Journal article
Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms
Plant biotechnology journal, Vol.11(7), pp.883-893
09/2013
Handle:
https://hdl.handle.net/2376/112107
PMCID: PMC3775899
PMID: 23763653
Abstract
Summary
Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Non‐sense mutations account for about 70 000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these non‐sense SNPs revealed several interesting results. First, non‐sense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison with peach, sweet cherry is found to have non‐sense SNPs in two 1‐aminocyclopropane‐1‐carboxylate synthase (ACS) genes and two 1‐aminocyclopropane‐1‐carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the nonclimacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of non‐sense SNP abundance in a genus being linked to specific GO terms.
Metrics
11 Record Views
Details
- Title
- Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms
- Creators
- Tyson Koepke - Washington State UniversityScott Schaeffer - Washington State UniversityArtemus Harper - Washington State UniversityFederico Dicenta - CEBAS‐CSICMark Edwards - Southern Cross UniversityRobert J Henry - The University of QueenslandBirger L Møller - University of CopenhagenLee Meisel - INTA‐Universidad de ChileNnadozie Oraguzie - Washington State UniversityHerman Silva - Universidad de ChileRaquel Sánchez‐Pérez - University of CopenhagenAmit Dhingra - Washington State University
- Publication Details
- Plant biotechnology journal, Vol.11(7), pp.883-893
- Academic Unit
- Crop and Soil Sciences, Department of; Horticulture, Department of
- Number of pages
- 11
- Grant note
- WSU ARC startup and Hatch Innova CORFO (07CN13 PBT‐167) ARCS fellowships (2008 ‐35300‐04676) NIH Protein Biotechnology Training Program (T32GM008336) Molecular Biology of Cyanogenesis in Almonds Séneca Foundation Mejora Genetica del Almendro Villum research center Pro‐Active Plants and the Novo Nordisk Foundation Center for Bio‐Sustainability US Department of Agriculture National Research Initiative (USDA‐NRI) CONICYT, FONDECYT (1120261)
- Identifiers
- 99900547607701842
- Language
- English
- Resource Type
- Journal article