A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons
A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons
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DOI：
10.1073/pnas.2101486118
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发表时间：
2021-06-08
影响因子：
11.1
通讯作者：
Chomicki, Guillaume
中科院分区：
文献类型：
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作者：
Renner, Susanne S.;Wu, Shan;Chomicki, Guillaume
作物的野生近缘种或祖先是育种和理解驯化的重要资源。然而，由于灭绝、杂交以及将它们与野生形式区分开来的挑战，识别它们是困难的。在这里，我们使用收集为基础的系统学，图像学，并重新测序加入西瓜和西瓜的其他物种，以寻找潜在的祖先驯化西瓜。一种苏丹类型的甜瓜，果肉无苦味，白色，被称为科尔多凡甜瓜（C。绵毛亚种cordophanus），似乎是驯化西瓜的近亲和可能的祖先，与新解释的埃及墓葬壁画相一致，这些壁画表明西瓜可能在公元前4360年在尼罗河谷作为甜点食用。为了深入了解从祖先到驯化西瓜发生的遗传变化，我们使用Pacific Biosciences和Illumina测序以及Hi-C作图技术的组合，在染色体水平上组装并注释了科尔多凡甜瓜的基因组。科尔多凡甜瓜基因组中存在苦味丧失的遗传标记，但红色果肉颜色仅在驯化西瓜中固定。我们在科尔多凡甜瓜和一个典型的现代栽培品种“97103”之间检测到15,824个基因组结构变异（SV），并在400多个西瓜品种中绘制SV图谱，揭示了等位基因频率的变化，这表明水果甜度在西瓜驯化过程中逐渐增加。这种西瓜的一个可能的祖先仍然存在于苏丹，这对有针对性的现代育种工作有影响。
Wild relatives or progenitors of crops are important resources for breeding and for understanding domestication. Identifying them, however, is difficult because of extinction, hybridization, and the challenge of distinguishing them from feral forms. Here, we use collection-based systematics, iconography, and resequenced accessions of Citrullus lanatus and other species of Citrullus to search for the potential progenitor of the domesticated watermelon. A Sudanese form with nonbitter whitish pulp, known as the Kordofan melon (C. lanatus subsp. cordophanus), appears to be the closest relative of domesticated watermelons and a possible progenitor, consistent with newly interpreted Egyptian tomb paintings that suggest that the watermelon may have been consumed in the Nile Valley as a dessert by 4360 BP. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofan melon at the chromosome level, using a combination of Pacific Biosciences and Illumina sequencing as well as Hi-C mapping technologies. The genetic signature of bitterness loss is present in the Kordofan melon genome, but the red fruit flesh color only became fixed in the domesticated watermelon. We detected 15,824 genome structural variants (SVs) between the Kordofan melon and a typical modern cultivar, "97103," and mapping the SVs in over 400 Citrullus accessions revealed shifts in allelic frequencies, suggesting that fruit sweetness has gradually increased over the course of watermelon domestication. That a likely progenitor of the watermelon still exists in Sudan has implications for targeted modern breeding efforts.