Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.
Biochem Genet. 2024 Dec;62(6):4396-4407. doi: 10.1007/s10528-023-10638-9. Epub 2024 Feb 2.
Insertion-deletion (InDel) markers are co-dominant, relatively abundant and practical for agarose gel genotyping. InDel polymorphism usually affects gene functions. Nucleotide sequences of durian (Durio zibethinus) are available, but InDel makers have not been well established. This study aimed to develop drought-related gene-based InDel markers for durian through bioinformatic analysis of RNA-Seq datasets. The polymorphism of the markers was verified in 24 durian genotypes local to Thailand. Bioinformatic analysis indicated 496 InDel loci having lengths more than 9 bp. To evaluate these InDel markers, 15 InDel loci were selected. Nine markers were successfully amplified a clear polymorphic band pattern on 2% agarose gel. The polymorphic information content (PIC) of these nine markers ranged from 0.1103 to 0.5808. The genetic distance between the 24 genotypes ranged from 0.222 to 0.889. The phylogeny based on the nine InDel loci distinguished the 24 genotypes and divided samples into four groups. This set of gene-based InDel markers on putative drought-responsive genes will be useful for genetic studies.
插入缺失（InDel）标记是共显性的，相对丰富且适用于琼脂糖凝胶基因分型。InDel 多态性通常会影响基因功能。榴莲（Durio zibethinus）的核苷酸序列是可用的，但 InDel 标记尚未得到很好的建立。本研究旨在通过对 RNA-Seq 数据集的生物信息学分析，为榴莲开发与干旱相关的基于基因的 InDel 标记。在 24 种泰国当地的榴莲基因型中验证了这些标记的多态性。生物信息学分析表明，有 496 个长度超过 9bp 的 InDel 位点。为了评估这些 InDel 标记，选择了 15 个 InDel 位点。9 个标记在 2%琼脂糖凝胶上成功扩增出清晰的多态性条带模式。这 9 个标记的多态信息含量（PIC）范围为 0.1103 至 0.5808。24 个基因型之间的遗传距离为 0.222 至 0.889。基于 9 个 InDel 位点的系统发育将 24 个基因型区分开来，并将样本分为四组。这组基于候选抗旱基因的 InDel 标记将有助于遗传研究。
