Chinese Journal OF Rice Science >
QTL-Seq Analysis for Identification of Resistance Locus to Bacterial Leaf Streak in Rice
Received date: 2022-06-14
Revised date: 2022-08-05
Online published: 2023-03-10
【Objective】 The aim is to identify new resistance genes to bacterial leaf streak(BLS) and enrich the disease-resistance gene resources in rice, so as to lay a foundation for resistance gene cloning and molecular breeding in rice. 【Method】 A population of 278 recombinant inbred lines (RILs) was developed by crossing WP1 and 9311. WP1 was derived from Guangxi common wild rice(Oryza rufipogon Griff.), which was resistant to BLS, while 9311 was highly susceptible to BLS. QTL-Seq was used to analyze the high resistant and susceptible pools and their parents for quickly locating the genomic regions harboring QTLs resistance to BLS. Subsequently the resistant locus was further verified by QTL mapping using Ici Mapping 4.1 and narrowed down by substitution mapping.【Result】 Three genomic regions harboring resistance QTLs to BLS were identified on chromosomes 4, 8 and 10, respectively. A major resistance locus was verified by ICIM on chromosome 4, designated as qBLS4.1 accounting for 10.65% of the phenotypic variation with a LOD score of 5.03. Finally, the qBLS4.1 locus was delimited in the region of 521 kb from 5.27 to 5.79 Mb by substitution mapping, and there were 41 predicted protein-encoding genes with a total of 252 non-synonymous mutations between the resistant and susceptible parents.【Conclusion】 QTL-Seq combined with ICIM method can locate QTLs in rice more quickly and efficiently. The QTL qBLS4.1, a new locus against BLS will lay a basis and provide a reference for locating and cloning new genes for BLS resistance.
Key words： rice; bacterial leaf streak(BLS); QTL-Seq; mapping
WEI Minyi, MA Zengfeng, HUANG Dahui, QIN Yuanyuan, LIU Chi, LU Yingping, LUO Tongping, LI Zhenjing, ZHANG Yuexiong, QIN Gang . QTL-Seq Analysis for Identification of Resistance Locus to Bacterial Leaf Streak in Rice[J]. Chinese Journal OF Rice Science, 2023 , 37(2) : 133 -141 . DOI: 10.16819/j.1001-7216.2023.220607
| [1] | Yang W, Ju Y H, Zuo L P, Shang L Y, Li X R, Li X M, Feng S Z, Ding X H, Chu Z H. OsHsfB4d binds the promoter and 11/11 regulates the expression of OsHsp18.0-CI to resistant against Xanthomonas oryzae[J]. Rice, 2020, 13(1): 28. |
| [2] | Liu W, Liu J, Triplett L, Leach J E, Wang G L. Novel insights into rice innate immunity against bacterial and fungal pathogens[J]. Annual Review of Phytopathology, 2013, 52: 213-241. |
| [3] | He W A, Huang D H, Li R B, Qiu Y F, Song J D, Yang H N, Zheng J X, Huang Y Y, Liu C, Zhang Y X, Ma Z F, Yang Y. Identification of a resistance gene bls1 to bacterial leaf streak in wild rice Oryza rufipogon Griff[J]. Journal of Integrative Agriculture, 2012, 11: 962-969. |
| [4] | Ma Z F, Qin G, Zhang Y X, Liu C, Wei M Y, Cen Z L, Yan Y, Luo T P, Li Z J, Liang H F, Huang D H, Deng G F. Bacterial Leaf Streak 1 encoding a mitogen-activated protein kinase confers the rice resistance to bacterial leaf streak[J]. The Plant Journal, 2021, 107(4): 1084-1101. |
| [5] | 吴为人, 唐定中, 李维明, 卢浩然, Worland A J. 水稻细菌性条斑病抗性基因定位[J]. 高技术通讯, 1998(7): 47-50. |
| [5] | Wu W R, Tang D Z, Li W M, Lu H R, Worland A J. Mapping of genes underlying resistance to bacterial leaf streak in rice[J]. Chinese High Technology Letters, 1998(7): 47-50. (in Chinese with English abstract) |
| [6] | Tang D Z, Wu W R, Li W M, Lu H R, Worland A J. Mapping of QTLs conferring resistance to bacterial leaf streak in rice[J]. Theoretical and Applied Genetics, 2000, 101: 286-291. |
| [7] | 陈志伟, 景艳军, 李小辉, 周元昌, 刁志娟, 李生平, 吴为人. 水稻细菌性条斑病抗性QTL qBlsr5a的验证和更精确定位[J]. 福建农林大学学报:自然科学版, 2006, 35(6): 619-622. |
| [7] | Chen Z W, Jing Y J, Li X H, Zhou Y C, Diao Z J, Li S P, Wu W R. Verification and more precise mapping of a QTL qBIsr5a underlying resistance to bacterial leaf streak in rice[J]. Journal of Fujian Agriculture and Forestry University: Natural Science, 2006, 35(6): 619-622. (in Chinese with English abstract) |
| [8] | Han Q D, Chen Z W, Deng Y L, Lan T, Guan H Z, Guan Y L, Zhou Y C, Lin M C, Wu W R. Fine mapping of qBlsr5a, a QTL controlling resistance to bacterial leaf streak in rice[J]. Acta Agronomica Sinica, 2008, 34(4): 587-590. |
| [9] | Xie X F, Chen Z W, Cao J L, Guan H Z, Lin D G, Li C L, Lan T, Duan Y L, Mao D M, Wu W R. Toward the positional cloning of qBlsr5a, a QTL underlying resistance to bacterial leaf streak, using overlapping sub-CSSLs in rice[J]. PLoS ONE, 2014, 9(4): e95751. |
| [10] | Triplett L R, Cohen S P, Heffelfinger C, Schmidt C L, Huerta A I, Tekete C, Verdier V, Bogdanove A J, Leach J E. A resistance locus in the American heirloom rice variety carolina gold select is triggered by TAL effectors with diverse predicted targets and is effective against African strains of Xanthomonas oryzae pv. oryzicola[J]. The Plant Journal, 2016, 87(5): 472-483. |
| [11] | 施力军, 罗登杰, 赵严, 岑贞陆, 刘芳, 李容柏. 普通野生稻抗细菌性条斑病基因的遗传分析与定位[J]. 华南农业大学学报, 2019, 40(2): 1-5. |
| [11] | Shi L J, Luo D J, Zhao Y, Cen Z L, Liu F, Li R B. Genetic analysis and mapping of bacterial leaf streak resistance genes in Oryzae rufipogon Griff[J]. Journal of South China Agricultural University, 2019, 40(2): 1-5. (in Chinese with English abstract) |
| [12] | 罗登杰, 万瑶, 覃雪梅, 施力军, 张慧, 李容柏, 刘芳. 水稻细菌性条斑病抗性基因bls2 SSR分子标记开发[J]. 南方农业学报, 2021, 52(5): 1167-1173. |
| [12] | Luo D J, Wan Y, Qin X M, Shi L J, Zhang H, Li R B, Liu F. Development of SSR molecular markers for bacterial leaf streak resistance gene bls2 in rice(Oryza sativa L.)[J]. Journal of Southern Agriculture, 2021, 52(5): 1167-1173. (in Chinese with English abstract) |
| [13] | Wu T, Peng C, Li B B, Wu W, Kong L G, Li F C, Chu Z H, Liu F, Ding X H. OsPGIP1-mediated resistance to bacterial leaf streak in rice is beyond responsive to the polygalacturonase of Xanthomonas oryzae pv. oryzicola[J]. Rice, 2019, 12: 90. |
| [14] | Shen X L, Yuan B, Liu H B, Li X H, Wang S P. Opposite functions of a rice mitogen-activated protein kinase during the process of resistance against Xanthomonas oryzae[J]. The Plant Journal, 2010, 64(1): 86-99. |
| [15] | Feng C S, Zhang X, Wu T, Yuan B, Ding X H, Yao F Y, Chu Z H. The polygalacturonase-inhibiting protein 4 (OsPGIP4), a potential component of the qBlsr5a locus, confers resistance to bacterial leaf streak in rice[J]. Planta, 2016, 243: 1297-1308. |
| [16] | Ma H G, Chen J, Zhang Z Z, Ma L, Yang Z Y, Zhang Q L, Li X H, Xiao J H, Wang S P. MAPK kinase 10.2 promotes disease resistance and drought tolerance by activating different MAPKs in rice[J]. The Plant Journal, 2017, 92: 557-570. |
| [17] | Ju Y H, Tian H J, Zhang R H, Zuo L P, Jin G X, Xu Q, Ding X H, Li X K, Chu Z H. Overexpression of OsHSP18.0-CI enhances resistance to bacterial leaf streak in rice[J]. Rice, 2017, 10: 12. |
| [18] | Yang W, Zhang B G, Qi G H, Shang L Y, Chu Z H. Identification of the phytosulfokine receptor 1 (OsPSKR1) confers resistance to bacterial leaf streak in rice[J]. Planta, 2019, 250: 1603-1612. |
| [19] | Jiang N, Yan J, Liang Y, Shi Y L, He Z Z, Wu Y T, Zeng Q, Liu X L, Peng J H. Resistance genes and their interactions with bacterial blight/leaf streak pathogens (Xanthomonas oryzae) in rice (Oryza sativa L.): An updated review[J]. Rice, 2020, 13: 3. |
| [20] | Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform[J]. Bioinformatics, 2009, 14(1): 1754-1760. |
| [21] | Mckenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristol M A. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data[J]. Genome Research, 2010, 20(9): 1297-1303. |
| [22] | Mansfeld B N, Grumet R. QTLseqr: An R package for bulk segregant analysis with next-generation sequencing[J]. Plant Genome, 2018, 11(2): 1-5. |
| [23] | Paterson A H, DeVerna J W, Lanini B, Tanksley S D. Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato[J]. Genetics, 1990, 124: 735-742. |
| [24] | 彭小群, 王梦龙. 水稻白叶枯病抗性基因研究进展[J]. 植物生理学报, 2022, 58(3): 472-482. |
| [24] | Peng X Q, Wang M L. Research advances on resistance genes to bacterial blight disease in rice[J]. Plant Physiology Journal, 2022, 58(3): 472-482. (in Chinese with English abstract) |
| [25] | 李仲惺, 楼珏, 卢华金. 水稻细菌性条斑病发病程度与发病因子关系探讨[J]. 中国稻米, 2016, 22(4): 62-64. |
| [25] | Li Z X, Lou J, Lu H. Relationship between incidence and disease factors of bacterial leaf streak in rice[J]. China Rice, 2016, 22(4): 62-64. (in Chinese with English abstract) |
| [26] | Xie X F, Zheng Y, Lu L B, Yuan J Z, Hu J, Bu S H, Lin Y Y, Liu Y S, Guan H Z, Wu W R. Genome-wide association study of QTLs conferring resistance to bacterial leaf streak in rice[J]. Plants (Basel), 2021, 10(10): 2039. |
/
| 〈 |
|
〉 |