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.
Highlights
The Eurasian grape (Vitis vinifera L.) is one of the most important crops worldwide for its global distribution and economic value[1]
single-nucleotide polymorphisms (SNPs) genotyping of a grapevine germplasm population A total of 92 wild and domesticated grapevine accessions were genotyped using the custom Illumina Infinium Vitis20K SNP array and a novel RAD-seq approach[6]
Most of the SNPs filtered out due to high missing rate came from RAD-seq. This result is a common issue of all methods of reduce representation sequencing, where several technical factors led all the sequenced regions not to be evenly covered in all the individuals of the population[35]
Summary
The Eurasian grape (Vitis vinifera L.) is one of the most important crops worldwide for its global distribution and economic value[1]. V. vinifera L. exists as the cultivated form V. vinifera subsp. Sativa (or vinifera; hereafter called sativa) and the wild-form V. vinifera subsp sylvestris (hereafter called sylvestris), which is assumed to be the ancestor of modern cultivars. The two subspecies exhibit several phenotypical differences, notably in flower sex, seed shape, bunch and berry size, and leaf morphology[2]. Sylvestris is dioecious with separate male and female individuals, and in general produces few bunches with small, black and juiceless berries. Sylvestris is less diverse than the domesticated form[6]. The present distribution of the wild vinifera is fragmented in relict populations with very few individuals. The decline of sylvestris has drastically increased over the last two centuries because of the introduction of pests and diseases (phylloxera, downy and powdery mildew) from North
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