Genome Wide Association Study Reveals New Genes for Resistance to Striped Stem Borer in Rice ( L.)

Overview

Journal Front Plant Sci

Date 2024 Sep 30

PMID 39345976

Authors

Xing Xiang

Shuhua Liu

Yuewen He

Deqiang Li

Andrews Danso Ofori

Abdul Ghani Kandhro

Tengda Zheng

Xiaoqun Yi

Ping Li

Fu Huang

Aiping Zheng

Affiliations

Soon will be listed here.

Abstract

Rice is one of the most important food crops in the world and is important for global food security. However, damage caused by striped stem borer (SSB) seriously threatens rice production and can cause significant yield losses. The development and use of resistant rice varieties or genes is currently the most effective strategy for controlling SSB. We genotyped 201 rice samples using 2849855 high-confidence single nucleotide polymorphisms (SNPs). We conducted a genome-wide association study (GWAS) based on observed variation data of 201 rice cultivars resistant to SSB. We obtained a quantitative trait locus (QTL)- that confers resistance to SSB. Through annotation and analysis of genes within the locus, as well as qRT-PCR detection in resistant rice cultivars, we ultimately selected the candidate gene (named ) for further analysis. Next, we overexpressed the candidate gene in Nipponbare through transgenic methods, resulting in overexpressing lines (). In addition, we evaluated the insect resistance of lines using wild type (Nipponbare) as a control. The bioassay experiment results of live plants showed that after 20 days of inoculation with SSB, the withering heart rate of and lines was only 8.3% and 0%, with resistance levels of 1 and 0, respectively; however, the withering heart rate of the wild-type reached 100%, with a resistance level of 9. The results of the stem bioassay showed that, compared with the wild-type, the average corrected mortality rate of the SSB fed on the line reached 94.3%, and the resistance reached a high level. In summary, we preliminarily confirmed that positively regulates the defense of rice against SSB. This research findings reveal new SSB resistance gene resources, providing an important genetic basis for SSB resistance breeding in rice crops.

References

Zhou X . A UNIFIED FRAMEWORK FOR VARIANCE COMPONENT ESTIMATION WITH SUMMARY STATISTICS IN GENOME-WIDE ASSOCIATION STUDIES. Ann Appl Stat. 2018; 11(4):2027-2051. PMC: 5836736. DOI: 10.1214/17-AOAS1052. View

Zhou X, Stephens M . Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012; 44(7):821-4. PMC: 3386377. DOI: 10.1038/ng.2310. View

Zhou G, Ren N, Qi J, Lu J, Xiang C, Ju H . The 9-lipoxygenase Osr9-LOX1 interacts with the 13-lipoxygenase-mediated pathway to regulate resistance to chewing and piercing-sucking herbivores in rice. Physiol Plant. 2014; 152(1):59-69. DOI: 10.1111/ppl.12148. View

Li Y, Hallerman E, Liu Q, Wu K, Peng Y . The development and status of Bt rice in China. Plant Biotechnol J. 2015; 14(3):839-48. PMC: 11388839. DOI: 10.1111/pbi.12464. View

Zeng J, Zhang T, Huangfu J, Li R, Lou Y . Both Allene Oxide Synthases Genes Are Involved in the Biosynthesis of Herbivore-Induced Jasmonic Acid and Herbivore Resistance in Rice. Plants (Basel). 2021; 10(3). PMC: 7996763. DOI: 10.3390/plants10030442. View

Lipka A, Tian F, Wang Q, Peiffer J, Li M, Bradbury P . GAPIT: genome association and prediction integrated tool. Bioinformatics. 2012; 28(18):2397-9. DOI: 10.1093/bioinformatics/bts444. View

Wang C, Duan W, Riquicho A, Jing Z, Liu T, Hou X . Genome-wide survey and expression analysis of the PUB family in Chinese cabbage (Brassica rapa ssp. pekinesis). Mol Genet Genomics. 2015; 290(6):2241-60. DOI: 10.1007/s00438-015-1075-x. View

Monaghan J, Xu F, Gao M, Zhao Q, Palma K, Long C . Two Prp19-like U-box proteins in the MOS4-associated complex play redundant roles in plant innate immunity. PLoS Pathog. 2009; 5(7):e1000526. PMC: 2709443. DOI: 10.1371/journal.ppat.1000526. View

Burghardt L, Young N, Tiffin P . A Guide to Genome-Wide Association Mapping in Plants. Curr Protoc Plant Biol. 2019; 2(1):22-38. DOI: 10.1002/cppb.20041. View

10.

Yaeno T, Li H, Chaparro-Garcia A, Schornack S, Koshiba S, Watanabe S . Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity. Proc Natl Acad Sci U S A. 2011; 108(35):14682-7. PMC: 3167543. DOI: 10.1073/pnas.1106002108. View

11.

Lu J, Li J, Ju H, Liu X, Erb M, Wang X . Contrasting effects of ethylene biosynthesis on induced plant resistance against a chewing and a piercing-sucking herbivore in rice. Mol Plant. 2014; 7(11):1670-1682. DOI: 10.1093/mp/ssu085. View

12.

Gilroy E, Taylor R, Hein I, Boevink P, Sadanandom A, Birch P . CMPG1-dependent cell death follows perception of diverse pathogen elicitors at the host plasma membrane and is suppressed by Phytophthora infestans RXLR effector AVR3a. New Phytol. 2011; 190(3):653-66. DOI: 10.1111/j.1469-8137.2011.03643.x. View

13.

Uzunova M, Ecke W, Weissleder K, Robbelen G . Mapping the genome of rapeseed (Brassica napus L.). I. Construction of an RFLP linkage map and localization of QTLs for seed glucosinolate content. Theor Appl Genet. 2013; 90(2):194-204. DOI: 10.1007/BF00222202. View

14.

Tong X, Qi J, Zhu X, Mao B, Zeng L, Wang B . The rice hydroperoxide lyase OsHPL3 functions in defense responses by modulating the oxylipin pathway. Plant J. 2012; 71(5):763-75. DOI: 10.1111/j.1365-313X.2012.05027.x. View

15.

Lu J, Ju H, Zhou G, Zhu C, Erb M, Wang X . An EAR-motif-containing ERF transcription factor affects herbivore-induced signaling, defense and resistance in rice. Plant J. 2011; 68(4):583-96. DOI: 10.1111/j.1365-313X.2011.04709.x. View

16.

Wang A, Shu X, Jing X, Jiao C, Chen L, Zhang J . Identification of rice (Oryza sativa L.) genes involved in sheath blight resistance via a genome-wide association study. Plant Biotechnol J. 2021; 19(8):1553-1566. PMC: 8384605. DOI: 10.1111/pbi.13569. View

17.

Hu L, Ye M, Kuai P, Ye M, Erb M, Lou Y . OsLRR-RLK1, an early responsive leucine-rich repeat receptor-like kinase, initiates rice defense responses against a chewing herbivore. New Phytol. 2018; 219(3):1097-1111. DOI: 10.1111/nph.15247. View

18.

Xiang X, Liu S, Li H, Danso Ofori A, Yi X, Zheng A . Defense Strategies of Rice in Response to the Attack of the Herbivorous Insect, . Int J Mol Sci. 2023; 24(18). PMC: 10531896. DOI: 10.3390/ijms241814361. View

19.

Chagnon M, Kreutzweiser D, Mitchell E, Morrissey C, Noome D, van der Sluijs J . Risks of large-scale use of systemic insecticides to ecosystem functioning and services. Environ Sci Pollut Res Int. 2014; 22(1):119-34. PMC: 4284381. DOI: 10.1007/s11356-014-3277-x. View

20.

Li R, Afsheen S, Xin Z, Han X, Lou Y . OsNPR1 negatively regulates herbivore-induced JA and ethylene signaling and plant resistance to a chewing herbivore in rice. Physiol Plant. 2012; 147(3):340-51. DOI: 10.1111/j.1399-3054.2012.01666.x. View