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Pandey S, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK. The potentialities of omics resources for millet improvement. Funct Integr Genomics 2023; 23:210. [PMID: 37355501 DOI: 10.1007/s10142-023-01149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.
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Affiliation(s)
- Saurabh Pandey
- Department of Agricultural, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Samastipur, Bihar, 848125, India.
| | - Priyanka Jaiswal
- Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Mithilesh Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
| | - Khem Raj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan, 305817, India
| | - Satish Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
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Song JS, Im JH, Park YH, Lim SH, Yook MJ, Lee BW, Kim JW, Kim DS. Modeling the Effects of Elevated Temperature and Weed Interference on Rice Grain Yield. FRONTIERS IN PLANT SCIENCE 2021; 12:663779. [PMID: 34354717 PMCID: PMC8330814 DOI: 10.3389/fpls.2021.663779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/16/2021] [Indexed: 06/01/2023]
Abstract
A 3-year phytotron study was conducted in Suwon (37.27°N, 126.99°E), Korea, to evaluate and model the effects of elevated temperature on rice-weed competition. The dry weight and the number of panicles in rice were the most susceptible components to weed interference during the early growth of rice, regardless of weed species, while other yield components, including the number of grains, % ripened grain, and 1000-grain weight, were more susceptible to elevated temperature. A rectangular hyperbolic model well demonstrated that rice grain yield was affected by weed interference under elevated temperature, showing that the competitiveness of late watergrass (Echinochloa oryzicola) and water chestnut (Eleocharis kuroguwai) increased under elevated temperature conditions. Quadratic and linear models well described the effects of elevated temperature on the weed-free rice grain yield and weed competitiveness values of the rectangular hyperbolic model for the two weed species, respectively. Thus, a combined rectangular hyperbolic model incorporated with the quadratic and linear models well demonstrated the effects of elevated temperature and weed interference on rice grain yield across years. Using the combined model and estimated parameters, the rice grain yields were estimated to be 58.9, 48.5, 41.3, and 35.9% of the yields under weed-free conditions for 80 plants m-2 of late watergrass and 86.8, 64.3, 51.1, and 42.3% of the yields under weed-free conditions for 80 plants m-2 of water chestnut at 1,300, 1,500, 1,700, and 1,900°C·days of accumulated growing degree days (GDD; from transplanting to flowering, 89 days), respectively. The combined model developed in this study can provide an empirical description of both the elevated temperature and weed interference effects on rice yield and can be used for predicting rice grain yields due to weed interference under future elevated temperature conditions.
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Affiliation(s)
- Jong-Seok Song
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Institute of Plasma Technology, Korea Institute of Fusion Energy, Gunsan, South Korea
| | - Ji-Hoon Im
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Mushroom Research Division, Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, South Korea
| | - Yeon-Ho Park
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Soo-Hyun Lim
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Min-Jung Yook
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byun-Woo Lee
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Won Kim
- Crop Protection Division, Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Do-Soon Kim
- Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Lim SH, Kim H, Noh TK, Lim JS, Yook MJ, Kim JW, Yi JH, Kim DS. Baseline Sensitivity of Echinochloa crus-gall and E. oryzicola to Florpyrauxifen-Benzyl, a New Synthetic Auxin Herbicide, in Korea. FRONTIERS IN PLANT SCIENCE 2021; 12:656642. [PMID: 34177979 PMCID: PMC8221188 DOI: 10.3389/fpls.2021.656642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Echinochloa species is one of the most problematic weed species due to its high competitiveness and increasing herbicide resistance. Florpyrauxifen-benzyl, a new auxin herbicide, was recently introduced for Echinochloa management; however, the potential risk for the development of herbicide resistance in Echinochloa species has not been well-investigated. Thus, this study was conducted to evaluate the baseline sensitivity of Echinochloa species to florpyrauxifen-benzyl to estimate the risk of future resistance development. A total of 70 and 71 accessions of Echinochloa crus-galli and Echinochloa oryzicola were collected from paddy fields in Korea, respectively. These two Echinochloa species were grown in plastic pots up to the 5-leaf stage, and treated with florpyrauxifen-benzyl at a range of doses from 2.2 g to 70.0 g a.i. ha-1. Nonlinear regression analyses revealed that GR50 values for E. oryzicola ranged from 4.54 g to 29.66 g a.i. ha-1, giving a baseline sensitivity index (BSI) of 6.53, while those for E. crus-galli ranged from 6.15 g to 16.06 g a.i. ha-1, giving a BSI of 2.61. Our findings suggest that E. oryzicola has a greater potential risk than E. crus-galli for the development of metabolism-based resistance to florpyrauxifen-benzyl.
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Affiliation(s)
- Soo-Hyun Lim
- Department of Plant Science, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Harim Kim
- Department of Plant Science, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Tae-Kyeong Noh
- Department of Plant Science, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Ji-Soo Lim
- Department of Plant Science, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Min-Jung Yook
- Department of Plant Science, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Won Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jee-Hwan Yi
- Integrated Field Science, Corteva Agriscience, Indianapolis, IN, United States
| | - Do-Soon Kim
- Department of Plant Science, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Singh RK, Muthamilarasan M, Prasad M. Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement. J Biotechnol 2021; 327:64-73. [PMID: 33422569 DOI: 10.1016/j.jbiotec.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi 110067, India.
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Genetic and genomic resources, and breeding for accelerating improvement of small millets: current status and future interventions. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00322-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AbstractCurrent agricultural and food systems encourage research and development on major crops, neglecting regionally important minor crops. Small millets include a group of small- seeded cereal crops of the grass family Poaceae. This includes finger millet, foxtail millet, proso millet, barnyard millet, kodo millet, little millet, teff, fonio, job’s tears, guinea millet, and browntop millet. Small millets are an excellent choice to supplement major staple foods for crop and dietary diversity because of their diverse adaptation on marginal lands, less water requirement, lesser susceptibility to stresses, and nutritional superiority compared to major cereal staples. Growing interest among consumers about healthy diets together with climate-resilient features of small millets underline the necessity of directing more research and development towards these crops. Except for finger millet and foxtail millet, and to some extent proso millet and teff, other small millets have received minimal research attention in terms of development of genetic and genomic resources and breeding for yield enhancement. Considerable breeding efforts were made in finger millet and foxtail millet in India and China, respectively, proso millet in the United States of America, and teff in Ethiopia. So far, five genomes, namely foxtail millet, finger millet, proso millet, teff, and Japanese barnyard millet, have been sequenced, and genome of foxtail millet is the smallest (423-510 Mb) while the largest one is finger millet (1.5 Gb). Recent advances in phenotyping and genomics technologies, together with available germplasm diversity, could be utilized in small millets improvement. This review provides a comprehensive insight into the importance of small millets, the global status of their germplasm, diversity, promising germplasm resources, and breeding approaches (conventional and genomic approaches) to accelerate climate-resilient and nutrient-dense small millets for sustainable agriculture, environment, and healthy food systems.
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Renganathan VG, Vanniarajan C, Karthikeyan A, Ramalingam J. Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction. Front Genet 2020; 11:500. [PMID: 32655612 PMCID: PMC7325689 DOI: 10.3389/fgene.2020.00500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/22/2020] [Indexed: 01/09/2023] Open
Abstract
Barnyard millet (Echinochloa species) has become one of the most important minor millet crops in Asia, showing a firm upsurge in world production. The genus Echinochloa comprises of two major species, Echinochloa esculenta and Echinochloa frumentacea, which are predominantly cultivated for human consumption and livestock feed. They are less susceptible to biotic and abiotic stresses. Barnyard millet grain is a good source of protein, carbohydrate, fiber, and, most notably, contains more micronutrients (iron and zinc) than other major cereals. Despite its nutritional and agronomic benefits, barnyard millet has remained an underutilized crop. Over the past decades, very limited attempts have been made to study the features of this crop. Hence, more concerted research efforts are required to characterize germplasm resources, identify trait-specific donors, develop mapping population, and discover QTL/gene (s). The recent release of genome and transcriptome sequences of wild and cultivated Echinochloa species, respectively has facilitated in understanding the genetic architecture and decoding the rapport between genotype and phenotype of micronutrients and agronomic traits in this crop. In this review, we highlight the importance of barnyard millet in the current scenario and discuss the up-to-date status of genetic and genomics research and the research gaps to be worked upon by suggesting directions for future research to make barnyard millet a potential crop in contributing to food and nutritional security.
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Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Adhimoolam Karthikeyan
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Jegadeesan Ramalingam
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
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Fukushima A, Kuroha T, Nagai K, Hattori Y, Kobayashi M, Nishizawa T, Kojima M, Utsumi Y, Oikawa A, Seki M, Sakakibara H, Saito K, Ashikari M, Kusano M. Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress. Metabolites 2020; 10:metabo10020068. [PMID: 32075002 PMCID: PMC7074043 DOI: 10.3390/metabo10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Yoko Hattori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Yoshinori Utsumi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata 997-8555, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 263-8522, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Correspondence:
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Kuroha T, Nagai K, Kurokawa Y, Nagamura Y, Kusano M, Yasui H, Ashikari M, Fukushima A. eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1753. [PMID: 29081784 PMCID: PMC5645499 DOI: 10.3389/fpls.2017.01753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/25/2017] [Indexed: 05/09/2023]
Abstract
To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.
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Affiliation(s)
- Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- *Correspondence: Takeshi Kuroha, Atsushi Fukushima,
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Yusuke Kurokawa
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Yoshiaki Nagamura
- Genome Resource Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- *Correspondence: Takeshi Kuroha, Atsushi Fukushima,
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Nah G, Lee M, Kim DS, Rayburn AL, Voigt T, Lee DK. Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress. PLoS One 2016; 11:e0152294. [PMID: 27032112 PMCID: PMC4816275 DOI: 10.1371/journal.pone.0152294] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/12/2016] [Indexed: 12/29/2022] Open
Abstract
Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.
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Affiliation(s)
- Gyoungju Nah
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea
| | - Moonsub Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
| | - Do-Soon Kim
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea
| | - A. Lane Rayburn
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
| | - Thomas Voigt
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
| | - D. K. Lee
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1120 S. Goodwin Ave, Urbana, Illinois 61801, United States of America
- * E-mail:
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Nah G, Im JH, Kim JW, Kim K, Lim J, Choi AY, Choi IY, Yang TJ, Park TS, Lee D, Kim DS. The complete chloroplast genomes of three Korean Echinochloa crus-galli accessions. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4357-4358. [PMID: 26466198 DOI: 10.3109/19401736.2015.1089499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast (cp) genomes of three Echinochloa crus-galli accessions (KR822684, KR822685, and KR822686) are reported in this work. The cp genome size is similar in three accessions, ranging from 139 846 bp to 139 860 bp. All three genomes have two inverted repeats (IR) of 22 748 bp per each IR with a large single copy (LSC) region of 81 833-81 844 bp and a small single copy (SSC) region of 12 517-12 520 bp. The total of 131 genes was identified in individual accession. Phylogenetic analysis revealed three Korean Echinochloa accessions belonged to E. crus-galli, and diverged less than 0.1 million years ago (Mya).
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Affiliation(s)
- Gyoungju Nah
- a Department of Plant Science , Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Ji-Hoon Im
- a Department of Plant Science , Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Jin-Won Kim
- a Department of Plant Science , Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Kyunghee Kim
- a Department of Plant Science , Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Jongsung Lim
- b National Instrumentation Center for Environment Management (NICEM), College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Ah Young Choi
- b National Instrumentation Center for Environment Management (NICEM), College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Ik-Young Choi
- b National Instrumentation Center for Environment Management (NICEM), College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Tae-Jin Yang
- a Department of Plant Science , Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
| | - Tae-Seon Park
- c National Academy of Agricultural Science , RDA, Wanju , Jeollabuk-Do , Korea , and
| | - DoKyoung Lee
- a Department of Plant Science , Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea.,d Department of Crop Science , University of Illinois , Urbana-Champaign , Champaign , IL , USA
| | - Do-Soon Kim
- a Department of Plant Science , Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Korea
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Correction: Uncovering the Differential Molecular Basis of Adaptive Diversity in Three Echinochloa Leaf Transcriptomes. PLoS One 2015; 10:e0139534. [PMID: 26407143 PMCID: PMC4583394 DOI: 10.1371/journal.pone.0139534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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