Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population

Wintai Kamolsukyeunyong,Watchareewan Jamboonsri,Ekawat Chaichoompu,Pantharika Chumwong,Siriphat Ruengphayak,Kunyakarn Phoonsiri,Chatree Saensuk,Theerayut Toojinda,Lucia Kusumawati,Apichart Vanavichit

doi:10.1186/s12284-019-0274-1

Abstract

BackgroundThe development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal.ResultsWe used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78–7.78 Mb (QBPH4.1) and 15.22–17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations.ConclusionOn the one hand, HPs of OsLekRK2–3, OsSTPS2, and BPH32 determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population, BPH9 together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.

Highlights

The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH)
In this study, we used ddRADseq with quantitative trait loci (QTL)-seq analysis to identify single nucleotide polymorphisms (SNPs) and candidate resistance genes associated with BPH resistance in Rathu Heenati (RH)-derived backcross inbred lines (BILs)
Two major genomic regions associated with broad-spectrum BPH resistance were localized between 5.78–7.78 Mb (QBPH4.1) and 15.22–17.22 Mb (QBPH4.2), forming three linkage disequilibrium (LD) blocks on the rice chromosome 4

Summary

Introduction

The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). Rice (Oryza sativa L.) is an important cereal crop that feeds almost half of the world’s population (Mohanty 2013), and is mostly grown in Asia (Muthayya et al 2014) Insect pests, such as brown planthopper (BPH), white-backed hopper, green leafhopper, stem borer, and gall midge, cause severe damage to the rice crop across the world (Ane and Hussain 2016). A significant threat to rice production was reported in the early 1970s, when new high yielding varieties and extensive use of fertilizers and pesticides caused the rapid evolution of pesticide-tolerant biotypes of insect pests. These newly introduced rice cultivars, lacking broad-spectrum resistance, exhibit short life spans. Only eight have been cloned, including BPH14 (Du et al 2009), BPH26 (Tamura et al 2014), BPH3 (Liu et al 2014), BPH29 (Wang et al 2015), BPH 9 (Zhao et al 2016), BPH18 (Ji et al 2016), BPH32 (Ren et al 2016), and BPH31 (Prahalada et al 2017)

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