Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by Fusarium fujikuroi.

Do-Yu Kang,Kyung-Hwan Kim,Jun Oh,Song Lim Kim,Nam-Jin Chung,Hyeonso Ji,Kyeong-Seong Cheon,Inchan Choi,Jeongho Baek,Eungyeong Lee,Nyunhee Kim,Hyoja Oh

doi:10.3390/ijms20102598

Abstract

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, ‘Samgwang’ and ‘Junam’, respectively. Resequencing of ‘Junam’ and ‘Samgwang’ genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, qFfR9, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24–7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the ‘Junam’ and ‘Samgwang’ genome sequence data, and are possibly candidate genes for qFfR9; therefore, qFfR9 could be utilized as a valuable resource for breeding BD-resistant rice varieties.

Highlights

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious global threat in the majority of the rice-cultivating regions, leading to high (3.0–95.4%) losses in yield [1,2,3,4,5]
Symptoms vary depending on the quantity of gibberellins and fusaric acid produced, which vary according to fungal strains and the resistance of rice varieties [6]
CIo(Fnivgeurrseel1yc, )t.hWe mhiolertaalmityajroartietyofotfrtehaetetdre‘aStaemdg‘Jwuannagm’ ’pplalnantstswdaised0%, aallttuhpe ttore3a2teDdA‘SIa(Fmigguwraen1gc)’. pWlahniltes asumrvaijvoeridtyato2f 4thDeAtrIe(aFteigdu‘rJeun1dam). ’ plants died, all the treated ‘Samgwang’ plants survived at 24 days following inoculation (DAI) (Figure 1d)

Summary

Introduction

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious global threat in the majority of the rice-cultivating regions, leading to high (3.0–95.4%) losses in yield [1,2,3,4,5]. “Bakanae” means a “foolish rice seedling” in colloquial Japanese and indicates the unusually early elongation of a seedling induced by pathogen-produced gibberellins [6]. Fusarium fujikuroi produces fusaric acid, a phytotoxin that causes stunted growth [6]. Symptoms vary depending on the quantity of gibberellins and fusaric acid produced, which vary according to fungal strains and the resistance of rice varieties [6]. The optimum growth temperature for the pathogen ranges between 27 ◦C and 30 ◦C, while 35 ◦C is optimum for infectious disease development [3]. The incidence of BD is predicted to increase with global warming and rising temperatures

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