Supplementary Dataset 1 from the paper "Syntenic cell wall QTLs as versatile breeding tools: intra-specific allelic variability and predictability of biomass quality loci in target plant species"

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). <br> 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. <br> 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. <br> <br>

本数据集收录了论文《Syntenic cell wall QTLs as versatile breeding tools: intra-specific allelic variability and predictability of biomass quality loci in target plant species》（目前处于同行评审阶段，论文正式发表后将补充资源标题与DOI）中，通过跨不同植物种质基因组的共线数量性状基因座（syntenic quantitative trait loci, SQTLs）比对分析种内基因组多样性时，所检测到的SQTLs包含的所有基因内的遗传多态性（单核苷酸多态性与插入缺失多态性，SNPs/INDELs）。
该数据集的多态性鉴定方法已在上述论文中详细说明。简言之，研究人员使用NUCmer工具将SQTL的核苷酸序列与六种植物物种（详见数据集）的不同种质基因组组装结果进行比对。NUCmer的输出结果记录了SQTL区域内的SNPs与INDELs位点，基于这些数据可推断SQTL基因的编码蛋白序列变化。
总体而言，本数据集共包含19列信息，具体如下：
1. SQTL编号
2. 该SQTL通过NUCmer比对所涉及的目标染色体
3. 报道存在SNPs/INDELs的基因编号（每一行对应一个SQTL中的单个基因）
4-5列：对应基因在细胞壁生物合成/生物学过程中的作用与功能（若该基因为细胞壁相关基因）
6-7列：参考SQTL的基因序列所编码的蛋白质序列及其长度
8-9列：与该SQTL进行比对的目标染色体的基因序列所编码的蛋白质序列及其长度
10-11列：每个基因的比对中检测到的SNPs与INDELs数量
12-15列：SNPs与INDELs的位点及其序列效应，包括终止密码子相关变化（第12-13列）与点/短氨基酸替换（第14-15列）
16-19列：比对中各基因所对应的基因组组装、物种及蛋白质首个氨基酸的通用信息。