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Gunasekaran A, Seshadri G, Ramasamy S, Muthurajan R, Karuppasamy KS. Identification of Newer Stable Genetic Sources for High Grain Number per Panicle and Understanding the Gene Action for Important Panicle Traits in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:250. [PMID: 36678963 PMCID: PMC9860970 DOI: 10.3390/plants12020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/24/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
Rice is an important food crop extensively cultivated worldwide, and rice's grain yield should be improved to meet future food demand. Grain number per panicle is the main trait that determines the grain yield in rice, and other panicle-related traits influence the grain number. To study the genetic diversity, 50 diverse Indian-origin germplasm were evaluated for grain number per panicle and other panicle traits for two consecutive seasons (Rabi 2019 and Kharif 2020). The maximum genotypic and phenotypic coefficient of variation was obtained for the number of spikelets and filled grains per panicle. The genotypes were grouped into eight clusters with Mahalanobis' D2 analysis and six groups using Principal component analysis. Based on, per se, performance for grain number per panicle and genetic distances, six parents were selected and subjected to full diallel mating. The genotypes CB12132, IET 28749, and BPT 5204 were the best general combiners for the number of filled grains per panicle and other panicle branching traits, viz., the number of primary and secondary branches per panicle. The hybrid BPT 5204 × CB 12132 identified as the best specific combination for most of the studied panicle traits. The additive gene effects were high for the number of filled grains per panicle, the number of primary branches, and secondary branches, whereas non-additive gene action was high for the number of productive tillers and grain yield per plant. The information obtained from this study will be useful in rice breeding programs to improve panicle traits, especially the grain number, which would result in higher grain yield.
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Affiliation(s)
- Ariharasutharsan Gunasekaran
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Geetha Seshadri
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India
- Department of Pulses, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Saraswathi Ramasamy
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India
- Department of Plant Genetic Resources, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Krishna Surendar Karuppasamy
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India
- Department of Seed Science and Technology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai 625104, India
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Dan Z, Chen Y, Li H, Zeng Y, Xu W, Zhao W, He R, Huang W. The metabolomic landscape of rice heterosis highlights pathway biomarkers for predicting complex phenotypes. PLANT PHYSIOLOGY 2021; 187:1011-1025. [PMID: 34608951 PMCID: PMC8491067 DOI: 10.1093/plphys/kiab273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Understanding the molecular mechanisms underlying complex phenotypes requires systematic analyses of complicated metabolic networks and contributes to improvements in the breeding efficiency of staple cereal crops and diagnostic accuracy for human diseases. Here, we selected rice (Oryza sativa) heterosis as a complex phenotype and investigated the mechanisms of both vegetative and reproductive traits using an untargeted metabolomics strategy. Heterosis-associated analytes were identified, and the overlapping analytes were shown to underlie the association patterns for six agronomic traits. The heterosis-associated analytes of four yield components and plant height collectively contributed to yield heterosis, and the degree of contribution differed among the five traits. We performed dysregulated network analyses of the high- and low-better parent heterosis hybrids and found multiple types of metabolic pathways involved in heterosis. The metabolite levels of the significantly enriched pathways (especially those from amino acid and carbohydrate metabolism) were predictive of yield heterosis (area under the curve = 0.907 with 10 features), and the predictability of these pathway biomarkers was validated with hybrids across environments and populations. Our findings elucidate the metabolomic landscape of rice heterosis and highlight the potential application of pathway biomarkers in achieving accurate predictions of complex phenotypes.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yunping Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ruifeng He
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6414, USA
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Labroo MR, Studer AJ, Rutkoski JE. Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review. Front Genet 2021; 12:643761. [PMID: 33719351 PMCID: PMC7943638 DOI: 10.3389/fgene.2021.643761] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Although hybrid crop varieties are among the most popular agricultural innovations, the rationale for hybrid crop breeding is sometimes misunderstood. Hybrid breeding is slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection and exploitation of heterosis simultaneously. Inbred parental lines can identically reproduce both themselves and their F1 progeny indefinitely, whereas outbred lines cannot, so uniform outbred lines must be bred indirectly through their inbred parents to harness heterosis. Heterosis is an expected consequence of whole-genome non-additive effects at the population level over evolutionary time. Understanding heterosis from the perspective of molecular genetic mechanisms alone may be elusive, because heterosis is likely an emergent property of populations. Hybrid breeding is a process of recurrent population improvement to maximize hybrid performance. Hybrid breeding is not maximization of heterosis per se, nor testing random combinations of individuals to find an exceptional hybrid, nor using heterosis in place of population improvement. Though there are methods to harness heterosis other than hybrid breeding, such as use of open-pollinated varieties or clonal propagation, they are not currently suitable for all crops or production environments. The use of genomic selection can decrease cycle time and costs in hybrid breeding, particularly by rapidly establishing heterotic pools, reducing testcrossing, and limiting the loss of genetic variance. Open questions in optimal use of genomic selection in hybrid crop breeding programs remain, such as how to choose founders of heterotic pools, the importance of dominance effects in genomic prediction, the necessary frequency of updating the training set with phenotypic information, and how to maintain genetic variance and prevent fixation of deleterious alleles.
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Affiliation(s)
| | | | - Jessica E. Rutkoski
- Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
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Dan Z, Chen Y, Zhao W, Wang Q, Huang W. Metabolome-based prediction of yield heterosis contributes to the breeding of elite rice. Life Sci Alliance 2019; 3:3/1/e201900551. [PMID: 31836628 PMCID: PMC6918511 DOI: 10.26508/lsa.201900551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 01/15/2023] Open
Abstract
Metabolite profiles obtained from parental seedlings can predict yield heterosis of rice hybrids with correctly dissected population structure across different growth conditions. Improvement of the breeding efficiencies of heterotic crops adaptive to different conditions can mitigate the food shortage crisis due to overpopulation and climate change. To date, diverse molecular markers have been used to guide field phenotypic selection, whereas accurate predictions of complex heterotic traits are rarely reported. Here, we present a practical metabolome-based strategy for predicting yield heterosis in rice. The dissection of population structure based on untargeted metabolite profiles as the initial critical step in multivariate modeling performed better than the screening of predictive variables. Then the assessment of each predictive variable’s contribution to predictive models according to all latent factors was more precise than the conventional first one. Metabolites belonging to specific pathways were closely associated with yield heterosis, and the up-regulation of galactose metabolism promoted robust yield heterosis in hybrids under different growth conditions. Our study demonstrates that metabolome-based predictive models with correctly dissected population structure and screened predictive variables can facilitate accurate predictions of yield heterosis and have great potential for establishing molecular marker–based precision breeding programs.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yunping Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiong Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, College of Life Sciences, Wuhan University, Wuhan, China
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Dan Z, Chen Y, Xu Y, Huang J, Huang J, Hu J, Yao G, Zhu Y, Huang W. A metabolome-based core hybridisation strategy for the prediction of rice grain weight across environments. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:906-913. [PMID: 30321482 PMCID: PMC6587747 DOI: 10.1111/pbi.13024] [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: 04/03/2018] [Revised: 08/21/2018] [Accepted: 10/10/2018] [Indexed: 05/05/2023]
Abstract
Marker-based prediction holds great promise for improving current plant and animal breeding efficiencies. However, the predictabilities of complex traits are always severely affected by negative factors, including distant relatedness, environmental discrepancies, unknown population structures, and indeterminate numbers of predictive variables. In this study, we utilised two independent F1 hybrid populations in the years 2012 and 2015 to predict rice thousand grain weight (TGW) using parental untargeted metabolite profiles with a partial least squares regression method. A stable predictive model for TGW was built based on hybrids from the population in 2012 (r = 0.75) but failed to properly predict TGW for hybrids from the population in 2015 (r = 0.27). After integrating hybrids from both populations into the training set, the TGW of hybrids could be predicted but was largely dependent on population structures. Then, core hybrids from each population were determined by principal component analysis and the TGW of hybrids in both environments were successfully predicted (r > 0.60). Moreover, adjusting the population structures and numbers of predictive analytes increased TGW predictability for hybrids in 2015 (r = 0.72). Our study demonstrates that the TGW of F1 hybrids across environments can be accurately predicted based on parental untargeted metabolite profiles with a core hybridisation strategy in rice. Metabolic biomarkers identified from early developmental stage tissues, which are grown under experimental conditions, may represent a workable approach towards the robust prediction of major agronomic traits for climate-adaptive varieties.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Yunping Chen
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Yanghong Xu
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Junran Huang
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Jishuai Huang
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Jun Hu
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Guoxin Yao
- School of Life and Science TechnologyHubei Engineering UniversityXiaoganChina
| | - Yingguo Zhu
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
| | - Wenchao Huang
- State Key Laboratory of Hybrid RiceKey Laboratory for Research and Utilization of Heterosis in Indica RiceThe Yangtze River Valley Hybrid Rice Collaboration & Innovation CenterCollege of Life SciencesWuhan UniversityWuhanChina
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Fan F, Li N, Chen Y, Liu X, Sun H, Wang J, He G, Zhu Y, Li S. Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice. FRONTIERS IN PLANT SCIENCE 2017. [PMID: 28638401 PMCID: PMC5461369 DOI: 10.3389/fpls.2017.00986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1, BPH-resistant genes Bph6 and Bph9, fertility restorer genes Rf3, Rf4, Rf5, and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties.
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Affiliation(s)
- Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
| | - Nengwu Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
| | - Yunping Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
| | - Xingdan Liu
- College of Agronomy, Hunan Agricultural UniversityChangsha, China
| | - Heng Sun
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
| | - Jie Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan UniversityWuhan, China
- *Correspondence: Shaoqing Li
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