Dataset Information

Genome-wide analysis of the "cut-and-paste" transposons of grapevine.

ABSTRACT: BACKGROUND: The grapevine is a widely cultivated crop and a high number of different varieties have been selected since its domestication in the Neolithic period. Although sexual crossing has been a major driver of grapevine evolution, its vegetative propagation enhanced the impact of somatic mutations and has been important for grapevine diversity. Transposable elements are known to be major contributors to genome variability and, in particular, to somatic mutations. Thus, transposable elements have probably played a major role in grapevine domestication and evolution. The recent publication of the complete grapevine genome opens the possibility for an in deep analysis of its transposon content. PRINCIPAL FINDINGS: We present here a detailed analysis of the "cut-and-paste" class II transposons present in the genome of grapevine. We characterized 1160 potentially complete grapevine transposons as well as 2086 defective copies. We report on the structure of each element, their potentiality to encode a functional transposase, and the existence of matching ESTs that could suggest their transcription. CONCLUSIONS: Our results show that these elements have transduplicated and amplified cellular sequences and some of them have been domesticated and probably fulfill cellular functions. In addition, we provide evidences that the mobility of these elements has contributed to the genomic variability of this species.

SUBMITTER: Benjak A

PROVIDER: S-EPMC2528002 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Genome-wide analysis of the "cut-and-paste" transposons of grapevine.

Benjak Andrej A Forneck Astrid A Casacuberta Josep M JM

PloS one 20080903 9

<h4>Background</h4>The grapevine is a widely cultivated crop and a high number of different varieties have been selected since its domestication in the Neolithic period. Although sexual crossing has been a major driver of grapevine evolution, its vegetative propagation enhanced the impact of somatic mutations and has been important for grapevine diversity. Transposable elements are known to be major contributors to genome variability and, in particular, to somatic mutations. Thus, transposable e ...[more]

PMID: 18769592

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Project description:An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.

Dataset Information

Genome-wide analysis of the "cut-and-paste" transposons of grapevine.

Publications

Genome-wide analysis of the "cut-and-paste" transposons of grapevine.

Similar Datasets

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