Genetic diversity of Asian rice gall midge based on mtCOI gene sequences and identification of a novel resistance locus gm12 in rice cultivar MN62M

The rice gall midge (RGM), Orseolia oryzae (Wood-Mason), is one of the most destructive insect pests of rice, and it causes significant yield losses annually in Asian countries. The development of resistant rice varieties is considered as the most effective and economical approach for maintaining yield stability by controlling RGM. Identification of resistance genes will help in marker-assisted selection (MAS) to pyramid the resistance genes and develop a durable resistance variety against RGM in areas with frequent outbreaks. In this study, a mitochondrial cytochrome oxidase subunit I (mtCOI) was used to analyze the genetic diversity among Thai RGM populations. The phylogenetic tree indicated that the Thai RGM populations were homogeneously distributed throughout the country. The reactions of the resistant rice varieties carrying different resistance genes revealed different RGM biotypes in Thailand. The Thai rice landrace MN62M showed resistance to all RGM populations used in this study. We identified a novel genetic locus for resistance to RGM, designated as gm12, on the short arm of rice chromosome 2. The locus was identified using linkage analysis in 144 F₂ plants derived from a cross between susceptible cultivar KDML105 and RGM-resistant cultivar MN62M with single nucleotide polymorphism (SNP) markers and F_2:3 phenotype. The locus was mapped between two flanking markers, S2_76222 and S2_419160. In conclusion, we identified a new RGM resistance gene, gm12, on rice chromosome 2 in the Thai rice landrace MN62M. This finding yielded DNA markers that can be used in MAS to develop cultivars with broad-spectrum resistance to RGM. Moreover, the new resistance gene provides essential information for the identification of RGM biotypes in Thailand and Southeast Asia.

Keywords: Asian rice gall midge; MN62M; Resistance gene; Simple sequence repeats (SSR); Single nucleotide polymorphism (SNP); mtCOI.