Publicação
Genomic characterization of Portuguese grapevine varieties
| Resumo: | Grapevine (Vitis vinifera ssp. sativa) is the most cultivated fruit crop in the world. However, extensive breeding programs and vegetative propagation of Vitis vinifera have lead to a reduction in the existing genetic diversity. Its wild ancestor, Vitis vinifera ssp. sylvestris, represents an invaluable genetic resource for the improvement of cultivated grapevines, and can be the key for the discovery of its domestication history. It is commonly assumed that grapevine was first domesticated in the Near East and gradually moved towards the Eastern Mediterranean Basin and Western Europe. However, recent data suggest multi-local domestication of grapevine, and the Iberian Peninsula stands as a plausible local where a grapevine domestication event occurred. Here, we present the first genome-wide approach to address whether the Iberian Peninsula was also a center of grapevine domestication. Genomic DNA extraction of 22 grapevine samples – Portuguese and international (non-Iberian), Portuguese sylvestris and non-vinifera Vitis sp. – was performed, culminating in an optimized protocol to extract genomic DNA from grapevine leaves for high throughput sequencing. CIBIO’s Illumina HiSeq sequencer was used to sequence all the samples. Reads were mapped to a reference genome, and genotype likelihood calling was performed for population structure analysis. Results indicate that three Portuguese varieties – Alvarinho, Melhorio and Espadeiro – may have introgression of wild genomic DNA, suggesting that these varieties may have suffered crossing with local wild populations during their domestication. Traditionally, genome wide studies require the sequencing of several genotypes with each of the phenotypes for the trait in study, which can be expensive and labour intensive. Pool-Seq emerges as a cost-effective alternative, where the genomic DNA of the genotypes is bulked and sequenced using the same library. To investigate which genes were responsible for the grapevine berry color by detection of selective sweep presence, we conducted an analysis of the Pool-Seq data of four different grapevine varieties, and subsequent di statistics for red versus white-skinned berry grapevines. Custom scripts in Python were written to analyze and simplify most of the generated data, and Circos was employed to graphically visualize the data. During this analysis, one COP1 ortholog in grapevine emerged as candidate gene for anthocyanin biosynthesis signaling in this species. Preliminary in silico phylogenetic and protein structure analysis were carried out as an attempt to extrapolate whether its function remains conserved in relation to its Arabidopsis ortholog. |
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| Autores principais: | Gonçalves, Luís Miguel Carvalho |
| Ano: | 2017 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso restrito |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | Grapevine (Vitis vinifera ssp. sativa) is the most cultivated fruit crop in the world. However, extensive breeding programs and vegetative propagation of Vitis vinifera have lead to a reduction in the existing genetic diversity. Its wild ancestor, Vitis vinifera ssp. sylvestris, represents an invaluable genetic resource for the improvement of cultivated grapevines, and can be the key for the discovery of its domestication history. It is commonly assumed that grapevine was first domesticated in the Near East and gradually moved towards the Eastern Mediterranean Basin and Western Europe. However, recent data suggest multi-local domestication of grapevine, and the Iberian Peninsula stands as a plausible local where a grapevine domestication event occurred. Here, we present the first genome-wide approach to address whether the Iberian Peninsula was also a center of grapevine domestication. Genomic DNA extraction of 22 grapevine samples – Portuguese and international (non-Iberian), Portuguese sylvestris and non-vinifera Vitis sp. – was performed, culminating in an optimized protocol to extract genomic DNA from grapevine leaves for high throughput sequencing. CIBIO’s Illumina HiSeq sequencer was used to sequence all the samples. Reads were mapped to a reference genome, and genotype likelihood calling was performed for population structure analysis. Results indicate that three Portuguese varieties – Alvarinho, Melhorio and Espadeiro – may have introgression of wild genomic DNA, suggesting that these varieties may have suffered crossing with local wild populations during their domestication. Traditionally, genome wide studies require the sequencing of several genotypes with each of the phenotypes for the trait in study, which can be expensive and labour intensive. Pool-Seq emerges as a cost-effective alternative, where the genomic DNA of the genotypes is bulked and sequenced using the same library. To investigate which genes were responsible for the grapevine berry color by detection of selective sweep presence, we conducted an analysis of the Pool-Seq data of four different grapevine varieties, and subsequent di statistics for red versus white-skinned berry grapevines. Custom scripts in Python were written to analyze and simplify most of the generated data, and Circos was employed to graphically visualize the data. During this analysis, one COP1 ortholog in grapevine emerged as candidate gene for anthocyanin biosynthesis signaling in this species. Preliminary in silico phylogenetic and protein structure analysis were carried out as an attempt to extrapolate whether its function remains conserved in relation to its Arabidopsis ortholog. |
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