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Yan X, Zhou W, Huang X, Ouyang J, Li S, Gao J, Wang X. RAL6 encodes a seed allergenic protein that positively regulates grain weight and seed germination. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01581-w. [PMID: 39242482 DOI: 10.1007/s10265-024-01581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
The rice albumin (RAG) gene family belongs to the Tryp_alpha_amyl family. RAG2, specifically expressed in 14-21 DAP (days after pollination) seeds, regulates grain yield and quality. In this study, we identified another RAG family gene, RAL6, which exhibits specific expression in developing seeds, particularly in 7, 10, and 15 DAP seeds. Employing the CRISPR/Cas9 system, we analyzed functions of RAL6 and found that the ral6 lines (ral6-1, ral6-2, ral6-3, and ral6-4) displayed thinner seeds with significantly decreased 1000-grain weight and grain thickness compared to ZH11. Additionally, the cell width of spikelet cells, total protein and glutelin contents were significantly reduced in ral6. The germination assay and 1% TTC staining revealed a significant decrease in seed vigor among the ral6 lines. The alpha-amylase activity in ral6 mutant seeds was also markedly lower than in ZH11 seeds after 2 days of imbibition. Furthermore, co-expression analysis and GO annotation showed that co-expressed genes were involved in immune response, oligopeptide transport, and the glucan biosynthetic process. Collectively, our findings suggest that RAL6 plays a coordinating role in regulating grain weight and seed germination in rice.
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Affiliation(s)
- Xin Yan
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China
| | - Wei Zhou
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Xirui Huang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China
| | - Jiexiu Ouyang
- 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
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, 510640, China.
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510555, China.
| | - Xin Wang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China.
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AlHusnain L, AlKahtani MDF, Attia KA, Sanaullah T, Elsharnoby DE. Application of CRISPR/Cas9 system to knock out GluB gene for developing low glutelin rice mutant. BOTANICAL STUDIES 2024; 65:27. [PMID: 39225765 PMCID: PMC11371991 DOI: 10.1186/s40529-024-00432-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
The nutritional quality improvement is among the most integral objective for any rice molecular breeding programs. The seed storage proteins (SSPs) have greater role to determine the nutritional quality of any cereal grains. Rice contains relatively balanced amino acid composition and the SSPs are fractioned into albumins (ALB), globulins (GLO), prolamins (PRO) and glutelins (GLU) according to differences in solubility. GLUs are further divided into subfamilies: GluA, GluB, GluC, and GluD depending on resemblance in amino acid. The GLU protein accounts for 60-80% of total protein contents, encoded by 15 genes located on different chromosomes of rice genome. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was employed to knockout Glu-B (LOC-Os02g15070) gene in non-basmati rice PK386 cultivar. The mutant displayed two base pair and three base pair mutation in the targeted regions. The homozygous mutant plant displayed reduction for both in total protein contents and GLU contents whereas, elevation in GLO, ALB and PRO. Moreover, the mutant plant also displayed reduction in physio-chemical properties e.g., total starch, amylose and gel consistency. The agronomic characteristics of both mutant and wild type displayed non-significant differences along with increase in higher percentage of chalkiness in mutant plants. The results obtained from scanning electron microscopy showed the loosely packed starch granules compared to wild type. The gene expression analysis displayed the lower expression of gene at 5 days after flowering (DAF), 10 DAF, 15 DAF and 20 DAF compared to wild type. GUS sub-cellular localization showed the staining in seed which further validated the results obtained from gene expression. Based on these findings it can be concluded Glu-B gene have significant role in controlling GLU contents and can be utilized in breeding programs to enhance the nutritional quality of rice, and may serve as healthy diet for patient allergic with high GLU contents.
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Affiliation(s)
- Latifa AlHusnain
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Muneera D F AlKahtani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Kotb A Attia
- Center of Excellence in Biotechnology Research, King Saud University, P.O. Box2455, Riyadh, 11451, Saudi Arabia.
| | - Tayyaba Sanaullah
- Department of Botany, Government Sadiq College Women University, Bahawalpur, 53100, Pakistan
| | - Dalia E Elsharnoby
- Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
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Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. Multi-model genome-wide association studies for appearance quality in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1304388. [PMID: 38273959 PMCID: PMC10808671 DOI: 10.3389/fpls.2023.1304388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024]
Abstract
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
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Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, International Crop Reseach Institute for Semi Arid Tropics (ICRISAT), Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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Liang C, Xu H, You H, Zhang O, Han Y, Li Q, Hu Y, Xiang X. Physicochemical properties and molecular mechanisms of different resistant starch subtypes in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1313640. [PMID: 38259949 PMCID: PMC10800921 DOI: 10.3389/fpls.2023.1313640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024]
Abstract
Resistant starch (RS) can help prevent diabetes and decrease calorie intake and that from plants are the main source of mankind consumption. Rice is many people's staple food and that with higher RS will help health management. A significantly positive correlation exists between apparent amylose content (AAC) of rice and its RS content. In this study, 72 accessions with moderate or high AAC were selected to explore the regulatory mechanisms and physicochemical properties on different proceeding types of rice RS. RS in raw milled rice (RSm), hot cooked rice (RSc), and retrogradation rice (RSr) showed a wide variation and distinct controlling mechanisms. They were co-regulated by Waxy (Wx), soluble starch synthase (SS) IIb and SSI. Besides that, RSm was also regulated by SSIIa and SSIVb, RSc by granule-bound starch synthase (GBSS) II and RSr by GBSSII and Pullulanase (PUL). Moreover, Wx had significant interactions with SSIIa, SSI, SSIIb and SSIVb on RSm, but only the dominant interactions with SSIIb and SSI on RSc and RSr. Wx was the key factor for the formation of RS, especially the RSc and RSr. The genes had the highest expression at 17 days after flowering and were beneficial for RS formation. The longer the chain length of starch, the higher the RS3 content. RSc and RSr were likely to be contained in medium-size starch granules. The findings favor understanding the biosynthesis of different subtypes of RS.
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Affiliation(s)
- Cheng Liang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Rice Research Institute, Southwest University of Science and Technology, Sichuan, Mianyang, China
| | - Haoyang Xu
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Rice Research Institute, Southwest University of Science and Technology, Sichuan, Mianyang, China
| | - Hui You
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Rice Research Institute, Southwest University of Science and Technology, Sichuan, Mianyang, China
| | - Ouling Zhang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Rice Research Institute, Southwest University of Science and Technology, Sichuan, Mianyang, China
| | - Yiman Han
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Rice Research Institute, Southwest University of Science and Technology, Sichuan, Mianyang, China
| | - Qingyu Li
- School of Medicine, Tsinghua University, Beijing, China
| | - Yungao Hu
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Rice Research Institute, Southwest University of Science and Technology, Sichuan, Mianyang, China
| | - Xunchao Xiang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Rice Research Institute, Southwest University of Science and Technology, Sichuan, Mianyang, China
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Ahn E, Botkin J, Ellur V, Lee Y, Poudel K, Prom LK, Magill C. Genome-Wide Association Study of Seed Morphology Traits in Senegalese Sorghum Cultivars. PLANTS (BASEL, SWITZERLAND) 2023; 12:2344. [PMID: 37375969 DOI: 10.3390/plants12122344] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Sorghum is considered the fifth most important crop in the world. Despite the potential value of Senegalese germplasm for various traits, such as resistance to fungal diseases, there is limited information on the study of sorghum seed morphology. In this study, 162 Senegalese germplasms were evaluated for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness and brightness by scanning and analyzing morphology-related traits with SmartGrain software at the USDA-ARS Plant Science Research Unit. Correlations between seed morphology-related traits and traits associated with anthracnose and head smut resistance were analyzed. Lastly, genome-wide association studies were performed on phenotypic data collected from over 16,000 seeds and 193,727 publicly available single nucleotide polymorphisms (SNPs). Several significant SNPs were found and mapped to the reference sorghum genome to uncover multiple candidate genes potentially associated with seed morphology. The results indicate clear correlations among seed morphology-related traits and potential associations between seed morphology and the defense response of sorghum. GWAS analysis listed candidate genes associated with seed morphologies that can be used for sorghum breeding in the future.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
| | - Jacob Botkin
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Vishnutej Ellur
- Molecular Plant Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yoonjung Lee
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Kabita Poudel
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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6
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Rice Labeling according to Grain Quality Features Using Laser-Induced Breakdown Spectroscopy. Foods 2023; 12:foods12020365. [PMID: 36673459 PMCID: PMC9858346 DOI: 10.3390/foods12020365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Rice is an important source of nutrition and energy consumed around the world. Thus, quality inspection is crucial for protecting consumers and increasing the rice's value in the productive chain. Currently, methods for rice labeling depending on grain quality features are based on image and/or visual inspection. These methods have shown subjectivity and inefficiency for large-scale analyses. Laser-induced breakdown spectroscopy (LIBS) is an analytical technique showing attractive features due to how quick the analysis can be carried out and its capability of providing spectra that are true fingerprints of the sample's elemental composition. In this work, LIBS performance was evaluated for labeling rice according to grain quality features. The LIBS spectra of samples with their grain quality numerically described as Type 1, 2, and 3 were measured. Several spectral processing methods were evaluated when modeling a k-nearest neighbors (k-NN) classifier. Variable selection was also carried out by principal component analysis (PCA), and then the optimal k-value was selected. The best result was obtained by applying spectrum smoothing followed by normalization by using the first fifteen principal components (PCs) as input variables and k = 9. Under these conditions, the method showed excellent performance, achieving sample classification with 94% overall prediction accuracy. The sensitivities ranged from 90 to 100%, and specificities were in the range of 92-100%. The proposed method has remarkable characteristics, e.g., analytical speed and analysis guided by chemical responses; therefore, the method is not susceptible to subjectivity errors.
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Chen Z, Du H, Tao Y, Xu Y, Wang F, Li B, Zhu QH, Niu H, Yang J. Efficient breeding of low glutelin content rice germplasm by simultaneous editing multiple glutelin genes via CRISPR/Cas9. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111449. [PMID: 36058302 DOI: 10.1016/j.plantsci.2022.111449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Chronic kidney disease (CKD) and phenylketonuria (PKU) patients need to eat rice with low glutelin content. Therefore, breeding low glutelin content rice varieties with high yield and delicious taste is one of the major goals of rice breeders due to the high demand for the product. In this study, we designed three sgRNAs targeting nine glutelin genes and generated nine T-DNA-free homozygous editing lines with reduced glutelin content compared with the wild-type due to simultaneous mutation(s) in 5-7 glutelin genes. The glutelin content of two lines is even significantly lower than that of the low glutelin content cultivar, LGC-1. Compared to the wild-type, these low glutelin lines showed similar agronomic traits, including yield components and viscosity properties, and can be used as new varieties or parental materials for further breeding.
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Affiliation(s)
- Zhihui Chen
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Hongxu Du
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Yajun Tao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China; Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Bin Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra ACT 2601, Australia.
| | - Hongbin Niu
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, Jiangsu, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, Jiangsu, China; Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
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Jiang L, Zhong H, Jiang X, Zhang J, Huang R, Liao F, Deng Y, Liu Q, Huang Y, Wang H, Tao Y, Zheng J. Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape. FRONTIERS IN PLANT SCIENCE 2022; 12:814928. [PMID: 35126437 PMCID: PMC8810533 DOI: 10.3389/fpls.2021.814928] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/20/2021] [Indexed: 05/31/2023]
Abstract
Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes have been cloned to date. In this study, the candidate gene GSE5 of a major quantitative trait locus (QTL) for rice chalkiness, qDEC5, was identified by map-based cloning. Phenotyping and haplotype analysis of proActin:GSE5 transgenic line, gse5-cr mutant, and 69 rice varieties further confirmed that GSE5 had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed GSE5 was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to GSE5 was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that GSE5 played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by GSE5 to affect the formation of chalkiness, including some newly discovered genes, such as OsCESA9, OsHSP70, OsTPS8, OsPFK04, OsSTA1, OsERdj3A, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly; OsDjC10 and OsSUS3 were upregulated at 6 and 12 DAP, respectively, and OsGSTL2 was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of qDEC5 dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.
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Affiliation(s)
- Liangrong Jiang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hui Zhong
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xianbin Jiang
- Guangxi Rice Genetics and Breeding Key Laboratory, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jiaoping Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Rongyu Huang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Furong Liao
- Xiamen Entry-Exit Inspection and Quarantine Bureau, Xiamen, China
| | - Yaqin Deng
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingqing Liu
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yumin Huang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Houcong Wang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yi Tao
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jingsheng Zheng
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
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Zombardo A, Crosatti C, Bagnaresi P, Bassolino L, Reshef N, Puccioni S, Faccioli P, Tafuri A, Delledonne M, Fait A, Storchi P, Cattivelli L, Mica E. Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality. BMC Genomics 2020; 21:468. [PMID: 32641089 PMCID: PMC7341580 DOI: 10.1186/s12864-020-06795-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/25/2020] [Indexed: 12/19/2022] Open
Abstract
Background In viticulture, rootstock genotype plays a critical role to improve scion physiology, berry quality and to adapt grapevine (Vitis vinifera L.) to different environmental conditions. This study aimed at investigating the effect of two different rootstocks (1103 Paulsen - P - and Mgt 101–14 - M) in comparison with not grafted plants - NGC - on transcriptome (RNA-seq and small RNA-seq) and chemical composition of berry skin in Pinot noir, and exploring the influence of rootstock-scion interaction on grape quality. Berry samples, collected at veraison and maturity, were investigated at transcriptional and biochemical levels to depict the impact of rootstock on berry maturation. Results RNA- and miRNA-seq analyses highlighted that, at veraison, the transcriptomes of the berry skin are extremely similar, while variations associated with the different rootstocks become evident at maturity, suggesting a greater diversification at transcriptional level towards the end of the ripening process. In the experimental design, resembling standard agronomic growth conditions, the vines grafted on the two different rootstocks do not show a high degree of diversity. In general, the few genes differentially expressed at veraison were linked to photosynthesis, putatively because of a ripening delay in not grafted vines, while at maturity the differentially expressed genes were mainly involved in the synthesis and transport of phenylpropanoids (e.g. flavonoids), cell wall loosening, and stress response. These results were supported by some differences in berry phenolic composition detected between grafted and not grafted plants, in particular in resveratrol derivatives accumulation. Conclusions Transcriptomic and biochemical data demonstrate a stronger impact of 1103 Paulsen rootstock than Mgt 101–14 or not grafted plants on ripening processes related to the secondary metabolite accumulations in berry skin tissue. Interestingly, the MYB14 gene, involved in the feedback regulation of resveratrol biosynthesis was up-regulated in 1103 Paulsen thus supporting a putative greater accumulation of stilbenes in mature berries.
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Affiliation(s)
- A Zombardo
- CREA Research Centre for Viticulture and Enology, viale Santa Margherita 80, 52100, Arezzo, Italy.,Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine 18, 50144, Florence, Italy
| | - C Crosatti
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - P Bagnaresi
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - L Bassolino
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.,CREA Research Centre for Cereal and Industrial Crops, via di Corticella 133, 40128, Bologna, Italy
| | - N Reshef
- French Associates institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel.,Present address: Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - S Puccioni
- CREA Research Centre for Viticulture and Enology, viale Santa Margherita 80, 52100, Arezzo, Italy
| | - P Faccioli
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - A Tafuri
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - M Delledonne
- Department of Biotechnologies, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - A Fait
- French Associates institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 84990, Israel
| | - P Storchi
- CREA Research Centre for Viticulture and Enology, viale Santa Margherita 80, 52100, Arezzo, Italy
| | - L Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - E Mica
- CREA Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
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Bertazzon N, Bagnaresi P, Forte V, Mazzucotelli E, Filippin L, Guerra D, Zechini A, Cattivelli L, Angelini E. Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties. BMC Genomics 2019; 20:526. [PMID: 31242866 PMCID: PMC6595628 DOI: 10.1186/s12864-019-5908-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/17/2019] [Indexed: 01/18/2023] Open
Abstract
Background Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible. Results The comparative analysis of the constitutive transcriptomic profiles suggests the existence of passive defense strategies against the insect and/or the phytoplasma in the scarcely-susceptible cultivar. Moreover, the attack by the infective vector on the scarcely-susceptible variety prompted immediate and substantial transcriptomic changes that led to the rapid erection of further active defenses. On the other hand, in the most susceptible variety the response was delayed and mainly consisted of the induction of phytoalexin synthesis. Surprisingly, the jasmonic acid- and ethylene-mediated defense reactions, activated by the susceptible cultivar following FD-free insect feeding, were not detected in the presence of the phytoplasma-infected vector. Conclusions The comparison of the transcriptomic response in two grapevine varieties with different levels of susceptibility to Flavescence dorèe highlighted both passive and active defense mechanisms against the vector and/or the pathogen in the scarcely-susceptible variety, as well as the capacity of the phytoplasmas to repress the defense reaction against the insect in the susceptible variety. Electronic supplementary material The online version of this article (10.1186/s12864-019-5908-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nadia Bertazzon
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy.
| | - Paolo Bagnaresi
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Vally Forte
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy
| | | | - Luisa Filippin
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy
| | - Davide Guerra
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Antonella Zechini
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, 29017, Fiorenzuola d'Arda (PC), Italy
| | - Elisa Angelini
- CREA Research Centre for Viticulture and Enology, 31015, Conegliano (TV), Italy
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Subedi SR, Sandhu N, Singh VK, Sinha P, Kumar S, Singh SP, Ghimire SK, Pandey M, Yadaw RB, Varshney RK, Kumar A. Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition. BMC Genomics 2019; 20:471. [PMID: 31182016 PMCID: PMC6558851 DOI: 10.1186/s12864-019-5840-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/23/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system. RESULTS Study identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10- 4, 0.0330 to 1.25 × 10- 4, and 0.0534 to 4.60 × 10- 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development. CONCLUSIONS Once validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR.
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Affiliation(s)
- Sushil Raj Subedi
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Agriculture and Forestry University, Rampur, Chitwan Nepal
- National Rice Research Program, Hardinath, Nepal
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Pallavi Sinha
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar India
| | - S. P. Singh
- Bihar Agricultural University, Sabour, Bihar India
| | | | - Madhav Pandey
- Agriculture and Forestry University, Rampur, Chitwan Nepal
| | | | - Rajeev K. Varshney
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Milc J, Bagnaresi P, Aragona M, Valente MT, Biselli C, Infantino A, Francia E, Pecchioni N. Comparative transcriptome profiling of the response to Pyrenochaeta lycopersici in resistant tomato cultivar Mogeor and its background genotype-susceptible Moneymaker. Funct Integr Genomics 2019; 19:811-826. [PMID: 31104179 DOI: 10.1007/s10142-019-00685-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/15/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Breeding for resistance is the most effective tool for controlling the corky root disease of tomato caused by Pyrenochaeta lycopersici. A comparative RNA-Seq-based transcriptomic analysis was conducted at 96 hpi (hours post infection) on two tomato cultivars: resistant Mogeor and its genetic background, and susceptible Moneymaker to investigate the differences in their transcriptomic response and identify the molecular bases of this plant-pathogen interaction. The number of differentially expressed genes (DEGs) identified was much higher in the susceptible than in the resistant genotype; however, the proportion of upregulated genes was higher in Mogeor (70.81%) than in Moneymaker (52.95%). Gene Ontology (GO) analysis enabled identification of 24 terms shared by the two cultivars that were consistent with responses to external stimulus, such as fungal infection. On the other hand, as many as 54 GO were enriched solely in Moneymaker, including terms related to defense response and cell wall metabolism. Our results could support the previous observations in other pathosystems, that susceptibility and resistance have overlapping signaling pathways and responses, suggesting that the P. lycopersici resistance gene pyl might be a recessive allele at a susceptibility locus, for which different candidate genes were identified based on the differences in induction or expression levels, observed between the resistant and susceptible genotype. MapMan analysis highlighted a complex hormone and transcription factors interplay where SA- and JA-induced pathways are modulated in a similar way in both genotypes and thus take part in a common response while the ethylene signaling pathways, induced mainly in susceptible Moneymaker, seem putatively contribute to its susceptibility.
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Affiliation(s)
- Justyna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy.
| | - P Bagnaresi
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Via San Protaso 37, 29017, Fiorenzuola d'Arda, PC, Italy
| | - M Aragona
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156, Rome, Italy
| | - M T Valente
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156, Rome, Italy
| | - C Biselli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Via San Protaso 37, 29017, Fiorenzuola d'Arda, PC, Italy
- Council for Agricultural Research and Economics (CREA), Research Centre for Forestry and Wood, Viale Santa Margherita 80, 52100, Arezzo, Italy
| | - A Infantino
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156, Rome, Italy
| | - E Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - N Pecchioni
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, S.S. 16 km 675, 71121, Foggia, Italy
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Lin YJ, Yu XZ, Zhang Q. Transcriptome analysis of Oryza sativa in responses to different concentrations of thiocyanate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:11696-11709. [PMID: 30806930 DOI: 10.1007/s11356-019-04544-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 02/13/2019] [Indexed: 05/21/2023]
Abstract
Effective concentrations of potassium thiocyanate (KSCN) to rice seedlings were experimentally determined using relative growth rate as a sensitive endpoint. Agilent 44-K rice microarray was used to profile the molecular responses of rice seedlings exposed to thiocyanate ion (SCN-) at three different effective concentrations (EC10, EC20, and EC50). A total of 18,498 known genes were collected from SCN-treated rice microarray analysis. Out of all, 1603, 1882, and 5085 differentially expressed genes (DEGs) were observed at EC10, EC20, and EC50 concentrations, respectively. More upregulated/downregulated DEGs were detected in shoots than in roots after SCN- exposure. Gene functions and pathway enrichment analysis of DEGs indicated that different effective concentrations of SCN- resulted in multiple enriched GO categories and KEGG pathways and outcomes were quite tissue-specific. Different regulations and adaptations of gene expression in molecular function (MF), biological process (BP), and cellular components (CC) were observed in rice tissues at different effective concentrations of SCN-, suggesting their different responsive and adaptive strategies. Information collected here presents a detailed description of SCN-induced alternations of gene expression in rice seedlings and provide valuable information for further searching specific genes participating in transportation, phytotoxic responses, and detoxification of SCN- in rice seedlings.
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Affiliation(s)
- Yu-Juan Lin
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Xiao-Zhang Yu
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China.
| | - Qing Zhang
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
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14
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Economic Performance of Traditional and Modern Rice Varieties under Different Water Management Systems. SUSTAINABILITY 2017. [DOI: 10.3390/su9030347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Mahender A, Anandan A, Pradhan SK, Pandit E. Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches. SPRINGERPLUS 2016; 5:2086. [PMID: 28018794 PMCID: PMC5148756 DOI: 10.1186/s40064-016-3744-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 11/25/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Rice breeding program needs to focus on development of nutrient dense rice for value addition and helping in reducing malnutrition. Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice. RESULTS Genes and QTLs are recently known for the nutritional quality of rice. By comprehensive literature survey and public domain database, we provided a critical review on nutritional aspects like grain protein and amino acid content, vitamins and minerals, glycemic index value, phenolic and flavonoid compounds, phytic acid, zinc and iron content along with QTLs linked to these traits. In addition, achievements through transgenic and advanced genomic approaches have been discussed. The information available on genes and/or QTLs involved in enhancement of micronutrient element and amino acids are summarized with graphical representation. CONCLUSION Compatible QTLs/genes may be combined together to design a desirable genotype with superior in multiple grain quality traits. The comprehensive review will be helpful to develop nutrient dense rice cultivars by integrating molecular markers and transgenic assisted breeding approaches with classical breeding.
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Affiliation(s)
- Anumalla Mahender
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Annamalai Anandan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Elssa Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
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Biscarini F, Cozzi P, Casella L, Riccardi P, Vattari A, Orasen G, Perrini R, Tacconi G, Tondelli A, Biselli C, Cattivelli L, Spindel J, McCouch S, Abbruscato P, Valé G, Piffanelli P, Greco R. Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions. PLoS One 2016; 11:e0155425. [PMID: 27228161 PMCID: PMC4881974 DOI: 10.1371/journal.pone.0155425] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/28/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions. RESULTS In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011). CONCLUSIONS We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.
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Affiliation(s)
| | | | | | | | | | - Gabriele Orasen
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Rosaria Perrini
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Gianni Tacconi
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Alessandro Tondelli
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Chiara Biselli
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Luigi Cattivelli
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Jennifer Spindel
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America
| | - Susan McCouch
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America
| | | | - Giampiero Valé
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
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