Weedy relatives of crop species infest agricultural fields worldwide, reducing harvests and threatening global food security. These weeds can potentially evolve and adapt through gene flow from both domesticated crop varieties and reproductively-compatible wild relatives. We studied populations of weedy rice in Thailand to investigate the role of introgression from cultivated and wild rice in their evolution. We examined two complementary sources of genetic data: allelic variation at three rice domestication genes (Bh4, controlling hull color; Rc, controlling pericarp color and seed dormancy; and sh4, controlling seed shattering), and 12 previously-published SSR markers. Sampling spanned three major rice growing regions in Thailand (Lower North, North East, and Central Plain) and included 124 cultivated rice accessions, 166 weedy rice accessions, and 98 wild rice accessions. Weedy rice strains were overall closely related to the cultivated varieties with which they co-occur. Domestication gene data revealed potential adaptive introgression of sh4 shattering alleles from wild rice. Introgression of potentially maladaptive rc crop alleles (conferring reduced dormancy) was also detected, with the frequency of the crop allele highest in northern populations. Although SSR markers also indicated introgression into weed populations from wild and cultivated rice, there was little overlap with domestication genes in the accessions showing admixed ancestry. This suggests that much of the introgression we detected at domestication genes most likely reflects past introgression rather than recent gene flow. This finding has implications for understanding long-term gene flow dynamics between rice and its weedy and wild relatives, including potential risks of transgene escape.

中文翻译：

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基因渗入的不一致模式表明历史基因从驯化和野生亲戚流入泰国杂草稻

作物物种的杂草近亲在世界范围内侵扰农田，减少收成并威胁全球粮食安全。这些杂草可以通过来自驯化作物品种和繁殖相容的野生近缘种的基因流进化和适应。我们研究了泰国的杂草稻种群，以研究栽培稻和野生稻的基因渗入在其进化中的作用。我们检查了两个互补的遗传数据来源：三个水稻驯化基因（Bh4，控制外壳颜色；Rc，控制果皮颜色和种子休眠；和 sh4，控制种子破碎）的等位基因变异，以及 12 个先前发表的 SSR 标记。抽样跨越泰国的三个主要水稻种植区（下北、东北和中原），包括 124 个栽培水稻品种、166 个杂草水稻品种、和 98 个野生稻种质。杂草水稻品系总体上与它们共同出现的栽培品种密切相关。驯化基因数据揭示了来自野生稻的 sh4 破碎等位基因的潜在适应性基因渗入。还检测到潜在不适应的 rc 作物等位基因（导致休眠减少）的渗入，北方种群中作物等位基因的频率最高。尽管 SSR 标记也表明从野生和栽培稻中渗入杂草种群，但与显示混合祖先的种质中的驯化基因几乎没有重叠。这表明我们在驯化基因上检测到的大部分基因渗入很可能反映了过去的基因渗入而不是最近的基因流。