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Gutaker RM, Purugganan MD. Adaptation and the Geographic Spread of Crop Species. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:679-706. [PMID: 38012052 DOI: 10.1146/annurev-arplant-060223-030954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Crops are plant species that were domesticated starting about 11,000 years ago from several centers of origin, most prominently the Fertile Crescent, East Asia, and Mesoamerica. From their domestication centers, these crops spread across the globe and had to adapt to differing environments as a result of this dispersal. We discuss broad patterns of crop spread, including the early diffusion of crops associated with the rise and spread of agriculture, the later movement via ancient trading networks, and the exchange between the Old and New Worlds over the last ∼550 years after the European colonization of the Americas. We also examine the various genetic mechanisms associated with the evolutionary adaptation of crops to their new environments after dispersal, most prominently seasonal adaptation associated with movement across latitudes, as well as altitudinal, temperature, and other environmental factors.
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Affiliation(s)
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY, USA;
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY, USA
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2
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [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: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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3
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Gao G, Chen M, Mo R, Li N, Xu Y, Lu Y. Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice. Genes (Basel) 2023; 14:2027. [PMID: 38002970 PMCID: PMC10671530 DOI: 10.3390/genes14112027] [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: 09/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.
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Affiliation(s)
- Guangtong Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoxian Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Mo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Xue P, Wen XX, Gong K, Wang BF, Xu P, Lin ZC, Peng ZQ, Fu JL, Yu P, Sun LP, Zhang YX, Cao LM, Cao LY, Cheng SH, Wu WX, Zhan XD. qHD5 encodes an AP2 factor that suppresses rice heading by down-regulating Ehd2 expression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111446. [PMID: 36041562 DOI: 10.1016/j.plantsci.2022.111446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/19/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Heading date is crucial for rice reproduction and the geographical expansion of cultivation. We fine-mapped qHD5 and identified LOC_Os05g03040, a gene that encodes an AP2 transcription factor, as the candidate gene of qHD5 in our previous study. In this article, using two near-isogenic lines NIL(BG1) and NIL(XLJ), which were derived from the progeny of the cross between BigGrain1 (BG1) and Xiaolijing (XLJ), we verified that LOC_Os05g03040 represses heading date in rice through genetic complementation and CRISPR/Cas9 gene-editing experiments. Complementary results showed that qHD5 is a semi-dominant gene and that the qHD5XLJ and qHD5BG1 alleles are both functional. The homozygous mutant line generated from knocking out qHD5XLJ in NIL(XLJ) headed earlier than NIL(XLJ) under both short-day and long-day conditions. In addition, the homozygous mutant line of qHD5BG1 in NIL(BG1) also headed slightly earlier than NIL(BG1). All of these results show that qHD5 represses the heading date in rice. Transient expression showed that the qHD5 protein localizes to the nucleus. Transactivation activity assays showed that the C-terminus is the critical site that affects self-activation in qHD5XLJ. qRT-PCR analysis revealed that qHD5 represses flowering by down-regulating Ehd2. qHD5 may have been selected during indica rice domestication.
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Affiliation(s)
- Pao Xue
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Xuzhou Institute of Agricultural Sciences, Xuzhou 221131, China
| | - Xiao-Xia Wen
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ke Gong
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Bei-Fang Wang
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Peng Xu
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ze-Chuan Lin
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ze-Qun Peng
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jun-Lin Fu
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ping Yu
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Lian-Ping Sun
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ying-Xin Zhang
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Li-Ming Cao
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Li-Yong Cao
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Northern Center of China National Rice Research Institute, Shuangyashan 155600, China
| | - Shi-Hua Cheng
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Wei-Xun Wu
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Xiao-Deng Zhan
- China National Center for Rice Improvement & State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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5
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Lee SJ, Kang K, Lim JH, Paek NC. Natural alleles of CIRCADIAN CLOCK ASSOCIATED1 contribute to rice cultivation by fine-tuning flowering time. PLANT PHYSIOLOGY 2022; 190:640-656. [PMID: 35723564 PMCID: PMC9434239 DOI: 10.1093/plphys/kiac296] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The timing of flowering is a crucial factor for successful grain production at a wide range of latitudes. Domestication of rice (Oryza sativa) included selection for natural alleles of flowering-time genes that allow rice plants to adapt to broad geographic areas. Here, we describe the role of natural alleles of CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1) in cultivated rice based on analysis of single-nucleotide polymorphisms deposited in the International Rice Genebank Collection Information System database. Rice varieties harboring japonica-type OsCCA1 alleles (OsCCA1a haplotype) flowered earlier than those harboring indica-type OsCCA1 alleles (OsCCA1d haplotype). In the japonica cultivar "Dongjin", a T-DNA insertion in OsCCA1a resulted in late flowering under long-day and short-day conditions, indicating that OsCCA1 is a floral inducer. Reverse transcription quantitative PCR analysis showed that the loss of OsCCA1a function induces the expression of the floral repressors PSEUDO-RESPONSE REGULATOR 37 (OsPRR37) and Days to Heading 8 (DTH8), followed by repression of the Early heading date 1 (Ehd1)-Heading date 3a (Hd3a)-RICE FLOWERING LOCUS T 1 (RFT1) pathway. Binding affinity assays indicated that OsCCA1 binds to the promoter regions of OsPRR37 and DTH8. Naturally occurring OsCCA1 alleles are evolutionarily conserved in cultivated rice (O. sativa). Oryza rufipogon-I (Or-I) and Or-III type accessions, representing the ancestors of O. sativa indica and japonica, harbored indica- and japonica-type OsCCA1 alleles, respectively. Taken together, our results demonstrate that OsCCA1 is a likely domestication locus that has contributed to the geographic adaptation and expansion of cultivated rice.
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Affiliation(s)
| | | | - Jung-Hyun Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
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6
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Fjellheim S, Young DA, Paliocha M, Johnsen SS, Schubert M, Preston JC. Major niche transitions in Pooideae correlate with variation in photoperiodic flowering and evolution of CCT domain genes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4079-4093. [PMID: 35394528 PMCID: PMC9232202 DOI: 10.1093/jxb/erac149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
The external cues that trigger timely flowering vary greatly across tropical and temperate plant taxa, the latter relying on predictable seasonal fluctuations in temperature and photoperiod. In the grass family (Poaceae) for example, species of the subfamily Pooideae have become specialists of the northern temperate hemisphere, generating the hypothesis that their progenitor evolved a flowering response to long days from a short-day or day-neutral ancestor. Sampling across the Pooideae, we found support for this hypothesis, and identified several secondary shifts to day-neutral flowering and one to short-day flowering in a tropical highland clade. To explain the proximate mechanisms for the secondary transition back to short-day-regulated flowering, we investigated the expression of CCT domain genes, some of which are known to repress flowering in cereal grasses under specific photoperiods. We found a shift in CONSTANS 1 and CONSTANS 9 expression that coincides with the derived short-day photoperiodism of our exemplar species Nassella pubiflora. This sets up the testable hypothesis that trans- or cis-regulatory elements of these CCT domain genes were the targets of selection for major niche shifts in Pooideae grasses.
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Affiliation(s)
| | - Darshan A Young
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Martin Paliocha
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Sylvia Sagen Johnsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Marian Schubert
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Jill C Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT 05405, USA
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7
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Zhou S, Zhu S, Cui S, Hou H, Wu H, Hao B, Cai L, Xu Z, Liu L, Jiang L, Wang H, Wan J. Transcriptional and post-transcriptional regulation of heading date in rice. THE NEW PHYTOLOGIST 2021; 230:943-956. [PMID: 33341945 PMCID: PMC8048436 DOI: 10.1111/nph.17158] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 05/04/2023]
Abstract
Rice is a facultative short day (SD) plant. In addition to serving as a model plant for molecular genetic studies of monocots, rice is a staple crop for about half of the world's population. Heading date is a critical agronomic trait, and many genes controlling heading date have been cloned over the last 2 decades. The mechanism of flowering in rice from recognition of day length by leaves to floral activation in the shoot apical meristem has been extensively studied. In this review, we summarise current progress on transcriptional and post-transcriptional regulation of heading date in rice, with emphasis on post-translational modifications of key regulators, including Heading date 1 (Hd1), Early heading date 1 (Ehd1), Grain number, plant height, and heading date7 (Ghd7). The contribution of heading date genes to heterosis and the expansion of rice cultivation areas from low-latitude to high-latitude regions are also discussed. To overcome the limitations of diverse genetic backgrounds used in heading date studies and to gain a clearer understanding of flowering in rice, we propose a systematic collection of genetic resources in a common genetic background. Strategies in breeding adapted cultivars by rational design are also discussed.
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Affiliation(s)
- Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haigang Hou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haoqin Wu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Benyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Liang Cai
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Zhuang Xu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
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8
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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9
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Fujino K. Days to heading, controlled by the heading date genes, Hd1 and DTH8, limits rice yield-related traits in Hokkaido, Japan. BREEDING SCIENCE 2020; 70:277-282. [PMID: 32714049 PMCID: PMC7372023 DOI: 10.1270/jsbbs.19151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/05/2019] [Indexed: 06/11/2023]
Abstract
A key aspect of rice breeding programs is the optimization of days to heading (DTH) for maximizing grain productivity in cultivation areas. Here, the effects of genotypes for heading date on yield-related traits in rice (culm and panicle length (CL and PL), panicle number (PN), and total number of seeds) were investigated. Heading date 1 (Hd1) and Days to heading 8 (DTH8) are the main controllers of the variation in heading date in the rice population of Hokkaido, Japan. Thus, an F2 population (n = 192) derived from a cross between Kitaibuki (Hd1dth8) and Akage (hd1DTH8) was developed. Significant differences in DTH were found among all combinations. Each genotype for heading date showed variations in the yield-related traits without a significant difference. However, DTH exhibited high positive coefficient values (more than 0.709) with the yield-related traits except for PN, which had a negative coefficient value of -0.431. A later heading date resulted in a longer growth duration and a higher yield with a combination of longer PL and CL and lower PN. These results suggest that DTH limits the yield-related traits rather than the genotype for heading date.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
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10
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Fujino K, Yamanouchi U. Genetic effect of a new allele for the flowering time locus Ghd7 in rice. BREEDING SCIENCE 2020; 70:342-346. [PMID: 32714056 PMCID: PMC7372035 DOI: 10.1270/jsbbs.19112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/02/2020] [Indexed: 06/11/2023]
Abstract
The optimization of flowering time is a key aspect in maximizing grain productivity in rice. Allelic variations in genes for flowering time are major drivers in the wide adaptability of cultivated rice around the world. Here, we identified a novel allele of flowering time gene Grain number, plant height and heading date 7 (Ghd7). Loss-of-function ghd7, Ghd7-0a, is important for extremely early flowering time for adaptability to cultivation in Hokkaido, Japan. However, the rice variety Sorachi lacks a key functional nucleotide polymorphism of Ghd7, which results in a loss of function of the gene. Based on the sequence of Ghd7 allele in Sorachi, we identified the insertion of a transposon-like sequence at an upstream site of Ghd7. Segregation analysis using an F2 population derived from the cross between Hoshinoyume and Sorachi demonstrated that the Ghd7 locus contributed to extremely early flowering time in Sorachi. This Ghd7 allele in Sorachi showed a weak function in terms of delay of flowering time, compared with loss-of-function allele, and a distinct distribution in northern Japan.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
| | - Utako Yamanouchi
- Institute of Crop Science, National Agricultural Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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11
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Fujino K, Ikegaya T. A novel genotype DATTO5 developed using the five genes exhibits the fastest heading date designed in rice. BREEDING SCIENCE 2020; 70:193-199. [PMID: 32523401 PMCID: PMC7272244 DOI: 10.1270/jsbbs.19113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 06/11/2023]
Abstract
The optimization of heading date is a key aspect for maximizing grain productivity in cereal crops including rice. The combinations of genes for heading date, a quantitative trait, are a major driver in the wide adaptability of cultivated rice worldwide. Here, we identified a novel QTL, qDTH3 (quantitative trait locus for days-to-heading on chromosome 3), for early flowering time in the F2 population derived from a cross between Hoshinoyume (HS) and Daichinohoshi (DH) among local rice populations with extremely early heading date. The DH allele at qDTH3, qDTH3DH , headed 2.7 days earlier than the HS allele at qDTH3, qDTH3HS . We sought to design a genotype for earlier heading date by pyramiding of five heading date genes. We designated this aggregate of the five genes as DATTO5. Plants with DATTO5 were selected from the F2 population derived from a cross between DH and HShd5, which is a near-isogenic line carrying a loss-of-function of days to heading 8 in a genetic background of HS. Plants with DATTO5 exhibited earlier heading date but reduced fitness, including shorter culm and panicle length and fewer seeds compared with HS, as a representative local rice variety with extremely early heading date.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
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12
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Leng Y, Gao Y, Chen L, Yang Y, Huang L, Dai L, Ren D, Xu Q, Zhang Y, Ponce K, Hu J, Shen L, Zhang G, Chen G, Dong G, Gao Z, Guo L, Ye G, Qian Q, Zhu L, Zeng D. Using Heading date 1 preponderant alleles from indica cultivars to breed high-yield, high-quality japonica rice varieties for cultivation in south China. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:119-128. [PMID: 31141272 PMCID: PMC6920332 DOI: 10.1111/pbi.13177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/22/2023]
Abstract
Heading date 1 (Hd1) is an important gene for the regulation of flowering in rice, but its variation in major cultivated rice varieties, and the effect of this variation on yield and quality, remains unknown. In this study, we selected 123 major rice varieties cultivated in China from 1936 to 2009 to analyse the relationship between the Hd1 alleles and yield-related traits. Among these varieties, 19 haplotypes were detected in Hd1, including two major haplotypes (H8 and H13) in the japonica group and three major haplotypes (H14, H15 and H16) in the indica group. Analysis of allele frequencies showed that the secondary branch number was the major aimed for Chinese indica breeding. In the five major haplotypes, SNP316 (C-T) was the only difference between the two major japonica haplotypes, and SNP495 (C-G) and SNP614 (G-A) are the major SNPs in the three indica haplotypes. Association analysis showed that H16 is the most preponderant allele in modern cultivated Chinese indica varieties. Backcrossing this allele into the japonica variety Chunjiang06 improved yield without decreasing grain quality. Therefore, our analysis offers a new strategy for utilizing these preponderant alleles to improve yield and quality of japonica varieties for cultivation in the southern areas of China.
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Affiliation(s)
- Yujia Leng
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yihong Gao
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Long Chen
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yaolong Yang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Lichao Huang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Liping Dai
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Deyong Ren
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Qiankun Xu
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Ya Zhang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Kimberly Ponce
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jiang Hu
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Lan Shen
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guangheng Zhang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guang Chen
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guojun Dong
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhenyu Gao
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Longbiao Guo
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guoyou Ye
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Qian Qian
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Li Zhu
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Dali Zeng
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
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13
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Cui Y, Wang J, Feng L, Liu S, Li J, Qiao W, Song Y, Zhang Z, Cheng Y, Zhang L, Zheng X, Yang Q. A Combination of Long-Day Suppressor Genes Contributes to the Northward Expansion of Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:864. [PMID: 32612630 PMCID: PMC7308711 DOI: 10.3389/fpls.2020.00864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/27/2020] [Indexed: 05/21/2023]
Abstract
Growing cultivated rice with a moderate heading date is the key to expanding its cultivation area and maintaining stable yields. The genes that regulate heading date are largely cloned; however, it remains unclear how genetic mutations and their combinations affect the heading date and adaptability of cultivated rice. Here, we report the analysis of genetic variation in eight long-day flowering suppressor genes (Hd1, DTH8, Ghd7, OsCOL4, DTH7, Hd6, Se5, and PhyB) and the phylogenetic relationship of eight genes. Genetic variations in DTH8, Ghd7, Hd1, DTH7, PhyB, and OsCOL4 are correlated with differences in heading date and the correlation between the genetic diversity of Hd6 and Se5 and rice heading data are weak. One group of haplotypes of DTH8, Ghd7, Hd1, DTH7, PhyB, and OsCOL4 are associated with earlier heading dates and appear to have accumulated during the northward expansion of rice cultivation. A minimum of four group A alleles of DTH8, Ghd7, Hd1, DTH7, PhyB, and OsCOL4 are required for the growth of cultivated rice at latitudes above 30°N. This study presents a preliminary investigation of the genetic patterns and adaptation mechanisms of long-day flowering suppressor genes and provides a useful reference for the molecular breeding of rice cultivars for various environments and farming systems.
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Affiliation(s)
- Yongxia Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junrui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Feng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sha Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zongqiong Zhang
- Department of Center for Crop Germplasm Resources, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xiaoming Zheng, ; Qingwen Yang,
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Department of Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xiaoming Zheng, ; Qingwen Yang,
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14
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Saito H, Okumoto Y, Tsukiyama T, Xu C, Teraishi M, Tanisaka T. Allelic Differentiation at the E1/Ghd7 Locus Has Allowed Expansion of Rice Cultivation Area. PLANTS 2019; 8:plants8120550. [PMID: 31795099 PMCID: PMC6963527 DOI: 10.3390/plants8120550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/22/2022]
Abstract
The photoperiod-insensitivity allele e1 is known to be essential for the extremely low photoperiod sensitivity of rice, and thereby enabled rice cultivation in high latitudes (42–53° north (N)). The E1 locus regulating photoperiod-sensitivity was identified on chromosome 7 using a cross between T65 and its near-isogenic line T65w. Sequence analyses confirmed that the E1 and the Ghd7 are the same locus, and haplotype analysis showed that the e1/ghd7-0a is a pioneer allele that enabled rice production in Hokkaido (42–45° N). Further, we detected two novel alleles, e1-ret/ghd7-0ret and E1-r/Ghd7-r, each harboring mutations in the promoter region. These mutant alleles alter the respective expression profiles, leading to marked alteration of flowering time. Moreover, e1-ret/ghd7-0ret, as well as e1/ghd7-0a, was found to have contributed to the establishment of Hokkaido varieties through the marked reduction effect on photoperiod sensitivity, whereas E1-r/Ghd7-r showed a higher expression than the E1/Ghd7 due to the nucleotide substitutions in the cis elements. The haplotype analysis showed that two photoperiod-insensitivity alleles e1/ghd7-0a and e1-ret/ghd7-0ret, originated independently from two sources. These results indicate that naturally occurring allelic variation at the E1/Ghd7 locus allowed expansion of the rice cultivation area through diversification and fine-tuning of flowering time.
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Affiliation(s)
- Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- Tropical Agriculture Research Front, Japan International Research Center of Agricultural Science, Ishigaki, Okinawa 907-0002, Japan
- Correspondence: ; Tel.: +81-980-82-2396
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
| | - Takuji Tsukiyama
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- Faculty of Agriculture, Kindai University, Nara, Nara 631-8505, Japan
| | - Chong Xu
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- School of Agriculture, Kibi International University, Minami-Awaji 656-0484, Japan
| | - Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
| | - Takatoshi Tanisaka
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan; (Y.O.); (T.T.); (C.X.); (M.T.); (T.T.)
- School of Agriculture, Kibi International University, Minami-Awaji 656-0484, Japan
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15
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Fujino K, Yamanouchi U, Nonoue Y, Obara M, Yano M. Switching genetic effects of the flowering time gene Hd1 in LD conditions by Ghd7 and OsPRR37 in rice. BREEDING SCIENCE 2019; 69:127-132. [PMID: 31086490 PMCID: PMC6507719 DOI: 10.1270/jsbbs.18060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/01/2018] [Indexed: 05/20/2023]
Abstract
Flowering time control in plants is a major limiting factor on the range of species. Day length, perceived via the photoperiodic pathway, is a critical factor for the induction of flowering. The module of GIGANTEA (GI)-CONSTANS (CO)-FLOWERING LOCUS T in the long day (LD) plant Arabidopsis is conserved in diverse plant species including the short day (SD) plant rice, where this module comprises OsGI-Heading date 1 (Hd1)-Heading date 3a. Hd1, the rice ortholog of Arabidopsis CO, has dual functions in the regulation of flowering time, promoting flowering in SD conditions and delaying it in LD conditions. We herein show genetic interactions among three LD repressor genes: Hd1, Grain number, plant height and heading date 7 (Ghd7), and Oryza sativa Pseudo-Response Regulator37 (OsPRR37). Genetic analyses, including segregation analyses, evaluations of near isogenic lines, and transformation for flowering time demonstrated that Hd1 promoted flowering time in inductive SD and non-inductive LD conditions in genetic condition of loss-of-function Ghd7 and OsPRR37 (ghd7osprr37) in rice. Functional Ghd7 or OsPRR37 may switch the genetic effects of Hd1 from the promotion to the delay of flowering times in LD conditions.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
- Corresponding author (e-mail: )
| | - Utako Yamanouchi
- Institute of Crop Science, National Agricultural Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Mari Obara
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
| | - Masahiro Yano
- Institute of Crop Science, National Agricultural Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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16
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Stephenson E, Estrada S, Meng X, Ourada J, Muszynski MG, Habben JE, Danilevskaya ON. Over-expression of the photoperiod response regulator ZmCCT10 modifies plant architecture, flowering time and inflorescence morphology in maize. PLoS One 2019; 14:e0203728. [PMID: 30726207 PMCID: PMC6364868 DOI: 10.1371/journal.pone.0203728] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/11/2019] [Indexed: 11/19/2022] Open
Abstract
Maize originated as a tropical plant that required short days to transition from vegetative to reproductive development. ZmCCT10 [CO, CONSTANS, CO-LIKE and TIMING OF CAB1 (CCT) transcription factor family] is a regulator of photoperiod response and was identified as a major QTL controlling photoperiod sensitivity in maize. We modulated expression of ZmCCT10 in transgenic maize using two constitutive promoters with different expression levels. Transgenic plants over expressing ZmCCT10 with either promoter were delayed in their transition from vegetative to reproductive development but were not affected in their switch from juvenile-to-adult vegetative growth. Strikingly, transgenic plants containing the stronger expressing construct had a prolonged period of vegetative growth accompanied with dramatic modifications to plant architecture that impacted both vegetative and reproductive traits. These plants did not produce ears, but tassels were heavily branched. In more than half of the transgenic plants, tassels were converted into a branched leafy structure resembling phyllody, often composed of vegetative plantlets. Analysis of expression modules controlling the floral transition and meristem identity linked these networks to photoperiod dependent regulation, whereas phase change modules appeared to be photoperiod independent. Results from this study clarified the influence of the photoperiod pathway on vegetative and reproductive development and allowed for the fine-tuning of the maize flowering time model.
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Affiliation(s)
- Elizabeth Stephenson
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Stacey Estrada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Xin Meng
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Jesse Ourada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Michael G. Muszynski
- University of Hawaii at Manoa, Tropical Plant and Soil Sciences, Honolulu, Hawaii; United States of America
| | - Jeffrey E. Habben
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Olga N. Danilevskaya
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
- * E-mail:
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17
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Wu W, Zheng XM, Chen D, Zhang Y, Ma W, Zhang H, Sun L, Yang Z, Zhao C, Zhan X, Shen X, Yu P, Fu Y, Zhu S, Cao L, Cheng S. OsCOL16, encoding a CONSTANS-like protein, represses flowering by up-regulating Ghd7 expression in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 260:60-69. [PMID: 28554475 DOI: 10.1016/j.plantsci.2017.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 05/22/2023]
Abstract
Flowering time is an important agronomic trait that coordinates the plant life cycle with regional adaptability and thereby impacts yield potentials for cereal crops. The CONSTANS (CO)-like gene family plays vital roles in the regulation of flowering time. CO-like proteins are typically divided into four phylogenetic groups in rice. Several genes from groups I, III, and IV have been functionally characterized, though little is known about the genes of group II in rice. We report the functional characterization in rice of a constitutive floral inhibitor, OsCOL16, encoding a group-II CO-like protein that delays flowering time and increases plant height and grain yield. Overexpression of OsCOL16 resulted in late heading under both long-day and short-day conditions. OsCOL16 expression exhibits a diurnal oscillation and serves as a transcription factor with transcriptional activation activity. We determined that OsCOL16 up-regulates the expression of the floral repressor Ghd7, leading to down-regulation of the expression of Ehd1, Hd3a, and RFT1. Moreover, genetic diversity and evolutionary analyses suggest that remarkable differences in flowering times correlate with two major alleles of OsCOL16. Our combined molecular biology and phylogeographic analyses revealed that OsCOL16 plays an important role in regulating rice photoperiodic flowering, allowing for environmental adaptation of rice.
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Affiliation(s)
- Weixun Wu
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Xiao-Ming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Daibo Chen
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Yingxin Zhang
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Weiwei Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Huan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lianping Sun
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Zhengfu Yang
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Chunde Zhao
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Xiaodeng Zhan
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Xihong Shen
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Ping Yu
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Yaping Fu
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Liyong Cao
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China.
| | - Shihua Cheng
- Zhejiang Key Laboratory of Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China.
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18
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Hori K, Matsubara K, Yano M. Genetic control of flowering time in rice: integration of Mendelian genetics and genomics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2241-2252. [PMID: 27695876 DOI: 10.1007/s00122-016-2773-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/12/2016] [Indexed: 05/20/2023]
Abstract
Integration of previous Mendelian genetic analyses and recent molecular genomics approaches, such as linkage mapping and QTL cloning, dramatically strengthened our current understanding of genetic control of rice flowering time. Flowering time is one of the most important agronomic traits for seed production in rice (Oryza sativa L.). It is controlled mainly by genes associated with photoperiod sensitivity, particularly in short-day plants such as rice. Since the early twentieth century, rice breeders and researchers have been interested in elucidating the genetic basis of flowering time because its modification is important for regional adaptation and yield optimization. Although flowering time is a complex trait controlled by many quantitative trait loci (QTLs), classical genetic studies have shown that many associated genes are inherited in accordance with Mendelian laws. Decoding the rice genome sequence opened a new era in understanding the genetic control of flowering time on the basis of genome-wide mapping and gene cloning. Heading date 1 (Hd1) was the first flowering time QTL to be isolated using natural variation in rice. Recent accumulation of information on rice genome has facilitated the cloning of other QTLs, including those with minor effects on flowering time. This information has allowed us to rediscover some of the flowering genes that were identified by classical Mendelian genetics. The genes characterized so far, including Hd1, have been assigned to specific photoperiod pathways. In this review, we provide an overview of the studies that led to an in-depth understanding of the genetic control of flowering time in rice, and of the current state of improving and fine-tuning this trait for rice breeding.
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