A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication. (21st June 2020)

• Record Type: Journal Article
• Authors: Pinosio, Sara; Marroni, Fabio; Zuccolo, Andrea; Vitulo, Nicola; Mariette, Stephanie; Sonnante, Gabriella; Aravanopoulos, Filippos A.; Ganopoulos, Ioannis; Palasciano, Marino; Vidotto, Michele; Magris, Gabriele; Iezzoni, Amy; Vendramin, Giovanni G.; Morgante, Michele
• Is Part Of: Plant journal. Volume 103:Number 4(2020)
• Page Start: 1420
• Page End: 1432
• Publication Date: 2020-06-21
• Subjects: genome structure and evolution -- domestication -- genetic diversity -- genome assembly -- Prunus avium; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14809
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: Sweet cherry ( Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety "Big Star*" and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry. Significance Statement: Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. In the present work, we assembled the genome of a sweet cherry variety and resequenced a total of 97 sweet cherry accessions to characterize the genome‐wide patterns of genetic variability in this species and to fine map the selection targets affected by domestication and breeding.