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. 2021 Sep 17;12(9):836.
doi: 10.3390/insects12090836.

Genome-Wide Association Study Reveals a New Quantitative Trait Locus in Rice Related to Resistance to Brown Planthopper Nilaparvata lugens (Stål)

Longqing Shi  1 , Meng Dong  1 , Ling Lian  1 , Junian Zhang  1 , Yongsheng Zhu  1 , Weilong Kong  2 , Liangmiao Qiu  3 , Dawei Liu  1 , Zhenxing Xie  1 , Zhixiong Zhan  1 , Zhaowei Jiang  1
Affiliations

Genome-Wide Association Study Reveals a New Quantitative Trait Locus in Rice Related to Resistance to Brown Planthopper Nilaparvata lugens (Stål)

Longqing Shi et al. Insects. .

Abstract

The brown planthopper (BPH) is one of the main pests endangering rice yields. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. To identify new BPH resistance-related genes, a total of 123 rice varieties were assessed for resistance and durable resistance. Three varieties were immune, and nine were highly resistant to BPH. After whole-genome resequencing of all 123 varieties, 1,897,845 single nucleotide polymorphisms (SNPs) were identified. Linkage disequilibrium (LD) decay analysis showed that the average LD of the SNPs at 20 kb was 0.30 (r2) and attenuated to half value (~0.30) at a distance of about 233 kb. A genome-wide association study (GWAS) of durable resistance to BPH was conducted using the Fast-MLM model. One quantitative trait locus, identified on chromosome 2, included 13 candidate genes. Two candidate genes contained a leucine-rich repeat and CC-NBS-LRR or NB-ARC domains, which might confer resistance to pests or diseases. Interestingly, LOC_Os02g27540 was highly expressed and was induced by BPH; GWAS identified potential rice genes coding for durable resistance to BPH. This study helps to elucidate the mechanism of durable resistance to BPH in rice and provides essential genetic information for breeding and functional verification of resistant varieties.

Keywords: GWAS; Host-plant resistance; durable resistance; resistance genes; rice pest.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phenotype identification of rice seedling resistance. (a) The phenotypic changes in TN1 rice (sensitive) seedlings inoculated with BPH nymphs after 0, 4, 8, and 12 days (the left tray); the right tray was treated without nymphs as a control. (b) Grading of rice seedling resistance to BPH. (c) Grading of the rice seedling durable resistance period for BPH. (d) Ratios of each resistance grade. (e) Ratios of each durable resistance grade.
Figure 2
Figure 2
SNP distribution density map on chromosomes and principal component analysis (PCA) of 123 rice varieties based on SNPs. (a) The distribution of SNPs on rice chromosomes; the number of SNPs per 0.1 Mb is displayed as a color index (lower right corner); (b) Principal component analysis of the genetic variation of the germplasm of 123 rice varieties.
Figure 3
Figure 3
Cross-validation, population linkage disequilibrium attenuation, and ADMIXTURE analysis of genetic relationships. (a) Cross-validation (CV) scores at different K values. The lowest value (K = 7) was selected as optimal for ADMIXTURE analysis. (b) Average LD attenuation for the whole genome. (c) Visualization of genetic relationships of each rice variety based on ADMIXTURE analysis.
Figure 4
Figure 4
Manhattan plot of genome association analysis and linkage disequilibrium block analysis. (a) Manhattan plot of FaST-LMM association mapping. (b) LD block module analysis of chromosome 2. (c) Graph of expected and observed p values.
Figure 5
Figure 5
The gene expression changes of six candidate genes after BPH inoculation by qRT-PCR, namely, LOC_Os02g27440 (a), LOC_Os02g27470 (b), LOC_Os02g27480 (c), LOC_Os02g27490 (d), LOC_Os02g27500 (e), and LOC_Os02g27540 (f).
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