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Badoni S, Pasion-Uy EA, Kor S, Kim SR, Tiozon RN, Misra G, Buenafe RJQ, Labarga LM, Ramos-Castrosanto AR, Pratap V, Slamet-Loedin I, Steimker JV, Alseekh S, Fernie AR, Kohli A, Khush GS, Sreenivasulu N. Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content. Proc Natl Acad Sci U S A 2024; 121:e2410598121. [PMID: 39190344 DOI: 10.1073/pnas.2410598121] [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: 05/27/2024] [Accepted: 07/26/2024] [Indexed: 08/28/2024] Open
Abstract
To counter the rising incidence of diabetes and to meet the daily protein needs, we created low glycemic index (GI) rice varieties with protein content (PC) surpassing 14%. In the development of recombinant inbred lines using Samba Mahsuri and IR36 amylose extender (IR36ae) as parental lines, we identified quantitative trait loci and genes associated with low GI, high amylose content (AC), and high PC. By integrating genetic techniques with classification models, this comprehensive approach identified candidate genes on chromosome 2 (qGI2.1/qAC2.1 spanning the region from 18.62 Mb to 19.95 Mb), exerting influence on low GI and high amylose. Notably, the phenotypic variant with high value was associated with the recessive allele of the starch branching enzyme 2b (sbeIIb). The genome-edited sbeIIb line confirmed low GI phenotype in milled rice grains. Further, combinations of alleles created by the highly significant SNPs from the targeted associations and epistatically interacting genes showed ultralow GI phenotypes with high amylose and high protein. Metabolomics analysis of rice with varying AC, PC, and GI revealed that the superior lines of high AC and PC, and low GI were preferentially enriched in glycolytic and amino acid metabolisms, whereas the inferior lines of low AC and PC and high GI were enriched with fatty acid metabolism. The high amylose high protein recombinant inbred line (HAHP_101) was enriched in essential amino acids like lysine. Such lines may be highly relevant for food product development to address diabetes and malnutrition.
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Affiliation(s)
- Saurabh Badoni
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
- International Rice Research Institute South Asia Regional Centre, Collectry farm, Varanasi, Uttar Pradesh 221006, India
| | - Erstelle A Pasion-Uy
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Sakshi Kor
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
| | - Sung-Ryul Kim
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
| | - Rhowell N Tiozon
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Gopal Misra
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
| | | | - Luster May Labarga
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
| | | | - Vipin Pratap
- International Rice Research Institute South Asia Regional Centre, Collectry farm, Varanasi, Uttar Pradesh 221006, India
| | - Inez Slamet-Loedin
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
| | - Julia von Steimker
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology, Plovdiv 4000, Bulgaria
| | - Ajay Kohli
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
| | - Gurudev S Khush
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Nese Sreenivasulu
- International Rice Research Institute, Los Banos, Laguna 4030, Philippines
- International Rice Research Institute South Asia Regional Centre, Collectry farm, Varanasi, Uttar Pradesh 221006, India
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Qiu CW, Richmond M, Ma Y, Zhang S, Liu W, Feng X, Ahmed IM, Wu F. Melatonin enhances cadmium tolerance in rice via long non-coding RNA-mediated modulation of cell wall and photosynthesis. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133251. [PMID: 38141306 DOI: 10.1016/j.jhazmat.2023.133251] [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: 10/11/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 12/25/2023]
Abstract
In plants, melatonin (MLT) is a versatile signaling molecule involved in promoting plant development and mitigating the damage caused by heavy metal exposure. Long non-coding RNAs (lncRNAs) are essential components in the plant's response to various abiotic stress, functioning within the gene regulatory network. Here, a hydroponic experiment was performed to explore the involvement of lncRNAs in MLT-mediated amelioration of cadmium (Cd) toxicity in rice plants. The results demonstrated that applying 250 mg L-1 MLT in a solution containing 10 μM Cd leads to an effective reduction of 30.0% in shoot Cd concentration. Remarkably, the treatment resulted in a 21.2% improvement in potassium and calcium uptake, a 164.5% enhancement in net photosynthetic rate, and a 33.2% decrease in malondialdehyde accumulation, resulting increases in plant height, root length, and biomass accumulation. Moreover, a transcriptome analysis revealed 2510 differentially expressed transcripts, including the Cd transporters (-3.82-fold downregulated) and the Cd tolerance-associated genes (1.24-fold upregulated). Notably, regulatory network prediction uncovered 6 differentially expressed lncRNAs that act as competitive endogenous RNA or in RNA complex interactions. These key lncRNAs regulate the expression of target genes that are involved in pectin and cellulose metabolism, scavenging of reactive oxygen species, salicylic acid-mediated defense response, and biosynthesis of brassinosteroids, which ultimately modify the cell wall for Cd adsorption, safeguard photosynthesis, and control hormone signaling to reduce Cd toxicity. Our results unveiled a crucial lncRNA-mediated mechanism underlying MLT's role in Cd detoxification in rice plants, providing potential applications in agricultural practices and environmental remediation.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Marvin Richmond
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xue Feng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Imrul Mosaddek Ahmed
- Plant Biotechnology Laboratory, Center for Viticulture & Small Fruit Research, Florida A&M University, FL 32317, USA
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Ren D, Liu H, Sun X, Zhang F, Jiang L, Wang Y, Jiang N, Yan P, Cui J, Yang J, Li Z, Lu P, Luo X. Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:66-85. [PMID: 37970747 DOI: 10.1111/jipb.13583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/29/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023]
Abstract
RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.
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Affiliation(s)
- Ding Ren
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xuejun Sun
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Fan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Ling Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinhao Cui
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhikang Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Pingli Lu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
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Nanda S, Rout P, Ullah I, Nag SR, Reddy VV, Kumar G, Kumar R, He S, Wu H. Genome-wide identification and molecular characterization of CRK gene family in cucumber (Cucumis sativus L.) under cold stress and sclerotium rolfsii infection. BMC Genomics 2023; 24:219. [PMID: 37101152 PMCID: PMC10131431 DOI: 10.1186/s12864-023-09319-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND The plant cysteine-rich receptor-like kinases (CRKs) are a large family having multiple roles, including defense responses under both biotic and abiotic stress. However, the CRK family in cucumbers (Cucumis sativus L.) has been explored to a limited extent. In this study, a genome-wide characterization of the CRK family has been performed to investigate the structural and functional attributes of the cucumber CRKs under cold and fungal pathogen stress. RESULTS A total of 15 C. sativus CRKs (CsCRKs) have been characterized in the cucumber genome. Chromosome mapping of the CsCRKs revealed that 15 genes are distributed in cucumber chromosomes. Additionally, the gene duplication analysis of the CsCRKs yielded information on their divergence and expansion in cucumbers. Phylogenetic analysis divided the CsCRKs into two clades along with other plant CRKs. Functional predictions of the CsCRKs suggested their role in signaling and defense response in cucumbers. The expression analysis of the CsCRKs by using transcriptome data and via qRT-PCR indicated their involvement in both biotic and abiotic stress responses. Under the cucumber neck rot pathogen, Sclerotium rolfsii infection, multiple CsCRKs exhibited induced expressions at early, late, and both stages. Finally, the protein interaction network prediction results identified some key possible interacting partners of the CsCRKs in regulating cucumber physiological processes. CONCLUSIONS The results of this study identified and characterized the CRK gene family in cucumbers. Functional predictions and validation via expression analysis confirmed the involvement of the CsCRKs in cucumber defense response, especially against S. rolfsii. Moreover, current findings provide better insights into the cucumber CRKs and their involvement in defense responses.
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Affiliation(s)
- Satyabrata Nanda
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Priyadarshini Rout
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Ikram Ullah
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Swapna Rani Nag
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Velagala Veerraghava Reddy
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Gagan Kumar
- Krishi Vigyan Kendra, Narkatiaganj, Dr. Rajendra Prasad Central Agricultural University, Pusa Samastipur, Bihar, 848125, India
| | - Ritesh Kumar
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongzhi Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China.
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Thapa R, Tabien RE, Johnson CD, Septiningsih EM. Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress. BMC Genomics 2023; 24:185. [PMID: 37024819 PMCID: PMC10080786 DOI: 10.1186/s12864-023-09262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Rice is one of the most important cereals consumed worldwide. Two major abiotic factors affecting rice plants in different growth stages are flooding stress and cold stress. These abiotic stresses can take place independently or simultaneously and significantly affect rice plants during germination and seedling growth. Fortunately, a wide array of phenotypic responses conferring flooding stress and chilling stress tolerance exist within the rice germplasm, indicating the presence of different molecular mechanisms underlying tolerance to these stresses. Understanding these differences may assist in developing improved rice cultivars having higher tolerance to both stresses. In this study, we conducted a comparative global gene expression analysis of two rice genotypes with contrasting phenotypes under cold stress, anaerobic stress, and combined cold and anaerobic stress during germination. RESULTS The differential gene expression analysis revealed that 5571 differentially expressed genes (DEGs), 7206 DEGs, and 13279 DEGs were identified under anaerobic stress, cold stress, and combined stress, respectively. Genes involved in the carbohydrate metabolic process, glucosyltransferase activity, regulation of nitrogen compound metabolic process, protein metabolic process, lipid metabolic process, cellular nitrogen compound biosynthetic process, lipid biosynthetic process, and a microtubule-based process were enriched across all stresses. Notably, the common Gene Ontology (GO) analysis identified three hub genes, namely Os08g0176800 (similar to mRNA-associated protein mrnp 41), Os11g0454200 (dehydrin), and OS10g0505900 (expressed protein). CONCLUSION A large number of differentially expressed genes were identified under anaerobic, cold conditions during germination and the combination of the two stress conditions in rice. These results will assist in the identification of promising candidate genes for possible manipulation toward rice crops that are more tolerant under flooding and cold during germination, both independently and concurrently.
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Affiliation(s)
- Ranjita Thapa
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
- Present address: Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | - Charles D Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.
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Guo Z, Ma W, Cai L, Guo T, Liu H, Wang L, Liu J, Ma B, Feng Y, Liu C, Pan G. Comparison of anther transcriptomes in response to cold stress at the reproductive stage between susceptible and resistant Japonica rice varieties. BMC PLANT BIOLOGY 2022; 22:500. [PMID: 36284279 PMCID: PMC9597962 DOI: 10.1186/s12870-022-03873-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Rice is one of the most important cereal crops in the world but is susceptible to cold stress (CS). In this study, we carried out parallel transcriptomic analysis at the reproductive stage on the anthers of two Japonica rice varieties with contrasting CS resistance: cold susceptible Longjing11 (LJ11) and cold resistant Longjing25 (LJ25). RESULTS According to the obtained results, a total of 16,762 differentially expressed genes (DEGs) were identified under CS, including 7,050 and 14,531 DEGs in LJ25 and LJ11, respectively. Examining gene ontology (GO) enrichment identified 35 up- and 39 down-regulated biological process BP GO terms were significantly enriched in the two varieties, with 'response to heat' and 'response to cold' being the most enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 33 significantly enriched pathways. Only the carbon metabolism and amino acid biosynthesis pathways with down-regulated DEGs were enriched considerably in LJ11, while the plant hormone signal transduction pathway (containing 153 DEGs) was dramatically improved. Eight kinds of plant hormones were detected in the pathway, while auxin, abscisic acid (ABA), salicylic acid (SA), and ethylene (ETH) signaling pathways were found to be the top four pathways with the most DEGs. Furthermore, the protein-protein interaction (PPI) network analysis identified ten hub genes (co-expressed gene number ≥ 30), including six ABA-related genes. Various DEGs (such as OsDREB1A, OsICE1, OsMYB2, OsABF1, OsbZIP23, OsCATC, and so on) revealed distinct expression patterns among rice types when the DEGs between LJ11 and LJ25 were compared, indicating that they are likely responsible for CS resistance of rice in cold region. CONCLUSION Collectively, our findings provide comprehensive insights into complex molecular mechanisms of CS response and can aid in CS resistant molecular breeding of rice in cold regions.
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Affiliation(s)
- Zhenhua Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Wendong Ma
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China
| | - Lijun Cai
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, 154007, Jiamusi, Heilongjiang, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Linan Wang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China
| | - Junliang Liu
- Jiamusi Longjing Seed Industry Co., LTD, 154026, Jiamusi, Heilongjiang, China
| | - Bo Ma
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, 161006, Qiqihar, Heilongjiang, China
| | - Yanjiang Feng
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China.
| | - Chuanxue Liu
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China.
| | - Guojun Pan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China.
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Source-To-Sink Transport of Sugar and Its Role in Male Reproductive Development. Genes (Basel) 2022; 13:genes13081323. [PMID: 35893060 PMCID: PMC9329892 DOI: 10.3390/genes13081323] [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: 05/15/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Sucrose is produced in leaf mesophyll cells via photosynthesis and exported to non-photosynthetic sink tissues through the phloem. The molecular basis of source-to-sink long-distance transport in cereal crop plants is of importance due to its direct influence on grain yield-pollen grains, essential for male fertility, are filled with sugary starch, and rely on long-distance sugar transport from source leaves. Here, we overview sugar partitioning via phloem transport in rice, especially where relevant for male reproductive development. Phloem loading and unloading in source leaves and sink tissues uses a combination of the symplastic, apoplastic, and/or polymer trapping pathways. The symplastic and polymer trapping pathways are passive processes, correlated with source activity and sugar gradients. In contrast, apoplastic phloem loading/unloading involves active processes and several proteins, including SUcrose Transporters (SUTs), Sugars Will Eventually be Exported Transporters (SWEETs), Invertases (INVs), and MonoSaccharide Transporters (MSTs). Numerous transcription factors combine to create a complex network, such as DNA binding with One Finger 11 (DOF11), Carbon Starved Anther (CSA), and CSA2, which regulates sugar metabolism in normal male reproductive development and in response to changes in environmental signals, such as photoperiod.
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8
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Omics: a tool for resilient rice genetic improvement strategies. Mol Biol Rep 2022; 49:5075-5088. [PMID: 35298758 DOI: 10.1007/s11033-022-07189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/24/2022] [Indexed: 10/18/2022]
Abstract
Rice is pivotal pyramid of about half of the world population. Bearing small genome size and worldwide utmost food crop rice has been known as ideal cereal crop for genome research. Currently, decreasing water table and soil fatigue are big challenges and intense consequences in changing climate. Whole sequenced genome of rice sized 389 Mb of which 95% is covered with excellent mapping order. Sequenced rice genome helps in molecular biology and transcriptomics of cereals as it provides whole genome sequence of indica and japonica sub species. Through rice genome sequencing and functional genomics, QTLs or genes, genetic variability and halophyte blocks for agronomic characters were identified which have proved much more useful in molecular breeding and direct selection. There are different numbers of genes or QTLs identified for yield related traits i.e., 6 QTLs/genes for plant architecture, 6 for panicle characteristics, 4 for grain number, 1 gene/QTL for tiller, HGW, grain filling and shattering. QTLS/genes for grain quality, biotic stresses and for abiotic stresses are 7, 23 and 13 respectively. Low yield, inferior quality and susceptibility to biotic and abiotic stresses of a crop is due to narrow genetic background of new evolving rice verities. Wild rice provides genetic resources for improvement of these characters, molecular and genomics tool at different stages can overcome these stresses and improve yield and quality of rice crop.
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9
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Yang L, Xing F, He Q, Tahir ul Qamar M, Chen LL, Xing Y. Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. Int J Mol Sci 2020; 21:ijms21249618. [PMID: 33348666 PMCID: PMC7765902 DOI: 10.3390/ijms21249618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/10/2020] [Accepted: 12/16/2020] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is an epigenetic phenomenon in which a subset of genes express dependent on the origin of their parents. In plants, it is unclear whether imprinted genes are conserved between subspecies in rice. Here we identified imprinted genes from embryo and endosperm 5-7 days after pollination from three pairs of reciprocal hybrids, including inter-subspecies, japonica intra-subspecies, and indica intra-subspecies reciprocal hybrids. A total of 914 imprinted genes, including 546 in inter-subspecies hybrids, 211 in japonica intra-subspecies hybrids, and 286 in indica intra-subspecies hybrids. In general, the number of maternally expressed genes (MEGs) is more than paternally expressed genes (PEGs). Moreover, imprinted genes tend to be in mini clusters. The number of shared genes by R9N (reciprocal crosses between 9311 and Nipponbare) and R9Z (reciprocal crosses between 9311 and Zhenshan 97), R9N and RZN (reciprocal crosses between Zhonghua11 and Nipponbare), R9Z and RZN was 72, 46, and 16. These genes frequently involved in energy metabolism and seed development. Five imprinted genes (Os01g0151700, Os07g0103100, Os10g0340600, Os11g0679700, and Os12g0632800) are commonly detected in all three pairs of reciprocal hybrids and were validated by RT-PCR sequencing. Gene editing of two imprinted genes revealed that both genes conferred grain filling. Moreover, 15 and 27 imprinted genes with diverse functions in rice were shared with Arabidopsis and maize, respectively. This study provided valuable resources for identification of imprinting genes in rice or even in cereals.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
| | - Feng Xing
- College of Life Science, Xinyang Normal University, Xinyang 464000, China;
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
| | - Muhammad Tahir ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China;
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
- Correspondence: (L.-L.C.); (Y.X.)
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
- Correspondence: (L.-L.C.); (Y.X.)
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10
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Vasumathy SK, Peringottillam M, Sundaram KT, Kumar SHK, Alagu M. Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing. Mol Biol Rep 2020; 47:7391-7402. [PMID: 32886328 DOI: 10.1007/s11033-020-05794-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 107 reads were generated, and among that 16.3 × 107 reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker- assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.
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Affiliation(s)
| | - Maya Peringottillam
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Krishna T Sundaram
- South Asia hub, ICRISAT Campus, International Rice Research Institute, Secundarabad, Telangana, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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11
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Nutan KK, Rathore RS, Tripathi AK, Mishra M, Pareek A, Singla-Pareek SL. Integrating the dynamics of yield traits in rice in response to environmental changes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:490-506. [PMID: 31410470 DOI: 10.1093/jxb/erz364] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/29/2019] [Indexed: 05/23/2023]
Abstract
Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.
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Affiliation(s)
- Kamlesh Kant Nutan
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ray Singh Rathore
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Amit Kumar Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Manjari Mishra
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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12
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Chen T, Li G, Islam MR, Fu W, Feng B, Tao L, Fu G. Abscisic acid synergizes with sucrose to enhance grain yield and quality of rice by improving the source-sink relationship. BMC PLANT BIOLOGY 2019; 19:525. [PMID: 31775620 PMCID: PMC6882056 DOI: 10.1186/s12870-019-2126-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/08/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Abscisic acid (ABA) and sucrose act as molecular signals in response to abiotic stress. However, how their synergy regulates the source-sink relationship has rarely been studied. This study aimed to reveal the mechanism underlying the synergy between ABA and sucrose on assimilates allocation to improve grain yield and quality of rice. The early indica rice cultivar Zhefu802 was selected and planted in an artificial climate chamber at 32/24 °C (day/night) under natural sunlight conditions. Sucrose and ABA were exogenously sprayed (either alone or in combination) onto rice plants at flowering and 10 days after flowering. RESULTS ABA plus sucrose significantly improved both the grain yield and quality of rice, which was mainly a result of the higher proportion of dry matter accumulation and non-structural carbohydrates in panicles. These results were mainly ascribed to the large improvement in sucrose transport in the sheath-stems in response to the ABA plus sucrose treatment. In this process, ABA plus sucrose significantly enhanced the contents of starch, gibberellic acids, and zeatin ribosides as well as the activities and gene expression of enzymes involved in starch synthesis in grains. Additionally, remarkable increases in trehalose content and expression levels of trehalose-6-phosphate synthase1, trehalose-6-phosphate phosphatase7, and sucrose non-fermenting related protein kinase 1A were also found in grains treated with ABA plus sucrose. CONCLUSION The synergy between ABA and sucrose increased grain yield and quality by improving the source-sink relationship through sucrose and trehalose metabolism in grains.
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Affiliation(s)
- Tingting Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Guangyan Li
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Mohammad Rezaul Islam
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
- Department of Agricultural Extension, Ministry of Agriculture, Dhaka, 1215 Bangladesh
| | - Weimeng Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Baohua Feng
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Longxing Tao
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Guanfu Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
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13
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Panigrahi R, Kariali E, Panda BB, Lafarge T, Mohapatra PK. Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:507-523. [PMID: 30961785 DOI: 10.1071/fp18153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
The advent of dwarf statured rice varieties enabled a major breakthrough in yield and production, but raising the ceiling of genetically determined yield potential even further has been the breeding priority. Grain filling is asynchronous in the rice panicle; the inferior spikelets particularly on secondary branches of the basal part do not produce grains of a quality suitable for human consumption. Of the various strategies being considered, the control of ethylene production at anthesis has been a valuable route to potentially enhance genetic yield level of rice. The physiology underlying spikelet development has revealed spikelet position-specific ethylene levels determine the extent of grain filling, with higher levels resulting in ill-developed spikelet embodying poor endosperm starch content. To break the yield barrier, breeders have increased spikelet number per panicle in new large-panicle rice plants. However, the advantage of panicles with numerous spikelets has not resulted in enhanced yield because of poor filling of inferior spikelets. High spikelet number stimulates ethylene production and downgrading of starch synthesis, suggesting a trade-off between spikelet number and grain filling. High ethylene production in inferior spikelets suppresses expression of genes encoding endosperm starch synthesising enzymes. Hence, ethylene could be a retrograde signal that dictates the transcriptome dynamics for the cross talk between spikelet number and grain filling in the rice panicle, so attenuation of its activity may provide a solution to the problem of poor grain filling in large-panicle rice. This physiological linkage that reduces starch biosynthesis of inferior kernels is not genetically constitutive and amenable for modification through chemical, biotechnological, surgical and allelic manipulations. Studies on plant genotypes with different panicle architecture have opened up possibilities of selectively improving starch biosynthesis of inferior spikelets and thereby increasing grain yield through a physiological route.
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Affiliation(s)
- Rashmi Panigrahi
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India
| | - Ekamber Kariali
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India
| | - Binay Bhusan Panda
- Environmental Biotechnology Laboratory, Institute of Life Science, Bhubaneswar, 751023, India
| | - Tanguy Lafarge
- CIRAD, UMR AGAP, F-34398 Montpellier, France; and AGAP, University of Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
| | - Pravat Kumar Mohapatra
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India; and Corresponding author. Emails:
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14
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Fu X, Xu J, Zhou M, Chen M, Shen L, Li T, Zhu Y, Wang J, Hu J, Zhu L, Gao Z, Dong G, Guo L, Ren D, Chen G, Lin J, Qian Q, Zhang G. Enhanced Expression of QTL qLL9/DEP1 Facilitates the Improvement of Leaf Morphology and Grain Yield in Rice. Int J Mol Sci 2019; 20:E866. [PMID: 30781568 PMCID: PMC6412340 DOI: 10.3390/ijms20040866] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 01/22/2023] Open
Abstract
In molecular breeding of super rice, it is essential to isolate the best quantitative trait loci (QTLs) and genes of leaf shape and explore yield potential using large germplasm collections and genetic populations. In this study, a recombinant inbred line (RIL) population was used, which was derived from a cross between the following parental lines: hybrid rice Chunyou84, that is, japonica maintainer line Chunjiang16B (CJ16); and indica restorer line Chunhui 84 (C84) with remarkable leaf morphological differences. QTLs mapping of leaf shape traits was analyzed at the heading stage under different environmental conditions in Hainan (HN) and Hangzhou (HZ). A major QTL qLL9 for leaf length was detected and its function was studied using a population derived from a single residual heterozygote (RH), which was identified in the original population. qLL9 was delimitated to a 16.17 kb region flanked by molecular markers C-1640 and C-1642, which contained three open reading frames (ORFs). We found that the candidate gene for qLL9 is allelic to DEP1 using quantitative real-time polymerase chain reaction (qRT-PCR), sequence comparison, and the clustered regularly interspaced short palindromic repeat-associated Cas9 nuclease (CRISPR/Cas9) genome editing techniques. To identify the effect of qLL9 on yield, leaf shape and grain traits were measured in near isogenic lines (NILs) NIL-qLL9CJ16 and NIL-qLL9C84, as well as a chromosome segment substitution line (CSSL) CSSL-qLL9KASA with a Kasalath introgressed segment covering qLL9 in the Wuyunjing (WYJ) 7 backgrounds. Our results showed that the flag leaf lengths of NIL-qLL9C84 and CSSL-qLL9KASA were significantly different from those of NIL-qLL9CJ16 and WYJ 7, respectively. Compared with NIL-qLL9CJ16, the spike length, grain size, and thousand-grain weight of NIL-qLL9C84 were significantly higher, resulting in a significant increase in yield of 15.08%. Exploring and pyramiding beneficial genes resembling qLL9C84 for super rice breeding could increase both the source (e.g., leaf length and leaf area) and the sink (e.g., yield traits). This study provides a foundation for future investigation of the molecular mechanisms underlying the source⁻sink balance and high-yield potential of rice, benefiting high-yield molecular design breeding for global food security.
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Affiliation(s)
- Xue Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jing Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Mengyu Zhou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Minmin Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Ting Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yuchen Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jiajia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jianrong Lin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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15
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Du L, Xu F, Fang J, Gao S, Tang J, Fang S, Wang H, Tong H, Zhang F, Chu J, Wang G, Chu C. Endosperm sugar accumulation caused by mutation of PHS8/ISA1 leads to pre-harvest sprouting in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:545-556. [PMID: 29775500 DOI: 10.1111/tpj.13970] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 05/18/2023]
Abstract
Pre-harvest sprouting (PHS) is an unfavorable trait in cereal crops that could seriously decrease grain yield and quality. Although some PHS-associated quantitative trait loci or genes in cereals have been reported, the molecular mechanism underlying PHS remains largely elusive. Here, we characterized a rice mutant, phs8, which exhibits PHS phenotype accompanied by sugary endosperm. Map-based cloning revealed that PHS8 encodes a starch debranching enzyme named isoamylase1. Mutation in PHS8 resulted in the phytoglycogen breakdown and sugar accumulation in the endosperm. Intriguingly, with increase of sugar contents, decreased expression of OsABI3 and OsABI5 as well as reduced sensitivity to abscisic acid (ABA) were found in the phs8 mutant. Using rice suspension cell system, we confirmed that exogenous sugar is sufficient to suppress the expression of both OsABI3 and OsABI5. Furthermore, overexpression of OsABI3 or OsABI5 could partially rescue the PHS phenotype of phs8. Therefore, our study presents important evidence supporting that endosperm sugar not only acts as an essential energy source for seed germination but also determines seed dormancy and germination by affecting ABA signaling.
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Affiliation(s)
- Lin Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fan Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaopei Gao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuang Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongru Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongning Tong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fengxia Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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16
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Gianinetti A, Finocchiaro F, Bagnaresi P, Zechini A, Faccioli P, Cattivelli L, Valè G, Biselli C. Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition. PLANTS 2018; 7:plants7020035. [PMID: 29671830 PMCID: PMC6026906 DOI: 10.3390/plants7020035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/11/2018] [Indexed: 01/18/2023]
Abstract
Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.
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Affiliation(s)
- Alberto Gianinetti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Franca Finocchiaro
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Antonella Zechini
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Primetta Faccioli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Chiara Biselli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
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17
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Gao M, Yin X, Yang W, Lam SM, Tong X, Liu J, Wang X, Li Q, Shui G, He Z. GDSL lipases modulate immunity through lipid homeostasis in rice. PLoS Pathog 2017; 13:e1006724. [PMID: 29131851 PMCID: PMC5703576 DOI: 10.1371/journal.ppat.1006724] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 11/27/2017] [Accepted: 10/31/2017] [Indexed: 12/04/2022] Open
Abstract
Lipids and lipid metabolites play important roles in plant-microbe interactions. Despite the extensive studies of lipases in lipid homeostasis and seed oil biosynthesis, the involvement of lipases in plant immunity remains largely unknown. In particular, GDSL esterases/lipases, characterized by the conserved GDSL motif, are a subfamily of lipolytic enzymes with broad substrate specificity. Here, we functionally identified two GDSL lipases, OsGLIP1 and OsGLIP2, in rice immune responses. Expression of OsGLIP1 and OsGLIP2 was suppressed by pathogen infection and salicylic acid (SA) treatment. OsGLIP1 was mainly expressed in leaf and leaf sheath, while OsGLIP2 showed high expression in elongating internodes. Biochemical assay demonstrated that OsGLIP1 and OsGLIP2 are functional lipases that could hydrolyze lipid substrates. Simultaneous down-regulation of OsGLIP1 and OsGLIP2 increased plant resistance to both bacterial and fungal pathogens, whereas disease resistance in OsGLIP1 and OsGLIP2 overexpression plants was significantly compromised, suggesting that both genes act as negative regulators of disease resistance. OsGLIP1 and OsGLIP2 proteins mainly localize to lipid droplets and the endoplasmic reticulum (ER) membrane. The proper cellular localization of OsGLIP proteins is indispensable for their functions in immunity. Comprehensive lipid profiling analysis indicated that the alteration of OsGLIP gene expression was associated with substantial changes of the levels of lipid species including monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). We show that MGDG and DGDG feeding could attenuate disease resistance. Taken together, our study indicates that OsGLIP1 and OsGLIP2 negatively regulate rice defense by modulating lipid metabolism, thus providing new insights into the function of lipids in plant immunity. Lipases are a large family of enzymes conferring lipid metabolism. Lipids and their metabolites play diverse roles in plant growth as well as response to environmental stimuli. Accumulating evidence implicates lipids as signaling molecules mediating plant immunity. Therefore, lipases are presumed to be actively involved in plant defense responses. Based on gene expression profiling, we have identified two functional GDSL lipases, encoded by OsGLIP1 and OsGLIP2, whose expression was suppressed by pathogen infection in the model cereal rice. Both OsGLIP1 and OsGLIP2 proteins localize to lipid droplets and the endoplasmic reticulum (ER) membrane, and they likely coordinate lipid metabolism with differential but complementary expression patterns in tissues and developmental stages. Consequently, alteration of OsGLIP gene expression was associated with substantial changes of lipid abundance and plant disease resistance. Our work identifies and characterizes two lipases that function as negative regulators of plant immune responses, strengthening the understanding of lipid metabolism in plant-microbe interactions.
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Affiliation(s)
- Mingjun Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Yin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Tong
- China National Rice Research Institute, Hangzhou, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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18
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Liu Y, Zhang C, Zhao Y, Sun S, Liu Z. Effects of growing seasons and genotypes on the accumulation of cadmium and mineral nutrients in rice grown in cadmium contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 579:1282-1288. [PMID: 27908623 DOI: 10.1016/j.scitotenv.2016.11.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Heavy metals naturally occur in soil but their concentrations may be changed by seasonal rainfall under double-rice cropping system. The field trials at three sites, which represent low, medium and high cadmium (Cd) content in soil, revealed significant genotypic and environmental variations in grain Cd concentrations. Most cultivars in late rice at three sites produced grains with Cd content over the maximum permissible concentration (MPC) 0.20mgkg-1. However, grain Cd content in early rice was over MPC only at high Cd site. When planted at same site, late rice showed remarkably higher content of Cd as well as K, Mg, Fe and Mn than that in early rice in both grains and rachises. Content of Ni, Pb and Cr was generally in the safe range and it was determined by the interactions between genotypes and environmental factors. Element concentrations in rachises were about 2-10 times higher than those in grains, depending on element species, cultivars, locations and seasons. Low-Cd-accumulation cultivars generally displayed both lower Cd content in rachis and lower Cd transportation ratio from rachises to grains than those of high-Cd-accumulation cultivars. There was a significant and positive correlation between Cd and Mn concentrations in grains. The most important factor that causes great variation in Cd accumulation in rachises and grains between early and later rice is water contents and levels in paddy soils mainly caused by different rainfall amount. Inhibiting Cd accumulation in rachises and Cd transportation from rachises to grains could efficiently decrease Cd content in rice grains produced in contaminated soil.
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Affiliation(s)
- Yang Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China; College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, 300384, China
| | - Changbo Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China
| | - Yanling Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China
| | - Shoujun Sun
- College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, 300384, China
| | - Zhongqi Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China.
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19
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Li X, Guo K, Zhu X, Chen P, Li Y, Xie G, Wang L, Wang Y, Persson S, Peng L. Domestication of rice has reduced the occurrence of transposable elements within gene coding regions. BMC Genomics 2017; 18:55. [PMID: 28068923 PMCID: PMC5223533 DOI: 10.1186/s12864-016-3454-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/22/2016] [Indexed: 11/19/2022] Open
Abstract
Background Transposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are thus proposed as an ideal model to study TEs roles in the context of plant genome evolution. As TEs may contribute to improved rice growth and grain quality, it is of pivotal significance for worldwide food security and biomass production. Results We analyzed three cultivated rice species and their closest five wild relatives for distribution and content of TEs in their genomes. Despite that the three cultivar rice species contained similar copies and more total TEs, their genomes contained much longer TEs as compared to their wild relatives. Notably, TEs were largely depleted from genomic regions that corresponded to genes in the cultivated species, while this was not the case for their wild relatives. Gene ontology and gene homology analyses revealed that while certain genes contained TEs in all the wild species, the closest homologs in the cultivated species were devoid of them. This distribution of TEs is surprising as the cultivated species are more distantly related to each other as compared to their closest wild relative. Hence, cultivated rice species have more similar TE distributions among their genes as compared to their closest wild relatives. We, furthermore, exemplify how genes that are conferring important rice traits can be regulated by TE associations. Conclusions This study demonstrate that the cultivation of rice has led to distinct genomic distribution of TEs, and that certain rice traits are closely associated with TE distribution patterns. Hence, the results provide means to better understand TE-dependent rice traits and the potential to genetically engineer rice for better performance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3454-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xukai Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Kai Guo
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xiaobo Zhu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Ying Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Guosheng Xie
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Staffan Persson
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,School of Biosciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
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20
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Huang BH, Chen YW, Huang CL, Gao J, Liao PC. Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes. Sci Rep 2016; 6:39031. [PMID: 27966614 PMCID: PMC5155217 DOI: 10.1038/srep39031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/16/2016] [Indexed: 01/19/2023] Open
Abstract
Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yi-Wen Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Jian Gao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
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21
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Huang LF, Tan CC, Yeh JF, Liu HY, Liu YK, Ho SL, Lu CA. Efficient Secretion of Recombinant Proteins from Rice Suspension-Cultured Cells Modulated by the Choice of Signal Peptide. PLoS One 2015; 10:e0140812. [PMID: 26473722 PMCID: PMC4608814 DOI: 10.1371/journal.pone.0140812] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/29/2015] [Indexed: 11/25/2022] Open
Abstract
Plant-based expression systems have emerged as a competitive platform in the large-scale production of recombinant proteins. By adding a signal peptide, αAmy3sp, the desired recombinant proteins can be secreted outside transgenic rice cells, making them easy to harvest. In this work, to improve the secretion efficiency of recombinant proteins in rice expression systems, various signal peptides including αAmy3sp, CIN1sp, and 33KDsp have been fused to the N-terminus of green fluorescent protein (GFP) and introduced into rice cells to explore the efficiency of secretion of foreign proteins. 33KDsp had better efficiency than αAmy3sp and CIN1sp for the secretion of GFP from calli and suspension-cultured cells. 33KDsp was further applied for the secretion of mouse granulocyte-macrophage colony-stimulating factor (mGM-CSF) from transgenic rice suspension-cultured cells; approximately 76%–92% of total rice-derived mGM-CSF (rmGM-CSF) was detected in the culture medium. The rmGM-CSF was bioactive and could stimulate the proliferation of a murine myeloblastic leukemia cell line, NSF-60. The extracellular yield of rmGM-CSF reached 31.7 mg/L. Our study indicates that 33KDsp is better at promoting the secretion of recombinant proteins in rice suspension-cultured cell systems than the commonly used αAmy3sp.
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Affiliation(s)
- Li-Fen Huang
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, 135 Yuan-Tung Road, Taoyuan, Taiwan, ROC
- * E-mail: (L-FH); (C-AL)
| | - Chia-Chun Tan
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, 135 Yuan-Tung Road, Taoyuan, Taiwan, ROC
| | - Ju-Fang Yeh
- Department of Life Science, National Central University, Taoyuan, Taiwan, ROC
| | - Hsin-Yi Liu
- Department of Life Science, National Central University, Taoyuan, Taiwan, ROC
| | - Yu-Kuo Liu
- Graduate Institute of Biochemical and Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Shin-Lon Ho
- Department of Agronomy, National Chi-Yi University, Chiayi, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Science, National Central University, Taoyuan, Taiwan, ROC
- * E-mail: (L-FH); (C-AL)
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22
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Yin C, Li H, Li S, Xu L, Zhao Z, Wang J. Genetic dissection on rice grain shape by the two-dimensional image analysis in one japonica × indica population consisting of recombinant inbred lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1969-86. [PMID: 26133732 PMCID: PMC4572083 DOI: 10.1007/s00122-015-2560-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/13/2015] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE This article used seven characters from the 2D image analysis to dissect the genetic architecture underlying rice grain shape in one japonica × indica population consisting of 215 recombinant inbred lines. Two-dimensional (2D) digital image analysis is efficient for investigating the rice grain shape characters in large genetic and breeding populations. In this study, we used 2D image analysis to investigate seven characters, i.e., grain length (GL), grain width (GW), length-to-width ratio (LW), grain area (GA), grain circumference (GC), grain diameter (GD), and grain roundness (GR), in one japonica × indica genetic population consisting of 215 recombinant inbred lines. GL and GW can be recorded manually as well, and have been extensively used together with LW (i.e., GL/GW) in genetic studies on grain shape. GC and GA can be hardly measured manually, and have not been used together with GD and GR. Results indicated that the seven characters could be precisely measured by 2D image analysis, genotype by environment interaction was low, and heritability was high. Each character was controlled by a few major stable genes and multiple minor additive genes. A total of 51 QTL were detected for the seven characters across four diverse environments, 22 from GL, GW, and LW, the three traditional characters, and 29 from the other four characters. The 51 QTL were clustered in eighteen marker intervals. Comparing with previous studies and analyzing the stability of identified QTL, we found six non-reported marker intervals, one each on chromosomes 2 and 3, and two each on chromosomes 6 and 8. The newly identified loci and the large-scale phenotyping system would greatly improve our knowledge about the genetic architecture and the future rice breeding on grain shape.
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Affiliation(s)
- Changbin Yin
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science and CIMMYT China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huihui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science and CIMMYT China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shanshan Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science and CIMMYT China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lidong Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhigang Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiankang Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science and CIMMYT China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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23
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Rao Y, Li Y, Qian Q. Recent progress on molecular breeding of rice in China. PLANT CELL REPORTS 2014; 33:551-64. [PMID: 24442397 PMCID: PMC3976512 DOI: 10.1007/s00299-013-1551-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 05/22/2023]
Abstract
Molecular breeding of rice for high yield, superior grain quality, and strong environmental adaptability is crucial for feeding the world's rapidly growing population. The increasingly cloned quantitative trait loci and genes, genome variations, and haplotype blocks related to agronomically important traits in rice have provided a solid foundation for direct selection and molecular breeding, and a number of genes have been successfully introgressed into mega varieties of rice. Here we summarize China's great achievements in molecular breeding of rice in the following five traits: high yield, biotic stress resistance, abiotic stress resistance, quality and physiology. Further, the prospect of rice breeding by molecular design is discussed.
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Affiliation(s)
- Yuchun Rao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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24
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Sun L, Yang DL, Kong Y, Chen Y, Li XZ, Zeng LJ, Li Q, Wang ET, He ZH. Sugar homeostasis mediated by cell wall invertase GRAIN INCOMPLETE FILLING 1 (GIF1) plays a role in pre-existing and induced defence in rice. MOLECULAR PLANT PATHOLOGY 2014; 15:161-73. [PMID: 24118770 PMCID: PMC6638756 DOI: 10.1111/mpp.12078] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Sugar metabolism and sugar signalling are not only critical for plant growth and development, but are also important for stress responses. However, how sugar homeostasis is involved in plant defence against pathogen attack in the model crop rice remains largely unknown. In this study, we observed that the grains of gif1, a loss-of-function mutant of the cell wall invertase gene GRAIN INCOMPLETE FILLING 1 (GIF1), were hypersusceptible to postharvest fungal pathogens, with decreased levels of sugars and a thinner glume cell wall in comparison with the wild-type. Interestingly, constitutive expression of GIF1 enhanced resistance to both the rice bacterial pathogen Xanthomonas oryzae pv. oryzae and the fungal pathogen Magnaporthe oryzae. The GIF1-overexpressing (GIF1-OE) plants accumulated higher levels of glucose, fructose and sucrose compared with the wild-type plants. More importantly, higher levels of callose were deposited in GIF1-OE plants during pathogen infection. Moreover, the cell wall was much thicker in the infection sites of the GIF1-OE plants when compared with the wild-type plants. We also found that defence-related genes were constitutively activated in the GIF1-OE plants. Taken together, our study reveals that sugar homeostasis mediated by GIF1 plays an important role in constitutive and induced physical and chemical defence.
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Affiliation(s)
- Li Sun
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China; National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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25
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Huang A, Xu S, Cai X. Whole-genome quantitative trait locus mapping reveals major role of epistasis on yield of rice. PLoS One 2014; 9:e87330. [PMID: 24489897 PMCID: PMC3906158 DOI: 10.1371/journal.pone.0087330] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/19/2013] [Indexed: 01/05/2023] Open
Abstract
Although rice yield has been doubled in most parts of the world since 1960s, thanks to the advancements in breeding technologies, the biological mechanisms controlling yield are largely unknown. To understand the genetic basis of rice yield, a number of quantitative trait locus (QTL) mapping studies have been carried out, but whole-genome QTL mapping incorporating all interaction effects is still lacking. In this paper, we exploited whole-genome markers of an immortalized F2 population derived from an elite rice hybrid to perform QTL mapping for rice yield characterized by yield per plant and three yield component traits. Our QTL model includes additive and dominance main effects of 1,619 markers and all pair-wise interactions, with a total of more than 5 million possible effects. The QTL mapping identified 54, 5, 28 and 4 significant effects involving 103, 9, 52 and 7 QTLs for the four traits, namely the number of panicles per plant, the number of grains per panicle, grain weight, and yield per plant. Most identified QTLs are involved in digenic interactions. An extensive literature survey of experimentally characterized genes related to crop yield shows that 19 of 54 effects, 4 of 5 effects, 12 of 28 effects and 2 of 4 effects for the four traits, respectively, involve at least one QTL that locates within 2 cM distance to at least one yield-related gene. This study not only reveals the major role of epistasis influencing rice yield, but also provides a set of candidate genetic loci for further experimental investigation.
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Affiliation(s)
- Anhui Huang
- Department of Electrical and Computer Engineering, University of Miami, Coral Gables, Florida, United State of America
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United State of America
| | - Xiaodong Cai
- Department of Electrical and Computer Engineering, University of Miami, Coral Gables, Florida, United State of America
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26
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Ruan YL. Sucrose metabolism: gateway to diverse carbon use and sugar signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:33-67. [PMID: 24579990 DOI: 10.1146/annurev-arplant-050213-040251] [Citation(s) in RCA: 709] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sucrose metabolism plays pivotal roles in development, stress response, and yield formation, mainly by generating a range of sugars as metabolites to fuel growth and synthesize essential compounds (including protein, cellulose, and starch) and as signals to regulate expression of microRNAs, transcription factors, and other genes and for crosstalk with hormonal, oxidative, and defense signaling. This review aims to capture the most exciting developments in this area by evaluating (a) the roles of key sucrose metabolic enzymes in development, abiotic stress responses, and plant-microbe interactions; (b) the coupling between sucrose metabolism and sugar signaling from extra- to intracellular spaces; (c) the different mechanisms by which sucrose metabolic enzymes could perform their signaling roles; and (d) progress on engineering sugar metabolism and transport for high yield and disease resistance. Finally, the review outlines future directions for research on sugar metabolism and signaling to better understand and improve plant performance.
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Affiliation(s)
- Yong-Ling Ruan
- School of Environment and Life Sciences and Australia-China Research Centre for Crop Improvement, University of Newcastle, Callaghan 2308, Australia;
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27
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Lee ST, Huang WL. Cytokinin, auxin, and abscisic acid affects sucrose metabolism conduce to de novo shoot organogenesis in rice (Oryza sativa L.) callus. BOTANICAL STUDIES 2013; 54:5. [PMID: 28510848 PMCID: PMC5383921 DOI: 10.1186/1999-3110-54-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 08/09/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Shoot regeneration frequency in rice callus is still low and highly diverse among rice cultivars. This study aimed to investigate the association of plant hormone signaling and sucrose uptake and metabolism in rice during callus induction and early shoot organogenesis. The immatured seeds of two rice cultivars, Ai-Nan-Tsao 39 (ANT39) and Tainan 11 (TN11) are used in this study. RESULTS Callus formation is earlier, callus fresh weight is higher, but water content is significant lower in ANT39 than in TN11 while their explants are inoculated on callus induction medium (CIM). Besides, the regeneration frequency is prominently higher in ANT39 (~80%) compared to TN11 callus (0%). Levels of glucose, sucrose, and starch are all significant higher in ANT39 than in TN11 either at callus induction or early shoot organogenesis stage. Moreover, high expression levels of Cell wall-bound invertase 1, Sucrose transporter 1 (OsSUT1) and OsSUT2 are detected in ANT39 at the fourth-day in CIM but it cannot be detected in TN11 until the tenth-day. It suggested that ANT39 has higher callus growth rate and shoot regeneration ability may cause from higher activity of sucrose uptake and metabolism. As well, the expression levels of ORYZA SATIVA RESPONSE REGULATOR 1 (ORR1), PIN-formed 1 and Late embryogenesis-abundant 1, representing endogenous cytokinin, auxin and ABA signals, respectively, were also up-regulated in highly regenerable callus, ANT39, but only ORR1 was greatly enhanced in TN11 at the tenth-day in CIM. CONCLUSION Thus, phytohormone signals may affect sucrose metabolism to trigger callus initiation and further de novo shoot regeneration in rice culture.
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Affiliation(s)
- Shiang-Ting Lee
- Department of Agronomy, National Chiayi University, Chiayi City 600, Taiwan
| | - Wen-Lii Huang
- Department of Agronomy, National Chiayi University, Chiayi City 600, Taiwan
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28
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Ikeda M, Miura K, Aya K, Kitano H, Matsuoka M. Genes offering the potential for designing yield-related traits in rice. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:213-20. [PMID: 23466256 DOI: 10.1016/j.pbi.2013.02.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/04/2013] [Indexed: 05/05/2023]
Abstract
Breeding of high-yielding rice is crucial for meeting the food demand of the increasing world population. New technologies have facilitated identification of genes involved in quantitative traits, and many genes underpinning quantitative trait loci involved in rice crop yield have been isolated. Meanwhile, various kinds of mutants have been intensively studied, leading to characterization of many genes related to yield traits. A combination of quantitative trait locus analysis and studies of such mutants has made it possible to compile a list of genes available for breeding rice with higher yield.
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Affiliation(s)
- Mayuko Ikeda
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
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29
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Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z. Genetic bases of rice grain shape: so many genes, so little known. TRENDS IN PLANT SCIENCE 2013; 18:218-26. [PMID: 23218902 DOI: 10.1016/j.tplants.2012.11.001] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 10/27/2012] [Accepted: 11/01/2012] [Indexed: 05/21/2023]
Abstract
Rice (Oryza sativa) grain shape is a key determinant of grain yield and market values. Facilitated by advancements in genomics and various molecular markers, more than 400 quantitative trait loci (QTLs) associated with rice grain traits have been identified. In this review, we examine the genetic bases of rice grain shape, focusing on the protein products of 13 genes that have been cloned and the chromosome locations of 15 QTLs that have been fine mapped. Although more genes affecting grain traits are likely to be cloned in the near future, characterizing their functions at the biochemical level and applying these molecular data to rice breeding programs will be a more challenging task.
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Affiliation(s)
- Rongyu Huang
- School of Life Sciences, Xiamen University, Xiamen 361005, China
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Olsen KM, Wendel JF. A bountiful harvest: genomic insights into crop domestication phenotypes. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:47-70. [PMID: 23451788 DOI: 10.1146/annurev-arplant-050312-120048] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Human selection during crop domestication has resulted in remarkable transformations of plant phenotypes, providing a window into the genetic basis of morphological evolution. Recent progress in our understanding of the genetic architecture of novel plant traits has emerged from combining advanced molecular technologies with improved experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies reveal a diversity of underlying causative mutations affecting phenotypes important in plant domestication and crop improvement, including coding sequence substitutions, presence/absence and copy number variation, transposon activation leading to novel gene structures and expression patterns, diversification following gene duplication, and polyploidy leading to altered combinatorial capabilities. The genomic regions unknowingly targeted by human selection include both structural and regulatory genes, often with results that propagate through the transcriptome as well as to other levels in the biosynthetic and morphogenetic networks.
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Affiliation(s)
- Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Abu-Zaitoon YM, Bennett K, Normanly J, Nonhebel HM. A large increase in IAA during development of rice grains correlates with the expression of tryptophan aminotransferase OsTAR1 and a grain-specific YUCCA. PHYSIOLOGIA PLANTARUM 2012; 146:487-99. [PMID: 22582989 DOI: 10.1111/j.1399-3054.2012.01649.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The indole-3-acetic acid (IAA) content of developing grains of Oryza sativa subsp. japonica was measured by combined liquid chromatography, tandem mass spectrometry in multiple-reaction-monitoring mode. The increase from 50 ng g(-1) fresh weight to 2.9 µg g(-1) fresh weight from 1 to 14 days after pollination was much larger than that previously reported by enzyme-linked immunoassay methods. The largest increase in IAA content coincided with the start of the major starch deposition phase of grain-fill. The increase in IAA content was strongly correlated with the expression of putative IAA biosynthesis genes, OsYUC9, OsYUC11 and OsTAR1, measured by quantitative reverse transcriptase polymerase chain reaction. These results confirm the importance of the tryptophan aminotransferase/YUCCA pathway in this system. All three genes were expressed in endosperm; expression of OsYUC11 appeared to be confined to endosperm tissue. Phylogenetic analysis indicated that OsYUC11 and AtYUC10 belong to a separate clade of YUCCAs, which do not have orthologues outside the Angiosperms. This clade may have evolved with a specific role in endosperm. Expression of tryptophan decarboxylase in developing rice grains did not correlate with IAA levels, indicating that tryptamine is unlikely to be important for IAA synthesis in this system. In light of these observations, we hypothesize that IAA production in developing rice grains is controlled via expression of OsTAR1, OsYUC9, OsYUC11 and that IAA may be important during starch deposition in addition to its previously suggested role early in grain development.
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Affiliation(s)
- Yousef M Abu-Zaitoon
- Molecular and Cellular Biology, University of New England, Armidale, New South Wales, Australia
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Bombarely A, Edwards KD, Sanchez-Tamburrino J, Mueller LA. Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. BMC Genomics 2012; 13:406. [PMID: 22900718 PMCID: PMC3582432 DOI: 10.1186/1471-2164-13-406] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 08/03/2012] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco) and parental genome donors, N. sylvesteris (S-Genome) and N. tomentosiformis (T-Genome), a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant. RESULTS A comparison between the genes present in the leaf transcriptomes of N. tabacum and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters) expressed above background level (more than 5 reads) showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes) of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total) showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks) and non-synonymous nucleotide substitution (Kn) provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place. CONCLUSIONS Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD) events, polyploid genomes usually maintain a high percentage of gene duplicates. The data provided little evidence of preferential maintenance of gene expression from either the T- or S-genome. Additionally there was little evidence of neofunctionalization in Nicotiana tabacum suggesting it occurs at a low frequency in young polyploidy.
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Affiliation(s)
- Aureliano Bombarely
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY, 14853-1801, USA
| | - Kieron D Edwards
- Advanced Technologies (Cambridge Ltd), 210 Cambridge Science Park, Milton Road, Cambridge, CB4 0WA, UK
| | - Juan Sanchez-Tamburrino
- Advanced Technologies (Cambridge Ltd), 210 Cambridge Science Park, Milton Road, Cambridge, CB4 0WA, UK
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY, 14853-1801, USA
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Singh D, Singh PK, Chaudhary S, Mehla K, Kumar S. Exome sequencing and advances in crop improvement. ADVANCES IN GENETICS 2012; 79:87-121. [PMID: 22989766 DOI: 10.1016/b978-0-12-394395-8.00003-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Next-generation sequencing strategies have opened new vistas for molecular plant breeding. The sequence information obtained by the advent of next-generation sequencing provides a valuable tool not only for improving domesticated crops but also for investigating the natural evolution of crops. Such information provides an enormous potential for sustainable agriculture. In this review, we discuss how such sequencing approaches have transformed exome sequencing into a practical utility that has enormous potential for crop improvement in agriculture. Furthermore, we also describe the future of crop improvement beyond the exome sequencing strategies.
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Affiliation(s)
- Devi Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, UP, India
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Liu X, Zhang C, Ou Y, Lin Y, Song B, Xie C, Liu J, Li XQ. Systematic analysis of potato acid invertase genes reveals that a cold-responsive member, StvacINV1, regulates cold-induced sweetening of tubers. Mol Genet Genomics 2011; 286:109-18. [PMID: 21691778 DOI: 10.1007/s00438-011-0632-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Accepted: 06/07/2011] [Indexed: 11/25/2022]
Abstract
Acid invertase is believed to play a regulatory role during plant developmental processes and to respond to environmental stimuli. The expression profiles of the entire acid invertase family are not yet available for potato. By searching existing databases, it was determined that there are at least six acid invertase genes in potato, including four cell-wall invertase genes and two vacuolar invertase genes. They were subjected to comparative expression profiling in various organs of potato plants and in stored tubers to exploit their potential functions. The results revealed that each gene exhibited a unique expression pattern, which differed in transcript abundance or showed organ-specific features, pointing to the possible involvement of individual genes in plant development. The vacuolar invertase gene StvacINV1 had the highest expression level among three genes detected in the potato tubers. Further storage experiments showed that StvacINV1 was strongly induced by low temperatures, which is consistent with glucose accumulation in cold-stored tubers. Suppression of StvacINV1 by the antisense transformation in potato confirmed that lower StvacINV1 transcript abundance in transgenic tubers is related to lower reducing sugar content and lighter chip color in comparison with the wild type. The evidence strongly suggests that StvacINV1 is a gene involved in regulation of cold-induced sweetening of potato tubers. This provides an avenue for studying the mechanism involved in the regulation of the cold-induced sweetening trait and for agronomic enhancement.
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Affiliation(s)
- Xun Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Centre for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan 430070, China
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Diversity in copy number and structure of a silkworm morphogenetic gene as a result of domestication. Genetics 2011; 187:965-76. [PMID: 21242537 DOI: 10.1534/genetics.110.124982] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The carotenoid-binding protein (CBP) of the domesticated silkworm, Bombyx mori, a major determinant of cocoon color, is likely to have been substantially influenced by domestication of this species. We analyzed the structure of the CBP gene in multiple strains of B. mori, in multiple individuals of the wild silkworm, B. mandarina (the putative wild ancestor of B. mori), and in a number of other lepidopterans. We found the CBP gene copy number in genomic DNA to vary widely among B. mori strains, ranging from 1 to 20. The copies of CBP are of several types, based on the presence of a retrotransposon or partial deletion of the coding sequence. In contrast to B. mori, B. mandarina was found to possess a single copy of CBP without the retrotransposon insertion, regardless of habitat. Several other lepidopterans were found to contain sequences homologous to CBP, revealing that this gene is evolutionarily conserved in the lepidopteran lineage. Thus, domestication can generate significant diversity of gene copy number and structure over a relatively short evolutionary time.
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