Identification of origin and analysis of population structure of field-selected imidazolinone-herbicide resistant red rice (<Emphasis Type="Italic">Oryza sativa</Emphasis>)

Several red rice biotypes have evolved resistance to imidazolinone herbicides. The origin of resistance has been attributed to gene flow from the herbicide-resistant rice cultivars, but independent evolution of spontaneous mutation can also contribute to the herbicide resistance. The objective of this study was to quantify the occurrence of gene flow and independent selection as the mechanisms of origin of imidazolinone-resistance in red rice to correctly define the management practices for red rice control. Three single nucleotide polymorphism markers were used to identify acetolactate synthase (ALS) gene mutations, and four simple sequence repeat markers were used to identify hybrids of imidazolinone-resistant rice cultivars and red rice. In addition, genetic diversity and population structure analyses were performed. Artificial hybrids were used as controls. Gene flow was the main origin of imidazolinone herbicide resistance, but independent selection occurred in 1.1 % of the evaluated red rice plants. Two red rice plants that independently evolved herbicide resistance had the ALS gene mutation, Gly₆₅₄Glu. Population structure analysis also indicated intense gene flow from rice cultivars to red rice, but some populations maintained a high genetic identity based on a small amount of gene introgression from the rice cultivars. These results indicate the importance of adopting controls of red rice escapees to avoid gene flow from the imidazolinone-resistant rice, and the necessity of biotechnological approaches to mitigating gene flow in the development of new herbicide-resistant rice cultivars.