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Yin M, Tong X, Yang J, Cheng Y, Zhou P, Li G, Wang Y, Ying J. Dissecting the Genetic Basis of Yield Traits and Validation of a Novel Quantitative Trait Locus for Grain Width and Weight in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:770. [PMID: 38592774 PMCID: PMC10975080 DOI: 10.3390/plants13060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Grain yield in rice is a complex trait and it is controlled by a number of quantitative trait loci (QTL). To dissect the genetic basis of rice yield, QTL analysis for nine yield traits was performed using an F2 population containing 190 plants, which was developed from a cross between Youyidao (YYD) and Sanfenhe (SFH), and each plant in the population evaluated with respect to nine yield traits. In this study, the correlations among the nine yield traits were analyzed. The grain yield per plant positively correlated with six yield traits, except for grain length and grain width, and showed the highest correlation coefficient of 0.98 with the number of filled grains per plant. A genetic map containing 133 DNA markers was constructed and it spanned 1831.7 cM throughout 12 chromosomes. A total of 36 QTLs for the yield traits were detected on nine chromosomes, except for the remaining chromosomes 5, 8, and 9. The phenotypic variation was explained by a single QTL that ranged from 6.19% to 36.01%. Furthermore, a major QTL for grain width and weight, qGW2-1, was confirmed to be newly identified and was narrowed down to a relatively smaller interval of about ~2.94-Mb. Collectively, we detected a total of 36 QTLs for yield traits and a major QTL, qGW2-1, was confirmed to control grain weight and width, which laid the foundation for further map-based cloning and molecular design breeding in rice.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiezheng Ying
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (M.Y.); (J.Y.); (Y.C.); (P.Z.); (G.L.); (Y.W.)
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2
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Guo J, Zhou X, Chen D, Chen K, Ye C, Liu J, Liu S, Chen Y, Chen G, Liu C. Effect of Fat Content on Rice Taste Quality through Transcriptome Analysis. Genes (Basel) 2024; 15:81. [PMID: 38254970 PMCID: PMC10815682 DOI: 10.3390/genes15010081] [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: 12/06/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Rice is an important crop in the word, and fat is one of the main important nutrient components of rice. The lipid content and fatty acid composition of grains significantly influences the quality of rice. In this study, 94 homozygous recombination inbred lines (RILs) were developed and the crude fat content of them displayed a normal distribution ranging from 0.44% to 2.62%. Based on their taste quality, a positive association between fat content and eating quality was revealed. Then, two lines (FH and FL) were selected with similar agronomic characteristics and different lipid content and taste quality for RNA sequencing analysis, and a total of 619 differentiable expressed genes were detected, primarily enriched in metabolic pathways such as starch and sucrose metabolism, fatty acid metabolism, and amino acid metabolism. The expression of two genes related to fatty acid synthesis and elongation was significantly up-regulated, while the expression of three genes related to fatty acid degradation was significantly down-regulated in FH grains. By using liquid chromatography, the relative levels of palmitic acid and oleic acid were discovered significantly higher in FH grains. Additionally, the comparative genomic analysis was conducted to visualize genomic differences of five genes. Ultimately, two genes (Os07g0417200 and Os12g0102100) were selected to be the key gene to affect the lipid metabolism, especially for the synthesis of unsaturated fatty acids, significantly changing the eating quality of rice. These results provide a theoretical basis for improving the taste quality of rice.
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Affiliation(s)
- Jie Guo
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xinqiao Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Dagang Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Juan Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Shaolong Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Youding Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Guorong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.G.); (X.Z.); (G.C.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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3
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Huang S, Zhang D, Wang Q, Shang B, Liu J, Xing X, Hong Y, Duan X, Sun H. Shotgun lipidomics reveals the changes in phospholipids of brown rice during accelerated aging. Food Res Int 2023; 171:113073. [PMID: 37330832 DOI: 10.1016/j.foodres.2023.113073] [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: 01/03/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/19/2023]
Abstract
Brown rice exhibits higher nutritional value and attracts more and more attentions; however, the change in phospholipid molecular species in brown rice during aging is poorly understood. In this study, shotgun lipidomics was employed to investigate the changes in phospholipid molecular species in four brown rice varieties (two japonica rice and two indica rice) during accelerated aging. A total of 64 phospholipid molecular species were identified, and most of them were rich in polyunsaturated fatty acids. For japonica rice, phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG) gradually decreased during accelerated aging. However, the content of PC, PE, and PG in indica rice showed no difference during accelerated aging. Significantly different phospholipid molecular species from four brown rice were screened during accelerated aging. Based on these significantly different phospholipids, the metabolic pathways including glycerophospholipid metabolism and linoleic acid metabolism during accelerated aging were depicted. The findings from this study could be helpful in explaining the impact of accelerated aging on phospholipids of brown rice, and offer an understanding on relationships between phospholipids degradation and brown rice deterioration.
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Affiliation(s)
- Shanshan Huang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Dong Zhang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China.
| | - Qian Wang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Bo Shang
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Jianlei Liu
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Xiaoting Xing
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Yu Hong
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
| | - Xiaoliang Duan
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China.
| | - Hui Sun
- Academy of National Food and Strategic Reserves Administration, Beijing 100037, China.
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Su S, Tang P, Zuo R, Chen H, Zhao T, Yang S, Yang J. Exogenous Jasmonic Acid Alleviates Blast Resistance Reduction Caused by LOX3 Knockout in Rice. Biomolecules 2023; 13:1197. [PMID: 37627262 PMCID: PMC10452216 DOI: 10.3390/biom13081197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
Lipoxygenase 3 (LOX3) is a lipid peroxidase found in rice embryos that is known to affect seed quality. Interestingly, deletion of the LOX3 gene has been shown to improve rice seed quality but decrease resistance to rice blast disease and drought. To investigate these opposing effects, we generated a LOX3 knockout construct (ΔLox3) in rice (Oryza sativa L.) plants. Blast resistance and transcription levels of rice genes in ΔLox3 rice plants and the effects of exogenous jasmonic acid (JA) on resistance and transcriptional levels of rice genes in Magnaporthe oryzae-infected ΔLox3 rice plants were further elucidated. The results showed that the ΔLox3 plants exhibited normal phenotypes, with high levels of methyl-linolenate and reactive oxygen species (ROS), and the genes involved in three Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways contributed to rice seed quality. M. oryzae-infected ΔLox3 plants exhibited serious blast symptoms with a reduced defense response but increased ROS-mediated cell death, and the genes involved in seven KEGG pathways contributed to rice seed quality. Exogenous JA treatment alleviated blast symptoms in infected ΔLox3 plants by hindering hyphal expansion, inhibiting ROS-mediated cell death, and increasing the defense response, and genes involved in 12 KEGG pathways contributed to rice seed quality. These findings demonstrate that LOX3 plays an important role in rice growth and defense, and its knockout improves rice quality at the expense of disease resistance. Exogenous JA provides a means to compensate for the reduction in defense responses of LOX3 knockout rice lines, suggesting potential applications in agricultural production.
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Affiliation(s)
- Shunyu Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (S.S.); (P.T.); (R.Z.); (H.C.); (T.Z.); (S.Y.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (S.S.); (P.T.); (R.Z.); (H.C.); (T.Z.); (S.Y.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Rubin Zuo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (S.S.); (P.T.); (R.Z.); (H.C.); (T.Z.); (S.Y.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Hongfeng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (S.S.); (P.T.); (R.Z.); (H.C.); (T.Z.); (S.Y.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Tianqi Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (S.S.); (P.T.); (R.Z.); (H.C.); (T.Z.); (S.Y.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shumin Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (S.S.); (P.T.); (R.Z.); (H.C.); (T.Z.); (S.Y.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (S.S.); (P.T.); (R.Z.); (H.C.); (T.Z.); (S.Y.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
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5
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Mai NTP, Nguyen LTT, Tran SG, To HTM. Genome-wide association study reveals useful QTL and genes controlling the fatty acid composition in rice bran oil using Vietnamese rice landraces. Funct Integr Genomics 2023; 23:150. [PMID: 37156920 DOI: 10.1007/s10142-023-01080-6] [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: 02/15/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/10/2023]
Abstract
In rice (Oryza sativa L.), rice bran contains valuable nutritional constituents, such as high unsaturated fat content, tocotrienols, inositol, γ-oryzanol, and phytosterols, all of which are of nutritional and pharmaceuticals interest. There is now a rising market demand for rice bran oil, which makes research into their content and fatty acid profile an area of interest. As it is evident that lipid content has a substantial impact on the eating, cooking, and storage quality of rice, an understanding of the genetic mechanisms that determine oil content in rice is of great importance, equal to that of rice quality. Therefore, in this study, we performed a genome-wide association study on the composition and oil concentration of 161 Vietnamese rice varieties. Five categories of fatty acids in rice bran were discovered and the bran oil concentration profile in different rice accessions was identified. We also identified 229 important markers related to the fatty acid composition of bran oil, distributed mainly on chromosomes 1 and 7. Seven quantitative trait loci and five potential genes related to unsaturated fatty acid content were detected, including OsKASI, OsFAD, OsARF, OsGAPDH, and OsMADS29. These results provide insights into the genetic basis of rice bran oil composition, which is pivotal to the metabolic engineering of rice plants with desirable bran oil content through candidate genes selection.
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Affiliation(s)
- Nga T P Mai
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Linh Thi Thuy Nguyen
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Son Giang Tran
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Huong Thi Mai To
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam.
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Xia D, Zhou H, Wang Y, Ao Y, Li Y, Huang J, Wu B, Li X, Wang G, Xiao J, Liu Q, He Y. qFC6, a major gene for crude fat content and quality in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2675-2685. [PMID: 35715647 DOI: 10.1007/s00122-022-04141-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
qFC6, a major quantitative trait locus for rice crude fat content, was fine mapped to be identical with Wx. FC6 negatively regulates crude fat content and rice quality. Starch, protein and lipids are the three major components in rice endosperm. The lipids content in rice influences both storage and quality. In this study, we identified a quantitative trait locus (QTL), qFC6, for crude fat (free lipids) content through association analysis and linkage analysis. Gene-based association analysis revealed that LOC_Os06g04200, also known as Wx, was the candidate gene for qFC6. Complementation and knockout transgenic lines revealed that Wx negatively regulates crude fat content. Lipid composition and content analysis by gas chromatography and taste evaluation analysis showed that FC6 positively influenced bound lipids content and negatively affected both free lipids content and taste. Besides, higher free lipids content rice varieties exhibit more lustrous appearance after cooking and by adding extra oil during cooking could improve rice luster and taste score, indicating that higher free lipids content may make rice more lustrous and delicious. Together, we cloned a QTL coordinating rice crude fat content and eating quality and assisted in uncovering the genetic basis of rice lipid content and in the improvement of rice eating quality.
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Affiliation(s)
- Duo Xia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yipei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiting Ao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinjie Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225000, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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7
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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8
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Chele KH, Steenkamp P, Piater LA, Dubery IA, Huyser J, Tugizimana F. A Global Metabolic Map Defines the Effects of a Si-Based Biostimulant on Tomato Plants under Normal and Saline Conditions. Metabolites 2021; 11:metabo11120820. [PMID: 34940578 PMCID: PMC8709197 DOI: 10.3390/metabo11120820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/10/2021] [Accepted: 11/13/2021] [Indexed: 01/19/2023] Open
Abstract
The ongoing unpredictability of climate changes is exponentially exerting a negative impact on crop production, further aggravating detrimental abiotic stress effects. Several research studies have been focused on the genetic modification of crop plants to achieve more crop resilience against such stress factors; however, there has been a paradigm shift in modern agriculture focusing on more organic, eco-friendly and long-lasting systems to improve crop yield. As such, extensive research into the use of microbial and nonmicrobial biostimulants has been at the core of agricultural studies to improve crop growth and development, as well as to attain tolerance against several biotic and abiotic stresses. However, the molecular mechanisms underlying the biostimulant activity remain enigmatic. Thus, this study is a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics approach to unravel the hypothetical biochemical framework underlying effects of a nonmicrobial biostimulant (a silicon-based formulation) on tomato plants (Solanum lycopersium) under salinity stress conditions. This metabolomics study postulates that Si-based biostimulants could alleviate salinity stress in tomato plants through modulation of the primary metabolism involving changes in the tricarboxylic acid cycle, fatty acid and numerous amino acid biosynthesis pathways, with further reprogramming of several secondary metabolism pathways such as the phenylpropanoid pathway, flavonoid biosynthesis pathways including flavone and flavanol biosynthesis. Thus, the postulated hypothetical framework, describing biostimulant-induced metabolic events in tomato plants, provides actionable knowledge necessary for industries and farmers to, confidently and innovatively, explore, design, and fully implement Si-based formulations and strategies into agronomic practices for sustainable agriculture and food production.
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Affiliation(s)
- Kekeletso H. Chele
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Paul Steenkamp
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa;
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa;
- Correspondence: ; Tel.: +27-011-559-7784
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9
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Li Y, Zheng YP, Zhou XH, Yang XM, He XR, Feng Q, Zhu Y, Li GB, Wang H, Zhao JH, Hu XH, Pu M, Zhou SX, Ji YP, Zhao ZX, Zhang JW, Huang YY, Fan J, Zhang LL, Wang WM. Rice miR1432 Fine-Tunes the Balance of Yield and Blast Disease Resistance via Different Modules. RICE (NEW YORK, N.Y.) 2021; 14:87. [PMID: 34674053 PMCID: PMC8531185 DOI: 10.1186/s12284-021-00529-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/12/2021] [Indexed: 05/02/2023]
Abstract
microRNAs act as fine-tuners in the regulation of plant growth and resistance against biotic and abiotic stress. Here we demonstrate that rice miR1432 fine-tunes yield and blast disease resistance via different modules. Overexpression of miR1432 leads to compromised resistance and decreased yield, whereas blocking miR1432 using a target mimic of miR1432 results in enhanced resistance and yield. miR1432 suppresses the expression of LOC_Os03g59790, which encodes an EF-hand family protein 1 (OsEFH1). Overexpression of OsEFH1 leads to enhanced rice resistance but decreased grain yield. Further study revealed that miR1432 and OsEFH1 are differentially responsive to chitin, a fungus-derived pathogen/microbe-associated molecular pattern (PAMP/MAMP). Consistently, blocking miR1432 or overexpression of OsEFH1 improves chitin-triggered immunity responses. In contrast, overexpression of ACOT, another target gene regulating rice yield traits, has no significant effects on rice blast disease resistance. Altogether, these results indicate that miR1432 balances yield and resistance via different target genes, and blocking miR1432 can simultaneously improve yield and resistance.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ya-Ping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xin-Hui Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xue-Mei Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Rong He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Qin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Guo-Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jing-Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Shi-Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yun-Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ji-Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ling-Li Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
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10
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Zhou H, Xia D, Li P, Ao Y, Xu X, Wan S, Li Y, Wu B, Shi H, Wang K, Gao G, Zhang Q, Wang G, Xiao J, Li X, Yu S, Lian X, He Y. Genetic architecture and key genes controlling the diversity of oil composition in rice grains. MOLECULAR PLANT 2021; 14:456-469. [PMID: 33307246 DOI: 10.1016/j.molp.2020.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/28/2020] [Accepted: 12/04/2020] [Indexed: 05/25/2023]
Abstract
Rice grain oil is a valuable nutrient source. However, the genetic basis of oil biosynthesis in rice grains remains unclear. In this study, we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions. High variation for 11 oil-related traits was observed, and the oil composition of rice grains showed differentiation among the subpopulations. We identified 46 loci that are significantly associated with grain oil concentration or composition, 16 of which were detected in three recombinant inbred line populations. Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci, four of which (PAL6, LIN6, MYR2, and ARA6) were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations. Interestingly, population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice. Based on these results, we propose a possible oil biosynthetic pathway in rice grains. Collectively, our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.
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Affiliation(s)
- Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yiting Ao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaodong Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shanshan Wan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huan Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kaiyue Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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11
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Sahu PK, Mondal S, Sao R, Vishwakarma G, Kumar V, Das BK, Sharma D. Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice ( Oryza sativa L.) landraces. 3 Biotech 2020; 10:487. [PMID: 33123454 DOI: 10.1007/s13205-020-02467-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
A core set of 190 rice landraces were used to decipher the genetic structure and to discover the chromosomal regions containing QTLs, affecting the grain micro-nutrients, fatty acids, and yield-related traits by using 148 molecular markers in this study. Landraces were categorized into three sub-groups based on population stratification study and followed by neighbor-joining tree and principal component analysis. Analysis of variance revealed abundant variations among the landraces for studied traits with less influence of environmental factors. Genome Wide Association Studies (GWAS) revealed 22 significant and consistent QTLs through marker trait association (MTAs) for 12 traits based on 2 years and pooled analysis. Out of 22 QTLs, three have been reported earlier while 19 QTLs are novel. Interestingly, 13 QTLs out of 22 were explained more than 10% phenotypic variance. Association of RM1148 and RM205 with Days to 50% flowering was comparable with flowering control genes Ghd8/qDTH8 and qDTH9, respectively. Similarly, Zn content was associated with RM44, which is situated within the QTL qZn8-1. Moreover, significant association of RM25 with oleic acid content was closely positioned with QTL qOle8. Association of RM7434 with grain yield/plant; RM184 with spikelet fertility %; R3M10, R9M42 with hundred seed weight; RM536, RM17467, RM484, RM26063 with Fe content; RM44, RM6839 with Zn content are the major outcomes of this study. In addition, association of R11M23 with days to 50% flowering, panicle length and total spikelets per panicle are explained the possible occurrence of pleiotropism among these traits. Prominent rice landraces viz., Anjani (early maturity); Sihar (extra dwarf); Gangabaru (highest grain yield/plant); Karhani (highest iron content); Byalo-2 (highest zinc content) and Kadamphool (highest oleic acid) were identified through this study. The present study will open many avenues towards utilization of these QTLs and superior landraces in rice breeding for developing nutrition-rich high yielding varieties.
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Affiliation(s)
- Parmeshwar K Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Vikash Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - B K Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
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12
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Singh RK, Prasad A, Muthamilarasan M, Parida SK, Prasad M. Breeding and biotechnological interventions for trait improvement: status and prospects. PLANTA 2020; 252:54. [PMID: 32948920 PMCID: PMC7500504 DOI: 10.1007/s00425-020-03465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/12/2020] [Indexed: 05/06/2023]
Abstract
Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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13
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Wang X, Yan X, Tian X, Zhang Z, Wu W, Shang J, Ouyang J, Yao W, Li S. Glycine- and Proline-Rich Protein OsGPRP3 Regulates Grain Size and Quality in Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7581-7590. [PMID: 32579349 DOI: 10.1021/acs.jafc.0c01803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The grain size and shape of rice are limited by the growth of the spikelet hulls and are important selective target during domestication and breeding. In this study, we identified a glycine- and proline-rich protein (OsGPRP3), which belongs to a conserved family rarely studied. We found that OsGPRP3 was highly expressed in the seed at 10 days after pollination (DAP) using qRT-PCR, pOsGPRP3::GUS and in situ hybridization. Knockout and knockdown of OsGPRP3 led to significant decrease of 1000-grain weight, grain width, and grain thickness. We further found that the content of storage protein and total lipid were decreased in osgprp3 lines. In particular, the contents of C14:0 (myristic acid), C16:0 (palmitic acid), C18:1 (oleic acid), and C18:2 (linoleic acid) were reduced in osgprp3 lines. Cytological experiments revealed that the cell width of spikelet hull in osgprp3 lines was significantly reduced than that in WT. Taken together, our results reveal that OsGPRP3 regulates the grain size and shape of rice by influencing the cell width of spikelet hulls and the accumulation of storage protein and lipids.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
| | - Xiaoxiao Tian
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
| | - Zongfei Zhang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
| | - Weiwei Wu
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
| | - Junjun Shang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life sciences, Nanchang University, Nanchang 330031, China
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14
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Hu W, Fitzgerald M, Topp B, Alam M, O'Hare TJ. A review of biological functions, health benefits, and possible de novo biosynthetic pathway of palmitoleic acid in macadamia nuts. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.103520] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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15
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Wang X, Yu C, Liu Y, Yang L, Li Y, Yao W, Cai Y, Yan X, Li S, Cai Y, Li S, Peng X. GmFAD3A, A ω-3 Fatty Acid Desaturase Gene, Enhances Cold Tolerance and Seed Germination Rate under Low Temperature in Rice. Int J Mol Sci 2019; 20:E3796. [PMID: 31382584 PMCID: PMC6696117 DOI: 10.3390/ijms20153796] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 11/17/2022] Open
Abstract
Low temperature is an environmental stress factor that is always been applied in research on improving crop growth, productivity, and quality of crops. Polyunsaturated fatty acids (PUFAs) play an important role in cold tolerance, so its genetic manipulation of the PUFA contents in crops has led to the modification of cold sensitivity. In this study, we over-expressed an ω-3 fatty acid desaturase from Glycine max (GmFAD3A) drove by a maize ubiquitin promoter in rice. Compared to the wild type (ZH11), ectopic expression of GmFAD3A increased the contents of lipids and total PUFAs. Seed germination rates in GmFAD3A transgenic rice were enhanced under low temperature (15 °C). Moreover, cold tolerance and survival ratio were significantly improved in GmFAD3A transgenic seedlings. Malondialdehyde (MDA) content in GmFAD3A transgenic rice was lower than that in WT under cold stress, while proline content obviously increased. Meanwhile, the activities of superoxide dismutase (SOD), hydroperoxidase (CAT), and peroxidase (POD) increased substantially in GmFAD3A transgenic rice after 4 h of cold treatment. Taken together, our results suggest that GmFAD3A can enhances cold tolerance and the seed germination rate at a low temperature in rice through the accumulation of proline content, the synergistic increase of the antioxidant enzymes activity, which finally ameliorated the oxidative damage.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Chao Yu
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yi Liu
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Lu Yang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yang Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yicong Cai
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Nanchang 330200, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaojue Peng
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China.
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16
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Zhao Y, Peng T, Sun H, Teotia S, Wen H, Du Y, Zhang J, Li J, Tang G, Xue H, Zhao Q. miR1432-OsACOT (Acyl-CoA thioesterase) module determines grain yield via enhancing grain filling rate in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:712-723. [PMID: 30183128 PMCID: PMC6419572 DOI: 10.1111/pbi.13009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 05/18/2023]
Abstract
Rice grain filling rate contributes largely to grain productivity and accumulation of nutrients. MicroRNAs (miRNAs) are key regulators of development and physiology in plants and become a novel key target for engineering grain size and crop yield. However, there is little studies, so far, showing the miRNA regulation of grain filling and rice yield, in consequence. Here, we show that suppressed expression of rice miR1432 (STTM1432) significantly improves grain weight by enhancing grain filling rate and leads to an increase in overall grain yield up to 17.14% in a field trial. Molecular analysis identified rice Acyl-CoA thioesterase (OsACOT), which is conserved with ACOT13 in other species, as a major target of miR1432 by cleavage. Moreover, overexpression of miR1432-resistant form of OsACOT (OXmACOT) resembled the STTM1432 plants, that is, a large margin of an increase in grain weight up to 46.69% through improving the grain filling rate. Further study indicated that OsACOT was involved in biosynthesis of medium-chain fatty acids. In addition, RNA-seq based transcriptomic analyses of transgenic plants with altered expression of miR1432 demonstrated that downstream genes of miR1432-regulated network are involved in fatty acid metabolism and phytohormones biosynthesis and also overlap with the enrichment analysis of co-expressed genes of OsACOT, which is consistent with the increased levels of auxin and abscisic acid in STTM1432 and OXmACOT plants. Overall, miR1432-OsACOT module plays an important role in grain filling in rice, illustrating its capacity for engineering yield improvement in crops.
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Affiliation(s)
- Ya‐Fan Zhao
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Ting Peng
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Hong‐Zheng Sun
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Sachin Teotia
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Department of Biological Sciences and Biotechnology Research Center (BRC)Michigan Technological UniversityHoughtonMIUSA
| | - Hui‐Li Wen
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Yan‐Xiu Du
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Jing Zhang
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Jun‐Zhou Li
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Gui‐Liang Tang
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Department of Biological Sciences and Biotechnology Research Center (BRC)Michigan Technological UniversityHoughtonMIUSA
| | - Hong‐Wei Xue
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of Sciences (CAS)ShanghaiChina
| | - Quan‐Zhi Zhao
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
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17
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Alseekh S, Bermudez L, de Haro LA, Fernie AR, Carrari F. Crop metabolomics: from diagnostics to assisted breeding. Metabolomics 2018; 14:148. [PMID: 30830402 DOI: 10.1007/s11306-018-1446-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding. AIM OF REVIEW We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality. KEY SCIENTIFIC CONCEPTS OF REVIEW Translational metabolomics applied to crop breeding programs.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luis Alejandro de Haro
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina.
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, 05508-090, Brazil.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
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An EMS-induced new sequence variant, TEMS5032, in the coding region of SRS3 gene leads to shorter grain length in rice (Oryza sativa L.). J Appl Genet 2018; 59:377-389. [PMID: 30014258 DOI: 10.1007/s13353-018-0455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/02/2018] [Accepted: 06/27/2018] [Indexed: 01/29/2023]
Abstract
Grain shape and size influence yield and consumer preferences in rice. In the present study, we characterized and mapped a short and bold grained mutant and named it as TEMS5032, as the mutant is a result of EMS-induced transition from C to T at the 5032nd bp of SRS3 gene, which is known to affect grain size in rice. The substitution led to creation of a stop codon in the motor domain of SRS3, a kinesin 13 family gene, translating into a truncated protein product. However, transcription of this gene remained unaffected in TEMS5032 compared to the wild type, N22. Further, the mutation was found to affect 13 of the 25 cell cycle-related genes as they showed differential expression with respect to N22. Based on rate of grain filling, dry matter accumulation in the endosperm and histological studies, the effect of mutation in TEMS5032 was found to be similar to a known variant, TCM758, but less severe than sar1 mutant. Sequencing of 88 rice germplasm lines in the kinesin motor domain region did not reveal the presence of this mutation, establishing it as a new variant of SRS3 gene.
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Meng X, Xing S, Perez LM, Peng X, Zhao Q, Redoña ED, Wang C, Peng Z. Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds. Sci Rep 2017; 7:17486. [PMID: 29235492 PMCID: PMC5727541 DOI: 10.1038/s41598-017-17756-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022] Open
Abstract
Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants. Functional annotation analyses indicated that a wide variety of vital biological processes were preferably targeted by lysine 2-hydroxyisobutyrylation, including glycolysis/gluconeogenesis, TCA cycle, starch biosynthesis, lipid metabolism, protein biosynthesis and processing. Our finding showed that 2-hydroxyisobutyrylated histone sites were conserved across plants, human, and mouse. A number of 2-hydroxyisobutyryl sites were shared with other lysine acylations in both histone and non-histone proteins. Comprehensive analysis of the lysine 2-hydroxyisobutyrylation sites illustrated that the modification sites were highly sequence specific with distinct motifs, and they had less surface accessibility than other lysine residues in the protein. Overall, our study provides the first systematic analysis of lysine 2-hydroxyisobutyrylation proteome in plants, and it serves as an important resource for future investigations of the regulatory mechanisms and functions of lysine 2-hydroxyisobutyrylation.
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Affiliation(s)
- Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
| | - Shihai Xing
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, Anhui, 230000, China
| | - Loida M Perez
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou, 310018, China
| | - Qingyong Zhao
- Institute of Crop Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Edilberto D Redoña
- Delta Research and Extension Center, Stoneville, P.O. Box 197, Mississippi, 38776, USA
| | - Cailin Wang
- Institute of Crop Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA.
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20
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Zhou W, Wang X, Zhou D, Ouyang Y, Yao J. Overexpression of the 16-kDa α-amylase/trypsin inhibitor RAG2 improves grain yield and quality of rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:568-580. [PMID: 27775871 PMCID: PMC5399008 DOI: 10.1111/pbi.12654] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/02/2016] [Accepted: 10/20/2016] [Indexed: 05/02/2023]
Abstract
Increasing grain yield and improving grain quality are two important goals for rice breeding. A better understanding of the factors that contribute to the overall grain quantity and nutritional quality of rice will lay the foundation for developing new breeding strategies. RAG2 is a member of 14-to-16-kDa α-amylase/trypsin inhibitors in rice, which belong to the albumin of seed storage proteins. We found that RAG2 was specifically expressed in ripening seed and its transcription peak was between 14 and 21 days after flowering. Grain size and 1000-grain weight were obviously increased in RAG2-overexpressed lines compared with wild type, and grain size was reduced in RAG2-suppressed lines. In addition, the major storage substances of the seeds differed significantly in RAG2-overexpressed and RAG2-suppressed lines compared to wild type. The protein content and amount of total lipids were increased and decreased, respectively, in the seeds of RAG2-overexpressed and RAG2-suppressed lines. Overexpression of RAG2 significantly increased grain size and improved grain quality and yield simultaneously. These results imply that RAG2 might play an important role in regulating grain weight and seed quality of rice. The functional characterization of rice RAG2 facilitates a further understanding of the mechanisms involved in grain size and seed quality and may be helpful in improving grain yield and quantity in cereal crops.
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Affiliation(s)
- Wei Zhou
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xin Wang
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Dan Zhou
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Jialing Yao
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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21
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Knoch D, Riewe D, Meyer RC, Boudichevskaia A, Schmidt R, Altmann T. Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1655-1667. [PMID: 28338798 PMCID: PMC5444479 DOI: 10.1093/jxb/erx049] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To gain insight into genetic factors controlling seed metabolic composition and its relationship to major seed properties, an Arabidopsis recombinant inbred line (RIL) population, derived from accessions Col-0 and C24, was studied using an MS-based metabolic profiling approach. Relative intensities of 311 polar primary metabolites were used to identify associated genomic loci and to elucidate their interactions by quantitative trait locus (QTL) mapping. A total of 786 metabolic QTLs (mQTLs) were unequally distributed across the genome, forming several hotspots. For the branched-chain amino acid leucine, mQTLs and candidate genes were elucidated in detail. Correlation studies displayed links between metabolite levels, seed protein content, and seed weight. Principal component analysis revealed a clustering of samples, with PC1 mapping to a region on the short arm of chromosome IV. The overlap of this region with mQTL hotspots indicates the presence of a potential master regulatory locus of seed metabolism. As a result of database queries, a series of candidate regulatory genes, including bZIP10, were identified within this region. Depending on the search conditions, metabolic pathway-derived candidate genes for 40-61% of tested mQTLs could be determined, providing an extensive basis for further identification and characterization of hitherto unknown genes causal for natural variation of Arabidopsis seed metabolism.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Rhonda Christiane Meyer
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Renate Schmidt
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
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22
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Sun R, Ye R, Gao L, Zhang L, Wang R, Mao T, Zheng Y, Li D, Lin Y. Characterization and Ectopic Expression of CoWRI1, an AP2/EREBP Domain-Containing Transcription Factor from Coconut ( Cocos nucifera L.) Endosperm, Changes the Seeds Oil Content in Transgenic Arabidopsis thaliana and Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:63. [PMID: 28179911 PMCID: PMC5263148 DOI: 10.3389/fpls.2017.00063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/11/2017] [Indexed: 05/10/2023]
Abstract
Coconut (Cocos nucifera L.) is a key tropical crop and a member of the monocotyledonous family Arecaceae (Palmaceae). Few genes and related metabolic processes involved in coconut endosperm development have been investigated. In this study, a new member of the WRI1 gene family was isolated from coconut endosperm and was named CoWRI1. Its transcriptional activities and interactions with the acetyl-CoA carboxylase (BCCP2) promoter of CoWRI1 were confirmed by the yeast two-hybrid and yeast one-hybrid approaches, respectively. Functional characterization was carried out through seed-specific expression in Arabidopsis and endosperm-specific expression in rice. In transgenic Arabidopsis, high over-expressions of CoWRI1 in seven independent T2 lines were detected by quantitative real-time PCR. The relative mRNA accumulation of genes encoding enzymes involved in either fatty acid biosynthesis or triacylglycerols assembly (BCCP2, KASI, MAT, ENR, FATA, and GPDH) were also assayed in mature seeds. Furthermore, lipid and fatty acids C16:0 and C18:0 significantly increased. In two homozygous T2 transgenic rice lines (G5 and G2), different CoWRI1 expression levels were detected, but no CoWRI1 transcripts were detected in the wild type. Analyses of the seed oil content, starch content, and total protein content indicated that the two T2 transgenic lines showed a significant increase (P < 0.05) in seed oil content. The transgenic lines also showed a significant increase in starch content, whereas total protein content decreased significantly. Further analysis of the fatty acid composition revealed that palmitic acid (C16:0) and linolenic acid (C18:3) increased significantly in the seeds of the transgenic rice lines, but oleic acid (C18:1) levels significantly declined.
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Affiliation(s)
- RuHao Sun
- Department of Bioengineering, College of Material and Chemical Engineering, Hainan UniversityHaikou, China
| | - Rongjian Ye
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Lingchao Gao
- Department of Bioengineering, College of Material and Chemical Engineering, Hainan UniversityHaikou, China
| | - Lin Zhang
- Department of Bioengineering, College of Material and Chemical Engineering, Hainan UniversityHaikou, China
| | - Rui Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Ting Mao
- Department of Bioengineering, College of Material and Chemical Engineering, Hainan UniversityHaikou, China
| | - Yusheng Zheng
- Department of Bioengineering, College of Material and Chemical Engineering, Hainan UniversityHaikou, China
| | - Dongdong Li
- Department of Bioengineering, College of Material and Chemical Engineering, Hainan UniversityHaikou, China
- *Correspondence: Dongdong Li, Yongjun Lin,
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Dongdong Li, Yongjun Lin,
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23
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Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1941-55. [PMID: 26990124 PMCID: PMC5043468 DOI: 10.1111/pbi.12559] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 05/18/2023]
Abstract
Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
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Affiliation(s)
- Cheng Zou
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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24
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Hong J, Yang L, Zhang D, Shi J. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci 2016; 17:ijms17060767. [PMID: 27258266 PMCID: PMC4926328 DOI: 10.3390/ijms17060767] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Litao Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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25
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Mustafiz A, Kumari S, Karan R. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics. Curr Genomics 2016; 17:155-76. [PMID: 27252584 PMCID: PMC4869004 DOI: 10.2174/1389202917666160202215135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.
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Affiliation(s)
- Ananda Mustafiz
- South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi
| | - Sumita Kumari
- Sher-e-Kashmir University of Agriculture Sciences and Technology, Jammu 180009, India
| | - Ratna Karan
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville - 32611, Florida, USA
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Zhang L, Wang SB, Li QG, Song J, Hao YQ, Zhou L, Zheng HQ, Dunwell JM, Zhang YM. An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants. PLoS One 2016; 11:e0154882. [PMID: 27159078 PMCID: PMC4861283 DOI: 10.1371/journal.pone.0154882] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/20/2016] [Indexed: 11/19/2022] Open
Abstract
Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Shi-Bo Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Statistical Genomics Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Qi-Gang Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People’s Republic of China
| | - Jian Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Yu-Qi Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Ling Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Institute of Biotechnology, Jiangsu Academy of Agricultural Science, Nanjing 210014, People’s Republic of China
| | - Huan-Quan Zheng
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AS, United Kingdom
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Statistical Genomics Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
- * E-mail: ;
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27
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Ting NC, Yaakub Z, Kamaruddin K, Mayes S, Massawe F, Sambanthamurthi R, Jansen J, Low LET, Ithnin M, Kushairi A, Arulandoo X, Rosli R, Chan KL, Amiruddin N, Sritharan K, Lim CC, Nookiah R, Amiruddin MD, Singh R. Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm. BMC Genomics 2016; 17:289. [PMID: 27079197 PMCID: PMC4832457 DOI: 10.1186/s12864-016-2607-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 03/28/2016] [Indexed: 12/21/2022] Open
Abstract
Background The commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called ‘palm oil’) with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil. Results In this study, a segregating E. oleifera x E. guineensis (OxG) hybrid population for FAC is used to identify quantitative trait loci (QTLs) linked to IV and various FAs. QTL analysis revealed 10 major and two putative QTLs for IV and six FAs, C14:0, C16:0, C16:1, C18:0, C18:1 and C18:2 distributed across six linkage groups (LGs), OT1, T2, T3, OT4, OT6 and T9. The major QTLs for IV and C16:0 on LGOT1 explained 60.0 – 69.0 % of the phenotypic trait variation and were validated in two independent BC2 populations. The genomic interval contains several key structural genes in the FA and oil biosynthesis pathways such as PATE/FATB, HIBCH, BASS2, LACS4 and DGAT1 and also a relevant transcription factor (TF), WRI1. The literature suggests that some of these genes can exhibit pleiotropic effects in the regulatory networks of these traits. Using the whole genome sequence data, markers tightly linked to the candidate genes were also developed. Clustering trait values according to the allelic forms of these candidate markers revealed significant differences in the IV and FAs of the palms in the mapping and validation crosses. Conclusions The candidate gene approach described and exploited here is useful to identify the potential causal genes linked to FAC and can be adopted for marker-assisted selection (MAS) in oil palm. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2607-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ngoot-Chin Ting
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.,School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Zulkifli Yaakub
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | | | - Sean Mayes
- Plant and Crop Sciences, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD, UK
| | - Festo Massawe
- School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | | | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, The Netherlands
| | - Leslie Eng Ti Low
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Maizura Ithnin
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Xaviar Arulandoo
- United Plantations Bhd., Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Rozana Rosli
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Nadzirah Amiruddin
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kandha Sritharan
- United Plantations Bhd., Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Chin Ching Lim
- United Plantations Bhd., Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.
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Jasinski S, Lécureuil A, Durandet M, Bernard-Moulin P, Guerche P. Arabidopsis Seed Content QTL Mapping Using High-Throughput Phenotyping: The Assets of Near Infrared Spectroscopy. FRONTIERS IN PLANT SCIENCE 2016; 7:1682. [PMID: 27891138 PMCID: PMC5103166 DOI: 10.3389/fpls.2016.01682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/25/2016] [Indexed: 05/04/2023]
Abstract
Seed storage compounds are of crucial importance for human diet, feed and industrial uses. In oleo-proteaginous species like rapeseed, seed oil and protein are the qualitative determinants that conferred economic value to the harvested seed. To date, although the biosynthesis pathways of oil and storage protein are rather well-known, the factors that determine how these types of reserves are partitioned in seeds have to be identified. With the aim of implementing a quantitative genetics approach, requiring phenotyping of 100s of plants, our first objective was to establish near-infrared reflectance spectroscopic (NIRS) predictive equations in order to estimate oil, protein, carbon, and nitrogen content in Arabidopsis seed with high-throughput level. Our results demonstrated that NIRS is a powerful non-destructive, high-throughput method to assess the content of these four major components studied in Arabidopsis seed. With this tool in hand, we analyzed Arabidopsis natural variation for these four components and illustrated that they all displayed a wide range of variation. Finally, NIRS was used in order to map QTL for these four traits using seeds from the Arabidopsis thaliana Ct-1 × Col-0 recombinant inbred line population. Some QTL co-localized with QTL previously identified, but others mapped to chromosomal regions never identified so far for such traits. This paper illustrates the usefulness of NIRS predictive equations to perform accurate high-throughput phenotyping of Arabidopsis seed content, opening new perspectives in gene identification following QTL mapping and genome wide association studies.
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Affiliation(s)
- Sophie Jasinski
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
- *Correspondence: Sophie Jasinski,
| | - Alain Lécureuil
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
| | - Monique Durandet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
| | | | - Philippe Guerche
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
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Butardo VM, Sreenivasulu N. Tailoring Grain Storage Reserves for a Healthier Rice Diet and its Comparative Status with Other Cereals. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 323:31-70. [DOI: 10.1016/bs.ircmb.2015.12.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Wang X, Zhou W, Lu Z, Ouyang Y, O CS, Yao J. A lipid transfer protein, OsLTPL36, is essential for seed development and seed quality in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 239:200-8. [PMID: 26398804 DOI: 10.1016/j.plantsci.2015.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 05/02/2023]
Abstract
Storage lipid is a vital component for maintaining structure of seed storage substances and valuable for rice quality and food texture. However, the knowledge of lipid transporting related genes and their function in seed development have not been well elucidated yet. In this study, we identified OsLTPL36, a homolog of putative lipid transport protein, and showed specific expression in rice developing seed. Transcriptional profiling and in situ hybridization analysis confirmed that OsLTPL36 was exclusively expressed in developing seed coat and endosperm aleurone cells. Down-regulated expression of OsLTPL36 led to decreased seed setting rate and 1000-grain weight in transgenic plants. Further studies showed that suppressed expression of OsLTPL36 caused chalky endosperm and resulted in reduced fat acid content in RNAi lines as compared with wild type (WT). Histological analysis showed that the embryo development was delayed after down regulation of OsLTPL36. Moreover, impeded seed germination and puny seedling were also observed in the OsLTPL36 RNAi lines. The data demonstrated that OsLTPL36, a lipid transporter, was critical important not only for seed quality but also for seed development and germination in rice.
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Affiliation(s)
- Xin Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Zhou
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zhanhua Lu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yidan Ouyang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chol Su O
- Life science Faculty, Kim Il Sung University, Pyongyang 999093, Democratic People's Republic of Korea.
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Kusano M, Yang Z, Okazaki Y, Nakabayashi R, Fukushima A, Saito K. Using metabolomic approaches to explore chemical diversity in rice. MOLECULAR PLANT 2015; 8:58-67. [PMID: 25578272 DOI: 10.1016/j.molp.2014.11.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/16/2014] [Indexed: 05/02/2023]
Abstract
Rice (Oryza sativa) is an excellent resource; it comprises 25% of the total caloric intake of the world's population, and rice plants yield many types of bioactive compounds. To determine the number of metabolites in rice and their chemical diversity, the metabolite composition of cultivated rice has been investigated with analytical techniques such as mass spectrometry (MS) and/or nuclear magnetic resonance spectroscopy and rice metabolite databases have been constructed. This review summarizes current knowledge on metabolites in rice including sugars, amino and organic acids, aromatic compounds, and phytohormones detected by gas chromatography-MS, liquid chromatography-MS, and capillary electrophoresis-MS. The biological properties and the activities of polar and nonpolar metabolites produced by rice plants are also presented. Challenges in the estimation of the structure(s) of unknown metabolites by metabolomic approaches are introduced and discussed. Lastly, examples are presented of the successful application of metabolite profiling of rice to characterize the gene(s) that are potentially critical for improving its quality by combining metabolite quantitative trait loci analysis and to identify potential metabolite biomarkers that play a critical role when rice is grown under abiotic stress conditions.
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Affiliation(s)
- Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.
| | - Zhigang Yang
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba 260-8675, Japan.
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Valluru R, Reynolds MP, Salse J. Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1463-89. [PMID: 24913362 DOI: 10.1007/s00122-014-2332-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 05/15/2014] [Indexed: 05/21/2023]
Abstract
Transferring the knowledge bases between related species may assist in enlarging the yield potential of crop plants. Being cereals, rice and wheat share a high level of gene conservation; however, they differ at metabolic levels as a part of the environmental adaptation resulting in different yield capacities. This review focuses on the current understanding of genetic and molecular regulation of yield-associated traits in both crop species, highlights the similarities and differences and presents the putative knowledge gaps. We focus on the traits associated with phenology, photosynthesis, and assimilate partitioning and lodging resistance; the most important drivers of yield potential. Currently, there are large knowledge gaps in the genetic and molecular control of such major biological processes that can be filled in a translational biology approach in transferring genomics and genetics informations between rice and wheat.
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Affiliation(s)
- Ravi Valluru
- Wheat Physiology, Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56130, Mexico DF, Mexico,
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Thambugala D, Cloutier S. Fatty acid composition and desaturase gene expression in flax (Linum usitatissimum L.). J Appl Genet 2014; 55:423-32. [PMID: 24871199 PMCID: PMC4185102 DOI: 10.1007/s13353-014-0222-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 10/29/2022]
Abstract
Little is known about the relationship between expression levels of fatty acid desaturase genes during seed development and fatty acid (FA) composition in flax. In the present study, we looked at promoter structural variations of six FA desaturase genes and their relative expression throughout seed development. Computational analysis of the nucleotide sequences of the sad1, sad2, fad2a, fad2b, fad3a and fad3b promoters showed several basic transcriptional elements including CAAT and TATA boxes, and several putative target-binding sites for transcription factors, which have been reported to be involved in the regulation of lipid metabolism. Using semi-quantitative reverse transcriptase PCR, the expression patterns throughout seed development of the six FA desaturase genes were measured in six flax genotypes that differed for FA composition but that carried the same desaturase isoforms. FA composition data were determined by phenotyping the field grown genotypes over four years in two environments. All six genes displayed a bell-shaped pattern of expression peaking at 20 or 24 days after anthesis. Sad2 was the most highly expressed. The expression of all six desaturase genes did not differ significantly between genotypes (P = 0.1400), hence there were no correlations between FA desaturase gene expression and variations in FA composition in relatively low, intermediate and high linolenic acid genotypes expressing identical isoforms for all six desaturases. These results provide further clues towards understanding the genetic factors responsible for FA composition in flax.
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Affiliation(s)
- Dinushika Thambugala
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, Canada, R3T 2N2
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Hegarty M, Yadav R, Lee M, Armstead I, Sanderson R, Scollan N, Powell W, Skøt L. Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.)). PLANT BIOTECHNOLOGY JOURNAL 2013; 11:572-81. [PMID: 23331642 DOI: 10.1111/pbi.12045] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 05/26/2023]
Abstract
Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially α-linolenic acid, an omega-3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high-sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction-associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n-6) on LGs 2 and 5; and α-linolenic acids (C18:3n-3) on LG 1 were identified. Two candidate genes (a lipase and a beta-ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n-6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop.
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Affiliation(s)
- Matthew Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
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Jasinski S, Lécureuil A, Miquel M, Loudet O, Raffaele S, Froissard M, Guerche P. Natural variation in seed very long chain fatty acid content is controlled by a new isoform of KCS18 in Arabidopsis thaliana. PLoS One 2012; 7:e49261. [PMID: 23145136 PMCID: PMC3493540 DOI: 10.1371/journal.pone.0049261] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/05/2012] [Indexed: 12/30/2022] Open
Abstract
Oil from oleaginous seeds is mainly composed of triacylglycerols. Very long chain fatty acids (VLCFAs) are major constituents of triacylglycerols in many seed oils and represent valuable feedstock for industrial purposes. To identify genetic factors governing natural variability in VLCFA biosynthesis, a quantitative trait loci (QTL) analysis using a recombinant inbred line population derived from a cross between accessions Bay-0 and Shahdara was performed in Arabidopsis thaliana. Two fatty acid chain length ratio (CLR) QTL were identified, with one major locus, CLR.2, accounting for 77% of the observed phenotypic variation. A fine mapping and candidate gene approach showed that a key enzyme of the fatty acid elongation pathway, the β-ketoacyl-CoA synthase 18 (KCS18), was responsible for the CLR.2 QTL detected between Bay-0 and Shahdara. Association genetics and heterologous expression in yeast cells identified a single point mutation associated with an alteration of KCS18 activity, uncovering the molecular bases for the modulation of VLCFA content in these two natural populations of Arabidopsis. Identification of this kcs18 mutant with altered activity opens new perspectives for the modulation of oil composition in crop plants.
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Affiliation(s)
- Sophie Jasinski
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France.
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Ying JZ, Gao JP, Shan JX, Zhu MZ, Shi M, Lin HX. Dissecting the Genetic Basis of Extremely Large Grain Shape in Rice Cultivar ‘JZ1560’. J Genet Genomics 2012; 39:325-33. [DOI: 10.1016/j.jgg.2012.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 03/08/2012] [Accepted: 03/08/2012] [Indexed: 10/28/2022]
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