Vol.:(0123456789) 1 3 Molecular Biology Reports https://doi.org/10.1007/s11033-020-05546-9 ORIGINAL ARTICLE Genetic diversity of Asian rice gall midge based on mtCOI gene sequences and identifcation of a novel resistance locus gm12 in rice cultivar MN62M P. Leelagud 1  · S. Kongsila 1  · P. Vejchasarn 1  · K. Darwell 2  · Y. Phansenee 1  · A. Suthanthangjai 1  · C. Uparang 1  · R. Kawichai 1  · P. Yajai 2  · K. Boonsa‑nga 3  · V. Chamarerk 4  · J. Jairin 1 Received: 10 February 2020 / Accepted: 23 May 2020 © Springer Nature B.V. 2020 Abstract The rice gall midge (RGM), Orseolia oryzae (Wood-Mason), is one of the most destructive insect pests of rice, and it causes signifcant yield losses annually in Asian countries. The development of resistant rice varieties is considered as the most efective and economical approach for maintaining yield stability by controlling RGM. Identifcation 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 diferent resist- ance genes revealed diferent RGM biotypes in Thailand. The Thai rice landrace MN62M showed resistance to all RGM populations used in this study. We identifed a novel genetic locus for resistance to RGM, designated as gm12, on the short arm of rice chromosome 2. The locus was identifed using linkage analysis in 144 F 2 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 fanking markers, S2_76222 and S2_419160. In conclusion, we identifed a new RGM resistance gene, gm12, on rice chromosome 2 in the Thai rice landrace MN62M. This fnding 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 identifcation of RGM biotypes in Thailand and Southeast Asia. Keywords MN62M · Asian rice gall midge · mtCOI · Resistance gene · Simple sequence repeats (SSR) · Single nucleotide polymorphism (SNP) Introduction The Asian rice gall midge (RGM), Orseolia oryzae (Wood- Mason) (Diptera: Cecidomyiidae), is a major pest of rice and widely spread in Asia. Its economic impacts are important for major rice-producing countries, especially in South and Southeast Asia [1]. The larvae of RGM feed on growing tips inside rice plant tillers, modulate host cell activities, and change regular tillers of rice plants into tubular leaf sheath galls called silver shoots that allow the RGM to complete its life cycle [2, 3]. No panicle is formed in the afected till- ers, leading to yield losses. Attempts to identify the genetic diversity of RGM have revealed the existence of genetic variations in RGM populations in Thailand [4–6]. Previous studies have suggested that RGM populations in South and Southeast Asia are isolated [4, 7]. The diferent reactions of resistant rice varieties to RGM populations have revealed various gall midge biotypes [8]. The biotypes difer in host range, depending on the resist- ance genes of the cultivars. Existence and emergence of new virulent RGM biotypes have been reported, and the resistance * J. Jairin jirapong.j@rice.mail.go.th 1 Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand 2 Phrae Rice Research Center, Mueang, Phrae, Thailand 3 Chiang Rai Rice Research Center, Phan, Chiang Rai, Thailand 4 Division of Rice Research and Development, Rice Department, Chatuchak, Bangkok, Thailand