Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou, 221131, China.
College of Horticulture, Hainan University, Haikou, 570228, China.
Mol Biol Rep. 2024 Nov 26;52(1):14. doi: 10.1007/s11033-024-10116-4.
The lack of genomic and genetic research on wild sweetpotato species has hindered the advancement of sweetpotato variety development through modern crop improvement techniques.
To facilitate the use of genomic and genetic approaches in sweetpotato variety development, we conducted a comprehensive assessment of the genome size and ploidy of six closely related wild sweetpotato species using flow cytometry and chromosome counting. Additionally, we acquired insights into their genomic characteristics through high-throughput sequencing. Based on the 17-mer frequency distribution, the genome sizes of these species ranged from 518.47 Mb to 1,505.04 Mb. Notably, most diploid species exhibited genome sizes of approximately 500 Mb, with the diploid wild species I. purpurea standing out as having a significantly larger genome size compared to other diploid species. A substantial proportion of repeats (ranging from 57.47 to 81.07%) was identified across the genomes of the six species. Heterozygosity levels varied from 0.24 to 2.21%. SSR analysis revealed that the distribution of microsatellite patterns was largely consistent among the genomes of I I. lacunosa, I. tenuissima, and I. tiliacea, with mono-, di-, and trinucleotide motifs dominated by A/T, AT/AT, and AAT/ATT, respectively, indicating a strong A/T base preference. SNPs in this study were unevenly distributed across chromosomes, and non-synonymous SNVs in exonic accounted for 3.199% of the total number of SNPs, which may lead to genetic functional variation between species. In addition, the cross-regional annotation of SNPs highlights the diversity of gene regulatory regions and may provide insights into gene regulation, the underlying genetics of complex traits, and genetic differences between species.
The current data reinforce the established positive correlation between genome size and ploidy in the genus Ipomoea. In particular, the diploid I. purpurea had a larger genome compared to other diploid species. The genome survey indicated that I. lacunosa(2x), I. tiliacea(2x), and I. tenuissima(2x) possess simple genomes with low heterozygosity (0.36%, 0.37%, and 0.24%, respectively). In contrast, I. purpurea(2x) has a simple genome but exhibits high heterozygosity (1.95%), while I. tabascana(4x) and I. trifida(6x) have complex genomes with high heterozygosity (2.21% and 1.54%, respectively). These results provide a reasonable basis for the selection of whole genome sequencing strategies for these species and would provide references for research into the genetic diversity of wild relatives of sweetpotato.
野生甘薯物种缺乏基因组和遗传研究，阻碍了通过现代作物改良技术开发甘薯品种。
为了促进基因组和遗传方法在甘薯品种开发中的应用，我们使用流式细胞术和染色体计数对六个密切相关的野生甘薯物种的基因组大小和倍性进行了全面评估。此外，我们通过高通量测序深入了解了它们的基因组特征。根据 17-mer 频率分布，这些物种的基因组大小范围为 518.47 Mb 至 1505.04 Mb。值得注意的是，大多数二倍体物种的基因组大小约为 500 Mb，其中二倍体野生种 Ipomoea purpurea 的基因组大小明显大于其他二倍体物种。六个物种的基因组中都存在大量的重复序列（57.47% 至 81.07%）。杂合度水平在 0.24% 至 2.21% 之间变化。SSR 分析表明，IIpomoea lacunosa、Ipomoea tenuissima 和 Ipomoea tiliacea 基因组中的微卫星模式分布大致一致，单、二和三核苷酸基序分别以 A/T、AT/AT 和 AAT/ATT 为主，表明强烈的 A/T 碱基偏好。本研究中的 SNPs 在染色体上的分布不均匀，外显子中的非同义 SNV 占 SNP 总数的 3.199%，这可能导致物种间的遗传功能变异。此外，跨区域 SNP 注释突出了基因调控区域的多样性，可能为基因调控、复杂性状的遗传基础以及物种间的遗传差异提供了线索。
目前的数据强化了在 Ipomoea 属中基因组大小与倍性之间存在的正相关关系。特别是二倍体 Ipomoea purpurea 的基因组大小大于其他二倍体物种。基因组调查表明，Ipomoea lacunosa（2x）、Ipomoea tiliacea（2x）和 Ipomoea tenuissima（2x）具有简单的基因组和低杂合度（分别为 0.36%、0.37%和 0.24%）。相比之下，Ipomoea purpurea（2x）具有简单的基因组，但表现出较高的杂合度（1.95%），而 Ipomoea tabascana（4x）和 Ipomoea trifida（6x）具有复杂的基因组和高杂合度（分别为 2.21%和 1.54%）。这些结果为这些物种的全基因组测序策略选择提供了合理的依据，并为甘薯野生近缘种遗传多样性的研究提供了参考。
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