Identification of Candidate Genes for Rice Resistance to Bacterial Blight via QTL Mapping and Gene Expression Analysis

doi:10.11983/CBB25059

Abstract

Abstract: INTRODUCTION: Bacterial blight is one of the three major diseases that threaten global rice production, seriously damaging the yield and quality of rice. The utilization of resistance genes is one of the most effective ways to control bacterial blight. RATIONALE: To cultivate rice varieties with both resistance to bacterial blight and high-yield characteristics, stable and efficient resistance genes need to be identified and used. To identify quantitative trait locus (QTL) related to bacterial blight resistance in rice, this study used the indica rice HZ, the japonica rice Nekken2 and their 120 recombinant inbred lines (RILs) as experimental materials. Four different races of bacterial blight pathogens were inoculated at the tillering stage of rice and the resistance phenotypes were evaluated. RESULTS: Based on the high-density genetic map constructed previously, we identified 19 QTLs for resistance to rice bacterial blight, with the maximum limit of detection (LOD) value being 5.49. Candidate genes within the detected QTL intervals were screened based on their expression levels analyzed by qRT-PCR. LOC_Os04g01310 and LOC_ Os04g01320, which are related to the regulatory pathway of STK receptor protein, showed significant upregulated expression after inoculation treatment. Meanwhile, the expression levels of the MYB transcription factor family gene LOC_Os05g10690 and the gene LOC_Os01g12320 related to GDSL-like lipase/acylhydrolase showed an extremely significant increase after inoculation treatment. The expression levels of the candidate genes LOC_Os02g13270 (Mpv17/PMP22 family domain containing protein), LOC_Os02g13410 (leucine rich repeat family protein), LOC_ Os02g13420 (leucine rich repeat receptor protein kinase EXS precursor), LOC_Os02g13430 (receptor-like protein kinase 5 precursor) and LOC_Os01g12130 (enodulin MtN3 family protein) were significantly different between the two parents and were induced after inoculation with the bacterial blight pathogen. CONCLUSION: By QTL mapping and gene expression analysis, we identified several candidate genes related to rice bacterial blight resistance. These results provide clues for further fine mapping and cloning of new bacterial blight resistance genes for future breeding of rice varieties with strong resistance to bacterial blight.

QTL mapping of resistance to bacterial blight in recombinant inbred lines of rice. QTLs can be used to reveal the structure of complex quantitative traits and identify candidate genes. Based on a high-density genetic map, a total of 19 QTLs were co-located and multiple candidate genes were screened out. To further locate and clone the related genes and lay a theoretical foundation for breeding new high-yield and disease-resistant rice varieties.

Key words: Oryza sativa, bacterial blight, QTL mapping, candidate genes

Chen Jun, Xu Jiangmin, Zhou Yinan, Jiang Yanan, Hu Chengxiang, Jin Qianyun, Zhao Beibei, Zhu Zhenan, Xu Yuqing, Zhang Luyi, Liu Xiaoyan, Liu Jun, Li Sanfeng, Wang Yuexing, Rao Yuchun. Identification of Candidate Genes for Rice Resistance to Bacterial Blight via QTL Mapping and Gene Expression Analysis[J]. Chinese Bulletin of Botany, 2025, 60(5): 831-845.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB25059

https://www.chinbullbotany.com/EN/Y2025/V60/I5/831

Figures/Tables 10

References 44

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Primer name	Forward primer (5'-3')	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os02g13270	TGGCCATTTCCTCCATAAAG	TTGGTATCCTTCTTCCCTTTGA
LOC_Os02g13350	AATGTCCATCGCACTGTTCA	GCTGCTTCAATCTCGGACTC
LOC_Os02g13410	TCAATTATCCGGCAGACTCC	TGCCTGTGCTACTGATCCTG
LOC_Os02g13420	TGCTCAGCTTTGGAGTTCCT	CCCAACGATAGCCTGTCAAT
LOC_Os02g13430	CCGATGAGTGATGTTCTCCA	CGCTATGTGTTCCGCTATGA
LOC_Os04g01310	TAATGGTACCAAGGGGGTGA	GAAGGCGATTCGTTGGATAA
LOC_Os04g01320	AGCCCGACTTCAAGCTAACA	ATGGATTCATTGGCATGGTT
LOC_Os01g12130	AATGGTGCTACCCGTTCTTG	CCGTGCGTATGAAACAGAAA
LOC_Os01g12160	CATCGCCTACTTCGAGTTCA	CATGCATGATGAGGACGAAC
LOC_Os01g12320	AGGTCCCGGAAAATACCACT	ATGGCATGAAGCCAATCATC
LOC_Os05g10690	TGGTGAAGGAGGAGGTTGTC	TAGCTCCAGGTCAGGCATCT

Primer name	Forward primer (5'-3')	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os02g13270	TGGCCATTTCCTCCATAAAG	TTGGTATCCTTCTTCCCTTTGA
LOC_Os02g13350	AATGTCCATCGCACTGTTCA	GCTGCTTCAATCTCGGACTC
LOC_Os02g13410	TCAATTATCCGGCAGACTCC	TGCCTGTGCTACTGATCCTG
LOC_Os02g13420	TGCTCAGCTTTGGAGTTCCT	CCCAACGATAGCCTGTCAAT
LOC_Os02g13430	CCGATGAGTGATGTTCTCCA	CGCTATGTGTTCCGCTATGA
LOC_Os04g01310	TAATGGTACCAAGGGGGTGA	GAAGGCGATTCGTTGGATAA
LOC_Os04g01320	AGCCCGACTTCAAGCTAACA	ATGGATTCATTGGCATGGTT
LOC_Os01g12130	AATGGTGCTACCCGTTCTTG	CCGTGCGTATGAAACAGAAA
LOC_Os01g12160	CATCGCCTACTTCGAGTTCA	CATGCATGATGAGGACGAAC
LOC_Os01g12320	AGGTCCCGGAAAATACCACT	ATGGCATGAAGCCAATCATC
LOC_Os05g10690	TGGTGAAGGAGGAGGTTGTC	TAGCTCCAGGTCAGGCATCT

Race	Significance test for all traits between their parents (t-test)			Variation for all traits tested in the RILs population
Race	HZ	Nekken2	P value	Means±SD	Range	Skewness	Kurtosis
P6	32.57±1.92	19.25±1.78	5.66E-08	22.01±7.71	0.50-46.83	0.33	1.54
P10	4.08±0.58	2.92±0.38	2.11E-03	4.43±2.47	0.50-17.08	2.27	7.93
C5	21.50±2.49	10.63±2.59	1.59E-04	14.89±5.98	0.45-32.40	0.19	0.62
T1	11.83±1.29	15.25±1.51	1.78E-03	12.03±6.61	0.60-30.25	0.47	-0.42

Race	Significance test for all traits between their parents (t-test)			Variation for all traits tested in the RILs population
Race	HZ	Nekken2	P value	Means±SD	Range	Skewness	Kurtosis
P6	32.57±1.92	19.25±1.78	5.66E-08	22.01±7.71	0.50-46.83	0.33	1.54
P10	4.08±0.58	2.92±0.38	2.11E-03	4.43±2.47	0.50-17.08	2.27	7.93
C5	21.50±2.49	10.63±2.59	1.59E-04	14.89±5.98	0.45-32.40	0.19	0.62
T1	11.83±1.29	15.25±1.51	1.78E-03	12.03±6.61	0.60-30.25	0.47	-0.42

Race	QTL locus	Chromo- some	Physical distance (bp)	Position of support (cM)	Limit of detection	Overlapped with known genes/QTL
P6	qP6-2	2	6987519-7215671	29.95-30.93	2.82	Novel
	qP6-6	6	22540408-24198880	96.62-103.73	2.10	Xa27 (Gu et al., 2004)
P10	qP10-4.1	4	46622-253174	0.20-1.09	4.09	Novel
	qP10-4.2	4	21662809-22843728	92.86-97.92	4.12	OsABA1 (Zhang et al., 2019)
	qP10-4.3	4	26889242-31662274	115.27-135.73	5.49	Xa1 (Yoshimura et al., 1998); Xa2 (He et al., 2006); Xa14 (Bao et al., 2010, in Chinese); Xa38 (Bhasin et al., 2012)
	qP10-5	5	5860546-5932385	25.12-25.43	2.17	Novel
	qP10-8	8	27210008-27435407	116.64-117.66	2.34	OsPDR1 (Zhang et al., 2020)
	qP10-9	9	11237877-11654883	48.17-49.96	2.50	Novel
	qP10-11	11	4880924-5893190	20.92-25.26	3.23	Novel
	qP10-12.1	12	3541703-5035843	15.18-21.59	3.52	OsSGS3a (Gu et al., 2023)
	qP10-12.2	12	9212254-11302449	39.49-48.45	3.47	ELL1 (Tian et al., 2020)
C5	qC5-1	1	6568005-6737416	28.16-28.88	2.41	Novel
	qC5-8	8	26765295-26912750	114.74-115.37	2.58	Xa-45(t) (Neelam et al., 2020)
T1	qT1-1.1	1	2317764-2649258	9.94-11.36	2.25	Novel
	qT1-1.2	1	5747788-6006625	24.64-25.75	2.17	TUT1 (Zhang et al., 2019)
	qT1-3	3	28465343-29876347	122.02-128.07	2.24	Xa11 (Goto et al., 2009); OsSLR1 (De Vleesschauwer et al., 2016)
	qT1-4	4	23759183-23831009	101.85-102.16	2.48	Novel
	qT1-5	5	5860546-5932385	25.12-25.43	2.51	Novel
	qT1-12	12	19717421-19889567	84.52-85.26	2.12	OsPR10a (Huang et al., 2016)