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.
Highlights
Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species
Based on an estimated time to the most recent common ancestor by estimating the divergence time between PL and PMC using all accessions in these two subgroups, we inferred that the unknown direct wild ancestor of cultivated P. persica originated at least 0.60 Mya in the Pleistocene. These results indicate that the emergence time of edible fruit in peach species occurred between 4.13–2.6 Mya and the direct wild ancestor of cultivated P. persica emerged between 2.47–0.60 Mya
We identified genes encoding cell wall synthases, cell wall lyases, and pectin lyase-like proteins that are known to contribute to fruit texture;[31,32,33] genes known to function in the synthesis and transport of sugars that have been reported as sugar-metabolism related QTLs which have contributed to sweetness in peach;[34] and genes encoding ion transport proteins that have been implicated in mesocarp development[35] (Supplementary Fig. 10 and 11 and Supplementary Data 11 and 12)
Summary
Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species. We explore the evolutionary history of peach using a largescale 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. Great morphological variation in fruit traits like fruit size, texture, taste, and skin color among cultivated peach and its wild relatives offers a natural diversity panel that presents an opportunity to explore the speciation and domestication history of peach, and to interpret the emergence and evolution of fruit edibility in perennial fruit crops more generally. Our study reveals the genetic basis of the emergence and evolution of fruit edibility in peach (Persica section) species and supports the hypothesis that frugivore-mediated selection may have occurred[5] several million years before the eventual domestication of peach. To gain insight into peach domestication, we identified genomic regions with strong selective signatures related to fruit texture, taste, size, and skin color, and propose that selection for fruit size occurred prior to the selection for fruit skin color that occurred during peach modern improvement
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