Identification of QTLs for stem borer resistance using chromosome segment substitution lines in rice

doi:10.3969/j.issn.1004-1524.20240217

Acta Agriculturae Zhejiangensis ›› 2025, Vol. 37 ›› Issue (3): 530-537.DOI: 10.3969/j.issn.1004-1524.20240217

• Crop Science • Previous Articles Next Articles

Identification of QTLs for stem borer resistance using chromosome segment substitution lines in rice

LEI Zhiwei¹^,²(), LI Xinxin²^,³, XU Heng², ZHANG Heng², ZHU Ying², ZHANG Hua²^,^*()

1. College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
2. State Key Laboratory for Quality and Safety of Agro-Products, Research Center for Crop Molecular Breeding at Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
3. College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, Zhejiang, China

Received:2024-03-08 Online:2025-03-25 Published:2025-04-02

Abstract

Abstract:

The rice stem borer disaster causes serious damage to rice production in China. However, the genetic mechanisms of stem borer resistance in rice is still unknown, and the breeding of stem borer resistant rice variety faces big challenges. In this study, a set of chromosome segment substitution lines with japonica rice ‘Nipponbare’ as the donor and indica rice ‘9311’ as the recipient were used as materials to conduct a genetic analysis of the traits related to resistance to the rice stem borer. Five quantitative trait loci (QTL) related to resistance to the rice stem borer were identified in the rice genome. Through phenotypic analysis of the relevant substitution lines, it was found that four QTLs derived from japonica rice ‘Nipponbare’ (qRSB1, qRSB3, qRSB4, and qRSB6) could significantly enhance the resistance of indica rice ‘9311’ to the rice stem borer. Meanwhile, based on the genotypic identification results of the relevant substitution lines, the candidate intervals of each QTL in the rice genome were initially determined through physical mapping. The above research results provide a basis for the further fine mapping and candidate gene isolation of these stem borer resistance QTLs and would be beneficial to the breeding of stem borer resistant rice varieties in future.

Key words: rice stem borer, chromosome segment substitution line, QTL mapping, molecular marker

CLC Number:

S511

LEI Zhiwei, LI Xinxin, XU Heng, ZHANG Heng, ZHU Ying, ZHANG Hua. Identification of QTLs for stem borer resistance using chromosome segment substitution lines in rice[J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 530-537.

Figures/Tables 6

Fig.1 Rice stem borer resistance results of japonica cultivar Nipponbare (NIP) and indica variety 9311 in field and netting house A and B, Rice stem borer resistance results of Nipponbare and 9311 in field condition, the higher the mortality rate of rice plants during the late filling stage indicates greater sensitivity to rice stem borer; C, Rice stem borer resistance results of Nipponbare and 9311 in netting house, after manual infestation, the higher the dead heart index of rice plants indicates greater sensitivity to rice stem borer. ** means significant differences at the levels of P<0.01. The same as below

Fig.2 Genotype of chromosome segment substitution lines of rice The blank represents background of 9311, the blue region represents substitution chromosome segment from Nipponbare, and the red region represents heterozygous genotype.

Fig.3 Statistical results of rice chromosome segment substitution lines resistant to stem borer

Fig.4 Analysis results of QTLs for rice stem borer resistance

Table 1 LOD score and linked molecular marker of QTL for rice stem borer resistance

QTL	LOD值 LOD score	连锁分子标记 Linked molecular marker
qRSB1	5.343	CS0138
qRSB3	4.608	CS0333
qRSB4	5.142	R4M43
qRSB6	5.067	CS0610
qRSB10	4.483	CS1002

Fig.5 Physical mapping results of QTLs (qRSB1, qRSB3, qRSB4, qRSB6 and qRSB10) for rice stem borer resistance The blank represents background of 9311, the black region represents substitution chromosome segment from Nipponbare. R and S represent resistant(L3)/susceptible(L1) to rice stem borer, respectively.

References 23

[1]	SAVARY S, WILLOCQUET L, PETHYBRIDGE S J, et al. The global burden of pathogens and pests on major food crops[J]. Nature Ecology & Evolution, 2019, 3(3):430-439.
[2]	CHEN M, SHELTON A, YE G Y. Insect-resistant genetically modified rice in China: from research to commercialization[J]. Annual Review of Entomology, 2011, 56: 81-101.
[3]	刘万才, 刘振东, 黄冲, 等. 近10年农作物主要病虫害发生危害情况的统计和分析[J]. 植物保护, 2016, 42(5): 1-9.
	LIU W C, LIU Z D, HUANG C, et al. Statistics and analysis of crop yield losses caused by main diseases and insect pests in recent 10 years[J]. Plant Protection, 2016, 42(5): 1-9. (in Chinese with English abstract)
[4]	叶恭银, 方琦, 徐红星, 等. 我国水稻螟虫发生及治理研究进展[J]. 植物保护, 2023, 49(5): 167-180.
	YE G Y, FANG Q, XU H X, et al. Research advances on the occurrence, damage and management of rice stem borers in China[J]. Plant Protection, 2023, 49(5): 167-180. (in Chinese with English abstract)
[5]	中华人民共和国农业农村部. 一类农作物病虫害名录[EB/OL]. 北京:(2023-03-07)[2023-07-18]. http://www.moa.gov.cn/govpublic//ZZYGLS/202303/t20230314_6422981.htm.
[6]	盛承发, 宣维健, 焦晓国, 等. 我国稻螟暴发成灾的原因、趋势及对策[J]. 自然灾害学报, 2002, 11(3): 103-108.
	SHENG C F, XUAN W J, JIAO X G, et al. Causes, trend and control strategies of disaster of rice borers in China[J]. Journal of Natural Disasters, 2002, 11(3): 103-108. (in Chinese with English abstract)
[7]	盛承发, 王红托, 盛世余, 等. 我国稻螟灾害的现状及损失估计[J]. 昆虫知识, 2003, 40(4): 289-294.
	SHENG C F, WANG H T, SHENG S Y, et al. Pest status and loss assessment of crop damage caused by the rice borers, Chilo suppressalis and Tryporyza incertulas in China[J]. Entomological Knowledge, 2003, 40(4): 289-294. (in Chinese with English abstract)
[8]	XU H X, YE X H, YANG Y J, et al. Comparative genomics sheds light on the convergent evolution of miniaturized wasps[J]. Molecular Biology and Evolution, 2021, 38(12): 5539-5554.
[9]	TANG R, BABENDREIER D, ZHANG F, et al. Assessment of Trichogramma japonicum and T. chilonis as potential biological control agents of yellow stem borer in rice[J]. Insects, 2017, 8(1): 19.
[10]	LU Y H, ZHAO Y Y, LU H, et al. Midgut transcriptional variation of Chilo suppressalis larvae induced by feeding on the dead-end trap plant, Vetiveria zizanioides[J]. Frontiers in Physiology, 2018, 9: 1067.
[11]	LU Y H, BAI Q, LI Q, et al. Two P450 genes, CYP6SN3 and CYP306A1 involved in the growth and development of Chilo suppressalis and the lethal effect caused by vetiver grass[J]. International Journal of Biological Macromolecules, 2022, 223: 860-869.
[12]	DEKA S, BARTHAKUR S. Overview on current status of biotechnological interventions on yellow stem borer Scirpophaga incertulas(Lepidoptera: Crambidae) resistance in rice[J]. Biotechnology Advances, 2010, 28(1): 70-81.
[13]	TU J, ZHANG G, DATTA K, et al. Field performance of transgenic elite commercial hybrid rice expressing Bacillus thuringiensis delta-endotoxin[J]. Nature Biotechnology, 2000, 18(10): 1101-1104.
[14]	顾正远, 肖英方, 王益民. 江苏省主要水稻品种对三种害虫的抗性[J]. 江苏农业学报, 1989, 5(2): 38-41.
	GU Z Y, XIAO Y F, WANG Y M. Resistance of main rice varieties or lines to brown planthopper, whitebacked planthopper and striped stem borer in Jiangsu[J]. Jiangsu Journal of Agricultural Sciences, 1989, 5(2): 38-41. (in Chinese with English abstract)
[15]	束兆林, 方继朝, 盛生兰, 等. 水稻品种(系)对二化螟抗性的初步研究[J]. 华东昆虫学报, 2003, 12(1): 14-18.
	SHU Z L, FANG J C, SHENG S L, et al. Study on resistance of the rice varieties to Chilo suppressalis(Walker)[J]. Entomological Journal of East China, 2003, 12(1): 14-18. (in Chinese with English abstract)
[16]	徐红星, 吕仲贤, 陈建明, 等. 不同水稻品种对二化螟的抗性及其与形态学和解剖学特征的关系[J]. 植物保护学报, 2006, 33(3): 241-245.
	XU H X, LV Z X, CHEN J M, et al. Resistance of different rice varieties to the striped stem borer, Chilo suppressalis, and its relationship with the morphological and anatomic characteristics of rice[J]. Journal of Plant Protection, 2006, 33(3): 241-245. (in Chinese with English abstract)
[17]	秦文婧, 黄水金, 黄建华, 等. 抗二化螟的水稻品种筛选[J]. 应用昆虫学报, 2015, 52(3): 721-727.
	QIN W J, HUANG S J, HUANG J H, et al. Resistance of rice varieties to the stripe stem borer Chilo suppressalis[J]. Chinese Journal of Applied Entomology, 2015, 52(3): 721-727. (in Chinese with English abstract)
[18]	SELVI A, SHANMUGASUNDARAM P, MOHAN KUMAR S, et al. Molecular markers for yellow stem borer Scirpophaga incertulas(Walker) resistance in rice[J]. Euphytica, 2002, 124(3): 371-377.
[19]	林贤文. 水稻抗螟虫及其相关性状的数量遗传分析与验证[D]. 杭州: 浙江大学, 2010.
	LIN X W. Genetic analysis and validation of the quantitative resistance and its related traits of rice to the stem borerp[D]. Hangzhou: Zhejiang University, 2010. (in Chinese with English abstract)
[20]	ZHU W Y, LIN J, YANG D W, et al. Development of chromosome segment substitution lines derived from backcross between two sequenced rice cultivars, indica recipient 93-11 and Japonica donor nipponbare[J]. Plant Molecular Biology Reporter, 2009, 27(2): 126-131.
[21]	ZHANG H, ZHAO Q, SUN Z Z, et al. Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of Japonica Nipponbare[J]. Journal of Genetics and Genomics, 2011, 38(12): 603-611.
[22]	BROMAN K W, WU H, SEN S, et al. R/QTL: QTL mapping in experimental crosses[J]. Bioinformatics, 2003, 19(7): 889-890.
[23]	HALEY C S, KNOTT S A. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers[J]. Heredity, 1992, 69(4): 315-324.

Identification of QTLs for stem borer resistance using chromosome segment substitution lines in rice

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 6

References 23

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	DONG Lili, XU Zhihao, YAN Canlong, FAN Xiaoping, JIN Zelan, WANG Zhonghua. Molecular identification and genetic relationship of different breeding populations in Fritillaria thunbergii based on phenotype and molecular markers [J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1719-1730.
[2]	LI Xuesong, SUN Dafeng, LIU Shaoxiong, ZHANG Junbo, YUE Wansong, LI Jianying, HUA Rong. Development of SSR molecular markers and application of fingerprint database based on whole genome of Stropharia rugosoannulata [J]. Acta Agriculturae Zhejiangensis, 2024, 36(1): 84-93.
[3]	XIE Meiqiong, WANG Longjiang, HE Yurong, LYU Lihua. Transcriptome sequencing and analysis of potential pathogenicity-related genes in Isaria fumosorosea [J]. Acta Agriculturae Zhejiangensis, 2023, 35(9): 2169-2180.
[4]	MENG Yusha, WANG Yin, LAI Qixian, LIU Lei, XIANG Chao, WU Yonghua, ZHENG Yanran, GU Xingguo, FANG Hao, MIAO Miao, WU Liehong, TANG Yong. Assessment of genetic diversity and variety identification based on insertion site-based polymorphism (ISBP) markers developed in wild species related to sweet potato [J]. Acta Agriculturae Zhejiangensis, 2023, 35(3): 489-498.
[5]	CUI Junjie, LYU Zhen, YANG Tianwen, WANG Jing, HONG Yu, CAO Yi. Construction of high-density bin marker genetic map and QTL mapping for fruit length in Luffa spp. [J]. Acta Agriculturae Zhejiangensis, 2023, 35(3): 590-597.
[6]	LI Xiaojuan, ZHAO Wenju, ZHAO Mengliang, SHAO Dengkui, MA Yidong, REN Yanjing. Development and application of SSR markers based on transcriptome sequencing of turnip (Brassica rapa ssp. rapa) [J]. Acta Agriculturae Zhejiangensis, 2023, 35(2): 319-328.
[7]	JIANG Haoliang, HUANG Yun, LIANG Shaofang, XIE Mengchen, XU Tiancheng, SONG Zhiting, XIANG Wenwen, CHEN Qingchun, WAN Xiaorong, SUN Wei. Influences of cadmium stress on seedling growth of different sweet corn inbred lines and screening of associated molecular markers via simple sequence repeats [J]. Acta Agriculturae Zhejiangensis, 2022, 34(8): 1582-1590.
[8]	WANG Zhiqi, SUN Jian, LIANG Junchao, ZHAO Yunyan, YAN Tingxian, YAN Xiaowen, WEI Wenliang, LE Meiwang. Study on genetic diversity of sesame germplasm in Jiangxi Province based on molecular markers [J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1565-1580.
[9]	MA Jie, QU Wen, CHEN Chunyan, WANG Lei, MA Jun, LIU Zhenshan, MA Wei, ZHOU Ping, HE Yuankuan, SUN Bo. Development of SSR markers based on transcriptome sequencing and genetic diversity analysis of Nainaiqingcai leaf mustard [J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1640-1649.
[10]	HUANG Xuan, JIN Lincan, YE Chaohui, JIANG Jiefeng, SHI Xianbo. Molecular detection and breeding application of some disease and insect resistance genes of japonica rice varieties/lines recently developed in Zhejiang Province [J]. Acta Agriculturae Zhejiangensis, 2021, 33(7): 1159-1169.
[11]	ZHANG Jingzhen, WANG Lianjun, LEI Jian, CHAI Shasha, YANG Xinsun, ZHANG Wenying. Genetic diversity analysis and construction of DNA fingerprint of yam (Dioscorea oppositeac Thunb.) germplasm by cpSSR marker [J]. Acta Agriculturae Zhejiangensis, 2021, 33(7): 1222-1233.
[12]	YANG Mei, HU Xiaolan, SHEN Tao, TAN Kang, LIU Dailing, QIU Hongbo. Construction of single fragment substitution lines of maize 8th chromosome and sreening of resistant maize germplasm to gray leaf spot [J]. Acta Agriculturae Zhejiangensis, 2021, 33(3): 383-389.
[13]	LIN Mengjie, WEN Huiping, XIAO Jianzhong, ZHENG Qiang. Construction of DNA fingerprint for 48 broccoli cultivars [J]. Acta Agriculturae Zhejiangensis, 2021, 33(12): 2304-2312.
[14]	ZHANG Xinyue, LI Youfa, LIU Jiangning, FU Haowei. Study on hybrid rice purity of special combining pattern testing with functional marker of wide compatibility gene S5-n [J]. , 2020, 32(1): 15-19.
[15]	HE Haiyan, CHAI Rongyao, QIU Haiping, MAO Xueqin, WANG Yanli, SUN Guocang. Distribution and resistance evaluation of 5 rice blast-resistant genes in cultivated rice varieties in Zhejiang [J]. , 2019, 31(6): 922-929.