1
|
Horgan FG, Almazan MLP, Bernal CC, Dilla-Ermita CJ, Ardestani G, Mundaca EA, Crisol-Martínez E. Origins of Susceptibility to Insect Herbivores in High-Yielding Hybrid and Inbred Rice Genotypes. INSECTS 2024; 15:608. [PMID: 39194813 DOI: 10.3390/insects15080608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/01/2024] [Accepted: 08/10/2024] [Indexed: 08/29/2024]
Abstract
Several studies have reported higher damage from insect herbivores to hybrid compared to inbred (pure line) rice. We used a collection of 20 hybrid and 12 inbred genotypes from diverse origins to test the hypotheses that hybrid rice susceptibility is due to (a) the hybrid plant type and/or (b) rice phylogeny. We challenged the genotypes with Nilaparvata lugans (BPH), Sogatella furcifera (WBPH) and Scirpophaga incertulas (YSB) in greenhouse and screenhouse bioassays and monitored herbivores in field plots. We used single nucleotide polymorphic (SNP) markers to assess genetic similarities between the genotypes and found that the hybrids and inbreds formed two distinct clusters regardless of origin. In the screenhouse, hybrids were more susceptible than inbreds to YSB; however, resistant hybrids and susceptible inbreds were also apparent from both the screenhouse and field plots. Plant biomass was the best predictor of susceptibility to YSB. Plant origin had a greater effect than plant type on susceptibility to BPH and WBPH. WBPH was the most abundant planthopper in the field plots where numbers were highly correlated with planthopper fitness in the greenhouse bioassays. Our results provide evidence that high-yielding hybrids that are relatively resistant to herbivores can be achieved through careful breeding. The avoidance of susceptible genotypes during breeding should remain a key element of integrated rice pest management.
Collapse
Affiliation(s)
- Finbarr G Horgan
- EcoLaVerna Integral Restoration Ecology, Bridestown, Kildinan, T56 P499 County Cork, Ireland
- School of Agronomy, Faculty of Agrarian and Forest Sciences, Catholic University of 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
| | | | | | - Christine Jade Dilla-Ermita
- International Rice Research Institute, Makati 1226, Manila, Philippines
- Department of Plant Sciences, UC Davis, One Shields Ave., Davis, CA 95616, USA
| | - Goli Ardestani
- International Rice Research Institute, Makati 1226, Manila, Philippines
- Boston IVF-IVIRMA Global Research Alliance, Waltham, MA 02451, USA
| | - Enrique A Mundaca
- School of Agronomy, Faculty of Agrarian and Forest Sciences, Catholic University of Maule Casilla 7-D, Curicó 3349001, Chile
| | - Eduardo Crisol-Martínez
- EcoLaVerna Integral Restoration Ecology, Bridestown, Kildinan, T56 P499 County Cork, Ireland
- International Rice Research Institute, Makati 1226, Manila, Philippines
- Association of Fruit and Vegetable Growers of Almeria (COEXPHAL), Carretera de Ronda 11, 04004 Almeria, Spain
| |
Collapse
|
2
|
Ahmed MS, Majeed A, Attia KA, Javaid RA, Siddique F, Farooq MS, Uzair M, Yang SH, Abushady AM. Country-wide, multi-location trials of Green Super Rice lines for yield performance and stability analysis using genetic and stability parameters. Sci Rep 2024; 14:9416. [PMID: 38658570 PMCID: PMC11043415 DOI: 10.1038/s41598-024-55510-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/24/2024] [Indexed: 04/26/2024] Open
Abstract
Rice (Oryza sativa L.) is an important member of the family Poaceae and more than half of world population depend for their dietary nutrition on rice. Rice cultivars with higher yield, resilience to stress and wider adaptability are essential to ensure production stability and food security. The fundamental objective of this study was to identify higher-yielding rice genotypes with stable performance and wider adaptability in a rice growing areas of Pakistan. A triplicate RCBD design experiment with 20 Green Super Rice (GSR) advanced lines was conducted at 12 rice growing ecologies in four Provinces of Pakistan. Grain yield stability performance was assessed by using different univariate and multivariate statistics. Analysis of variance revealed significant differences among genotypes, locations, and G x E interaction for mean squares (p < 0.05) of major yield contributing traits. All the studied traits except for number of tillers per plant revealed higher genotypic variance than environmental variance. Broad sense heritability was estimated in the range of 44.36% to 98.60%. Based on ASV, ASI, bi, Wi2, σ2i and WAAS statistics, the genotypes G1, G4, G5, G8, G11 and G12 revealed lowest values for parametric statistics and considered more stable genotypes based on paddy yield. The additive main effects and multiplicative interaction (AMMI) model revealed significant variation (p < 0.05) for genotypes, non-signification for environment and highly significant for G × E interaction. The variation proportion of PC1 and PC2 from interaction revealed 67.2% variability for paddy yield. Based on 'mean verses stability analysis of GGE biplot', 'Which-won-where' GGE Biplot, 'discriminativeness vs. representativeness' pattern of stability, 'IPCA and WAASB/GY' ratio-based stability Heat-map, and ranking of genotypes, the genotypes G1, G2, G3, G5, G8, G10, G11 and G13 were observed ideal genotypes with yield potential more than 8 tons ha-1. Discriminativeness vs. representativeness' pattern of stability identifies two environments, E5 (D.I Khan, KPK) and E6 (Usta Muhammad, Baluchistan) were best suited for evaluating genotypic yield performance. Based on these findings we have concluded that the genotypes G1, G2, G3, G5, G8, G10, G11 and G13 could be included in the commercial varietal development process and future breeding program.
Collapse
Affiliation(s)
- Muhammad Shahzad Ahmed
- Rice Research Program, Crop Sciences Institute, National Agricultural Research Center, Islamabad, Pakistan.
| | - Abid Majeed
- Rice Research Program, Crop Sciences Institute, National Agricultural Research Center, Islamabad, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
| | - Rana Arsalan Javaid
- Rice Research Program, Crop Sciences Institute, National Agricultural Research Center, Islamabad, Pakistan
| | - Faiza Siddique
- Rice Research Program, Crop Sciences Institute, National Agricultural Research Center, Islamabad, Pakistan
| | - Muhammad Shahbaz Farooq
- Rice Research Program, Crop Sciences Institute, National Agricultural Research Center, Islamabad, Pakistan
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Centre (NARC), Park Road, Islamabad, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, 59626, Republic of Korea.
| | - Asmaa M Abushady
- Biotechnology School, 26th of July Corridor, Nile University, Sheikh Zayed City, 12588, Giza, Egypt
- Department of Genetics, Agriculture College, Ain Shams University, Cairo, Egypt
| |
Collapse
|
3
|
Zheng X, Wei F, Cheng C, Qian Q. A historical review of hybrid rice breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:532-545. [PMID: 38103034 DOI: 10.1111/jipb.13598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/17/2023]
Abstract
The development of germplasm resources and advances in breeding methods have led to steady increases in yield and quality of rice (Oryza sativa L.). Three milestones in the recent history of rice breeding have contributed to these increases: dwarf rice breeding, hybrid rice breeding, and super rice breeding. On the 50th anniversary of the success of three-line hybrid rice, we highlight important scientific discoveries in rice breeding that were made by Chinese scientists and summarize the broader history of the field. We discuss the strategies that could be used in the future to optimize rice breeding further in the hope that China will continue to play a leading role in international rice breeding.
Collapse
Affiliation(s)
- Xiaoming Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fei Wei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng Cheng
- Yazhouwan National Laboratory, Sanya City, 572024, China
| | - Qian Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Yazhouwan National Laboratory, Sanya City, 572024, China
| |
Collapse
|
4
|
Zahra N, Uzair M, Zaid IU, Attia KA, Inam S, Fiaz S, Abdallah RM, Naeem MK, Farooq U, Rehman N, Ali GM, Xu J, Li Z, Khan MR. The comparative transcriptome analysis of two green super rice genotypes with varying tolerance to salt stress. Mol Biol Rep 2023; 51:22. [PMID: 38110786 DOI: 10.1007/s11033-023-08998-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Salinity is one of the main abiotic factors that restrict plant growth, physiology, and crop productivity is salt stress. About 33% of the total irrigated land suffers from severe salinity because of intensive underground water extraction and irrigation with brackish water. Thus, it is important to understand the genetic mechanism and identify the novel genes involved in salt tolerance for the development of climate-resilient rice cultivars. METHODS AND RESULTS In this study, two rice genotypes with varying tolerance to salt stress were used to investigate the differential expressed genes and molecular pathways to adapt under saline soil by comparative RNA sequencing at 42 days of the seedling stage. Salt-susceptible (S3) and -tolerant (S13) genotypes revealed 3982 and 3463 differentially expressed genes in S3 and S13 genotypes. The up-regulated genes in both genotypes were substantially enriched in different metabolic processes and binding activities. Biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and plant signal transduction mechanisms were highly enriched. Salt-susceptible and -tolerant genotypes shared the same salt adaptability mechanism with no significant quantitative differences at the transcriptome level. Moreover, bHLH, ERF, NAC, WRKY, and MYB transcription factors were substantially up-regulated under salt stress. 391 out of 1806 identified novel genes involved in signal transduction mechanisms. Expression profiling of six novel genes further validated the findings from RNA-seq data. CONCLUSION These findings suggest that the differentially expressed genes and molecular mechanisms involved in salt stress adaptation are conserved in both salt-susceptible and salt-tolerant rice genotypes. Further molecular characterization of novel genes will help to understand the genetic mechanism underlying salt tolerance in rice.
Collapse
Affiliation(s)
- Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Imdad Ullah Zaid
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan.
| | - Rizk M Abdallah
- Department of Rice, Field Crops Research Institute, ARC, Sakha, Kafrelshiekh, 33717, Egypt
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | | | - Jianlong Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan.
| |
Collapse
|
5
|
Yanting L, Bingkui W, Mengchao Z, Jing Y, Shenghai Y. Sensitivity of genotypically diverse rice varieties to radiation and the related changes to antioxidant enzyme activities. Int J Radiat Biol 2023; 100:453-465. [PMID: 38029339 DOI: 10.1080/09553002.2023.2290293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
PURPOSE Radiation mutagenesis, which typically involves gamma rays, is important for generating new rice germplasm resources. Determining the appropriate radiation dose range is critical for the success of radiation mutagenesis. Clarifying the sensitivity and tolerance of genotypically diverse rice varieties to gamma irradiation as well as the radiation-induced changes to reactive oxygen species (ROS) generation and antioxidant enzyme activities is crucial for increasing the utility of radiation mutagenesis in rice breeding programs. MATERIALS AND METHODS The seeds of the following four rice varieties with different genotypes were used as test materials: indica Zhe 1613, glutinous indica Zhe 1708, japonica Zhejing 100, and glutinous japonica Zhenuo 65. Additionally,60Co was used as the source of gamma rays. The rice seeds were irradiated with 14 doses (0, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, and 750 Gy). Non-irradiated seeds were used as the control. The seedling survival rate for each variety was recorded at 3, 7, 14, and 28 days after sowing. Moreover, the median lethal dose (LD50) and critical dose (LD40) were calculated according to the seedling survival rates at 28 days after sowing. The seedling superoxide anion (O2•-), hydrogen peroxide (H2O2), and malondialdehyde (MDA) contents and the superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) activities were analyzed at 7 days after sowing. RESULTS As the radiation dose increased, the seedling survival rate decreased. The seedling survival rate also decreased significantly as the number of days after sowing increased. Among the rice genotypes, the rank-order of the radiation tolerance was as follows: indica Zhe 1613 > glutinous indica Zhe 1708 > japonica Zhejing 100 > glutinous japonica Zhenuo 65. The LD50 values were 426.7 Gy for Zhe 1613, 329.2 Gy for Zhe 1708, 318.3 Gy for Zhejing 100, and 316.6 Gy for Zhenuo 65. Increases in the radiation dose resulted in significant increases in the seedling O2•- and H2O2 contents, but only up to a certain point. Further increases in the radiation dose caused the seedling O2•- and H2O2 contents to decrease. The H2O2 content for each variety peaked when the radiation dose was very close to the LD50. We propose that the radiation dose associated with the highest H2O2 content (±50 Gy) should be used as the recommended dose for the gamma irradiation of rice. The radiation dose that resulted in peak seedling O2•- contents in the analyzed rice varieties was very close to the LD40. In all rice varieties, the MDA content increased as the radiation dose increased. The SOD, CAT, POD, and APX activities increased as the radiation dose increased within a certain range (less than 600 Gy for Zhe 1613 and 400 Gy for the other varieties), but there were slight differences among the rice varieties. CONCLUSIONS Genotypically diverse rice varieties vary regarding their sensitivity to gamma irradiation. Our findings suggest that ROS generation and antioxidant enzyme activities are important factors associated with the radiation mutagenesis of rice. The close relationship between the activities of key antioxidant enzymes, such as SOD, POD, APX, and CAT, and the LD50 and LD40 may be exploited to enhance radiation mutagenesis through the use of plant growth regulators.
Collapse
Affiliation(s)
- Lu Yanting
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wang Bingkui
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhang Mengchao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ye Jing
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ye Shenghai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
6
|
Zhao M, Du C, Zeng J, Gao Z, Zhu Y, Wang J, Zhang Y, Zhu Z, Wang Y, Chen M, Wang Y, Chang J, Yang G, He G, Li Y, Chen X. Integrated omic analysis provides insights into the molecular regulation of stress tolerance by partial root-zone drying in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1156514. [PMID: 37360728 PMCID: PMC10288491 DOI: 10.3389/fpls.2023.1156514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/26/2023] [Indexed: 06/28/2023]
Abstract
Partial root-zone drying (PRD) is an effective water-saving irrigation strategy that improves stress tolerance and facilitates efficient water use in several crops. It has long been considered that abscisic acid (ABA)-dependent drought resistance may be involved during partial root-zone drying. However, the molecular mechanisms underlying PRD-mediated stress tolerance remain unclear. It's hypothesized that other mechanisms might contribute to PRD-mediated drought tolerance. Here, rice seedlings were used as a research model and the complex transcriptomic and metabolic reprogramming processes were revealed during PRD, with several key genes involved in osmotic stress tolerance identified by using a combination of physiological, transcriptome, and metabolome analyses. Our results demonstrated that PRD induces transcriptomic alteration mainly in the roots but not in the leaves and adjusts several amino-acid and phytohormone metabolic pathways to maintain the balance between growth and stress response compared to the polyethylene glycol (PEG)-treated roots. Integrated analysis of the transcriptome and metabolome associated the co-expression modules with PRD-induced metabolic reprogramming. Several genes encoding the key transcription factors (TFs) were identified in these co-expression modules, highlighting several key TFs, including TCP19, WRI1a, ABF1, ABF2, DERF1, and TZF7, involved in nitrogen metabolism, lipid metabolism, ABA signaling, ethylene signaling, and stress regulation. Thus, our work presents the first evidence that molecular mechanisms other than ABA-mediated drought resistance are involved in PRD-mediated stress tolerance. Overall, our results provide new insights into PRD-mediated osmotic stress tolerance, clarify the molecular regulation induced by PRD, and identify genes useful for further improving water-use efficiency and/or stress tolerance in rice.
Collapse
Affiliation(s)
- Minhua Zhao
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Canghao Du
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jian Zeng
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhihong Gao
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yongyong Zhu
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Jinfei Wang
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yupeng Zhang
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Zetao Zhu
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Yaqiong Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyuan Chen
- Henry Fok School of Biology and Agriculture, Guangdong Engineering Technology Research Center for Efficient Utilization of Water and Soil Resources in North Region, Shaoguan University, Shaoguan, Guangdong, China
| |
Collapse
|
7
|
Basu U, Parida SK. Restructuring plant types for developing tailor-made crops. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1106-1122. [PMID: 34260135 DOI: 10.1111/pbi.13666] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 05/27/2023]
Abstract
Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.
Collapse
Affiliation(s)
- Udita Basu
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Swarup K Parida
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| |
Collapse
|
8
|
Xu Y, Zhang X, Li H, Zheng H, Zhang J, Olsen MS, Varshney RK, Prasanna BM, Qian Q. Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction. MOLECULAR PLANT 2022; 15:1664-1695. [PMID: 36081348 DOI: 10.1016/j.molp.2022.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 05/12/2023]
Abstract
The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, by incorporation of molecular marker genotypes. However, plant performance or phenotype (P) is determined by the combined effects of genotype (G), envirotype (E), and genotype by environment interaction (GEI). Phenotypes can be predicted more precisely by training a model using data collected from multiple sources, including spatiotemporal omics (genomics, phenomics, and enviromics across time and space). Integration of 3D information profiles (G-P-E), each with multidimensionality, provides predictive breeding with both tremendous opportunities and great challenges. Here, we first review innovative technologies for predictive breeding. We then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy, particularly envirotypic data, which have largely been neglected in data collection and are nearly untouched in model construction. We propose a smart breeding scheme, integrated genomic-enviromic prediction (iGEP), as an extension of genomic prediction, using integrated multiomics information, big data technology, and artificial intelligence (mainly focused on machine and deep learning). We discuss how to implement iGEP, including spatiotemporal models, environmental indices, factorial and spatiotemporal structure of plant breeding data, and cross-species prediction. A strategy is then proposed for prediction-based crop redesign at both the macro (individual, population, and species) and micro (gene, metabolism, and network) scales. Finally, we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding initiatives. We call for coordinated efforts in smart breeding through iGEP, institutional partnerships, and innovative technological support.
Collapse
Affiliation(s)
- Yunbi Xu
- Institute of Crop Sciences, CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China; CIMMYT-China Tropical Maize Research Center, School of Food Science and Engineering, Foshan University, Foshan, Guangdong 528231, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China.
| | - Xingping Zhang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Huihui Li
- Institute of Crop Sciences, CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai 201400, China
| | - Jianan Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, Hebei 050035, China
| | - Michael S Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Australia
| | - Boddupalli M Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Qian Qian
- Institute of Crop Sciences, CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
9
|
Zhang F, Zhang C, Zhao X, Zhu S, Chen K, Zhou G, Wu Z, Li M, Zheng T, Wang W, Yan Z, Fei Q, Li Z, Chen J, Xu J. Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations. RICE (NEW YORK, N.Y.) 2022; 15:49. [PMID: 36181551 PMCID: PMC9526777 DOI: 10.1186/s12284-022-00595-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F1 (BCF1) hybrids derived from QYSM's parents across three environments and gene-based analyses. RESULTS Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF1 hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM. CONCLUSIONS The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis.
Collapse
Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Conghe Zhang
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuangbing Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Guixiang Zhou
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhi Yan
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Qinyong Fei
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China.
| | - Jinjie Chen
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China.
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China.
| |
Collapse
|
10
|
Rokonuzzaman MD, Li WC, Wu C, Ye ZH. Human health impact due to arsenic contaminated rice and vegetables consumption in naturally arsenic endemic regions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119712. [PMID: 35798190 DOI: 10.1016/j.envpol.2022.119712] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Rice and vegetables cultivated in naturally arsenic (As) endemic areas are the substantial source of As body loading for persons using safe drinking water. However, tracing As intake, particularly from rice and vegetables by biomarker analysis, has been poorly addressed. This field investigation was conducted to trace the As transfer pathway and measure health risk associated with consuming As enriched rice and vegetables. Purposively selected 100 farmers from five sub-districts of Chandpur, Bangladesh fulfilling specific requirements constituted the subjects of this study. A total of 100 Irrigation water, soils, rice, and vegetable samples were collected from those farmers' who donated scalp hair. Socio-demographic and food consumption data were collected face to face through questionnaire administration. The mean As level in irrigation water, soils, rice, vegetables, and scalp hairs exceeded the acceptable limit, while As content was significant at 0.1%, 5%, 0.1%, 1%, and 0.1% probability levels, respectively, in all five locations. Arsenic in scalp hair is significantly (p ≤ 0.01) correlated with that in rice and vegetables. The bioconcentration factor (BCF) for rice and vegetables is less than one and significant at a 1% probability level. The average daily intake (ADI) is higher than the RfD limit for As. Both grains and vegetables have an HQ (hazard quotient) > 1. Maximum incremental lifetime cancer risk (ILCR) showed 2.8 per 100 people and 1.6 per 1000 people are at considerable and threshold risk, respectively. However, proteinaceous and nutritious food consumption might have kept the participants asymptomatic. The PCA analysis showed that the first principle component (PC1) explains 91.1% of the total variance dominated by As in irrigation water, grain, and vegetables. The dendrogram shows greater variations in similarity in rice and vegetables As, while the latter has been found to contribute more to human body loading compared to grain As.
Collapse
Affiliation(s)
- M D Rokonuzzaman
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong Special Administrative Region, 999077, PR China
| | - W C Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong Special Administrative Region, 999077, PR China.
| | - C Wu
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong Special Administrative Region, 999077, PR China; School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Z H Ye
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| |
Collapse
|
11
|
Wu W, Guo W, Ni G, Wang L, Zhang H, Ng WL. Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the Invasive Sphagneticola trilobata and the Native S. calendulacea in South China, and Implications for Its Invasiveness. Front Genet 2022; 13:833406. [PMID: 35664338 PMCID: PMC9160872 DOI: 10.3389/fgene.2022.833406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
The role of hybridization is significant in biological invasion, and thermotolerance is a trait critical to range expansions. The South American Sphagneticola trilobata is now widespread in South China, threatening the native S. calendulacea by competition and hybridization. Furthermore, upon formation, their F1 hybrid can quickly replace both parents. In this study, the three taxa were used as a model to investigate the consequences of hybridization on cold tolerance, particularly the effect of subgenome dominance in the hybrid. Upon chilling treatments, physiological responses and transcriptome profiles were compared across different temperature points to understand their differential responses to cold. While both parents showed divergent responses, the hybrid’s responses showed an overall resemblance to S. calendulacea, but the contribution of homeolog expression bias to cold stress was not readily evident in the F1 hybrid possibly due to inherent bias that comes with the sampling location. Our findings provided insights into the role of gene expression in differential cold tolerance, and further contribute to predicting the invasive potential of other hybrids between S. trilobata and its congeners around the world.
Collapse
Affiliation(s)
- Wei Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Guangyan Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Longyuan Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hui Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Malaysia
- *Correspondence: Wei Lun Ng,
| |
Collapse
|
12
|
Upadhayay VK, Singh AV, Khan A, Singh J, Pareek N, Raghav A. FE-SEM/EDX Based Zinc Mobilization Analysis of Burkholderia cepacia and Pantoea rodasii and Their Functional Annotation in Crop Productivity, Soil Quality, and Zinc Biofortification of Paddy. Front Microbiol 2022; 13:852192. [PMID: 35602065 PMCID: PMC9120762 DOI: 10.3389/fmicb.2022.852192] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
The experimental study was contrived to characterize two zinc-solubilizing bacteria (ZSB), namely BMRR126 and BMAR64, and their role in zinc (Zn) biofortification of rice. These bacteria solubilized Zn profoundly, determined qualitatively by halo-zone formation on a solid medium and quantitatively in a liquid broth by AAS and SEM-EDX. The lowering of pH and contact angle assessment of the liquid broth unveiled the establishment of the acidic conditions in a medium suitable for Zn solubilization. The characterization of both isolates on the basis of 16S rRNA gene analysis was identified as Burkholderia cepacia and Pantoea rodasii, respectively. These strains were also found to have some plant probiotic traits namely phosphate solubilization, production of siderophore, indole acetic acid (IAA), exopolysaccharide (EPS), and ammonia. The field experiments were performed at two diverse locations and under all treatments; the simultaneous use of BMRR126 and BMAR64 with zinc oxide (ZnO) resulted in the highest growth and productivity of the paddy crop. The utmost Zn achievement in the grain was estimated in a treatment (T9) (25.07 mg/kg) containing a consortium of BMRR126 and BMAR64 along with ZnO for the Terai region. The treatment containing single ZSB bioinoculant BMRR126 (T7) showed an elevated Zn amount in the rice grain (33.25 mg/kg) for the Katchar region. The soil parameters (pH, EC, organic carbon, NPK, available Zn, and dehydrogenase activity) were also positively influenced under all bacterial treatments compared to the uninoculated control. Our study clearly accentuates the need for Zn solubilizing bacteria (ZSB) to provide the benefits of Zn-biofortification in different regions.
Collapse
Affiliation(s)
- Viabhav Kumar Upadhayay
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Ajay Veer Singh
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
- *Correspondence: Ajay Veer Singh,
| | - Amir Khan
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Jyoti Singh
- Department of Microbiology, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Navneet Pareek
- Department of Soil Science, College of Agriculture, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Alok Raghav
- Multidisciplinary Research Unit, Department of Health Research, Ministry of Health and Family Welfare, Ganesh Shankar Vidyarthi Memorial Medical College, Kanpur, India
| |
Collapse
|
13
|
Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
Collapse
Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
| |
Collapse
|
14
|
Hao Z, Ma S, Liang L, Feng T, Xiong M, Lian S, Zhu J, Chen Y, Meng L, Li M. Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network. Int J Mol Sci 2022; 23:ijms23074016. [PMID: 35409377 PMCID: PMC8999833 DOI: 10.3390/ijms23074016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 01/24/2023] Open
Abstract
Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the ‘gcHap-network pathway’. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.
Collapse
Affiliation(s)
- Zhiqi Hao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sai Ma
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Mengyuan Xiong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Shangshu Lian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jingyan Zhu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lijun Meng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (L.M.); (M.L.)
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Correspondence: (L.M.); (M.L.)
| |
Collapse
|
15
|
Ahmad H, Zafar SA, Naeem MK, Shokat S, Inam S, Rehman MAU, Naveed SA, Xu J, Li Z, Ali GM, Khan MR. Impact of Pre-Anthesis Drought Stress on Physiology, Yield-Related Traits, and Drought-Responsive Genes in Green Super Rice. Front Genet 2022; 13:832542. [PMID: 35401708 PMCID: PMC8987348 DOI: 10.3389/fgene.2022.832542] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022] Open
Abstract
Optimum soil water availability is vital for maximum yield production in rice which is challenged by increasing spells of drought. The reproductive stage drought is among the main limiting factors leading to the drastic reduction in grain yield. The objective of this study was to investigate the molecular and morphophysiological responses of pre-anthesis stage drought stress in green super rice. The study assessed the performance of 26 rice lines under irrigated and drought conditions. Irrigated treatment was allowed to grow normally, while drought stress was imposed for 30 days at the pre-anthesis stage. Three important physiological traits including pollen fertility percentage (PFP), cell membrane stability (CMS), and normalized difference vegetative index (NDVI) were recorded at anthesis stage during the last week of drought stress. Agronomic traits of economic importance including grain yield were recorded at maturity stage. The analysis of variance demonstrated significant variation among the genotypes for most of the studied traits. Correlation and principal component analyses demonstrated highly significant associations of particular agronomic traits with grain yield, and genetic diversity among genotypes, respectively. Our study demonstrated a higher drought tolerance potential of GSR lines compared with local cultivars, mainly by higher pollen viability, plant biomass, CMS, and harvest index under drought. In addition, the molecular basis of drought tolerance in GSR lines was related to upregulation of certain drought-responsive genes including OsSADRI, OsDSM1, OsDT11, but not the DREB genes. Our study identified novel drought-responsive genes (LOC_Os11g36190, LOC_Os12g04500, LOC_Os12g26290, and LOC_Os02g11960) that could be further characterized using reverse genetics to be utilized in molecular breeding for drought tolerance.
Collapse
Affiliation(s)
- Hassaan Ahmad
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Syed Adeel Zafar
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Sajid Shokat
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Malik Attique ur Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Shahzad Amir Naveed
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ghulam Muhammad Ali
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
- *Correspondence: Muhammad Ramzan Khan,
| |
Collapse
|
16
|
Understanding the genetic and molecular constitutions of heterosis for developing hybrid rice. J Genet Genomics 2022; 49:385-393. [PMID: 35276387 DOI: 10.1016/j.jgg.2022.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/31/2022]
Abstract
The wide adoption of hybrid rice has greatly increased rice yield in the last several decades. The utilization of heterosis facilitated by male sterility has been a common strategy for hybrid rice development. Here, we summarize our efforts in the genetic and molecular understanding of heterosis and male sterility together with the related progress from other research groups. Analyses of F1 diallel crosses show that strong heterosis widely exists in hybrids of diverse germplasms, and inter-subspecific hybrids often display higher heterosis. Using the elite hybrid Shanyou 63 as a model, an immortalized F2 population design is conducted for systematic characterization of the biological mechanism of heterosis, with identification of loci controlling heterosis of yield and yield component traits. Dominance, overdominance, and epistasis all play important roles in the genetic basis of heterosis; quantitative assessment of these components well addressed the three classical genetic hypotheses for heterosis. Environment-sensitive genic male sterility (EGMS) enables the development of two-line hybrids, and long noncoding RNAs often function as regulators of EGMS. Inter-subspecific hybrids show greatly reduced fertility; the identification and molecular characterization of hybrid sterility genes offer strategies for overcoming inter-subspecific hybrid sterility. These developments have significant implications for future hybrid rice improvement using genomic breeding.
Collapse
|
17
|
Ge J, Wang J, Pang H, Li F, Lou D, Fan W, Liu Z, Li J, Li D, Nong B, Zhang Z, Wang Y, Huang J, Xing M, Nie Y, Xiao X, Zhang F, Wang W, Xu J, Kim SR, Kohli A, Ye G, Qiao W, Yang Q, Zheng X. Genome-wide selection and introgression of Chinese rice varieties during breeding. J Genet Genomics 2022; 49:492-501. [DOI: 10.1016/j.jgg.2022.02.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/15/2022]
|
18
|
Yu S, Ali J, Zhou S, Ren G, Xie H, Xu J, Yu X, Zhou F, Peng S, Ma L, Yuan D, Li Z, Chen D, Zheng R, Zhao Z, Chu C, You A, Wei Y, Zhu S, Gu Q, He G, Li S, Liu G, Liu C, Zhang C, Xiao J, Luo L, Li Z, Zhang Q. From Green Super Rice to green agriculture: Reaping the promise of functional genomics research. MOLECULAR PLANT 2022; 15:9-26. [PMID: 34883279 DOI: 10.1016/j.molp.2021.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.
Collapse
Affiliation(s)
- Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shaochuan Zhou
- Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guangjun Ren
- Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Huaan Xie
- Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Fasong Zhou
- China National Seed Group Co., Ltd, Beijing, China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangyong Ma
- China National Rice Research Institute, Hangzhou, China
| | | | - Zefu Li
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Dazhou Chen
- Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | | | | | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Aiqing You
- Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yu Wei
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Susong Zhu
- Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Qiongyao Gu
- Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Shigui Li
- Sichuan Agricultural University, Chengdu, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Changhua Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
19
|
Zhu M, He Y, Zhu M, Ahmad A, Xu S, He Z, Jiang S, Huang J, Li Z, Liu S, Hou X, Zhang Z. ipa1 improves rice drought tolerance at seedling stage mainly through activating abscisic acid pathway. PLANT CELL REPORTS 2022; 41:221-232. [PMID: 34694441 DOI: 10.1007/s00299-021-02804-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE: ipa1 enhances rice drought tolerance mainly through activating the ABA pathway. It endows rice seedlings with a more developed root system, smaller leaf stomata aperture, and enhanced carbon metabolism. Drought is a major abiotic stress to crop production. IPA1 (IDEAL PLANT ARCHITECTURE 1)/OsSPL14 encodes a transcription factor and has been reported to function in both rice ideal plant architecture and biotic resistance. Here, with a pair of IPA1 and ipa1-NILs (Near Iso-genic Lines), we found that ipa1 could significantly improve rice drought tolerance at seedling stage. The ipa1 plants had a better-developed root system and smaller leaf stomatal aperture. Analysis of carbon-nitrogen metabolism-associated enzyme activity, gene expression, and metabolic profile indicated that ipa1 could tip the carbon-nitrogen metabolism balance towards an increased carbon metabolism pattern. In both the control and PEG-treated conditions, ABA content in the ipa1 seedlings was significantly higher than that in the IPA1 seedlings. Expression of the ABA biosynthesis genes was detected to be up-regulated, whereas the expression of ABA catabolism genes was down-regulated in the ipa1 seedlings. In addition, based on yeast one-hybrid assay and dual-luciferase assay, IPA1 was found to directly activate the promoter activity of OsHOX12, a transcription factor promoting ABA biosynthesis, and OsNAC52, a positive regulator of the ABA pathway. The expression of OsHOX12 and OsNAC52 was significantly up-regulated in the ipa1 plants. Combined with the previous studies, our results suggested that ipa1 could improve rice seedling drought tolerance mainly through activating the ABA pathway and that regulation of the ipa1-mediated ABA pathway will be an important strategy for improving drought resistance of rice.
Collapse
Affiliation(s)
- Menghao Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China
| | - Yonggang He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China
| | - Mingqiang Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ayaz Ahmad
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shuang Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zijun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shan Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jinqiu Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihui Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shaojia Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China
| | - Xin Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihong Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Ezhou Seed Technology Research Institute of Hubei Province, Ezhou, 436043, China.
| |
Collapse
|
20
|
Labroo MR, Ali J, Aslam MU, de Asis EJ, Dela Paz MA, Sevilla MA, Lipka AE, Studer AJ, Rutkoski JE. Genomic Prediction of Yield Traits in Single-Cross Hybrid Rice ( Oryza sativa L.). Front Genet 2021; 12:692870. [PMID: 34276796 PMCID: PMC8278103 DOI: 10.3389/fgene.2021.692870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
Hybrid rice varieties can outyield the best inbred varieties by 15 – 30% with appropriate management. However, hybrid rice requires more inputs and management than inbred rice to realize a yield advantage in high-yielding environments. The development of stress-tolerant hybrid rice with lowered input requirements could increase hybrid rice yield relative to production costs. We used genomic prediction to evaluate the combining abilities of 564 stress-tolerant lines used to develop Green Super Rice with 13 male sterile lines of the International Rice Research Institute for yield-related traits. We also evaluated the performance of their F1 hybrids. We identified male sterile lines with good combining ability as well as F1 hybrids with potential further use in product development. For yield per plant, accuracies of genomic predictions of hybrid genetic values ranged from 0.490 to 0.822 in cross-validation if neither parent or up to both parents were included in the training set, and both general and specific combining abilities were modeled. The accuracy of phenotypic selection for hybrid yield per plant was 0.682. The accuracy of genomic predictions of male GCA for yield per plant was 0.241, while the accuracy of phenotypic selection was 0.562. At the observed accuracies, genomic prediction of hybrid genetic value could allow improved identification of high-performing single crosses. In a reciprocal recurrent genomic selection program with an accelerated breeding cycle, observed male GCA genomic prediction accuracies would lead to similar rates of genetic gain as phenotypic selection. It is likely that prediction accuracies of male GCA could be improved further by targeted expansion of the training set. Additionally, we tested the correlation of parental genetic distance with mid-parent heterosis in the phenotyped hybrids. We found the average mid-parent heterosis for yield per plant to be consistent with existing literature values at 32.0%. In the overall population of study, parental genetic distance was significantly negatively correlated with mid-parent heterosis for yield per plant (r = −0.131) and potential yield (r = −0.092), but within female families the correlations were non-significant and near zero. As such, positive parental genetic distance was not reliably associated with positive mid-parent heterosis.
Collapse
Affiliation(s)
- Marlee R Labroo
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - M Umair Aslam
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Erik Jon de Asis
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Madonna A Dela Paz
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - M Anna Sevilla
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Anthony J Studer
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jessica E Rutkoski
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|
21
|
Varshney RK, Bohra A, Yu J, Graner A, Zhang Q, Sorrells ME. Designing Future Crops: Genomics-Assisted Breeding Comes of Age. TRENDS IN PLANT SCIENCE 2021; 26:631-649. [PMID: 33893045 DOI: 10.1016/j.tplants.2021.03.010] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 05/18/2023]
Abstract
Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.
Collapse
Affiliation(s)
- Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crops Plant Research (IPK), Gatersleben, Germany
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| |
Collapse
|
22
|
Fiaz S, Ahmar S, Saeed S, Riaz A, Mora-Poblete F, Jung KH. Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security. Int J Mol Sci 2021; 22:5585. [PMID: 34070430 PMCID: PMC8197453 DOI: 10.3390/ijms22115585] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.
Collapse
Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Sajjad Saeed
- Department of Forestry and Wildlife Management, University of Haripur, Haripur 22620, Pakistan
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| |
Collapse
|
23
|
Zhang Q, Xu M, Xia X, Komatsuda T, Varshney RK, Shi K. Crop genetics research in Asia: improving food security and nutrition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1339-1344. [PMID: 32306095 DOI: 10.1007/s00122-020-03597-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Mingliang Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
| | - Kai Shi
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| |
Collapse
|