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Genomics technologies to study structural variations in the grapevine genome
- Source :
- BIO Web of Conferences, Vol 7, p 01016 (2016)
- Publication Year :
- 2016
- Publisher :
- EDP Sciences, 2016.
-
Abstract
- Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs) on plant genomes, few data are available on copy number variation (CNV). Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV) for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.
- Subjects :
- Molecular breeding
Genetics
Environmental Engineering
lcsh:QP1-981
lcsh:QR1-502
Genomics
Single-nucleotide polymorphism
Biology
Genome
Phenotype
Industrial and Manufacturing Engineering
lcsh:Microbiology
lcsh:Physiology
Structural variation
Evolutionary biology
lcsh:Zoology
Copy-number variation
lcsh:QL1-991
Gene
Subjects
Details
- Language :
- English
- ISSN :
- 21174458
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- BIO Web of Conferences
- Accession number :
- edsair.doi.dedup.....ab46583940758107fb29a922bd34f649