Browse Articles

Article|01 Jul 2018|OPEN
Genomic signatures of different adaptations to environmental stimuli between wild and cultivated Vitis vinifera L
Annarita Marrano1, Diego Micheletti2, Silvia Lorenzi1, David Neale3 & M. Stella Grando1,4
1Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
2Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
3Department of Plant Sciences, University of California, Davis, CA 95616, USA
4Center Agriculture Food Environment (C3A), University of Trento, San Michele all ‘Adige (TN), Italy

Horticulture Research 5,
Article number: 34 (2018)
doi: 10.1038/hortres.2018.34
Views: 511

Received: 07 Dec 2017
Revised: 23 Mar 2018
Accepted: 06 Apr 2018
Published online: 01 Jul 2018

Abstract

The application of population genetic methods in combination with gene mapping strategies can help to identify genes and mutations selected during the evolution from wild plants to crops and to explore the considerable genetic variation still maintained in natural populations. We genotyped a grapevine germplasm collection of 44 wild (Vitis vinifera subsp. sylvestris) and 48 cultivated (V. vinifera subsp. sativa) accessions at 54 K single-nucleotide polymorphisms (SNPs) to perform a whole-genome comparison of the main population genetic statistics. The analysis of Wright Fixation Index (FST) along the whole genome allowed us to identify several putative “signatures of selection” spanning over two thousand SNPs significantly differentiated between sativa and sylvestris. Many of these genomic regions included genes involved in the adaptation to environmental changes. An overall reduction of nucleotide diversity was observed across the whole genome within sylvestris, supporting a small effective population size of the wild grapevine. Tajima’s D resulted positive in both wild and cultivated subgroups, which may indicate an ongoing balancing selection. Association mapping for six domestication-related traits was performed in combination with population genetics, providing further evidence of different perception and response to environmental stresses between sativa and sylvestris.