Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
BMC Genomics. 2023 Jun 15;24(1):332. doi: 10.1186/s12864-023-09443-w.
The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.
厚皮甜瓜和其他六种西瓜属物种丰富的遗传多样性为西瓜育种提供了重要资源。在这里，我们根据 400 份西瓜属重测序数据构建了西瓜属泛基因组，结果表明，在西瓜参考基因组中存在 477Mb 序列和 6249 个蛋白编码基因缺失。在西瓜属泛基因组中，共有 8795 个（30.5%）基因存在/缺失变异（PAV）。存在/缺失变异（PAV）分析表明，在驯化和改良过程中，大量基因 PAV 被选择，如在 C. mucosospermus 到 C. lanatus 地方品种的驯化过程中鉴定出 53 个有利基因和 40 个不利基因。我们还在西瓜属泛基因组中鉴定了 661 个抗病基因类似物（RGA），其中包含 90 个 RGA（89 个可变和 1 个核心基因）位于泛基因组额外的序列上。通过基于基因 PAV 的 GWAS，发现 8 个基因存在/缺失变异与果肉颜色相关。最后，基于不同果实颜色西瓜群体之间基因 PAV 选择分析的结果，我们鉴定出四个与类胡萝卜素积累相关的非参考候选基因，它们在白肉中出现的频率明显更高。这些结果将为西瓜育种提供重要资源。
