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Yu B, Geng M, Xue Y, Yu Q, Lu B, Liu M, Shao Y, Li C, Xu J, Li J, Hu W, Tang H, Li P, Liu Q, Jing S. Combined miRNA and mRNA sequencing reveals the defensive strategies of resistant YHY15 rice against differentially virulent brown planthoppers. FRONTIERS IN PLANT SCIENCE 2024; 15:1366515. [PMID: 38562566 PMCID: PMC10982320 DOI: 10.3389/fpls.2024.1366515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024]
Abstract
Introduction The brown planthopper (BPH) poses a significant threat to rice production in Asia. The use of resistant rice varieties has been effective in managing this pest. However, the adaptability of BPH to resistant rice varieties has led to the emergence of virulent populations, such as biotype Y BPH. YHY15 rice, which carries the BPH resistance gene Bph15, exhibits notable resistance to biotype 1 BPH but is susceptible to biotype Y BPH. Limited information exists regarding how resistant rice plants defend against BPH populations with varying levels of virulence. Methods In this study, we integrated miRNA and mRNA expression profiling analyses to study the differential responses of YHY15 rice to both avirulent (biotype 1) and virulent (biotype Y) BPH. Results YHY15 rice demonstrated a rapid response to biotype Y BPH infestation, with significant transcriptional changes occurring within 6 hours. The biotype Y-responsive genes were notably enriched in photosynthetic processes. Accordingly, biotype Y BPH infestation induced more intense transcriptional responses, affecting miRNA expression, defenserelated metabolic pathways, phytohormone signaling, and multiple transcription factors. Additionally, callose deposition was enhanced in biotype Y BPH-infested rice seedlings. Discussion These findings provide comprehensive insights into the defense mechanisms of resistant rice plants against virulent BPH, and may potentially guide the development of insect-resistant rice varieties.
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Affiliation(s)
- Bin Yu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Mengjia Geng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yu Xue
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Qingqing Yu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Miao Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yuhan Shao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Chenxi Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jingang Xu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jintao Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Wei Hu
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hengmin Tang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Peng Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Qingsong Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shengli Jing
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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Li X, Zhang J, Shangguan X, Yin J, Zhu L, Hu J, Du B, Lv W. Knockout of OsWRKY71 impairs Bph15-mediated resistance against brown planthopper in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1260526. [PMID: 38023936 PMCID: PMC10652391 DOI: 10.3389/fpls.2023.1260526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
The Bph15 gene, known for its ability to confer resistance to the brown planthopper (BPH; Nilaparvata lugens Stål), has been extensively employed in rice breeding. However, the molecular mechanism by which Bph15 provides resistance against BPH in rice remains poorly understood. In this study, we reported that the transcription factor OsWRKY71 was highly responsive to BPH infestation and exhibited early-induced expression in Bph15-NIL (near-isogenic line) plants, and OsWRKY71 was localized in the nucleus of rice protoplasts. The knockout of OsWRKY71 in the Bph15-NIL background by CRISPR-Cas9 technology resulted in an impaired Bph15-mediated resistance against BPH. Transcriptome analysis revealed that the transcript profiles responsive to BPH differed between the wrky71 mutant and Bph15-NIL, and the knockout of OsWRKY71 altered the expression of defense genes. Subsequent quantitative RT-PCR analysis identified three genes, namely sesquiterpene synthase OsSTPS2, EXO70 family gene OsEXO70J1, and disease resistance gene RGA2, which might participate in BPH resistance conferred by OsWRKY71 in Bph15-NIL plants. Our investigation demonstrated the pivotal involvement of OsWRKY71 in Bph15-mediated resistance and provided new insights into the rice defense mechanisms against BPH.
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Affiliation(s)
- Xiaozun Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jian Zhang
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinxin Shangguan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Jingjing Yin
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wentang Lv
- Shandong Academy of Agricultural Sciences, Jinan, China
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Shar SBD, Nguyen CD, Sanada-Morimura S, Yasui H, Zheng SH, Fujita D. Development and characterization of near-isogenic lines for brown planthopper resistance genes in the genetic background of japonica rice 'Sagabiyori'. BREEDING SCIENCE 2023; 73:382-392. [PMID: 38106508 PMCID: PMC10722098 DOI: 10.1270/jsbbs.23017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 12/19/2023]
Abstract
The brown planthopper (BPH: Nilaparvata lugens Stål) is one of the most destructive insects in rice production. The use of host plant resistance has potential to reduce damage caused by BPH. The heat tolerance japonica rice 'Sagabiyori', with superior grain quality and high soluble starch in the stem, is highly susceptible to damage by BPH. Here, to enhance its BPH resistance, we developed seven near-isogenic lines (NILs) carrying BPH2, BPH17-ptb, BPH32, BPH3, BPH17, BPH20, and BPH21 through marker-assisted selection and evaluated resistance to two BPH populations. Most lines were more resistant to the Hadano-1966 BPH population than Sagabiyori but were less effective against the highly virulent Koshi-2013 population. Nevertheless, in antixenosis tests, Koshi-2013 settled less on all NILs than on Sagabiyori. In addition, adult mortality and the percentage of fresh weight loss of lines carrying BPH17 and BPH3 indicated that these lines have higher resistance to Koshi-2013 than Sagabiyori. Current study revealed that BPH resistance of Sagabiyori became stronger by transferring BPH3 and BPH17 genes. Thus, BPH3 and BPH17 might be valuable for breeding programs to enhance BPH resistance of high grain quality rice varieties with heat tolerance.
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Affiliation(s)
- Saw Bo Day Shar
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Loikaw Research Center, Department of Agricultural Research, Loikaw 09011, Kayah State, Myanmar
| | - Cuong Dinh Nguyen
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Biotechnology Department, College of Food Industry, 101B Le Huu Trac Street, Son Tra District, Da Nang City 550000, Vietnam
| | - Sachiyo Sanada-Morimura
- Agro-Environment Research Division, Kyushu Okinawa Agricultural Research Center, NARO, 2421 Suya, Koshi, Kumamoto 861-1192, Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Shao-Hui Zheng
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Daisuke Fujita
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
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Yan L, Luo T, Huang D, Wei M, Ma Z, Liu C, Qin Y, Zhou X, Lu Y, Li R, Qin G, Zhang Y. Recent Advances in Molecular Mechanism and Breeding Utilization of Brown Planthopper Resistance Genes in Rice: An Integrated Review. Int J Mol Sci 2023; 24:12061. [PMID: 37569437 PMCID: PMC10419156 DOI: 10.3390/ijms241512061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Over half of the world's population relies on rice as their staple food. The brown planthopper (Nilaparvata lugens Stål, BPH) is a significant insect pest that leads to global reductions in rice yields. Breeding rice varieties that are resistant to BPH has been acknowledged as the most cost-effective and efficient strategy to mitigate BPH infestation. Consequently, the exploration of BPH-resistant genes in rice and the development of resistant rice varieties have become focal points of interest and research for breeders. In this review, we summarized the latest advancements in the localization, cloning, molecular mechanisms, and breeding of BPH-resistant rice. Currently, a total of 70 BPH-resistant gene loci have been identified in rice, 64 out of 70 genes/QTLs were mapped on chromosomes 1, 2, 3, 4, 6, 8, 10, 11, and 12, respectively, with 17 of them successfully cloned. These genes primarily encode five types of proteins: lectin receptor kinase (LecRK), coiled-coil-nucleotide-binding-leucine-rich repeat (CC-NB-LRR), B3-DNA binding domain, leucine-rich repeat domain (LRD), and short consensus repeat (SCR). Through mediating plant hormone signaling, calcium ion signaling, protein kinase cascade activation of cell proliferation, transcription factors, and miRNA signaling pathways, these genes induce the deposition of callose and cell wall thickening in rice tissues, ultimately leading to the inhibition of BPH feeding and the formation of resistance mechanisms against BPH damage. Furthermore, we discussed the applications of these resistance genes in the genetic improvement and breeding of rice. Functional studies of these insect-resistant genes and the elucidation of their network mechanisms establish a strong theoretical foundation for investigating the interaction between rice and BPH. Furthermore, they provide ample genetic resources and technical support for achieving sustainable BPH control and developing innovative insect resistance strategies.
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Affiliation(s)
- Liuhui Yan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou 545000, China;
| | - Tongping Luo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Dahui Huang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Minyi Wei
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Zengfeng Ma
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Chi Liu
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Yuanyuan Qin
- Agricultural Science and Technology Information Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Xiaolong Zhou
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Yingping Lu
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou 545000, China;
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Gang Qin
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Yuexiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
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Kamal MM, Nguyen CD, Sanada-Morimura S, Zheng SH, Fujita D. Near-isogenic lines for resistance to brown planthopper with the genetic background of Indica Group elite rice ( Oryza sativa L.) variety 'IR64'. BREEDING SCIENCE 2023; 73:278-289. [PMID: 37840984 PMCID: PMC10570883 DOI: 10.1270/jsbbs.22093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/25/2023] [Indexed: 10/17/2023]
Abstract
The brown planthopper (BPH), Nilaparvata lugens Stål, is an insect pest that severely damages rice (Oryza sativa L.) in Asia, causing huge yield loss. Use of resistant variety is a cost-effective and eco-friendly strategy for maintaining BPH populations below the economic injury level. However, current BPH populations have been changed to virulence against resistant varieties. In this study, to estimate effective combinations among eight BPH resistance genes (BPH32, BPH17-ptb, BPH20, BPH17, BPH3, BPH25, BPH26 and qBPH6), eight near-isogenic lines with the genetic background of an Indica Group rice variety 'IR64' (IR64-NIL) were developed using marker-assisted selection. The genome recoveries of these NILs ranged from 89.3% to 98.8% and agronomic traits of them were similar to those of 'IR64'. In modified seed box screening test, resistance level of IR64-NILs was higher than that of 'IR64'. In antibiosis test, high adult mortalities of BPH (from 56.0% to 97.0%) were observed among NILs, in comparison with that of 'IR64'. Among IR64-NILs, the line carrying BPH17 showed the highest resistance level at all tests. Thus, these IR64-NILs with multiple BPH resistance genes could be valuable breeding lines for enhancing resistance levels by gene pyramiding and multiline variety.
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Affiliation(s)
- Md. Mostofa Kamal
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Agrotechnology Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Cuong Dinh Nguyen
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Biotechnology Department, College of Food Industry, 101B Le Huu Trac Street, Son Tra District, Da Nang City 550000, Vietnam
| | - Sachiyo Sanada-Morimura
- Agro-Enviroment Research Division, Kyushu Okinawa Agricultural Research Center, NARO, 2421 Suya, Koshi, Kumamoto 861-1192, Japan
| | - Shao-Hui Zheng
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Daisuke Fujita
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
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Horgan FG. Slowing virulence adaptation in Asian rice planthoppers through migration-based deployment of resistance genes. CURRENT OPINION IN INSECT SCIENCE 2023; 55:101004. [PMID: 36640841 DOI: 10.1016/j.cois.2023.101004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Advances in molecular biology have accelerated rice breeding for resistance to Asian planthoppers. However, experience shows that planthoppers quickly adapt to resistance in tropical overwintering areas. With only limited sources available, the large-scale deployment of resistance genes can rapidly reduce the utility of these public goods. Planthoppers that migrate from tropical to temperate Asia carry virulence against many resistance genes, but adapt more slowly to resistant rice in temperate regions. Therefore, by restricting deployment of selected genes to temperate regions, virulence-adaptation rates and the volume of migrants returning to overwintering sites could be reduced. The current open exchange of breeding materials throughout Asia urgently requires an international, multidisciplinary, stakeholder coalition to promote a more sustainable deployment of planthopper-resistant rice.
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Affiliation(s)
- Finbarr G Horgan
- EcoLaVerna Integral Restoration Ecology, Bridestown, Kildinan, T56 P499 County Cork, Ireland; Escuela de AgronomÃa, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Casilla 7-D, Curicó 3349001, Chile; Centre for Pesticide Suicide Prevention, University/BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK.
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Lin SC, Li Y, Hu FY, Wang CL, Kuang YH, Sung CL, Tsai SF, Yang ZW, Li CP, Huang SH, Liao CT, Hechanova SL, Jena KK, Chuang WP. Effect of nitrogen fertilizer on the resistance of rice near-isogenic lines with BPH resistance genes. BOTANICAL STUDIES 2022; 63:16. [PMID: 35604579 PMCID: PMC9127031 DOI: 10.1186/s40529-022-00347-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Nitrogen is an essential macronutrient for plant growth and development. Crops with a high nitrogen input usually have high yields. However, outbreaks of brown planthoppers (Nilaparvata lugens; BPH) frequently occur on rice farms with excessive nitrogen inputs. Rice plants carrying BPH resistance genes are used for integrated pest management. Thus, the impact of nitrogen on the resistance of rice near-isogenic lines (NILs) with BPH resistance genes was investigated. RESULTS We tested these NILs using a standard seedbox screening test and a modified bulk seedling test under different nitrogen treatments. The amount of nitrogen applied had an impact on the resistance of some lines with BPH resistance genes. In addition, three NILs (NIL-BPH9, NIL-BPH17, and NIL-BPH32) were further examined for antibiosis and antixenosis under varying nitrogen regimes. The N. lugens nymph population growth rate, honeydew excretion, female fecundity, and nymph survival rate on the three NILs were not affected by different nitrogen treatments except the nymph survival rate on NIL-BPH9 and the nymph population growth rate on NIL-BPH17. Furthermore, in the settlement preference test, the preference of N. lugens nymphs for IR24 over NIL-BPH9 or NIL-BPH17 increased under the high-nitrogen regime, whereas the preference of N. lugens nymphs for IR24 over NIL-BPH32 was not affected by the nitrogen treatments. CONCLUSIONS Our results indicated that the resistance of three tested NILs did not respond to different nitrogen regimes and that NIL-BPH17 exerted the most substantial inhibitory effect on N. lugens growth and development.
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Affiliation(s)
- Shau-Ching Lin
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi Li
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Fang-Yu Hu
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Chih-Lu Wang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Yun-Hung Kuang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Chang-Lin Sung
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Shin-Fu Tsai
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Zhi-Wei Yang
- Crop Improvement Division, Taoyuan District Agricultural Research and Extension Station, Council of Agriculture, 32745, Taoyuan City, Taiwan
| | - Charng-Pei Li
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taichung City, 413008, Taiwan
| | - Shou-Horng Huang
- Department of Plant Protection, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Council of Agriculture, Chiayi, 60044, Taiwan
| | - Chung-Ta Liao
- Crop Environment Division, Taichung District Agricultural Research and Extension Station, Council of Agriculture, Changhua County, 51544, Taiwan
| | - Sherry Lou Hechanova
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, Odisha, India
| | - Wen-Po Chuang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan.
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Multiparent-Derived, Marker-Assisted Introgression Lines of the Elite Indian Rice Cultivar, ‘Krishna Hamsa’ Show Resistance against Bacterial Blight and Blast and Tolerance to Drought. PLANTS 2022; 11:plants11050622. [PMID: 35270092 PMCID: PMC8912774 DOI: 10.3390/plants11050622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
Major biotic stresses viz., bacterial blight (BB) and blast and brown plant hopper (BPH) coupled with abiotic stresses like drought stress, significantly affect rice yields. To address this, marker-assisted intercross (IC) breeding involving multiple donors was used to combine three BB resistance genes—xa5, xa13 and Xa21, two blast resistance genes—Pi9 and Pi54, two BPH resistance genes—Bph20 and Bph21, and four drought tolerant quantitative trait loci (QTL)—qDTY1.1, qDTY2.1, qDTY3.1 and qDTY12.1—in the genetic background of the elite Indian rice cultivar ‘Krishna Hamsa’. Three cycles of selective intercrossing followed by selfing coupled with foreground selection and phenotyping for the target traits resulted in the development of 196 introgression lines (ILs) with a myriad of gene/QTL combinations. Based on the phenotypic reaction, the ILs were classified into seven phenotypic classes of resistance/tolerance to the following: (1) BB, blast and drought—5 ILs; (2) BB and blast—10 ILs; (3) BB and drought—9 ILs; (4) blast and drought—42 ILs; (5) BB—3 ILs; (6) blast—84 ILs; and (7) drought—43 ILs; none of the ILs were resistant to BPH. Positive phenotypic response (resistance) was observed to both BB and blast in 2 ILs, BB in 9 ILs and blast in 64 ILs despite the absence of corresponding R genes. Inheritance of resistance to BB and/or blast in such ILs could be due to the unknown genes from other parents used in the breeding scheme. Negative phenotypic response (susceptibility) was observed in 67 ILs possessing BB-R genes, 9 ILs with blast-R genes and 9 ILs harboring QTLs for drought tolerance. Complex genic interactions and recombination events due to the involvement of multiple donors explain susceptibility in some of the marker positive ILs. The present investigation successfully demonstrates the possibility of rapid development of multiple stress-tolerant/resistant ILs in the elite cultivar background involving multiple donors through selective intercrossing and stringent phenotyping. The 196 ILs in seven phenotypic classes with myriad of gene/QTL combinations will serve as a useful genetic resource in combining multiple biotic and abiotic stress resistance in future breeding programs.
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Nigro D, Fortunato S, Giove SL, Mazzucotelli E, Gadaleta A. Functional Validation of Glutamine synthetase and Glutamate synthase Genes in Durum Wheat near Isogenic Lines with QTL for High GPC. Int J Mol Sci 2020; 21:ijms21239253. [PMID: 33291583 PMCID: PMC7730160 DOI: 10.3390/ijms21239253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is a minor crop grown on about 17 million hectares of land worldwide. Several grain characteristics determine semolina's high end-use quality, such as grain protein content (GPC) which is directly related to the final products' nutritional and technological values. GPC improvement could be pursued by considering a candidate gene approach. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a bottleneck in the first step of nitrogen assimilation. QTL for GPC have been located on all chromosomes, and several major ones have been reported on 2A and 2B chromosomes, where GS2 and Fd-GOGAT genes have been mapped. A useful and efficient method to validate a putative QTL is the constitution of near-isogenic lines (NILs) by using the marker found to be associated to that QTL. Here, we present the development of two distinct sets of heterogeneous inbred family (HIF)- based NILs segregating for GS2 and Fd-GOGAT genes obtained from heterozygous lines at those loci, as well as their genotypic and phenotypic characterizations. The results allow the validation of the previously identified GPC QTL on 2A and 2B chromosomes, along with the role of these key genes in GPC control.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
| | | | - Stefania Lucia Giove
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
| | | | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy;
- Correspondence: (D.N.); (A.G.); Tel.: +39-0805442997(D.N.); +39-0805442995 (A.G.)
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Yu S, Ali J, Zhang C, Li Z, Zhang Q. Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1427-1442. [PMID: 31915875 PMCID: PMC7214492 DOI: 10.1007/s00122-019-03516-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/17/2019] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE The "Green Super Rice" (GSR) project aims to fundamentally transform crop production techniques and promote the development of green agriculture based on functional genomics and breeding of GSR varieties by whole-genome breeding platforms. Rice (Oryza sativa L.) is one of the leading food crops of the world, and the safe production of rice plays a central role in ensuring food security. However, the conflicts between rice production and environmental resources are becoming increasingly acute. For this reason, scientists in China have proposed the concept of Green Super Rice for promoting resource-saving and environment-friendly rice production, while still achieving a yield increase and quality improvement. GSR is becoming one of the major goals for agricultural research and crop improvement worldwide, which aims to mine and use vital genes associated with superior agronomic traits such as high yield, good quality, nutrient efficiency, and resistance against insects and stresses; establish genomic breeding platforms to breed and apply GSR; and set up resource-saving and environment-friendly cultivation management systems. GSR has been introduced into eight African and eight Asian countries and has contributed significantly to rice cultivation and food security in these countries. This article mainly describes the GSR concept and recent research progress, as well as the significant achievements in GSR breeding and its application.
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Affiliation(s)
- Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- College of Agronomy, Anhui Agricultural University, Hefei, China.
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Nguyen CD, Verdeprado H, Zita D, Sanada-Morimura S, Matsumura M, Virk PS, Brar DS, Horgan FG, Yasui H, Fujita D. The Development and Characterization of Near-Isogenic and Pyramided Lines Carrying Resistance Genes to Brown Planthopper with the Genetic Background of Japonica Rice ( Oryza sativa L.). PLANTS 2019; 8:plants8110498. [PMID: 31726710 PMCID: PMC6918374 DOI: 10.3390/plants8110498] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 11/16/2022]
Abstract
The brown planthopper (BPH: Nilaparvata lugens Stål.) is a major pest of rice, Oryza sativa, in Asia. Host plant resistance has tremendous potential to reduce the damage caused to rice by the planthopper. However, the effectiveness of resistance genes varies spatially and temporally according to BPH virulence. Understanding patterns in BPH virulence against resistance genes is necessary to efficiently and sustainably deploy resistant rice varieties. To survey BPH virulence patterns, seven near-isogenic lines (NILs), each with a single BPH resistance gene (BPH2-NIL, BPH3-NIL, BPH17-NIL, BPH20-NIL, BPH21-NIL, BPH32-NIL and BPH17-ptb-NIL) and fifteen pyramided lines (PYLs) carrying multiple resistance genes were developed with the genetic background of the japonica rice variety, Taichung 65 (T65), and assessed for resistance levels against two BPH populations (Hadano-66 and Koshi-2013 collected in Japan in 1966 and 2013, respectively). Many of the NILs and PYLs were resistant against the Hadano-66 population but were less effective against the Koshi-2013 population. Among PYLs, BPH20+BPH32-PYL and BPH2+BPH3+BPH17-PYL granted relatively high BPH resistance against Koshi-2013. The NILs and PYLs developed in this research will be useful to monitor BPH virulence prior to deploying resistant rice varieties and improve rice’s resistance to BPH in the context of regionally increasing levels of virulence.
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Affiliation(s)
- Cuong D. Nguyen
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan;
- College of Food Industry, 101B Le Huu Trac Street, Son Tra District, Da Nang City 550000, Vietnam
| | - Holden Verdeprado
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
| | - Demeter Zita
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan;
| | - Sachiyo Sanada-Morimura
- NARO Kyushu Okinawa Agricultural Research Center, 2421 Suya, Koshi, Kumamoto 861–1192, Japan; (S.S.-M.); (M.M.)
| | - Masaya Matsumura
- NARO Kyushu Okinawa Agricultural Research Center, 2421 Suya, Koshi, Kumamoto 861–1192, Japan; (S.S.-M.); (M.M.)
| | - Parminder S. Virk
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
- International Center for Tropical Agriculture, A.A, 6713 Cali, Colombia
| | - Darshan S. Brar
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141027, India
| | - Finbarr G. Horgan
- EcoLaVerna Integral Restoration Ecology, Bridestown, Kildinan, Co. Cork, T56 CD39, Ireland;
| | - Hideshi Yasui
- Plant Breeding Laboratory, Graduate School, Kyushu University, Fukuoka 812-8581, Japan;
| | - Daisuke Fujita
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan;
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines; (H.V.); (P.S.V.); (D.S.B.)
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan;
- Plant Breeding Laboratory, Graduate School, Kyushu University, Fukuoka 812-8581, Japan;
- Correspondence: ; Tel.: +81-952-28-8724
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Wang H, Gao Y, Mao F, Xiong L, Mou T. Directional upgrading of brown planthopper resistance in an elite rice cultivar by precise introgression of two resistance genes using genomics-based breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110211. [PMID: 31521227 DOI: 10.1016/j.plantsci.2019.110211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 05/23/2023]
Abstract
Brown planthopper (BPH) is a devastating pest that threatens the food security of rice-producing countries. At present, most cultivars planted in farmers' paddies lack effective BPH resistance, which constitutes a potential threat to rice yield. Moreover, developing BPH-resistant rice varieties using traditional breeding approaches is time-consuming, labor-intensive, and unpredictable. In this study, we successfully enhanced BPH resistance of the elite rice cultivar Wushansimiao by introgressing the resistance genes BPH14 and BPH15 through positive selection, negative selection, and whole genome background selection. Through backcrossing, the introgression fragments were reduced to 428.3 kb for BPH14 and 413.1 kb for BPH15. Except for these two fragments, the residual genetic background of the selected near-isogenic lines (NILs) was nearly identical to that of the recurrent parent, with a genetic background recovery rate of 99.78%. As a result, the selected NILs exhibited much stronger BPH resistance at the seedling and adult stages compared to the recurrent parent. Moreover, field tests showed that grain yield, major agronomic traits, and grain quality of the five selected NILs were statistically indistinguishable from those of the recurrent parent. Our results provide an effective approach for directionally upgrading the target traits and will inform and facilitate rice breeding.
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Affiliation(s)
- Hongbo Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Fangming Mao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Tongmin Mou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Yang D, Tang J, Yang D, Chen Y, Ali J, Mou T. Improving rice blast resistance of Feng39S through molecular marker-assisted backcrossing. RICE (NEW YORK, N.Y.) 2019; 12:70. [PMID: 31502096 PMCID: PMC6733936 DOI: 10.1186/s12284-019-0329-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/30/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Rice blast caused by Magnaporthe oryzae is one of the most widespread biotic constraints that threaten rice production. Using major resistance genes for rice blast resistance improvement is considered to be an efficient and technically feasible approach to achieve optimal grain yield. RESULTS We report here the introgression of the broad-spectrum blast resistance gene Pi2 into the genetic background of an elite PTGMS line, Feng39S, for enhancing it and its derived hybrid blast resistance through marker-assisted backcrossing (MABC) coupled with genomics-based background selection. Two PTGMS lines, designated as DB16206-34 and DB16206-38, stacking homozygous Pi2 were selected, and their genetic background had recurrent parent genome recovery of 99.67% detected by the SNP array RICE6K. DB16206-34 and DB16206-38 had high resistance frequency, with an average of 94.7%, when infected with 57 blast isolates over 2 years, and the resistance frequency of their derived hybrids ranged from 68.2% to 95.5% under inoculation of 22 blast isolates. The evaluation of results under natural blast epidemic field conditions showed that the selected PTGMS lines and their derived hybrids were resistant against leaf and neck blast. The characterizations of the critical temperature point of fertility-sterility alternation of the selected PTGMS lines, yield, main agronomic traits, and rice quality of the selected PTGMS lines and their hybrids were identical to those of the recurrent parent and its hybrids. DB16206-34/9311 or DB16206-38/9311 can be used as a blast-resistant version to replace the popular hybrid Fengliangyou 4. Likewise, DB16206-34/FXH No.1 or DB16206-38/FXH No.1 can also be used as a blast-resistant version to replace another popular hybrid Fengliangyou Xiang 1. CONCLUSIONS Our evaluation is the first successful case to apply MABC with genomics-based background selection to improve the blast resistance of PTGMS lines for two-line hybrid rice breeding.
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Affiliation(s)
- Dabing Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jianhao Tang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Di Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Ying Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Tongmin Mou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
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Arbelaez JD, Tandayu E, Reveche MY, Jarana A, van Rogen P, Sandager L, Stolt P, Ng E, Varshney RK, Kretzschmar T, Cobb J. Methodology: ssb- MASS: a single seed-based sampling strategy for marker-assisted selection in rice. PLANT METHODS 2019; 15:78. [PMID: 31367224 PMCID: PMC6652012 DOI: 10.1186/s13007-019-0464-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers' nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. RESULTS Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7-8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost-benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. CONCLUSION This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Erwin Tandayu
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Maria Ymber Reveche
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Annalhea Jarana
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Petra van Rogen
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Line Sandager
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Patrik Stolt
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Enghwa Ng
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
| | - Joshua Cobb
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
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Application of high-throughput amplicon sequencing-based SSR genotyping in genetic background screening. BMC Genomics 2019; 20:444. [PMID: 31159719 PMCID: PMC6547574 DOI: 10.1186/s12864-019-5800-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/14/2019] [Indexed: 12/05/2022] Open
Abstract
Background Host genetic backgrounds affect gene functions. The genetic backgrounds of genetically engineered organisms must be identified to confirm their genetic backgrounds identity with those of recipients. Marker-assisted backcrossing (MAB), transgenesis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) editing are three commonly used genetic engineering techniques. However, methods for genetic background screening between genetically engineered organisms and corresponding recipients suffer from low efficiency, low accuracy or high cost. Results Here, we improved our previously reported AmpSeq-SSR method, an amplicon sequencing-based simple sequence repeat (SSR) genotyping method, by selecting SSR loci with high polymorphism among varieties. Ultimately, a set of 396 SSRs was generated and applied to evaluate the genetic backgrounds identity between rice lines developed through MAB, transgenesis, and CRISPR/Cas9 editing and the respective recipient rice. We discovered that the percentage of different SSRs between the MAB-developed rice line and its recipient was as high as 23.5%. In contrast, only 0.8% of SSRs were different between the CRISPR/Cas9-system-mediated rice line and its recipient, while no SSRs showed different genotypes between the transgenic rice line and its recipient. Furthermore, most differential SSRs induced by MAB technology were located in non-coding regions (62.9%), followed by untranslated regions (21.0%) and coding regions (16.1%). Trinucleotide repeats were the most prevalent type of altered SSR. Most importantly, all altered SSRs located in coding regions were trinucleotide repeats. Conclusions This method is not only useful for the background evaluation of genetic resources but also expands our understanding of the unintended effects of different genetic engineering techniques. While the work we present focused on rice, this method can be readily extended to other organisms. Electronic supplementary material The online version of this article (10.1186/s12864-019-5800-4) contains supplementary material, which is available to authorized users.
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Yang G, Chen S, Chen L, Sun K, Huang C, Zhou D, Huang Y, Wang J, Liu Y, Wang H, Chen Z, Guo T. Development of a core SNP arrays based on the KASP method for molecular breeding of rice. RICE (NEW YORK, N.Y.) 2019; 12:21. [PMID: 30963280 PMCID: PMC6453994 DOI: 10.1186/s12284-019-0272-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/20/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The development and utilization of genetic markers play a pivotal role in marker-assisted breeding of rice cultivars during pyramiding of valuable genes. Among molecular markers, SNPs have become the most promising due to their wide distribution within genomes and suitability for high -throughput automated genotyping. Although metadata of SNPs have been identified via next generation sequencing in rice, a large gap between the development of SNP markers and the application in breeding still exists. To promote the application of SNP markers based on the KASP (Kompetitive Allele-Specific PCR) method in rice breeding, a set of core SNP arrays was built via the screening of SNP databases and literature resources based on the KASP method. RESULTS Five hundred and ninety six SNPs classified into eight subsets including quality control, indica-indica variation, highly polymorphic, functional genes, key genes targeting sites, gene cloned region, important trait associated and gap filling sites were chosen to design KASP primers and 565 out of them were successfully designed, and the assay design success rate was 94.8%. Finally, 467 out of the 565 successfully-designed SNPs can display diversity at the loci were used to develop a set of core SNP arrays. To evaluate the application value of the core SNP markers in rice breeding, 481 rice germplasms were genotyped with three functional KASP markers designed from the sequences of GBSSI, SSIIa, and Badh2 from the core SNP arrays for estimation of their grain quality performance. Eighteen rice lines, including Xiangwanxian 13, Basmati 370, Ruanhua A, and PR 33319-9-1-1-5-3-5-4-1, harbor all three favorable alleles. The core KASP arrays were also used for rice germplasm assessment, genetic diversity and population evaluation. Four hundred and eighty-one rice germplasms were divided into 3 groups: POP1, POP2 and POP3. POP1 and POP2 were indica rice subgroups consisting of 263 and 186 rice germplasms, respectively. POP3 was a japonica rice subgroup consisting of 32 rice germplasms. The average FST value for the three subgroups was 0.3501; the FST value of POP1 and POP3 was the largest (0.5482), while that of POP1 and POP2 was the smallest (0.0721). The results showed that the genetic distance between the japonica and indica rice subspecies was large, indicating that the core SNP markers were effective at discriminating the population structure of the germplasms. Finally, the core KASP arrays were used for association analysis with milled grain traits. A total of 31 KASP markers were significantly associated (P < 0.01) with ML and the LWR. Among the 31 markers, 13 were developed based on cloned genes or on identified loci related to yield traits. Notably, several KASP markers associated with grain quality were also found to be associated with brown planthopper resistance or green leafhopper resistance simultaneously. CONCLUSIONS The core KASP arrays developed in our study were efficient and versatile for rice germplasm assessment, genetic diversity and population evaluation and are valuable for promoting SNP molecular breeding in rice. Our study demonstrated that useful assays combined with molecular breeding can be exploited for important economic trait improvement in rice breeding.
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Affiliation(s)
- Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Siping Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Likai Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Sun
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Danhua Zhou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yuting Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
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Yadav S, Sandhu N, Majumder RR, Dixit S, Kumar S, Singh SP, Mandal NP, Das SP, Yadaw RB, Singh VK, Sinha P, Varshney RK, Kumar A. Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress. Sci Rep 2019; 9:2616. [PMID: 30796339 PMCID: PMC6385343 DOI: 10.1038/s41598-019-39084-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL (qDTY) combinations in the genetic background of IR64, TDK1-Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1-Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.
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Affiliation(s)
- Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ratna Rani Majumder
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - S P Singh
- Bihar Agricultural University, Sabour, Bihar, India
| | - N P Mandal
- Central Rainfed Upland Rice Research station, National Rice Research Institute, Hazaribagh, Jharkhand, India
| | - S P Das
- ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, Tripura, India
| | | | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-arid Tropics, Patancheru, Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-arid Tropics, Patancheru, Hyderabad, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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18
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Resistance to Nilaparvata lugens in rice lines introgressed with the resistance genes Bph14 and Bph15 and related resistance types. PLoS One 2018; 13:e0198630. [PMID: 29856853 PMCID: PMC5983517 DOI: 10.1371/journal.pone.0198630] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022] Open
Abstract
Crop resistance is a cost-effective and environmentally friendly strategy for pest management. The brown planthopper (BPH, Nilaparvata lugens) is a devastating rice insect pest due to its ability to rapidly overcome plant resistance and the lack of sufficient resistance resources. BR4831 (a rice breeding line derived from the pyramiding of two BPH resistance genes, Bph14 and Bph15, into the elite rice variety Huang-Hua-Zhan, HHZ) and two single-gene introgression lines (HF106, carrying Bph14, and C602, carrying Bph15, in the elite rice cultivar 9311) were evaluated for their resistance to BPH using a standard seed box screening test coupled with field tests. The related resistance types were determined using laboratory assays. The seed box test and laboratory biological assays showed that BR4831 exhibited strong antibiotic resistance, and the behavioral assay showed that this line also exhibited strong antixenotic resistance, while both HF106 and C602 exhibited only weak antibiosis and no antixenotic resistance. Field tests showed significantly improved resistance in BR4831 compared to that of its recipient parent HHZ and slightly increased resistance in HF106 and C602 in comparison with their recipient parent 9311. These results demonstrate that the rice line BR4831, with pyramided resistance genes, exhibits higher resistance than the monogenic lines HF106 and C602 and highlight the benefits of combining the seed box seedling test, field tests and laboratory assays to thoroughly analyze plant resistance types.
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Jena KK, Hechanova SL, Verdeprado H, Prahalada GD, Kim SR. Development of 25 near-isogenic lines (NILs) with ten BPH resistance genes in rice (Oryza sativa L.): production, resistance spectrum, and molecular analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2345-2360. [PMID: 28795219 DOI: 10.1007/s00122-017-2963-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/01/2017] [Indexed: 05/21/2023]
Abstract
A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection. The linked DNA markers for each of the R genes were used for foreground selection and confirming the introgressed regions of the BPH R genes. Modified seed box screening and feeding rate of BPH were used to evaluate the spectrum of resistance. BPH reaction of each of the NILs carrying different single genes was variable at the antibiosis level with the four BPH populations of the Philippines. The NILs with two- to three-pyramided genes showed a stronger level of antibiosis (49.3-99.0%) against BPH populations compared with NILs with a single R gene NILs (42.0-83.5%) and IR24 (10.0%). Background genotyping by high-density SNPs markers revealed that most of the chromosome regions of the NILs (BC3F5) had IR24 genome recovery of 82.0-94.2%. Six major agronomic data of the NILs showed a phenotypically comparable agronomic performance with IR24. These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries.
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Affiliation(s)
- Kshirod K Jena
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
| | - Sherry Lou Hechanova
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Holden Verdeprado
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - G D Prahalada
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Plant Breeding Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Wu Y, Lv W, Hu L, Rao W, Zeng Y, Zhu L, He Y, He G. Identification and analysis of brown planthopper-responsive microRNAs in resistant and susceptible rice plants. Sci Rep 2017; 7:8712. [PMID: 28821824 PMCID: PMC5562839 DOI: 10.1038/s41598-017-09143-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/20/2017] [Indexed: 11/27/2022] Open
Abstract
The brown planthopper (BPH) is the most devastating insect pest of rice. The rice gene BPH15 confers resistance to BPH. MicroRNAs (miRNAs) regulate a spectrum of development and defense response processes in plants. In this study, we analyzed six miRNA profiles of a BPH15 introgression line (P15) and a susceptible recipient line (PC) at three time points (0 h, 6 h and 48 h) after BPH attack, and identified 464 known miRNAs and 183 potential novel miRNAs. Before the BPH feeding, we identified 23 miRNAs differentially expressed in P15 and PC. We speculated that the resistant plant is in a priming state by the regulation of miRNAs. After the BPH feeding, 104 miRNAs were found to be expressed differentially in P15 (68 in P15-6/P15-0, 36 in P15-48/P15-0), and 80 miRNAs were found expressed differentially in PC (32 in PC-6/PC-0, 48 in PC-48/PC-0), which illustrated that miRNA expression is activated upon attack. These miRNAs regulate different pathways that contribute to the basal defense and specific resistance of rice to the BPH. Our study provides additional data for scientists to further explore the mechanism of plant defense against insect attack and to find a way for efficient insect control.
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Affiliation(s)
- Yan Wu
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wentang Lv
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Liang Hu
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weiwei Rao
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ya Zeng
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lili Zhu
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangcun He
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Zhu J, Hao P, Lu C, Ma Y, Feng Y, Yu X. Expression and RNA Interference of Ribosomal Protein L5 Gene in Nilaparvata lugens (Hemiptera: Delphacidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:3832884. [PMID: 28973571 PMCID: PMC5538327 DOI: 10.1093/jisesa/iex047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Indexed: 05/05/2023]
Abstract
The ribosomal proteins play important roles in the growth and development of organisms. This study aimed to explore the function of NlRPL5 (GenBank KX379234), a ribosomal protein L5 gene, in the brown planthopper Nilaparvata lugens. The open reading frame of NlRPL5 was cloned from N. lugens based on a previous transcriptome analysis. The results revealed that the open reading frame of NlRPL5 is of 900 bp, encoding 299 amino acid residues. The reverse transcription quantitative PCR results suggested that the expression of NlRPL5 gene was stronger in gravid females, but was relatively low in nymphs, males, and newly emerged females. The expression level of NlRPL5 in the ovary was about twofolds of that in the head, thorax, or fat body. RNAi of dsNlRPL5 resulted in a significant reduction of mRNA levels, ∼50% decrease in comparison with the dsGFP control at day 6. Treatment of dsNlRPL5 significantly restricted the ovarian development, and decreased the number of eggs laid on the rice (Oryza sativa) plants. This study provided a new clue for further study on the function and regulation mechanism of NlRPL5 in N. lugens.
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Affiliation(s)
- Jiajun Zhu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China (; ; ; ; ; )
| | - Peiying Hao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China (; ; ; ; ; )
- Corresponding author, e-mail:
| | - Chaofeng Lu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China (; ; ; ; ; )
| | - Yan Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China (; ; ; ; ; )
| | - Yalin Feng
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China (; ; ; ; ; )
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China (; ; ; ; ; )
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