessions and 14 accessions from a previous study. Our analyses suggest that peach originated about 2.47 Mya in southwest China in glacial refugia generated by the uplift of the Tibetan plateau. Our exploration of genomic selection signatures and demographic history supports the hypothesis that frugivore-mediated selection occurred several million years before the eventual human-mediated domestication of peach. We also identify a large set of SNPs and/or CNVs, and candidate genes associated with fruit texture, taste, size, and skin color, with implications for genomic-selection breeding in peach. Collectively, this study provides valuable information for understanding the evolution and domestication of perennial fruit tree crops.

The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events

“…A compelling hypothesis for the origin of divergence between peach and almond is that climatic changes after Tibetan Plateau uplift and Himalayan orogeny led to isolation and subsequent divergence of peach (on the Eastern part of Himalaya) and almond (on the Western part) lineages from a common ancestral species (Chin et al, ; Velasco et al, ). The uplift of the Himalayan Mountains is indeed known to have resulted in the formation of geographical barriers and in climate changes, which fostered plant diversification (Beer et al, ; Yu et al, ; Zhisheng, Kutzbach, Prell, & Porter, ). These paleogeographic events probably also played an important role in wild apricot demographic history.…”

“…The (Chin et al, 2014;Velasco et al, 2016). The uplift of the Himalayan Mountains is indeed known to have resulted in the formation of geographical barriers and in climate changes, which fostered plant diversification (Beer et al, 2008;Yu et al, 2018;Zhisheng, Kutzbach, Prell, & Porter, 2001). These paleogeographic events probably also played an important role in wild apricot demographic history.…”

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

“…In principle, one can reconstruct the demographic history of a species from the genome sequences of its present‐day representatives (Beichman, Huerta‐Sanchez, & Lohmueller, ). These reconstructions can be used to answer various biological questions, such as the influence of climatic events on population size and structure (Miller et al, ), the timing of major events in the evolutionary history of modern humans (Fu et al, ; Li & Durbin, ), human impacts on wild animal populations (Johnson et al, ; Pujolar, Dalén, Hansen, & Madsen, ), and the effects of domestication (Frantz et al, ; Yu et al, ).…”

Association between blooming time and climatic adaptation in Prunus mume

“…Next‐generation sequencing (NGS) technologies are faster and cheaper than Sanger sequencing, which is frequently used in plant studies and allows for a deeper genome variant analysis (Deschamps & Campbell, ; Jackson, Iwata, Lee, Schmutz, & Shoemaker, ). So far, genome sequencing and evolutionary genetics have provided information about the origin, evolution (Ellegren, ; Sedivy, Wu, & Hanzawa, ; Velasco, Hough, Aradhya, & Ross‐Ibarra, ; Wu, Terol, et al, ; Yu et al, ), and domestication (Akagi, Hanada, Yaegaki, Gradziel, & Tao, ; Myles et al, ; Qiu et al, ; Velasco et al, ; Wu, Wang, et al, ). The first 237M long genomic map of P. mume was constructed in 2012, and the actual size of the genome of P. mume was estimated to be about 280M.…”

“…So far, genome sequencing and evolutionary genetics have provided information about the origin, evolution (Ellegren, 2014;Sedivy, Wu, & Hanzawa, 2017;Velasco, Hough, Aradhya, & Ross-Ibarra, 2016;Wu, Terol, et al, 2018;Yu et al, 2018), and domestication (Akagi, Hanada, Yaegaki, Gradziel, & Tao, 2016;Myles et al, 2011;Qiu et al, 2015;Velasco et al, 2016;Wu, Wang, et al, 2018). The first 237M long genomic map of P. mume was constructed in 2012, and the actual size of the genome of P. mume was estimated to be about 280M.…”