This dataset reports all the genetic polymorphisms (SNPs/INDELs) that were detected in all the genes included in the syntenic quantitative trait loci (SQTLs) for which intra-specific genomic diversity was studied by SQTLs alignment across genomes representing different plant accessions in the paper "Syntenic cell wall QTLs as versatile breeding tools: intra-specific allelic variability and predictability of biomass quality loci in target plant species" (currently under peer review; resource title and DOI will be added once the paper is published).
The methodology followed for polymorphisms identification is detailly reported in the paper "Syntenic cell wall QTLs as versatile breeding tools: intra-specific allelic variability and predictability of biomass quality loci in target plant species". In brief, SQTL nucleotide sequences were aligned by NUCmer against diverse genomic assemblies from different accessions of six plant species (reported in the dataset). NUCmer outputs report SNPs and INDELs positions along SQTLs, whose data were used to infer changes in translated protein sequences in SQTL genes.
Overall, the dataset contains 19 columns:
- 1: SQTL ID
- 2: The target chromosome over which SQTL produced alignment with NUCmer
- 3: Gene ID for which SNPs/INDELs were reported (each row represents one gene from a SQTL)
- 4-5: Process and function of a gene in the context of cell wall biosynthesis/biology (in the case a gene is a cell wall gene)
- 6-7: The protein sequence and its length as coded by the gene sequence of the reference SQTLs
- 8-9: The protein sequence and its length as coded by the gene sequence of the target chromosome against which SQTL produced alignment
- 10-11: The number of SNPs and INDELs detected in the alignment of each gene
- 12-15: Position and sequence effect of SNPs and INDELs in terms of stop codons (columns 12-13) and point/short amino acid changes (columns 14-15);
- 16-19: General information on the assembly, species, and protein's first amino acid for each gene in alignment.