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Li Q, Hou Y, Wang Q, Pan X, Sun Y, Zhu X, Li H, Guo M, Gao Y. Phytochrome interacting factor ZmPIF6 simultaneously enhances chilling tolerance and grain size in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108954. [PMID: 39053314 DOI: 10.1016/j.plaphy.2024.108954] [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: 03/20/2024] [Revised: 07/13/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Chilling is a prevalent type of abiotic stress that adversely affects agricultural productivity worldwide. Phytochrome interacting factors (PIFs) are a group of transcription factor that are crucial for plant abiotic stress response. Our research reveals that the maize PIF family gene ZmPIF6 is responsive to chilling stress, which mitigates the negative impacts of chilling through reducing reactive oxygen species content and enhancing cell membrane stability at the physiological and biochemical levels. We also found that the ZmPIF6 overexpression lines showed a significant increase in grain size, encompassing both length and width, which mainly due to the increase in cell size. In addition, digital gene expression results suggested that ZmPIF6 regulates the expression of cold-related and grain size-related genes in rice. In light of these findings, ZmPIF6 has a hopeful prospect as a candidate gene of chilling tolerance and crop productivity in the transgenic breeding.
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Affiliation(s)
- Qian Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yingxian Hou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Qingwen Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Xiaowen Pan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yixuan Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoqi Zhu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Hua Li
- Hezhou Academy of Agricultural Sciences, Hezhou, 542813, China
| | - Minliang Guo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
| | - Yong Gao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
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Terletskaya NV, Shadenova EA, Litvinenko YA, Ashimuly K, Erbay M, Mamirova A, Nazarova I, Meduntseva ND, Kudrina NO, Korbozova NK, Djangalina ED. Influence of Cold Stress on Physiological and Phytochemical Characteristics and Secondary Metabolite Accumulation in Microclones of Juglans regia L. Int J Mol Sci 2024; 25:4991. [PMID: 38732208 PMCID: PMC11084536 DOI: 10.3390/ijms25094991] [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: 04/16/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
The current study investigated the impact of cold stress on the morphological, physiological, and phytochemical properties of Juglans regia L. (J. regia) using in vitro microclone cultures. The study revealed significant stress-induced changes in the production of secondary antioxidant metabolites. According to gas chromatography-mass spectrometry (GC-MS) analyses, the stress conditions profoundly altered the metabolism of J. regia microclones. Although the overall spectrum of metabolites was reduced, the production of key secondary antioxidant metabolites significantly increased. Notably, there was a sevenfold (7×) increase in juglone concentration. These findings are crucial for advancing walnut metabolomics and enhancing our understanding of plant responses to abiotic stress factors. Additionally, study results aid in identifying the role of individual metabolites in these processes, which is essential for developing strategies to improve plant resilience and tolerance to adverse conditions.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Elvira A. Shadenova
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Yuliya A. Litvinenko
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Kazhybek Ashimuly
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Malika Erbay
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Aigerim Mamirova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
| | - Irada Nazarova
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Nataliya D. Meduntseva
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Nataliya O. Kudrina
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Nazym K. Korbozova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Erika D. Djangalina
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
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Bhupenchandra I, Chongtham SK, Gangarani Devi A, Dutta P, Lamalakshmi E, Mohanty S, Choudhary AK, Das A, Sarika K, Kumar S, Yumnam S, Sagolsem D, Rupert Anand Y, Bhutia DD, Victoria M, Vinodh S, Tania C, Dhanachandra Sharma A, Deb L, Sahoo MR, Seth CS, Swapnil P, Meena M. Harnessing weedy rice as functional food and source of novel traits for crop improvement. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38436101 DOI: 10.1111/pce.14868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.
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Affiliation(s)
- Ingudam Bhupenchandra
- ICAR-Farm Science Centre Tamenglong, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, Manipur, India
| | - Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Ayam Gangarani Devi
- ICAR Research Complex for North Eastern Hill Region, Tripura Centre Lembucherra, Tripura, India
| | - Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Elangbam Lamalakshmi
- ICAR Research Complex for North Eastern Hill Region, Sikkim Centre, Tadong, Sikkim, India
| | - Sansuta Mohanty
- Molecular Biology and Biotechnology Department, Faculty of Agricultural Sciences, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Anil K Choudhary
- Division of Crop Production, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Anup Das
- ICAR Research Complex for North Eastern Hill Region, Lembucherra, Tripura, India
| | - Konsam Sarika
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Plant Pathology, B.M. College of Agriculture, Khandwa, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, Madhya Pradesh, India
| | - Sonika Yumnam
- All India Coordinated Research Project on Chickpea, Central Agricultural University, Imphal, Manipur, India
| | - Diana Sagolsem
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Y Rupert Anand
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Dawa Dolma Bhutia
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - M Victoria
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - S Vinodh
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Chongtham Tania
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Lipa Deb
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Manas Ranjan Sahoo
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Prashant Swapnil
- Department of Botany, School of Basic Science, Central University of Punjab, Bhatinda, Punjab, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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Kalve S, House MA, Tar’an B. Freezing stress response of wild and cultivated chickpeas. FRONTIERS IN PLANT SCIENCE 2024; 14:1310459. [PMID: 38375446 PMCID: PMC10876003 DOI: 10.3389/fpls.2023.1310459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024]
Abstract
Chickpea is an economically and nutritionally important grain legume globally, however, cold stress has adverse effects on its growth. In cold countries, like Canada where the growing season is short, having cold stress-tolerant varieties is crucial. Crop wild relatives of chickpea, especially Cicer reticulatum, can survive in suboptimal environments and are an important resource for crop improvement. In this study, we explored the performance of eleven C. reticulatum wild accessions and two chickpea cultivars, CDC Leader and CDC Consul, together with a cold sensitive check ILC533 under freezing stress. Freezing tolerance was scored based on a 1-9 scale. The wild relatives, particularly Kesen_075 and CudiA_152, had higher frost tolerance compared to the cultivars, which all died after frost treatment. We completed transcriptome analysis via mRNA sequencing to assess changes in gene expression in response to freezing stress and identified 6,184 differentially expressed genes (DEGs) in CDC Consul, and 7,842 DEGs in Kesen_075. GO (gene ontology) analysis of the DEGs revealed that those related to stress responses, endogenous and external stimuli responses, secondary metabolite processes, and photosynthesis were significantly over-represented in CDC Consul, while genes related to endogenous stimulus responses and photosynthesis were significantly over-represented in Kesen_075. These results are consistent with Kesen_075 being more tolerant to freezing stress than CDC Consul. Moreover, our data revealed that the expression of CBF pathway-related genes was impacted during freezing conditions in Kesen_075, and expression of these genes is believed to alleviate the damage caused by freezing stress. We identified genomic regions associated with tolerance to freezing stress in an F2 population derived from a cross between CDC Consul and Kesen_075 using QTL-seq analysis. Eight QTLs (P<0.05) on chromosomes Ca3, Ca4, Ca6, Ca7, Ca8, and two QTLs (P<0.01) on chromosomes Ca4 and Ca8, were associated with tolerance to freezing stress. Interestingly, 58 DEGs co-located within these QTLs. To our knowledge, this is the first study to explore the transcriptome and QTLs associated with freezing tolerance in wild relatives of chickpea under controlled conditions. Altogether, these findings provide comprehensive information that aids in understanding the molecular mechanism of chickpea adaptation to freezing stress and further provides functional candidate genes that can assist in breeding of freezing-stress tolerant varieties.
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Affiliation(s)
| | | | - Bunyamin Tar’an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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5
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Kumari A, Sharma P, Rani M, Laxmi V, Sahil, Sahi C, Satturu V, Katiyar-Agarwal S, Agarwal M. Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:93-108. [PMID: 38435852 PMCID: PMC10902255 DOI: 10.1007/s12298-024-01412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/13/2023] [Accepted: 01/10/2024] [Indexed: 03/05/2024]
Abstract
Rice, a critical cereal crop, grapples with productivity challenges due to its inherent sensitivity to low temperatures, primarily during the seedling and booting stages. Recognizing the polygenic complexity of cold stress signaling in rice, a meta-analysis was undertaken, focusing on 20 physiological traits integral to cold tolerance. This initiative allowed the consolidation of genetic data from 242 QTLs into 58 meta-QTLs, thereby significantly constricting the genetic and physical intervals, with 84% of meta-QTLs (MQTLs) being reduced to less than 2 Mb. The list of 10,505 genes within these MQTLs, was further refined utilizing expression datasets to pinpoint 46 pivotal genes exhibiting noteworthy differential regulation during cold stress. The study underscored the presence of several TFs such as WRKY, NAC, CBF/DREB, MYB, and bHLH, known for their roles in cold stress response. Further, ortho-analysis involving maize, barley, and Arabidopsis identified OsWRKY71, among others, as a prospective candidate for enhancing cold tolerance in diverse crop plants. In conclusion, our study delineates the intricate genetic architecture underpinning cold tolerance in rice and propounds significant candidate genes, offering crucial insights for further research and breeding strategies focused on fortifying crops against cold stress, thereby bolstering global food resilience. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01412-1.
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Affiliation(s)
- Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Mamta Rani
- Department of Botany, University of Delhi, Delhi, India
| | - Vijay Laxmi
- Department of Botany, University of Delhi, Delhi, India
| | - Sahil
- Department of Botany, University of Delhi, Delhi, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066 India
| | - Vanisree Satturu
- Professor Jayashankar, Telangana State Agricultural University, Hyderabad, India
| | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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Schläppi MR, Jessel AR, Jackson AK, Phan H, Jia MH, Edwards JD, Eizenga GC. Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1303651. [PMID: 38162313 PMCID: PMC10755946 DOI: 10.3389/fpls.2023.1303651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024]
Abstract
Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.
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Affiliation(s)
- Michael R. Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Avery R. Jessel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Aaron K. Jackson
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Huy Phan
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Melissa H. Jia
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
| | - Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United States
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Yang S, Zhou J, Li Y, Wu J, Ma C, Chen Y, Sun X, Wu L, Liang X, Fu Q, Xu Z, Li L, Huang Z, Zhu J, Jia X, Ye X, Chen R. AP2/EREBP Pathway Plays an Important Role in Chaling Wild Rice Tolerance to Cold Stress. Int J Mol Sci 2023; 24:14441. [PMID: 37833888 PMCID: PMC10572191 DOI: 10.3390/ijms241914441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Cold stress is the main factor limiting rice production and distribution. Chaling wild rice can survive in cold winters. AP2/EREBP is a known transcription factor family associated with abiotic stress. We identified the members of the AP2/EREBP transcription factor family in rice, maize, and Arabidopsis, and conducted collinearity analysis and gene family analysis. We used Affymetrix array technology to analyze the expression of AP2/EREBP family genes in Chaling wild rice and cultivated rice cultivar Pei'ai64S, which is sensitive to cold. According to the GeneChip results, the expression levels of AP2/EREBP genes in Chaling wild rice were different from those in Pei'ai64S; and the increase rate of 36 AP2/EREBP genes in Chaling wild rice was higher than that in Pei'ai64S. Meanwhile, the MYC elements in cultivated rice and Chaling wild rice for the Os01g49830, Os03g08470, and Os03g64260 genes had different promoter sequences, resulting in the high expression of these genes in Chaling wild rice under low-temperature conditions. Furthermore, we analyzed the upstream and downstream genes of the AP2/EREBP transcription factor family and studied the conservation of these genes. We found that the upstream transcription factors were more conserved, indicating that these upstream transcription factors may be more important in regulating cold stress. Meanwhile, we found the expression of AP2/EREBP pathway genes was significantly increased in recombinant inbred lines from Nipponbare crossing with Chaling wild rice, These results suggest that the AP2/EREBP signaling pathway plays an important role in Chaling wild rice tolerance to cold stress.
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Affiliation(s)
- Songjin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jingming Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Yaqi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jiacheng Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Chuan Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Yulin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Xingzhuo Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Lingli Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Xin Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Qiuping Fu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Zhengjun Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Lihua Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Zhengjian Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jianqing Zhu
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Xiaomei Jia
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Xiaoying Ye
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Rongjun Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
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8
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Pan YH, Nong BX, Chen L, Yang XH, Xia XZ, Zhang ZQ, Qing DJ, Gao J, Huang CC, Li DT, Deng GF. QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice. Genes Genomics 2023; 45:867-885. [PMID: 37209287 DOI: 10.1007/s13258-023-01394-6] [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: 05/11/2022] [Accepted: 05/01/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe. OBJECTIVE This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment. METHODS A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage. RESULTS A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11. CONCLUSIONS This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.
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Affiliation(s)
- Ying-Hua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Bao-Xuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Lei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xing-Hai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xiu-Zhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zong-Qiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Dong-Jin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Cheng-Cui Huang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Dan-Ting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Guo-Fu Deng
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
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9
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Yang J, Chen A, Wei J, Xu J, Chen S, Tang W, Liu J, Wang H. Identification of QTLs and candidate genes for rice seed germinability under low temperature using high‐density genetic mapping and RNA‐seq. Food Energy Secur 2023. [DOI: 10.1002/fes3.452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Aie Chen
- Teaching Affairs Department Yunnan Normal University Kunming China
| | - Ji Wei
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Jifen Xu
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Shengnan Chen
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
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10
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Wang W, Huang R, Wu G, Sun J, Zhu Y, Wang H. Transcriptomic and QTL Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6. PLANTS (BASEL, SWITZERLAND) 2023; 12:871. [PMID: 36840221 PMCID: PMC9961040 DOI: 10.3390/plants12040871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Low temperature is one of the major factors affecting rice germination, and low temperature germination (LTG) is an important agronomic trait. Although significant progress has been made in the study of rice LTG, the molecular mechanism of LTG remains poorly understood. To explore more rice LTG gene resources, we first demonstrated that weedy rice WR04-6 (Oryza sativa f. spontanea) had significantly higher LTG ability at 10 °C than the cultivated rice Qishanzhan (QSZ Oryza sativa L. ssp. indica). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10 °C for 10, 12 and 14 days after imbibition (DAI) of seed germination. The results of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that the differentially expressed genes (DEGs) between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to abscisic acid (ABA). This is consistent with the results of α-amylase activity, ABA and gibberellins (GA) treatment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high-density SNP genetic map were used to detect quantitative trait loci (QTL) for LTG rates. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq DEGs, sixteen candidate genes potentially associated with LTG were identified. Validation of the expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to understand the genetic basis of LTG in weedy rice and provide new genetic resources for the generation of rice germplasm with improved LTG.
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Affiliation(s)
- Wenjia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ruizhi Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Gengwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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11
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Li Z, Wang B, Luo W, Xu Y, Wang J, Xue Z, Niu Y, Cheng Z, Ge S, Zhang W, Zhang J, Li Q, Chong K. Natural variation of codon repeats in COLD11 endows rice with chilling resilience. SCIENCE ADVANCES 2023; 9:eabq5506. [PMID: 36608134 PMCID: PMC9821855 DOI: 10.1126/sciadv.abq5506] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 12/06/2022] [Indexed: 06/07/2023]
Abstract
Abnormal temperature caused by global climate change threatens the rice production. Defense signaling network for chilling has been uncovered in plants. However, less is known about repairing DNA damage produced from overwhelmed defense and its evolution during domestication. Here, we genetically identified a major QTL, COLD11, using the data-merging genome-wide association study based on an algorithm combining polarized data from two subspecies, indica and japonica, into one system. Rice loss-of-function mutations of COLD11 caused reduced chilling tolerance. Genome evolution analysis of representative rice germplasms suggested that numbers of GCG sequence repeats in the first exon of COLD11 were subjected to strong domestication selection during the northern expansion of rice planting. The repeat numbers affected the biochemical activity of DNA repair protein COLD11/RAD51A1 in renovating DNA damage under chilling stress. Our findings highlight a potential way to finely manipulate key genes in rice genome and effectively improve chilling tolerance through molecular designing.
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Affiliation(s)
- Zhitao Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Luo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinjuan Wang
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing, 100181, China
| | - Zhihui Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuda Niu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Song Ge
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Zhang
- LSC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Jingyu Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qizhai Li
- University of Chinese Academy of Sciences, Beijing 100049, China
- LSC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Wang H, Tu R, Ruan Z, Wu D, Peng Z, Zhou X, Liu Q, Wu W, Cao L, Cheng S, Sun L, Zhan X, Shen X. STRIPE3, encoding a human dNTPase SAMHD1 homolog, regulates chloroplast development in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111395. [PMID: 35878695 DOI: 10.1016/j.plantsci.2022.111395] [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: 05/12/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Chloroplast is an important organelle for photosynthesis and numerous essential metabolic processes, thus ensuring plant fitness or survival. Although many genes involved in chloroplast development have been identified, mechanisms underlying such development are not fully understood. Here, we isolated and characterized the stripe3 (st3) mutant which exhibited white-striped leaves with reduced chlorophyll content and abnormal chloroplast development during the seedling stage, but gradually produced nearly normal green leaves as it developed. Map-based cloning and transgenic tests demonstrated that a splicing mutation in ST3, encoding a human deoxynucleoside triphosphate triphosphohydrolase (dNTPase) SAMHD1 homolog, was responsible for st3 phenotypes. ST3 is highly expressed in the third leaf at three-leaf stage and expressed constitutively in root, stem, leaf, sheath, and panicle, and the encoded protein, OsSAMHD1, is localized to the cytoplasm. The st3 mutant showed more severe albino leaf phenotype under exogenous 1-mM dATP/dA, dCTP/dC, and dGTP/dG treatments compared with the control conditions, indicating that ST3 is involved in dNTP metabolism. This study reveals a gene associated with dNTP catabolism, and propose a model in which chloroplast development in rice is regulated by the dNTP pool, providing a potential application of these results to hybrid rice breeding.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Ranran Tu
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Zheyan Ruan
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Duo Wu
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Zequn Peng
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Xingpeng Zhou
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Qunen Liu
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Weixun Wu
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Liyong Cao
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Shihua Cheng
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China
| | - Lianping Sun
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China.
| | - Xiaodeng Zhan
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China.
| | - Xihong Shen
- State Key Laboratory of Rice Biology, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311401 China.
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13
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Pan T, Bao Z, Ning L, Tong S. Change of Rice Paddy and Its Impact on Human Well-Being from the Perspective of Land Surface Temperature in the Northeastern Sanjiang Plain of China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9690. [PMID: 35955046 PMCID: PMC9368393 DOI: 10.3390/ijerph19159690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Large-scale and high-speed paddy land expansion has appeared in Northeast China since the 21st century, causing the change in land surface temperature. The lack of continuous investigation limits the exploration of discoveries in this region. To address this limitation, a collaborative approach that combined human-computer interaction technology, gravity center model and spatial analysis was established. It provided some new findings in spatiotemporal evolution, migration trajectory and surface cooling effect of the paddy field in Northeastern Sanjiang Plain, a center of paddy field planting in China. The results show that: (1) A sustained paddy expansion was monitored, with a total area ranging from 2564.58 km2 to 11430.94 km2, along with a rate of growth of 345.72% from 2000 to 2020. Correspondingly, its reclamation rate changed to 47.53% from 10.66%, showing the improved planting level of the paddy field. (2) Gravity center of paddy field continued to be revealed northward with a 5-year interval from 2000 to 2020. Migration distance of the straight line reached 23.94 km2, with the direction offset of 27.20° from east to north. (3) Throughout the growing season of crops, the land surface temperature of paddy field was 27.73°, 29.38°, 27.01°, 25.62° and 22.97° from May to October; and the cooling temperature effect of paddy field was investigated, with the reduced values of 0.61°, 0.79° and 1.10° in the low-, medium- and high-paddy field density regions from 2000 to 2020, respectively. Overall, these new findings in the cold temperate zone, high latitude region of the Northern Hemisphere, provided the reference for the investigation of paddy field monitoring and its environmental effects in China and other regions.
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Affiliation(s)
- Tao Pan
- School of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengyi Bao
- College of Computer Science and Technology, Inner Mongolian Normal University, Hohhot 010070, China
| | - Letian Ning
- School of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Siqin Tong
- College of Geographical Science, Inner Mongolia Normal University, Hohhot 010022, China
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14
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Lou Q, Guo H, Li J, Han S, Khan NU, Gu Y, Zhao W, Zhang Z, Zhang H, Li Z, Li J. Cold-adaptive evolution at the reproductive stage in Geng/japonica subspecies reveals the role of OsMAPK3 and OsLEA9. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1032-1051. [PMID: 35706359 DOI: 10.1111/tpj.15870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Cold stress at the reproductive stage severely affects the production and geographic distribution of rice. The Geng/japonica subpopulation gradually developed stronger cold adaptation than the Xian/indica subpopulation during the long-term domestication of cultivated rice. However, the evolutionary path and natural alleles underlying the cold adaptability of intra-Geng subspecies remain largely unknown. Here, we identified MITOGEN-ACTIVATED PROTEIN KINASE 3 (OsMAPK3) and LATE EMBRYOGENESIS ABUNDANT PROTEIN 9 (OsLEA9) as two important regulators for the cold adaptation of Geng subspecies from a combination of transcriptome analysis and genome-wide association study. Transgenic validation showed that OsMAPK3 and OsLEA9 confer cold tolerance at the reproductive stage. Selection and evolution analysis suggested that the Geng version of OsMAPK3 (OsMAPK3Geng ) directly evolved from Chinese Oryza rufipogon III and was largely retained in high-latitude and high-altitude regions with low temperatures during domestication. Later, the functional nucleotide polymorphism (FNP-776) in the Kunmingxiaobaigu and Lijiangxiaoheigu version of the OsLEA9 (OsLEA9KL ) promoter originated from novel variation of intra-Geng was selected and predominantly retained in temperate Geng to improve the adaptation of Geng together with OsMAPK3Geng to colder climatic conditions in high-latitude areas. Breeding potential analysis suggested that pyramiding of OsMAPK3Geng and OsLEA9KL enhanced the cold tolerance of Geng and promotes the expansion of cultivated rice to colder regions. This study not only highlights the evolutionary path taken by the cold-adaptive differentiation of intra-Geng, but also provides new genetic resources for rice molecular breeding in low-temperature areas.
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Affiliation(s)
- Qijin Lou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jin Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shichen Han
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Najeeb Ullah Khan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yunsong Gu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Weitong Zhao
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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15
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Jiang L, Peng Y, Seo J, Jeon D, Jo MG, Lee JH, Jeong JC, Kim CY, Park HC, Lee J. Subtercola endophyticus sp. nov., a cold-adapted bacterium isolated from Abies koreana. Sci Rep 2022; 12:12114. [PMID: 35840645 PMCID: PMC9287328 DOI: 10.1038/s41598-022-16116-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/05/2022] [Indexed: 11/09/2022] Open
Abstract
A novel Gram-stain-positive, aerobic bacterial strain, designated AK-R2A1-2 T, was isolated from the surface-sterilized needle leaves of an Abies koreana tree. Strain AK-R2A1-2 T had 97.3% and 96.7% 16S rRNA gene sequence similarities with Subtercola boreus K300T and Subtercola lobariae 9583bT, respectively, but formed a distinct phyletic lineage from these two strains. Growth of strain AK-R2A1-2 T was observed at 4–25 °C at pH 5.0–8.0. Strain AK-R2A1-2 T contained menaquinone 9 (MK-9) and menaquinone 10 (MK-10) as the predominant respiratory quinones. The major cellular fatty acids were anteiso-C15:0 and summed feature 8 (C18:1ω7c or/and C18:1ω6c), and the polar lipids included diphosphatidylglycerol (DPG) and three unknown aminolipids, AKL2, AKL3, and AKL4. The complete genome of strain AK-R2A1-2 T was sequenced to understand the genetic basis of its survival at low temperatures. Multiple copies of cold-associated genes involved in cold-active chaperon, stress response, and DNA repair supported survival of the strain at low temperatures. Strain AK-R2A1-2 T was also able to significantly improve rice seedling growth under low temperatures. Thus, this strain represents a novel species of the genus Subtercola, and the proposed name is Subtercola endophyticus sp. nov. The type strain is AK-R2A1-2 T (= KCTC 49721 T = GDMCC 1.2921 T).
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Affiliation(s)
- Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Jiyoon Seo
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Doeun Jeon
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Mi Gyeong Jo
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Jae Cheol Jeong
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Hyeong Cheol Park
- Team of Vulnerable Ecological Research, Division of Climate and Ecology, Bureau of Conservation & Assessment Research, National Institute of Ecology (NIE), Seocheon, 33657, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeollabuk-do, 56212, Republic of Korea.
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16
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Screening Technique Based on Seed and Early Seedling Parameters for Cold Tolerance of Selected F2-Derived F3 Rice Genotypes under Controlled Conditions. SUSTAINABILITY 2022. [DOI: 10.3390/su14148447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The cold tolerance studies were carried out in a bi-parental F2 population of a cross between tolerant and susceptible parents (SKUA-529 and HEERA, respectively). The purpose was to screen the individuals of a population for primary cold-tolerance-related attributes. The information generated has a direct application and use in identifying cold tolerance quantitative trait loci (QTLs) and further can be used for genotyping with an appropriate marker system. The screening was carried out on F2-derived F3 seeds and F3 plants for seedling and agronomic traits, respectively. Two tests measuring cold tolerance were conducted. In experiment I, seeds were germinated for 28 days at 13 °C and 7 days at 28 °C, and in experiment II, the seeds were germinated for 72 h at 28 °C, 96 h at 13 °C, and once more for 72 h at 28 °C. Coleoptile length, germination percentage, and radical reduction percentages were all measured in experiment I. The radicle and coleoptile regeneration in experiment II were measured after the cold period. The improvement in cold tolerance was achieved through radicle regrowth, as evidenced by the difference between the second and first measurements. The individual lines from the F2:3 population that recorded high germination (%) were #21, #13, #14, and #15. The percentage of coleoptile length (PERCOL %) was observed to be between the ranges of 23.33% to 53.00%. The reduction in coleoptile length (REDCOL %) was also obtained, and there was less reduction in #15, #16, and #14 and it had a range between 38.46% and 75%. Radicle regrowth (REDRAG) was high at 13 °C in #7, #11, #30, #35, and #36. Survival of the seedling range was between 33.33% and up to 100%, and the highest survival rate was observed in #16. The main objective of this rotation in temperature was to emulate field conditions where there has been a drop in temperature. The evaluations were done for primary cold stress tolerance traits, and it was found that most of these traits exhibited high variability. The mapping population developed may be utilized to generate a linkage map and locate QTLs for tolerance to cold stress in rice. Further, the identified donors for cold tolerance may be utilized for breeding programs aimed at the transfer of low-temperature stress tolerance into susceptible backgrounds. In general, a genotype with improved seedling germination rates, growth rates, and leaf yellowing scores; high seedling survival; lesser reduction in coleoptile length and in radicle development; and recovery following a cold shock at the seedling stage demonstrated its cold resistance. Genotypes with a low germination percentage, a greater number of days to germination, slow growth rate and higher leaf yellowing score, high reduction in coleoptile and radicle growth, and reduced seedling survival indicated cold susceptibility.
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17
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Burnett AC, Kromdijk J. Can we improve the chilling tolerance of maize photosynthesis through breeding? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3138-3156. [PMID: 35143635 PMCID: PMC9126739 DOI: 10.1093/jxb/erac045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/02/2022] [Indexed: 05/11/2023]
Abstract
Chilling tolerance is necessary for crops to thrive in temperate regions where cold snaps and lower baseline temperatures place limits on life processes; this is particularly true for crops of tropical origin such as maize. Photosynthesis is often adversely affected by chilling stress, yet the maintenance of photosynthesis is essential for healthy growth and development, and most crucially for yield. In this review, we describe the physiological basis for enhancing chilling tolerance of photosynthesis in maize by examining nine key responses to chilling stress. We synthesize current knowledge of genetic variation for photosynthetic chilling tolerance in maize with respect to each of these traits and summarize the extent to which genetic mapping and candidate genes have been used to understand the genomic regions underpinning chilling tolerance. Finally, we provide perspectives on the future of breeding for photosynthetic chilling tolerance in maize. We advocate for holistic and high-throughput approaches to screen for chilling tolerance of photosynthesis in research and breeding programmes in order to develop resilient crops for the future.
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Affiliation(s)
- Angela C Burnett
- Department of Plant Sciences, University of CambridgeCambridge, UK
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18
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Lopes MS. Will temperature and rainfall changes prevent yield progress in Europe? Food Energy Secur 2022. [DOI: 10.1002/fes3.372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Marta S. Lopes
- Sustainable Field Crops Programme IRTA (Institute for Food and Agricultural Research and Technology) Lleida Spain
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19
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Long-Term Dynamic of Cold Stress during Heading and Flowering Stage and Its Effects on Rice Growth in China. ATMOSPHERE 2022. [DOI: 10.3390/atmos13010103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Short episodes of low-temperature stress during reproductive stages can cause significant crop yield losses, but our understanding of the dynamics of extreme cold events and their impact on rice growth and yield in the past and present climate remains limited. In this study, by analyzing historical climate, phenology and yield component data, the spatial and temporal variability of cold stress during the rice heading and flowering stages and its impact on rice growth and yield in China was characterized. The results showed that cold stress was unevenly distributed throughout the study region, with the most severe events observed in the Yunnan Plateau with altitudes higher than 1800 m. With the increasing temperature, a significant decreasing trend in cold stress was observed across most of the three ecoregions after the 1970s. However, the phenological-shift effects with the prolonged growing period during the heading and flowering stages have slowed down the cold stress decreasing trend and led to an underestimation of the magnitude of cold stress events. Meanwhile, cold stress during heading and flowering will still be a potential threat to rice production. The cold stress-induced yield loss is related to both the intensification of extreme cold stress and the contribution of related components to yield in the three regions.
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20
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Liu Z, Su J, Luo X, Meng J, Zhang H, Li P, Sun Y, Song J, Peng X, Yu C. Nitrogen limits zinc‐mediated stimulation of tillering in rice by modifying phytohormone balance under low‐temperature stress. Food Energy Secur 2021. [DOI: 10.1002/fes3.359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Zhilei Liu
- College of Resources and Environment Northeast Agricultural University Harbin China
- Key Laboratory of Germplasm Innovation Ministry of Education Physiology and Ecology of Grain Crop in Cold Region (Northeast Agricultural University) Harbin China
| | - Jinkai Su
- College of Resources and Environment Northeast Agricultural University Harbin China
| | - Xiangyu Luo
- College of Resources and Environment Northeast Agricultural University Harbin China
| | - Jingrou Meng
- College of Resources and Environment Northeast Agricultural University Harbin China
| | - Haonan Zhang
- College of Resources and Environment Northeast Agricultural University Harbin China
| | - Pengfei Li
- College of Resources and Environment Northeast Agricultural University Harbin China
- Key Laboratory of Germplasm Innovation Ministry of Education Physiology and Ecology of Grain Crop in Cold Region (Northeast Agricultural University) Harbin China
| | - Yankun Sun
- College of Resources and Environment Northeast Agricultural University Harbin China
| | - Jiamei Song
- College of Resources and Environment Northeast Agricultural University Harbin China
| | - Xianlong Peng
- College of Resources and Environment Northeast Agricultural University Harbin China
- Key Laboratory of Germplasm Innovation Ministry of Education Physiology and Ecology of Grain Crop in Cold Region (Northeast Agricultural University) Harbin China
| | - Cailian Yu
- The School of Material Science and Chemical Engineering Harbin University of Science and Technology Harbin China
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21
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Irshad A, Rehman RNU, Kareem HA, Yang P, Hu T. Addressing the challenge of cold stress resilience with the synergistic effect of Rhizobium inoculation and exogenous melatonin application in Medicago truncatula. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 226:112816. [PMID: 34597844 DOI: 10.1016/j.ecoenv.2021.112816] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 05/17/2023]
Abstract
Cold stress is an adverse environmental condition that limits the growth and yield of leguminous plants. Thus, discovering an effective way of ameliorating cold-mediated damage is important for sustainable legume production. In this study, the combined use of Rhizobium inoculation (RI) and melatonin (MT) pretreatment was investigated in Medicago truncatula plants under cold stress. Eight-week-old seedlings were divided into eight groups: (i) CK (no stress, noninoculated, no MT), (ii) RI (Rhizobium inoculated), (iii) MT (75 μM melatonin), (iv) RI+MT, (v) CS (cold stress at 4 °C without Rhizobium inoculation and melatonin), (vi) CS+RI, (vii) CS+MT, and (viii) CS+RI+MT. Plants were exposed to cold stress for 24 hrs. Cold stress decreased photosynthetic pigments and increased oxidative stress. Pretreatment with RI and MT alone or combined significantly improved root activity and plant biomass production under cold stress. Interestingly, chlorophyll contents increased by 242.81% and MDA levels dramatically decreased by 34.22% in the CS+RI+MT treatment compared to the CS treatment. Moreover, RI+MT pretreatment improved the antioxidative ability by increasing the activities of peroxidase (POD; 8.45%), superoxide dismutase (SOD; 50.36%), catalase (CAT; 140.26%), and ascorbate peroxidase (APX; 42.63%) over CS treated plants. Additionally, increased osmolyte accumulation, nutrient uptake, and nitrate reductase activity due to the combined use of RI and MT helped the plants counteract cold-mediated damage by strengthening the nonenzymatic antioxidant system. These data indicate that pretreatment with a combined application of RI and MT can attenuate cold damage by enhancing the antioxidation ability of legumes.
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Affiliation(s)
- Annie Irshad
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rana Naveed Ur Rehman
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hafiz Abdul Kareem
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
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22
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Ali MK, Sun ZH, Yang XM, Pu XY, Duan CL, Li X, Wang LX, Yang JZ, Zeng YW. NILs of Cold Tolerant Japonica Cultivar Exhibited New QTLs for Mineral Elements in Rice. Front Genet 2021; 12:789645. [PMID: 34868277 PMCID: PMC8637755 DOI: 10.3389/fgene.2021.789645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Chilling stress at booting stage can cause floret deterioration and sterility by limiting the supply of food chain and the accumulation of essential mineral elements resulting in reduction of yield and grain quality attributes in rice. Genomic selection of chilling tolerant rice with reference to the accumulation of mineral elements will have great potential to cope with malnutrition and food security in times of climate change. Therefore, a study was conducted to explore the genomic determinants of cold tolerance and mineral elements content in near-isogenic lines (NILs) of japonica rice subjected to chilling stress at flowering stage. Detailed morphological analysis followed by quantitative analysis of 17 mineral elements revealed that the content of phosphorus (P, 3,253 mg/kg) and potassium (K, 2,485 mg/kg) were highest while strontium (Sr, 0.26 mg/kg) and boron (B, 0.34 mg/kg) were lowest among the mineral elements. The correlation analysis revealed extremely positive correlation of phosphorus (P) and copper (Cu) with most of the cold tolerance traits. Among all the effective ear and the second leaf length correlation was significant with half of the mineral elements. As a result of comparative analysis, some QTLs (qBRCC-1, qBRCIC-2, qBRZC-6, qBRCHC-6, qBRMC-6, qBRCIC-6a, qBRCIC-6b, qBRCHC-6, and qBRMC-6) identified for calcium (Ca), zinc (Zn), chromium (Cr) and magnesium (Mg) on chromosome number 1, 2, and 6 while, a novel QTL (qBCPC-1) was identified on chromosome number 1 for P element only. These findings provided bases for the identification of candidate genes involved in mineral accumulation and cold tolerance in rice at booting stage.
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Affiliation(s)
- Muhammad Kazim Ali
- Biotechnology and Germplasm Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan
| | - Zheng-Hai Sun
- School of Horticulture and Gardening, Southwest Forestry University, Kunming, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xiao-Meng Yang
- Biotechnology and Germplasm Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xiao-Ying Pu
- Biotechnology and Germplasm Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Cheng-Li Duan
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xia Li
- Biotechnology and Germplasm Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Lu-Xiang Wang
- Institute of Quality Standards and Testing Technology, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jia-Zhen Yang
- Biotechnology and Germplasm Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ya-Wen Zeng
- Biotechnology and Germplasm Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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23
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Lai K, Nguyen NT, Yasuda M, Dastogeer KMG, Toyoda A, Higashi K, Kurokawa K, Nguyen NTT, Komatsu K, Okazaki S. Leaf Bleaching in Rice: A New Disease in Vietnam Caused by Methylobacterium indicum, Its Genomic Characterization and the Development of a Suitable Detection Technique. Microbes Environ 2021; 36. [PMID: 34732597 PMCID: PMC8674445 DOI: 10.1264/jsme2.me21035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new disease in rice that is characterized by leaf bleaching was recently identified in some fields in the Mekong Delta region of Vietnam. The present study was the first to isolate and identify the pathogen of this disease. We confirmed that leaf bleaching symptoms were due to infection with Methylobacterium indicum bacteria using molecular biology approaches. A full-length genome analysis of pathogenic Methylobacterium strain VL1 revealed that it comprises a single chromosome and six plasmids, with a total size of 7.05 Mbp and GC content of 70.5%. The genomic features of VL1 were similar to those of the non-pathogenic M. indicum strain SE2.11T; however, VL1 possessed additional unique genes, including those related to homoserine lactone biosynthesis. We established a loop-mediated isothermal amplification (LAMP) assay using the unique sequences of VL1 as target sequences for the rapid and simple detection of pathogenic M. indicum strains. Our initial evaluation demonstrated that the LAMP assay successfully distinguished between pathogenic and non-pathogenic strains infecting rice plants in a rapid and sensitive manner. The present results provide insights into the pathogenesis and development of control measures for novel rice diseases.
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Affiliation(s)
- Khoa Lai
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology.,National Agro-Forestry-Fisheries Quality Assurance Department branch 4
| | - Ngoc Thai Nguyen
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
| | - Michiko Yasuda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Khondoker M G Dastogeer
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Department of Plant Pathology, Bangladesh Agricultural University
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics
| | - Koichi Higashi
- Genome Evolution Laboratory, National Institute of Genetics
| | - Ken Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics
| | - Nga Thi Thu Nguyen
- Department of Plant Protection, College of Agriculture and Applied Biology, CanTho University
| | - Ken Komatsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology.,Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Shin Okazaki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology.,Graduate School of Agriculture, Tokyo University of Agriculture and Technology
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24
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Transcriptome Profiling of Maize ( Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage. Genes (Basel) 2021; 12:genes12101638. [PMID: 34681032 PMCID: PMC8535276 DOI: 10.3390/genes12101638] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 01/22/2023] Open
Abstract
Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 779 and 877 DEGs, which were significantly enhanced in the tolerant and sensitive lines, respectively. Functional analysis of the 1656 DEGs highlighted the enrichment of signaling, carotenoid, lipid metabolism, transcription factors (TFs), peroxisome, and amino acid metabolism. A total of 147 TFs belonging to 32 families, including MYB, ERF, NAC, WRKY, bHLH, MIKC MADS, and C2H2, were strongly altered by cold stress. Moreover, the tolerant lines’ 779 enhanced DEGs were predominantly associated with carotenoid, ABC transporter, glutathione, lipid metabolism, and amino acid metabolism. In comparison, the cold-sensitive lines’ 877 enhanced DEGs were significantly enriched for MAPK signaling, peroxisome, ribosome, and carbon metabolism pathways. The biggest proportion of the unannotated DEGs was implicated in the roles of long non-coding RNAs (lncRNAs). Taken together, this study provides valuable insights that offer a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to cold stress.
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25
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Li J, Zeng Y, Pan Y, Zhou L, Zhang Z, Guo H, Lou Q, Shui G, Huang H, Tian H, Guo Y, Yuan P, Yang H, Pan G, Wang R, Zhang H, Yang S, Guo Y, Ge S, Li J, Li Z. Stepwise selection of natural variations at CTB2 and CTB4a improves cold adaptation during domestication of japonica rice. THE NEW PHYTOLOGIST 2021; 231:1056-1072. [PMID: 33892513 DOI: 10.1111/nph.17407] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The improvement of cold adaptation has contributed to the increased growing area of rice. Standing variation and de novo mutation are distinct natural sources of beneficial alleles in plant adaptation. However, the genetic mechanisms and evolutionary patterns underlying these sources in a single population during crop domestication remain elusive. Here we cloned the CTB2 gene, encoding a UDP-glucose sterol glucosyltransferase, for cold tolerance in rice at the booting stage. A single standing variation (I408V) in the conserved UDPGT domain of CTB2 originated from Chinese Oryza rufipogon and contributed to the cold adaptation of Oryza sativa ssp. japonica. CTB2 is located in a 56.8 kb region, including the previously reported gene CTB4a in which de novo mutation arose c. 3200 yr BP in Yunnan province, China, conferring cold tolerance. Standing variation of CTB2 and de novo mutation of CTB4a underwent stepwise selection to facilitate cold adaptation to expand rice cultivation from high-altitude to high-latitude regions. These results provide an example of stepwise selection on two kinds of variation and describe a new molecular mechanism of cold adaptation in japonica rice.
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Affiliation(s)
- Jilong Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yawen Zeng
- Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yinghua Pan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Lei Zhou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qijin Lou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Lipid ALL Technologies Ltd, Changzhou, 213000, China
| | - Hanguang Huang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - He Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongmei Guo
- Institute of Crop Science, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Pingrong Yuan
- Institute of Crop Science, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Hong Yang
- Lijiang Institute of Agricultural Science, Lijiang, 674100, China
| | - Guojun Pan
- Rice Research Institute, Heilongjiang Academy of Agricultural Science, Jiamusi, 154026, China
| | - Ruiying Wang
- Rice Research Institute, Heilongjiang Academy of Agricultural Science, Jiamusi, 154026, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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26
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Zhou Y, Sommer ML, Hochholdinger F. Cold response and tolerance in cereal roots. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab334. [PMID: 34270744 DOI: 10.1093/jxb/erab334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Indexed: 05/02/2023]
Abstract
Cold stress adversely affects plant growth and is a limiting factor in crop productivity. Temperature volatility as a consequence of climate change will increase the effects of cold stress on crop cultivation. Low temperatures frequently occur early after planting in temperate climates and severely affect root development in cereals. In this review we address the question how cereal root systems respond to cold on different scales. First, we summarize the morphological, physiological and cellular responses of cereal roots to cold stress and how these processes are regulated by phytohormones. Subsequently, we highlight the status of the genetic and molecular dissection of cold tolerance with emphasis on the role of cold-responsive genes in improving cold tolerance in cereal roots. Finally, we discuss the role of beneficial microorganisms and mineral nutrients in ameliorating the effects of cold stress in cereal roots. A comprehensive knowledge of the molecular mechanisms underlying cold tolerance will ensure yield stability by enabling the generation of cold-tolerant crop genotypes.
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Affiliation(s)
- Yaping Zhou
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Mauritz Leonard Sommer
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
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27
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Yarra R, Wei W. The NAC-type transcription factor GmNAC20 improves cold, salinity tolerance, and lateral root formation in transgenic rice plants. Funct Integr Genomics 2021; 21:473-487. [PMID: 34191184 DOI: 10.1007/s10142-021-00790-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/22/2021] [Accepted: 05/06/2021] [Indexed: 02/08/2023]
Abstract
NAC-type transcription factors are crucial players in the abiotic stress responses of plants. Soybean NAC-type transcription factor GmNAC20 was transformed into rice genome via Agrobacterium method of transformation to improve abiotic stress tolerance. Integration and expression of GmNAC20 were verified by the DNA blot hybridization, immunoblotting, RT-PCR, and quantitative RT-PCR in T3 generation of transgenic rice plants. Significant expression of GmNAC20 was found in transgenic plants under salinity, cold, and IAA treatments. The transgenic rice plants expressing GmNAC20 displayed enhanced salinity and cold stress tolerance via upregulating the abiotic stress-responsive genes. Furthermore, T3 transgenic plants retained relative water content, chlorophyll content with enhanced accumulation of proline content than wild-type plants under salinity, and cold stress environments. The decrease in MDA content and electrolyte leakage with a significant increase in antioxidant enzyme activities were noticed in transgenic rice plants under either salinity or cold stress conditions, compared to wild-type plants. Overexpression of GmNAC20 in rice plants also induced the lateral root formation, associated with upregulation of auxin signaling-related genes. Taken together, our results indicated that GmNAC20 acts as a positive regulator for conferring salinity and cold tolerance in rice plants and appropriate candidate for improving salinity and cold stress in other important food crops.
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Affiliation(s)
- Rajesh Yarra
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wei Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Melo FV, Oliveira MM, Saibo NJM, Lourenço TF. Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:640193. [PMID: 33833769 PMCID: PMC8021960 DOI: 10.3389/fpls.2021.640193] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Plants are unable to physically escape environmental constraints and have, therefore, evolved a range of molecular and physiological mechanisms to maximize survival in an ever-changing environment. Among these, the post-translational modification of ubiquitination has emerged as an important mechanism to understand and improve the stress response. The ubiquitination of a given protein can change its abundance (through degradation), alter its localization, or even modulate its activity. Hence, ubiquitination increases the plasticity of the plant proteome in response to different environmental cues and can contribute to improve stress tolerance. Although ubiquitination is mediated by different enzymes, in this review, we focus on the importance of E3-ubiquitin ligases, which interact with the target proteins and are, therefore, highly associated with the mechanism specificity. We discuss their involvement in abiotic stress response and place them as putative candidates for ubiquitination-based development of stress-tolerant crops. This review covers recent developments in this field using rice as a reference for crops, highlighting the questions still unanswered.
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Rativa AGS, Junior ATDA, Friedrich DDS, Gastmann R, Lamb TI, Silva ADS, Adamski JM, Fett JP, Ricachenevsky FK, Sperotto RA. Root responses of contrasting rice genotypes to low temperature stress. JOURNAL OF PLANT PHYSIOLOGY 2020; 255:153307. [PMID: 33142180 DOI: 10.1016/j.jplph.2020.153307] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/05/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
Rice (Oryza sativa L.) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as the number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H2O2 accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.
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Affiliation(s)
| | | | | | - Rodrigo Gastmann
- Biological Sciences and Health Center, University of Taquari Valley - Univates, Lajeado, Brazil
| | - Thainá Inês Lamb
- Biological Sciences and Health Center, University of Taquari Valley - Univates, Lajeado, Brazil
| | | | | | - Janette Palma Fett
- Graduate Program in Cellular and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil; Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Felipe Klein Ricachenevsky
- Graduate Program in Cellular and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil; Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Raul Antonio Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, Brazil; Biological Sciences and Health Center, University of Taquari Valley - Univates, Lajeado, Brazil.
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Yang J, Yang M, Su L, Zhou D, Huang C, Wang H, Guo T, Chen Z. Genome-wide association study reveals novel genetic loci contributing to cold tolerance at the germination stage in indica rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110669. [PMID: 33218635 DOI: 10.1016/j.plantsci.2020.110669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 08/13/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
Low temperature at the germination stage is one of the major abiotic stresses limiting rice (Oryza sativa L.) production, especially in regions where rice seeds are sown directly. However, few relevant genetic loci and genes have been identified. In this study, we report the phenotypic analysis of low temperature germination (LTG) in 200 indica rice varieties and a genome-wide association study (GWAS) of LTG in this collection using 161,657 high-quality SNPs, which were identified via genotyping-by-sequencing (GBS) of all the rice varieties. A total of 159 genetic loci were detected, and they were evenly distributed on all 12 chromosomes. Among them, 51 loci were detected more than twice; in particular, 23 loci were detected repeatedly in both the wet and dry seasons, and 569 genes were predicted in the 200-kb genomic region harbouring these 23 loci. Furthermore, 14,742 differentially expressed genes (DEGs) were identified using RNA sequencing. By integrating GWAS and RNA sequencing, 179 candidate DEGs were obtained. Sequence variation in the region of loci 95 was analyzed using 20 varieties with extreme phenotype. The polymorphisms of three DEGs (Os07g0585500, Os07g0585700, Os07g0585900) were associated with their phenotypes. Haplotype analysis of the three genes demonstrated that almost all the varieties with the same haplotype as japonica Nipponbare on the three DEGs showed high LTG ability. These findings provide valuable information for understanding the genetic control of LTG and performing molecular breeding with marker-assisted selection in indica rice.
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Affiliation(s)
- Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Meng Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Ling Su
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Danhua Zhou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
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Guo H, Zeng Y, Li J, Ma X, Zhang Z, Lou Q, Li J, Gu Y, Zhang H, Li J, Li Z. Differentiation, evolution and utilization of natural alleles for cold adaptability at the reproductive stage in rice. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2491-2503. [PMID: 32490579 PMCID: PMC7680545 DOI: 10.1111/pbi.13424] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Genetic studies on cold tolerance at the reproductive stage in rice could lead to significant reductions in yield losses. However, knowledge about the genetic basis and adaptive differentiation, as well as the evolution and utilization of the underlying natural alleles, remains limited. Here, 580 rice accessions in two association panels were used to perform genome-wide association study, and 156 loci associated with cold tolerance at the reproductive stage were identified. Os01g0923600 and Os01g0923800 were identified as promising candidate genes in qCTB1t, a major associated locus. Through population genetic analyses, 22 and 29 divergent regions controlling cold adaptive differentiation inter-subspecies (Xian/Indica and Geng/Japonica) and intra-Geng, respectively, were identified. Joint analyses of four cloned cold-tolerance genes showed that they had different origins and utilizations under various climatic conditions. bZIP73 and OsAPX1 differentiating inter-subspecies evolved directly from wild rice, whereas the novel mutations CTB4a and Ctb1 arose in Geng during adaptation to colder climates. The cold-tolerant Geng accessions have undergone stronger selection under colder climate conditions than other accessions during the domestication and breeding processes. Additive effects of dominant allelic variants of four identified genes have been important in adaptation to cold in modern rice varieties. Therefore, this study provides valuable information for further gene discovery and pyramiding breeding to improve cold tolerance at the reproductive stage in rice.
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Affiliation(s)
- Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yawen Zeng
- Biotechnology and Genetic Resources InstituteYunnan Academy of Agricultural SciencesKunmingChina
| | - Jilong Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Xiaoqian Ma
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Qijin Lou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jin Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yunsong Gu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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Koper K, Hwang SK, Wood M, Singh S, Cousins A, Kirchhoff H, Okita TW. The Rice Plastidial Phosphorylase Participates Directly in Both Sink and Source Processes. ACTA ACUST UNITED AC 2020; 62:125-142. [DOI: 10.1093/pcp/pcaa146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/11/2020] [Indexed: 12/19/2022]
Abstract
Abstract
The plastidial starch phosphorylase (Pho1) functions in starch metabolism. A distinctive structural feature of the higher Pho1 is a 50–82-amino-acid long peptide (L50–L82), which is absent in phosphorylases from non-plant organisms. To study the function of the rice Pho1 L80 peptide, we complemented a pho1− rice mutant (BMF136) with the wild-type Pho1 gene or with a Pho1 gene lacking the L80 region (Pho1ΔL80). While expression of Pho1 in BMF136 restored normal wild-type phenotype, the introduction of Pho1ΔL80 enhanced the growth rate and plant productivity above wild-type levels. Mass spectrometry analysis of proteins captured by anti-Pho1 showed the surprising presence of PsaC, the terminal electron acceptor/donor subunit of photosystem I (PSI). This unexpected interaction was substantiated by reciprocal immobilized protein pull-down assays of seedling extracts and supported by the presence of Pho1 on isolated PSI complexes resolved by blue-native gels. Spectrophotometric studies showed that Pho1ΔL80 plants exhibited modified PSI and enhanced CO2 assimilation properties. Collectively, these findings indicate that the higher plant Pho1 has dual roles as a potential modulator of source and sink processes.
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Affiliation(s)
- Kaan Koper
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Magnus Wood
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013, India
| | - Asaph Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
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Hong WJ, Jiang X, Ahn HR, Choi J, Kim SR, Jung KH. Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes. Int J Mol Sci 2020; 21:E6872. [PMID: 32961678 PMCID: PMC7554834 DOI: 10.3390/ijms21186872] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 11/16/2022] Open
Abstract
Rice (Oryza sativa L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein-protein interaction network encompassing four hub genes and analyzed the roles of the Stay-Green (SGR) gene in regulating crosstalk with sgr mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
| | - Xu Jiang
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
| | - Hye Ryun Ahn
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
| | - Juyoung Choi
- Department of Life Science, Sogang University, Seoul 04107, Korea;
| | - Seong-Ryong Kim
- Department of Life Science, Sogang University, Seoul 04107, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; (W.-J.H.); (X.J.); (H.R.A.)
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Ermilova E. Cold Stress Response: An Overview in Chlamydomonas. FRONTIERS IN PLANT SCIENCE 2020; 11:569437. [PMID: 33013991 PMCID: PMC7494811 DOI: 10.3389/fpls.2020.569437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/18/2020] [Indexed: 06/01/2023]
Abstract
Low temperature (or cold) is one of the major environmental factors that limit the growth and development of many plants. Various plant species have evolved complex mechanisms to adjust to decreased temperature. Mesophilic chlorophytes are a widely distributed group of eukaryotic photosynthetic organisms, but there is insufficient information about the key molecular processes of their cold acclimation. The best available model for studying how chlorophytes respond to and cope with variations in temperature is the unicellular green alga Chlamydomonas reinhardtii. Chlamydomonas has been widely used for decades as a model system for studying the fundamental mechanisms of the plant heat stress response. At present, unraveling novel cold-regulated events in Chlamydomonas has attracted increasing research attention. This mini-review summarizes recent progress on low-temperature-dependent processes in the model alga, while information on other photosynthetic organisms (cyanobacteria and land plants) was used to strengthen generalizations or specializations of cold-induced mechanisms in plant evolution. Here, we describe recent advances in our understanding of cold stress response in Chlamydomonas, discuss areas of controversy, and highlight potential future directions in cold acclimation research.
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35
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Shim JS, Jang G. Environmental Signal-Dependent Regulation of Flowering Time in Rice. Int J Mol Sci 2020; 21:ijms21176155. [PMID: 32858992 PMCID: PMC7504671 DOI: 10.3390/ijms21176155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 01/11/2023] Open
Abstract
The transition from the vegetative to the reproductive stage of growth is a critical event in the lifecycle of a plant and is required for the plant’s reproductive success. Flowering time is tightly regulated by an internal time-keeping system and external light conditions, including photoperiod, light quality, and light quantity. Other environmental factors, such as drought and temperature, also participate in the regulation of flowering time. Thus, flexibility in flowering time in response to environmental factors is required for the successful adaptation of plants to the environment. In this review, we summarize our current understanding of the molecular mechanisms by which internal and environmental signals are integrated to regulate flowering time in Arabidopsis thaliana and rice (Oryza sativa).
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Shimoyama N, Johnson M, Beaumont A, Schläppi M. Multiple Cold Tolerance Trait Phenotyping Reveals Shared Quantitative Trait Loci in Oryza sativa. RICE (NEW YORK, N.Y.) 2020; 13:57. [PMID: 32797316 PMCID: PMC7427827 DOI: 10.1186/s12284-020-00414-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/29/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species. RESULTS The Rice Diversity Panel 1 (RDP1) was used to investigate a core set of Oryza sativa accessions. The tools available for this panel allowed for a comprehensive analysis of two chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches using all 354 accessions yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL covering 25% of the rice genome, while 40 QTL were identified by multiple traits. QTL mappings using subsets of rice accession clusters yielded another 255 QTL, for a total of 500 QTL. The genes within these multiple trait QTL were analyzed for Gene Ontology (GO) term and potential pathway enrichments. Terms related to "carbohydrate biosynthesis", "carbohydrate transmembrane transport", "small molecule protein modification", and "plasma membrane" were enriched from this list. Filtering was done to identify more likely candidate pathways involved in conferring chilling tolerance, resulting in enrichment of terms related to "Golgi apparatus", "stress response", "transmembrane transport", and "signal transduction". CONCLUSIONS Taken together, these GO term clusters revealed a likely involvement of Golgi-mediated subcellular and extracellular vesicle and intracellular carbohydrate transport as a general cold stress tolerance response mechanism to achieve cell and metabolic homeostasis under chilling stress.
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Affiliation(s)
- Naoki Shimoyama
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Melineeh Johnson
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - André Beaumont
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Michael Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
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Pan Y, Liang H, Gao L, Dai G, Chen W, Yang X, Qing D, Gao J, Wu H, Huang J, Zhou W, Huang C, Liang Y, Deng G. Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice. BMC PLANT BIOLOGY 2020; 20:371. [PMID: 32762649 PMCID: PMC7409433 DOI: 10.1186/s12870-020-02569-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/22/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. RESULTS This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44-68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. CONCLUSION Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.
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Affiliation(s)
- Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Lijun Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Gaoxing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Weiwei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Dongjin Qing
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Ju Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Hao Wu
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Weiyong Zhou
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Chengcui Huang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Yuntao Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
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Prinzenberg AE, Campos‐Dominguez L, Kruijer W, Harbinson J, Aarts MGM. Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions. PLANT, CELL & ENVIRONMENT 2020; 43:2000-2013. [PMID: 32495939 PMCID: PMC7497054 DOI: 10.1111/pce.13811] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 03/29/2020] [Accepted: 05/18/2020] [Indexed: 05/18/2023]
Abstract
Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (ΦPSII ) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in ΦPSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in ΦPSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.
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Affiliation(s)
- Aina E. Prinzenberg
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Plant BreedingWageningen University and ResearchPO Box 386Wageningen6700 AJThe Netherlands
| | - Lucia Campos‐Dominguez
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUnited Kingdom
| | - Willem Kruijer
- BiometrisWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
| | - Jeremy Harbinson
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Laboratory of BiophysicsWageningen University and ResearchWageningenThe Netherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
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Leng Y, Sun J, Wang J, Liu H, Zheng H, Zhang M, Zhao H, Zou D. Genome-wide lncRNAs identification and association analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L.). THE PLANT GENOME 2020; 13:e20020. [PMID: 33016612 DOI: 10.1002/tpg2.20020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/03/2020] [Accepted: 03/28/2020] [Indexed: 05/26/2023]
Abstract
Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. The spectacular progress made in next-generation sequencing technologies has enabled a genome-wide identification of lncRNAs in multiple plant species. In this study, a genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparing a tolerant variety, Kongyu131 (KY131) and a sensitive variety, Dongnong422 (DN422). A total of 1485 lncRNAs were identified, and 566 of these lncRNAs were defined as differential lncRNAs by comparing four samples. GO and KEGG enrichment analyses were performed, focusing on the cis- and trans- target genes of the differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate 35 cold-tolerant QTLs at the booting stage. In summary, 12 candidate genes and their target lncRNAs were identified by qRT-PCR. LncTar was used to identify the interaction between lncRNAs and the candidate genes. In addition, 130 rice cultivars with rich genetic diversity were collected to verify the association of candidate genes with cold-resistance. The results revealed that five SNPs in LOC_Os07g42940, three SNP and one InDel in LOC_Os02g03410 were associated with cold-resistance at a significant level using association analysis. This study provides new gene resources and insights into cold-resistance research for rice.
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Affiliation(s)
- Yue Leng
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Jian Sun
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Minghui Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Hongwei Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Detang Zou
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
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40
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Kim JH, Lim SD, Jang CS. Oryza sativa drought-, heat-, and salt-induced RING finger protein 1 (OsDHSRP1) negatively regulates abiotic stress-responsive gene expression. PLANT MOLECULAR BIOLOGY 2020; 103:235-252. [PMID: 32206999 DOI: 10.1007/s11103-020-00989-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/02/2020] [Indexed: 05/13/2023]
Abstract
Plants are sessile and unable to avoid environmental stresses, such as drought, high temperature, and high salinity, which often limit the overall plant growth. Plants have evolved many complex mechanisms to survive these abiotic stresses via post-translational modifications. Recent evidence suggests that ubiquitination plays a crucial role in regulating abiotic stress responses in plants by regulating their substrate proteins. Here, we reported the molecular function of a RING finger E3 ligase, Oryza sativa Drought, Heat and Salt-induced RING finger protein 1 (OsDHSRP1), involved in regulating plant abiotic stress tolerance via the Ub/26S proteasome system. The OsDHSRP1 gene transcripts were highly expressed under various abiotic stresses such as NaCl, drought, and heat and the phytohormone abscisic acid (ABA). In addition, in vitro ubiquitination assays demonstrated that the OsDHSRP1 protein possesses a RING-H2 type domain that confers ligase functionality. The results of yeast two-hybrid (Y2H), in vitro pull-down, and bimolecular fluorescence complementation assays support that OsDHSRP1 is able to regulate two substrates, O. sativa glyoxalase (OsGLYI-11.2) and O. sativa abiotic stress-induced cysteine proteinase 1 (OsACP1). We further confirmed that these two substrate proteins were ubiquitinated by OsDHSRP1 E3 ligase and caused protein degradation via the Ub/26S proteasome system. The Arabidopsis plants overexpressing OsDHSRP1 exhibited hypersensitivity to drought, heat, and NaCl stress and a decrease in their germination rates and root lengths compared to the control plants because the degradation of the OsGLYI-11.2 protein maintained lower glyoxalase levels, which increased the methylglyoxal amount in transgenic Arabidopsis plants. However, the OsDHSRP1-overexpressing plants showed no significant difference when treated with ABA. Our finding supports the hypothesis that the OsDHSRP1 E3 ligase acts as a negative regulator, and the degradation of its substrate proteins via ubiquitination plays important roles in regulating various abiotic stress responses via an ABA-independent pathway.
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Affiliation(s)
- Ju Hee Kim
- Plant Genomics Laboratory, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 200-713, South Korea
| | - Sung Don Lim
- Plant Genomics Laboratory, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 200-713, South Korea
| | - Cheol Seong Jang
- Plant Genomics Laboratory, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 200-713, South Korea.
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Shi Y, Phan H, Liu Y, Cao S, Zhang Z, Chu C, Schläppi MR. Glycosyltransferase OsUGT90A1 helps protect the plasma membrane during chilling stress in rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2723-2739. [PMID: 31974553 PMCID: PMC7210772 DOI: 10.1093/jxb/eraa025] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 05/09/2023]
Abstract
Due to its subtropical origins, rice (Oryza sativa) is sensitive to low-temperature stress. In this study, we identify LOC_Os04g24110, annotated to encode the UDP-glycosyltransferase enzyme UGT90A1, as a gene associated with the low-temperature seedling survivability (LTSS) quantitative trait locus qLTSS4-1. Differences between haplotypes in the control region of OsUGT90A1 correlate with chilling tolerance phenotypes, and reflect differential expression between tolerant and sensitive accessions rather than differences in protein sequences. Expression of OsUGT90A1 is initially enhanced by low temperature, and its overexpression helps to maintain membrane integrity during cold stress and promotes leaf growth during stress recovery, which are correlated with reduced levels of reactive oxygen species due to increased activities of antioxidant enzymes. In addition, overexpression of OsUGT90A1 in Arabidopsis improves freezing survival and tolerance to salt stress, again correlated with enhanced activities of antioxidant enzymes. Overexpression of OsUGT90A1 in rice decreases root lengths in 3-week-old seedlings while gene-knockout increases the length, indicating that its differential expression may affect phytohormone activities. We conclude that higher OsUGT90A1 expression in chilling-tolerant accessions helps to maintain cell membrane integrity as an abiotic stress-tolerance mechanism that prepares plants for the resumption of growth and development during subsequent stress recovery.
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Affiliation(s)
- Yao Shi
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Present address: The University of Pennsylvania School of Dental Medicine, Levy Building, Biochemistry Department, Rm538, 240 S 40th St, Philadelphia, PA 19104, USA
| | - Huy Phan
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Yaju Liu
- National Sweet Potato Improvement Center, Sweet Potato Research Institute, Xuzhou, P.R. China
| | - Shouyun Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhihua Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Michael R Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Correspondence:
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Adamski JM, Rosa LMG, Menezes Peixoto CRD, Pinheiro CL, Fett JP, Sperotto RA. Photosynthetic activity of indica rice sister lines with contrasting cold tolerance. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:955-964. [PMID: 32377045 PMCID: PMC7196564 DOI: 10.1007/s12298-020-00792-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 06/11/2023]
Abstract
Incidence of cold during early stages is an obstacle for the growing progress of rice plants. Cold stress has strong negative effects on photosynthetic activity. Previously, our group evaluated plant survival of 90 indica rice genotypes after cold treatment. Two sister lines were characterized as cold-tolerant and cold-sensitive. Transcriptomic analyses of the same genotypes had indicated differential expression of genes related to photosynthesis. Previous work with japonica rice had suggested that cold sensitivity was more related to photosystem II (PSII) than to photosystem I (PSI). Using our previously identified contrasting genotypes, we investigated the role of specific steps of the photosynthetic process in cold tolerance/sensitivity of indica rice plants during and after (recovery period) cold exposure. During both cold treatment and recovery period, the photochemical activity (including PSII and PSI) presented higher levels in the low temperature-tolerant genotype, when compared with the sensitive one. The higher photochemical efficiency during the cold treatment appears to be related to a lower fraction of reduced QA - in PSII. We also observed lower transpiration rates and higher water use efficiency in the cold-tolerant genotype, due to stomatal closure. After the recovery period, the higher efficiency in the cold-tolerant genotype seems to be related to a lower fraction of reduced QA - and a larger pool of final electron acceptors at the PSI. This work uncovered changes in photosynthetic performance including both photosystems and improved water use efficiency which may be important components of cold tolerance mechanisms in indica rice.
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Affiliation(s)
- Janete Mariza Adamski
- Programa de Pós-Graduação em Botânica (PPGBot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Luis Mauro Gonçalves Rosa
- Programa de Pós-Graduação em Botânica (PPGBot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | | | - Clodoaldo Leites Pinheiro
- Programa de Pós-Graduação em Botânica (PPGBot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Janette Palma Fett
- Programa de Pós-Graduação em Botânica (PPGBot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Raul Antonio Sperotto
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade do Vale do Taquari - Univates, Lajeado, RS Brazil
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43
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Fei M, Jin Y, Jin L, Su J, Ruan Y, Wang F, Liu C, Sun C. Adaptation of Rice to the Nordic Climate Yields Potential for Rice Cultivation at Most Northerly Site and the Organic Production of Low-Arsenic and High-Protein Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:329. [PMID: 32425956 PMCID: PMC7212348 DOI: 10.3389/fpls.2020.00329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
There is an urgent demand for low-arsenic rice in the global market, particularly for consumption by small children. Soils in Uppsala, Sweden, contain low concentrations of arsenic (As). We hypothesize that if certain japonica paddy rice varieties can adapt to the cold climate and long day length in Uppsala and produce normal grains, such a variety could be used for organic production of low-arsenic rice for safe rice consumption. A japonica paddy rice variety, "Heijing 5," can be cultivated in Uppsala, Sweden, after several years' adaptation, provided that the rice plants are kept under a simple plastic cover when the temperature is below 10°C. Uppsala-adapted "Heijing 5" has a low concentration of 0.1 mg per kg and high protein content of 12.6% per dry weight in brown rice grain, meaning that it thus complies with all dietary requirements determined by the EU and other countries for small children. The high protein content is particularly good for small children in terms of nutrition. Theoretically, Uppsala-adapted "Heijing 5" can produce a yield of around 5100 kg per ha, and it has a potential for organic production. In addition, we speculate that cultivation of paddy rice can remove nitrogen and phosphorus from Swedish river water and reduce nutrient loads to the Baltic Sea and associated algae blooms.
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Affiliation(s)
- Mingliang Fei
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Hunan Agricultural University, Changsha, China
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yunkai Jin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lu Jin
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Hunan Agricultural University, Changsha, China
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jun Su
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ying Ruan
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Hunan Agricultural University, Changsha, China
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Feng Wang
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Chunlin Liu
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Thapa R, Tabien RE, Thomson MJ, Septiningsih EM. Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice. Front Genet 2020; 11:22. [PMID: 32153631 PMCID: PMC7047875 DOI: 10.3389/fgene.2020.00022] [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: 09/20/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.
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Affiliation(s)
- Ranjita Thapa
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
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Hu Y, Li L, Tian J, Zhang C, Wang J, Yu E, Xing Z, Guo B, Wei H, Huo Z, Zhang H. Effects of dynamic low temperature during the grain filling stage on starch morphological structure, physicochemical properties, and eating quality of soft
japonica
rice. Cereal Chem 2020. [DOI: 10.1002/cche.10268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yajie Hu
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Luan Li
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Jinyu Tian
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Chengxin Zhang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Jie Wang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Enwei Yu
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Zhipeng Xing
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Baowei Guo
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Haiyan Wei
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Zhongyang Huo
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Hongcheng Zhang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
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Han B, Ma X, Cui D, Wang Y, Geng L, Cao G, Zhang H, Han L. Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings. RICE (NEW YORK, N.Y.) 2020; 13:12. [PMID: 32056019 PMCID: PMC7018935 DOI: 10.1186/s12284-019-0363-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
In this study, the cold-tolerance capacity of 133 varieties of weedy rice was evaluated based on the comprehensive evaluation index D, with Kongyu 131 used as a cold-tolerant control. A total of 39.8% of the 133 varieties were considered 'strong', indicating that weedy rice populations indeed have relatively strong cold-tolerance capacity as a whole, and the robust cold-tolerant varieties WR29 and WR157 were identified. Regression analysis showed that the metrics including the nitrogen recovery index, superoxide dismutase (SOD) content and malondialdehyde (MDA) content correlated significantly (P < 0.05) with cold tolerance and could be used as indicators of cold tolerance. On the basis of a transcriptome analysis of WR157, a robust cold-tolerant variety identified in this study, a total of 4645 putative DEGs were identified in treated groups compared to the control groups, with 2123 upregulated DEGs and 2522 downregulated DEGs. All upregulated DEGs were enriched on 1388 terms, all downregulated DEGs were enriched on 1566 terms; 911 of the 2123 upregulated DEGs fell into 98 KEGG categories and 1103 of the 2522 downregulated DEGs were in 115 categories. Further analysis showed that GO:0019740 and GO:0006808 are involved in nitrogen utilization; GO:0009269 and GO:0009414 are related to the stress response; and GO:0016491 and GO:0016614 are related to oxidoreductase activity. BACKGROUND: Weedy rice (Oryza) is a related pest species of cultivated rice (Oryza sativa L.) that has strong abiotic stress resistance; however, the comprehensive mechanism governing its cold tolerance is poorly understood. CONCLUSION: Our comprehensive evaluation based on five morphological indices and nine physiological indicators revealed outstanding levels of cold-tolerance capacity among weedy rice varieties from different regions and revealed some terms related to cold tolerance via transcriptome analysis. Our results underscored the reliable evaluation methods for additional cold tolerance studies and revealed several genes related to cold tolerance, which will help researchers breed cultivated rice varieties to increase their cold-tolerance capacity. These traits have the ability to increase seedling survival rate and growth, as well as future yields.
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Affiliation(s)
- Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanjie Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Leiyue Geng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Coastal Agriculture Institute, Hebei Academy of Agricultural and Forestry Sciences, Tangshan, 063299 China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing. Mol Phylogenet Evol 2020; 146:106737. [PMID: 31982455 DOI: 10.1016/j.ympev.2020.106737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/27/2023]
Abstract
Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.
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Najeeb S, Ali J, Mahender A, Pang Y, Zilhas J, Murugaiyan V, Vemireddy LR, Li Z. Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2020; 40:10. [PMID: 31975784 PMCID: PMC6944268 DOI: 10.1007/s11032-019-1090-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7 ) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT 1 , qLTT 2 , qLTT 3 , qLTT 5 , qLTT 6 , qLTT 8 , qLTT 9 , and qLTT 11 . A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.
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Affiliation(s)
- S. Najeeb
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Science & Technology (SKAUST), Khudwani, Kashmir 190025 India
| | - J. Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - A. Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Y.L. Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 People’s Republic of China
| | - J. Zilhas
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - V. Murugaiyan
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Plant Nutrition, Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, 53012 Bonn, Germany
| | - Lakshminarayana R. Vemireddy
- Department of Genetics and Plant Breeding, Sri Venkateswara Agricultural College, Acharya NG Ranga Agricultural University, Tirupati, Andhra Pradesh 517502 India
| | - Z. Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 People’s Republic of China
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Lai K, Thai Nguyen N, Miwa H, Yasuda M, Huu Nguyen H, Okazaki S. Diversity of Methylobacterium spp. in the Rice of the Vietnamese Mekong Delta. Microbes Environ 2020; 35:ME19111. [PMID: 31969531 PMCID: PMC7104282 DOI: 10.1264/jsme2.me19111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/27/2019] [Indexed: 11/12/2022] Open
Abstract
The Vietnamese Mekong delta is one of the largest rice-producing areas globally. Methylobacterium spp. are persistent colonizers of the rice plant and exert beneficial effects on plant growth and health. Sixty-one Methylobacterium strains belonging to seven species were predominantly isolated from the phyllosphere of rice cultivated in six Mekong delta provinces. Inoculation tests revealed that some strains exhibited plant growth-promoting activity. Moreover, three strains possessed the novel characteristics of inducing leaf bleaching and killing rice seedlings. These results revealed the complex diversity of Methylobacterium in Mekong delta rice and that healthy and productive rice cultivation requires a proper balance of Methylobacterium.
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Affiliation(s)
- Khoa Lai
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
- National Agro-Forestry-Fisheries Quality Assurance Department branch 4, 271—To Ngoc Van St, Linh Dong ward, Thu Duc district, Ho Chi Minh City, Vietnam
| | - Ngoc Thai Nguyen
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
| | - Hiroki Miwa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
| | - Michiko Yasuda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
| | - Hiep Huu Nguyen
- Department of Microbial Biotechnology, Biotechnology Research and Development Institute, Cantho University, II—St 3/2, Ninh Kieu ward, Cantho City, Vietnam
| | - Shin Okazaki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
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50
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Chai C, Shankar R, Jain M, Subudhi PK. Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Sci Rep 2018; 8:14218. [PMID: 30242197 PMCID: PMC6155081 DOI: 10.1038/s41598-018-32513-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
Analyzing the genome level DNA polymorphisms between weedy and cultivated rice is crucial to elucidate the molecular basis of weedy and agronomic traits, which in turn can enhance our ability to control weedy rice and its utilization for rice improvement. Here, we presented the genome-wide genetic variations between a weedy rice accession PSRR-1 and two cultivated rice accessions, Bengal and Nona Bokra, belonging to japonica and indica subspecies, respectively. The total number of SNPs and InDels in PSRR/Bengal was similar to that of Nona Bokra/Bengal, but was three times greater than that of PSRR/Nona Bokra. There were 11546 large-effect SNPs/InDels affecting 5673 genes, which most likely differentiated weedy rice from cultivated rice. These large effect DNA polymorphisms were mostly resulted in stop codon gain and least by start codon loss. Analysis of the molecular functions and biological processes of weedy rice specific SNPs/InDels indicated that most of these genes were involved in protein modification/phosphorylation, protein kinase activity, and protein/nucleotide binding. By integrating previous QTL mapping results with the DNA polymorphisms data, the candidate genes for seed dormancy and seed shattering were narrowed down. The genomic resource generated in this study will facilitate discovery of functional variants for weedy and agronomic traits.
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Affiliation(s)
- Chenglin Chai
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Rama Shankar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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