Identifying genetically redundant accessions in the world’s largest cassava collection

A diverse panel of cultivated cassava landraces and improved lines were genotyped using DArTSeq Technology to identify genetic redundancy within the genebank collection. Metodology:Leaf samples were collected from in vitro plants for DNA extraction. The extracted DNA samples were subsequently sent to DArT P/L and genotyped using the DArTseq platform and sequencing, resulting in approximately 2.5 million reads per sample. Libraries were generated using the PstI and MseI restriction enzymes. To call SNPs and SilicoDArT genomic variants, the DS14 software was implemented. Genomic variants were reported in .csv files. SilicoDArT Format: SilicoDArTs are scored in a binary fashion, representing genetically 'dominant' markers, with '1' indicating the presence and '0' indicating the absence of a restriction fragment with the marker sequence in the genomic representation of the sample. 'NA' is used for missing data. SNP Format: '0' represents a reference allele homozygote, '2' represents an SNP allele homozygote, '1' represents a heterozygote, and 'NA' represents a double null/null allele homozygote (absence of a fragment with SNP in the genomic representation).

本研究采用DArTseq技术（DArTseq Technology）对一组涵盖多样栽培木薯地方品种与改良品系的材料开展基因分型，旨在鉴定种质库收集材料内的遗传冗余现象。
方法学：从离体培养植株采集叶片样本以提取DNA。提取得到的DNA样本随后被寄送至DArT P/L公司，借助DArTseq平台及测序技术完成基因分型，每个样本可获得约250万条测序读段。实验采用PstI与MseI两种限制性内切酶构建测序文库。为鉴定单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与SilicoDArT基因组变异位点，本研究使用了DS14软件。基因组变异数据以.csv格式文件进行输出。
SilicoDArT标记格式：SilicoDArT标记采用二元计分方式，属于遗传显性标记。其中，"1"代表样本基因组表征中存在携带该标记序列的限制性片段，"0"代表不存在此类片段；"NA"用于表示缺失数据。
SNP标记格式："0"代表参考等位基因纯合子，"2"代表SNP等位基因纯合子，"1"代表杂合子，"NA"代表双无效/零等位基因纯合子（即样本基因组表征中不存在携带该SNP位点的限制性片段）。