Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication.
Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication.
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DOI：
10.1186/s13059-022-02720-z
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发表时间：
2022-07-04
期刊：
影响因子：
12.3
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中科院分区：
文献类型：
--
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波斯核桃，核桃，自然发生从希腊到中国西部，而其最近的亲戚，铁核桃，核桃，是中国西南部特有的;这两个物种都是为了它们的坚果和木材而种植的。在这里，我们推断他们的人口历史和时间和方向可能的杂交和渗入他们之间。我们使用全基因组重测序数据，不同的群体遗传学方法（PSMC和GONE）以及来自欧洲，伊朗，哈萨克斯坦，巴基斯坦和中国的个体的隔离迁移模型（IMA 3）。IMa 3分析表明，这两个物种在85万年前彼此分化，从东部的J. regia和它的祖先到J. sigillata的单向基因流，包括壳厚度基因。在J. regia中，一个位于欧洲到伊朗的西方群体和一个来自中国北方的东方群体在大约80代前（大约2400至4000年）经历了人口规模的急剧下降，然后在大约40代时扩大，而J. sigillata在大约100至20代前的人口规模保持不变，然后迅速下降。核桃和核桃在驯化过程中似乎都遭受了突然的种群数量下降，这表明植物驯化的瓶颈情景可能至少适用于一些多年生作物物种。从引进的J. regia的渐渗似乎在J. sigillata的驯化中发挥了作用。在线版本包含补充材料，可通过10.1186/s13059-022-02720-z获得。
Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them. We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline. Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata. The online version contains supplementary material available at 10.1186/s13059-022-02720-z.
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影响因子：
5.6
作者：
Bernard A;Crabier J;Donkpegan ASL;Marrano A;Lheureux F;Dirlewanger E
通讯作者：
Dirlewanger E
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4.6
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影响因子：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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