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Cao S, Liu B, Wang D, Rasheed A, Xie L, Xia X, He Z. Orchestrating seed storage protein and starch accumulation toward overcoming yield-quality trade-off in cereal crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:468-483. [PMID: 38409921 DOI: 10.1111/jipb.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/22/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024]
Abstract
Achieving high yield and good quality in crops is essential for human food security and health. However, there is usually disharmony between yield and quality. Seed storage protein (SSP) and starch, the predominant components in cereal grains, determine yield and quality, and their coupled synthesis causes a yield-quality trade-off. Therefore, dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality. Here, we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops, including maize, rice and wheat. We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights. We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding. Finally, future perspectives on major challenges are proposed.
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Affiliation(s)
- Shuanghe Cao
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Bingyan Liu
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Daowen Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Awais Rasheed
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lina Xie
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Xianchun Xia
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
| | - Zhonghu He
- State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center, Institute of Crop Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Wang Q, Gao H, Liu K, Wang H, Zhang F, Wei L, Lu K, Li M, Shi Y, Zhao J, Zhou W, Peng B, Yuan H. CRISPR/Cas9-mediated enhancement of semi-dwarf glutinous traits in elite Xiangdaowan rice ( Oryza sativa L.): targeting SD1 and Wx genes for yield and quality improvement. FRONTIERS IN PLANT SCIENCE 2024; 15:1333191. [PMID: 38434426 PMCID: PMC10904601 DOI: 10.3389/fpls.2024.1333191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
In rice cultivation, the traits of semi-dwarfism and glutinous texture are pivotal for optimizing yield potential and grain quality, respectively. Xiangdaowan (XDW) rice, renowned for its exceptional aromatic properties, has faced challenges due to its tall stature and high amylose content, resulting in poor lodging resistance and suboptimal culinary attributes. To address these issues, we employed CRISPR/Cas9 technology to precisely edit the SD1 and Wx genes in XDW rice, leading to the development of stable genetically homozygous lines with desired semi-dwarf and glutinous characteristics. The sd1-wx mutant lines exhibited reduced gibberellin content, plant height, and amylose content, while maintaining hardly changed germination rate and other key agronomic traits. Importantly, our study demonstrated that exogenous GA3 application effectively promoted growth by compensating for the deficiency of endogenous gibberellin. Based on this, a semi-dwarf glutinous elite rice (Oryza sativa L.) Lines was developed without too much effect on most agronomic traits. Furthermore, a comparative transcriptome analysis unveiled that differentially expressed genes (DEGs) were primarily associated with the anchored component of the membrane, hydrogen peroxide catabolic process, peroxidase activity, terpene synthase activity, and apoplast. Additionally, terpene synthase genes involved in catalyzing the biosynthesis of diterpenoids to gibberellins were enriched and significantly down-regulated. This comprehensive study provides an efficient method for simultaneously enhancing rice plant height and quality, paving the way for the development of lodging-resistant and high-quality rice varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Hongyu Yuan
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
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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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He L, Chen T, Liang W, Zhao C, Zhao L, Yao S, Zhou L, Zhu Z, Zhao Q, Lu K, Wang C, Zhu L, Zhang Y. The RING-Type Domain-Containing Protein GNL44 Is Essential for Grain Size and Quality in Rice ( Oryza sativa L.). Int J Mol Sci 2024; 25:589. [PMID: 38203760 PMCID: PMC10779214 DOI: 10.3390/ijms25010589] [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: 11/22/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Grain size in rice (Oryza sativa L.) shapes yield and quality, but the underlying molecular mechanism is not fully understood. We functionally characterized GRAIN NUMBER AND LARGE GRAIN SIZE 44 (GNL44), encoding a RING-type protein that localizes to the cytoplasm. The gnl44 mutant has fewer but enlarged grains compared to the wild type. GNL44 is mainly expressed in panicles and developing grains. Grain chalkiness was higher in the gnl44 mutant than in the wild type, short-chain amylopectin content was lower, middle-chain amylopectin content was higher, and appearance quality was worse. The amylose content and gel consistency of gnl44 were lower, and protein content was higher compared to the wild type. Rapid Visco Analyzer results showed that the texture of cooked gnl44 rice changed, and that the taste value of gnl44 was lower, making the eating and cooking quality of gnl44 worse than that of the wild type. We used gnl44, qgl3, and gs3 monogenic and two-gene near-isogenic lines to study the effects of different combinations of genes affecting grain size on rice quality-related traits. Our results revealed additive effects for these three genes on grain quality. These findings enrich the genetic resources available for rice breeders.
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Affiliation(s)
- Lei He
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Tao Chen
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Wenhua Liang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Chunfang Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Ling Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Shu Yao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Lihui Zhou
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Zhen Zhu
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Kai Lu
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Cailin Wang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yadong Zhang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
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Yang X, Pan Y, Xia X, Qing D, Chen W, Nong B, Zhang Z, Zhou W, Li J, Li D, Dai G, Deng G. Molecular basis of genetic improvement for key rice quality traits in Southern China. Genomics 2023; 115:110745. [PMID: 37977332 DOI: 10.1016/j.ygeno.2023.110745] [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: 07/11/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.
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Affiliation(s)
- Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Dongjin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Weiwei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Weiyong Zhou
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Jingcheng Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
| | - Gaoxing Dai
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
| | - Guofu Deng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
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6
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Wang L, Liu L, Zhao J, Li C, Wu H, Zhao H, Wu Q. Granule-bound starch synthase in plants: Towards an understanding of their evolution, regulatory mechanisms, applications, and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111843. [PMID: 37648115 DOI: 10.1016/j.plantsci.2023.111843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Amylose content (AC) is a significant quality trait in starchy crops, affecting their processing and application by the food and non-food industries. Therefore, fine-tuning AC in these crops has become a focus for breeders. Granule-bound starch synthase (GBSS) is the core enzyme that directly determines the AC levels. Several excellent reviews have summarized key progress in various aspects of GBSS research in recent years, but they mostly focus on cereals. Herein, we provide an in-depth review of GBSS research in monocots and dicots, focusing on the molecular characteristics, evolutionary relationships, expression patterns, molecular regulation mechanisms, and applications. We also discuss future challenges and directions for controlling AC in starchy crops, and found simultaneously increasing both the PTST and GBSS gene expression levels may be an effective strategy to increase amylose content.
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Affiliation(s)
- Lei Wang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Linling Liu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Jiali Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Huala Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Haixia Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China.
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Guo X, Wang L, Zhu G, Xu Y, Meng T, Zhang W, Li G, Zhou G. Impacts of Inherent Components and Nitrogen Fertilizer on Eating and Cooking Quality of Rice: A Review. Foods 2023; 12:2495. [PMID: 37444233 DOI: 10.3390/foods12132495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
With the continuous improvement of living standards, the preferences of consumers are shifting to rice varieties with high eating and cooking quality (ECQ). Milled rice is mainly composed of starch, protein, and oil, which constitute the physicochemical basis of rice taste quality. This review summarizes the relationship between rice ECQ and its intrinsic ingredients, and also briefly introduces the effects of nitrogen fertilizer management on rice ECQ. Rice varieties with higher AC usually have more long branches of amylopectin, which leach less when cooking, leading to higher hardness, lower stickinesss, and less panelist preference. High PC impedes starch pasting, and it may be hard for heat and moisture to enter the rice interior, ultimately resulting in worse rice eating quality. Rice with higher lipid content had a brighter luster and better eating quality, and starch lipids in rice have a greater impact on rice eating quality than non-starch lipids. The application of nitrogen fertilizer can enhance rice yield, but it also decreases the ECQ of rice. CRNF has been widely used in cereal crops such as maize, wheat, and rice as a novel, environmentally friendly, and effective fertilizer, and could increase rice quality to a certain extent compared with conventional urea. This review shows a benefit to finding more reasonable nitrogen fertilizer management that can be used to regulate the physical and chemical indicators of rice grains in production and to improve the taste quality of rice without affecting yield.
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Affiliation(s)
- Xiaoqian Guo
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
- China-Sudan Joint Laboratory of Crop Salinity and Drought Stress Physiology, The Ministry of Education of China, Yangzhou 225000, China
| | - Luqi Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guanglong Zhu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Yunji Xu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Tianyao Meng
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Weiyang Zhang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225000, China
| | - Guohui Li
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225000, China
| | - Guisheng Zhou
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
- China-Sudan Joint Laboratory of Crop Salinity and Drought Stress Physiology, The Ministry of Education of China, Yangzhou 225000, China
- College for Overseas Education, Yangzhou University, Yangzhou 225000, China
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8
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Hu Z, Niu F, Yan P, Wang K, Zhang L, Yan Y, Zhu Y, Dong S, Ma F, Lan D, Liu S, Xin X, Wang Y, Yang J, Cao L, Wu S, Luo X. The kinase OsSK41/OsGSK5 negatively regulates amylose content in rice endosperm by affecting the interaction between OsEBP89 and OsBP5. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36965127 DOI: 10.1111/jipb.13488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
Amylose content (AC) is the main factor determining the palatability, viscosity, transparency, and digestibility of rice (Oryza sativa) grains. AC in rice grains is mainly controlled by different alleles of the Waxy (Wx) gene. The AP2/EREBP transcription factor OsEBP89 interacts with the MYC-like protein OsBP5 to synergistically regulate the expression of Wx. Here, we determined that the GLYCOGEN SYNTHASE KINASE 5 (OsGSK5, also named SHAGGY-like kinase 41 [OsSK41]) inhibits the transcriptional activation activity of OsEBP89 in rice grains during amylose biosynthesis. The loss of OsSK41 function enhanced Wx expression and increased AC in rice grains. By contrast, the loss of function of OsEBP89 reduced Wx expression and decreased AC in rice grains. OsSK41 interacts with OsEBP89 and phosphorylates four of its sites (Thr-28, Thr-30, Ser-238, and Thr-257), which makes OsEBP89 unstable and attenuates its interaction with OsBP5. Wx promoter activity was relatively weak when regulated by the phosphomimic variant OsEBP89E -OsBP5 but relatively strong when regulated by the nonphosphorylatable variant OsEBP89A -OsBP5. Therefore, OsSK41-mediated phosphorylation of OsEBP89 represents an additional layer of complexity in the regulation of amylose biosynthesis during rice grain development. In addition, our findings provide four possible sites for regulating rice grain AC via precise gene editing.
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Affiliation(s)
- Zejun Hu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Fuan Niu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Kai Wang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Lixia Zhang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Ying Yan
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Yu Zhu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Shiqing Dong
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Fuying Ma
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dengyong Lan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Siwen Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaoyun Xin
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Liming Cao
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Shujun Wu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
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9
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Li J, Zhang C, Luo X, Zhang T, Zhang X, Liu P, Yang W, Lei Y, Tang S, Kang L, Huang L, Li T, Wang Y, Chen W, Yuan H, Qin P, Li S, Ma B, Tu B. Fine mapping of the grain chalkiness quantitative trait locus qCGP6 reveals the involvement of Wx in grain chalkiness formation. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad112. [PMID: 36964899 DOI: 10.1093/jxb/erad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Indexed: 06/18/2023]
Abstract
Grain chalkiness is an important index of rice appearance quality and is negatively associated with rice processing and eating qualities. However, the genetic mechanism underlying chalkiness formation is largely unknown. To identify the genetic basis of chalkiness, 410 recombinant inbred lines (RILs) derived from two representative indica rice varieties, Shuhui498 (R498) and Yihui3551 (R3551), were used to discover quantitative trait loci (QTL). The two parental lines and RILs were grown in three locations in China under three controlled fertilizer application level. Analyses indicated that chalkiness was significantly affected by genotype, the environment, and the interaction between the two, and that heritability was high. Several QTLs were isolated, including the two stable QTLs, i.e., qCGP6 and qCGP8. Fine mapping and candidate gene verification of qCGP6 showed that Wx may play a key role in chalkiness formation. Chromosomal segment substitution lines (CSSLs) and near-isogenic lines (NILs) carrying the Wxa or Wxin allele produced more chalky grain than the R498 parent. A similar result was also observed in the 3611 background. Notably, the effect of the Wx genotype on rice chalkiness was shown to be dependent on environmental conditions and Wx alleles exhibited different sensitivities to shading treatment. Using CRISPR/Cas9, the Wxa promoter region was successfully edited, down-regulating Wx alleviates chalkiness formation in NILR498-Wxa. This study developed a new strategy for synergistic improvement of eating and appearance qualities in rice, and created a novel Wx allele with great potential in breeding applications.
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Affiliation(s)
- Jialian Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang, Liaoning 110101, China
| | - Xia Luo
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyu Zhang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Pin Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Wen Yang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yuekun Lei
- Chengdu Juannong Intelligent Agriculture Technology Development Co., Ltd
| | - Siwen Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Liangzhu Kang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Weilan Chen
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Peng Qin
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Bingtian Ma
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
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10
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Tian Y, Zhou Y, Gao G, Zhang Q, Li Y, Lou G, He Y. Creation of Two-Line Fragrant Glutinous Hybrid Rice by Editing the Wx and OsBADH2 Genes via the CRISPR/Cas9 System. Int J Mol Sci 2023; 24:ijms24010849. [PMID: 36614293 PMCID: PMC9820973 DOI: 10.3390/ijms24010849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023] Open
Abstract
Global food security has benefited from the development and promotion of the two-line hybrid rice system. Excellent eating quality determines the market competitiveness of hybrid rice varieties based on achieving the fundamental requirements of high yield and good adaptability. Developing sterile and restorer lines with improved quality for two-line hybrid breeding by editing quality genes with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 is an efficient and practical alternative to the lengthy and laborious process of conventional breeding to improve rice quality. We edited Wx and OsBADH2 using CRISPR/Cas9 technology to produce both homozygous male sterile mutant lines and homozygous restorer mutant lines with Cas9-free. These mutants have a much lower amylose content while having a significantly higher 2-acetyl-1-pyrroline aroma content. Based on this, a fragrant glutinous hybrid rice was developed without too much effect on most agronomic traits. This study demonstrates the use of CRISPR/Cas9 in creating two-line fragrant glutinous hybrid rice by editing the components of the male sterile and the restorative lines.
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11
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Deng Z, Liu Y, Gong C, Chen B, Wang T. Waxy is an important factor for grain fissure resistance and head rice yield as revealed by a genome-wide association study. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6942-6954. [PMID: 36052968 PMCID: PMC9629786 DOI: 10.1093/jxb/erac330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Head rice yield (HRY) is an essential quality trait, and is sensitive to environmental stresses during the grain-filling, harvest, and postharvest stages. It is therefore important for rice production and global food security to select for superior HRY traits; however, the molecular basis of this trait remains unknown. Using diverse rice germplasm material, we performed a genome-wide association study of grain fissure resistance (GFR), the phenotype most associated with HRY, and found that the granule-bound starch synthase I gene Waxy is an important gene controlling GFR. Analysis of near-isogenic lines demonstrated that genetic variations in Waxy conferred different levels of tolerance to fissuring in grains. The null allele wx resulted in the highest GFR, while alleles that increased amylose synthesis reduced GFR. Increases in amylose content led to increases in the ratio of the widths of the amorphous layer to the semi-crystalline layer of the starch granules, and also to increased occurrence of chalkiness. The layer structure determined GFR by affecting the degree of swelling of granules in response to moisture, and chalkiness acted as an accelerator of moisture infiltration to rapidly increase the number of swelling granules. Our study reveals the molecular basis of GFR and HRY, thus opening the door for further understanding of the molecular networks of GFR and HRY.
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Affiliation(s)
| | | | - Chunyan Gong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bingtang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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12
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Identification of volatile organic compounds related to the eating quality of cooked japonica rice. Sci Rep 2022; 12:18133. [PMID: 36307468 PMCID: PMC9616908 DOI: 10.1038/s41598-022-21863-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 12/30/2022] Open
Abstract
Eating quality (EQ) of rice has a complex nature composed of physicochemical properties. Nevertheless, breeding programs evaluating EQ through sensory test or taste-evaluation instruments have been laborious, time-consuming and inefficient. EQ is affected by both taste and aroma. However, in actual breeding programs, aroma of cooked rice has been considered the least due to lack of information. Here we identified a total of 41 volatile compounds potentially affecting the EQ of non-aromatic, cooked japonica rice, identified by GC-MS, sensory panel test, and Toyo taste-meter analyses. Partial least squares discriminant analysis demonstrated an outstanding classification effect of the identified volatile compounds on eating-quality discrimination. Several volatile compounds related to lipid oxidation and fatty acid degradation were identified to affect the EQ in japonica rice. Of them, 1-octen-3-ol, 1-ethyl-3,5-dimethylbenzene, 2,6,11-trimethyldodecane, 3-ethyloctane, 2,7,10-trimethyldodecane, methyl salicylate, 2-octanone, and heptanal were selected as important compounds. The discriminant model for the classification of the quality of cultivars was robust and accurate, an r-squared value was 0.91, a q squared value was 0.85, and an accuracy was 1.0. Overall, the results of this study characterize EQ of rice cultivars based on volatile compounds, suggesting the application of metabolite profiling data for rice breeding of high eating quality.
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13
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Liu X, Tian D, Li C, Tang B, Wang Z, Zhang R, Pan Y, Wang Y, Zou D, Zhang Z, Song S. GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals. Nucleic Acids Res 2022; 51:D969-D976. [PMID: 36263826 PMCID: PMC9825481 DOI: 10.1093/nar/gkac924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 01/30/2023] Open
Abstract
GWAS Atlas (https://ngdc.cncb.ac.cn/gwas/) is a manually curated resource of genome-wide genotype-to-phenotype associations for a wide range of species. Here, we present an updated implementation of GWAS Atlas by curating and incorporating more high-quality associations, with significant improvements and advances over the previous version. Specifically, the current release of GWAS Atlas incorporates a total of 278,109 curated genotype-to-phenotype associations for 1,444 different traits across 15 species (10 plants and 5 animals) from 830 publications and 3,432 studies. A collection of 6,084 lead SNPs of 439 traits and 486 experiment-validated causal variants of 157 traits are newly added. Moreover, 1,056 trait ontology terms are newly defined, resulting in 1,172 and 431 terms for Plant Phenotype and Trait Ontology and Animal Phenotype and Trait Ontology, respectively. Additionally, it is equipped with four online analysis tools and a submission platform, allowing users to perform data analysis and data submission. Collectively, as a core resource in the National Genomics Data Center, GWAS Atlas provides valuable genotype-to-phenotype associations for a diversity of species and thus plays an important role in agronomic trait study and molecular breeding.
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Affiliation(s)
| | | | | | - Bixia Tang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhonghuang Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongqin Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yitong Pan
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformatics, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhang Zhang
- Correspondence may also be addressed to Zhang Zhang. Tel: +86 10 84097261; Fax: +86 10 84097720;
| | - Shuhui Song
- To whom correspondence should be addressed. Tel: +86 10 84097620; Fax: +86 10 84097720;
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14
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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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15
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Xia D, Wang Y, Shi Q, Wu B, Yu X, Zhang C, Li Y, Fu P, Li M, Zhang Q, Liu Q, Gao G, Zhou H, He Y. Effects of Wx Genotype, Nitrogen Fertilization, and Temperature on Rice Grain Quality. FRONTIERS IN PLANT SCIENCE 2022; 13:901541. [PMID: 35937336 PMCID: PMC9355397 DOI: 10.3389/fpls.2022.901541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Quality is a complex trait that is not only the key determinant of the market value of the rice grain, but is also a major constraint in rice breeding. It is influenced by both genetic and environmental factors. However, the combined effects of genotypes and environmental factors on rice grain quality remain unclear. In this study, we used a three-factor experimental design to examine the grain quality of different Wx genotypes grown under different nitrogen fertilization and temperature conditions during grain development. We found that the three factors contributed differently to taste, appearance, and nutritional quality. Increased Wx function and nitrogen fertilization significantly reduced eating quality, whereas high temperature (HT) had almost no effect. The main effects of temperature on appearance quality and moderate Wx function at low temperatures (LTs) contributed to better appearance, and higher nitrogen fertilization promoted appearance at HTs. With regard to nutritional quality, Wx alleles promoted amylose content (AC) as well as starch-lipids content (SLC); nitrogen fertilization increased storage protein content (PC); and higher temperature increased lipid content but decreased the PC. This study helps to broaden the understanding of the major factors that affect the quality of rice and provides constructive messages for rice quality improvement and the cultivation of high-quality rice varieties.
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Affiliation(s)
- Duo Xia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yipei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qingyun Shi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaoman Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Changquan Zhang
- 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, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Pei Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Minqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 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, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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16
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Ke F, Zhang K, Li Z, Wang J, Zhang F, Wu H, Zhang Z, Lu F, Wang Y, Duan Y, Liu Z, Zou J, Zhu K. Transcriptomic analysis of starch accumulation patterns in different glutinous sorghum seeds. Sci Rep 2022; 12:11133. [PMID: 35778525 PMCID: PMC9249802 DOI: 10.1038/s41598-022-15394-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Sorghum is a high-quality raw material for brewing white wine, and the starch content in seeds has a large impact on brewing quality. Transcriptomic data obtained from a glutinous variety (Liaonian3) and a non-glutinous variety (Liaoza10) at 3, 18, and 30 days after pollination were analyzed to identify genes associated with starch accumulation. The amylopectin content was significantly higher in Liaonian3 compared to Liaoza10, but the amylose content and total starch content were lower. There were 6634 differentially expressed genes found in Liaoza10 between 3 and 18 d after pollination, and 779 differentially expressed genes between 18 and 30 d after pollination. In Liaonian3, there were 6768 differentially expressed genes between 3 and 18 d after pollination, and 7630 differentially expressed genes between 18 and 30 d after pollination. Genes were grouped by expression profiles over the three time points and the profiles were analyzed for enrichment of gene ontology terms and biochemical pathways. Profile 1 (decreasing expression from 3 to 30 d) for Liaoza10 was enriched in ribosomes, metabolic pathways, and carbon metabolic pathways. Profile 0 (decreasing expression from 3 to 18 d and consistent expression from 18 to 30 d) was enriched in pathways related to sugar or starch metabolism. Although the starch accumulation rate in Liaonian3 and Liaoza10 showed a profile of increasing and then decreasing, the expression of genes related to starch synthesis gradually decreased with time since pollination, demonstrating the complexity of starch synthesis. According to orthologous gene alignment and expression analysis, 19 genes such as entrzID_8068390 and entrzID_8066807 were found to be the key genes for starch synthesis and glutinous and non-glutinous differentiation in sorghum grains.
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Affiliation(s)
- Fulai Ke
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Kuangye Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Zhihua Li
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Jiaxu Wang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Fei Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Han Wu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Zhipeng Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Feng Lu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Yanqiu Wang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Youhou Duan
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Zhiqiang Liu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Jianqiu Zou
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China
| | - Kai Zhu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, Liaoning Province, People's Republic of China.
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17
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Zhao D, Zhang C, Li Q, Liu Q. Genetic control of grain appearance quality in rice. Biotechnol Adv 2022; 60:108014. [PMID: 35777622 DOI: 10.1016/j.biotechadv.2022.108014] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/27/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023]
Abstract
Grain appearance, one of the key determinants of rice quality, reflects the ability to attract consumers, and is characterized by four major properties: grain shape, chalkiness, transparency, and color. Mining of valuable genes, genetic mechanisms, and breeding cultivars with improved grain appearance are essential research areas in rice biology. However, grain appearance is a complex and comprehensive trait, making it challenging to understand the molecular details, and therefore, achieve precise improvement. This review highlights the current findings of grain appearance control, including a detailed description of the key genes involved in the formation of grain appearance, and the major environmental factors affecting chalkiness. We also discuss the integration of current knowledge on valuable genes to enable accurate breeding strategies for generation of rice grains with superior appearance quality.
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Affiliation(s)
- Dongsheng Zhao
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Changquan Zhang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China.
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18
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Analysis of Related Metabolites Affecting Taste Values in Rice under Different Nitrogen Fertilizer Amounts and Planting Densities. Foods 2022; 11:foods11101508. [PMID: 35627078 PMCID: PMC9141971 DOI: 10.3390/foods11101508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was to explore the differences in metabolites related to rice quality formation under different nitrogen (N) fertilizers and planting densities. In this study, Yangnongxiang 28 was used as the experimental material with the following conditions: high nitrogen and low density (HNLD; high nitrogen: 360 kg·hm−2, low density: the row spacing of rice plants was 16 cm × 30 cm), medium nitrogen and medium density (MNMD; medium nitrogen: 270 kg·hm−2, medium density: the row spacing of rice plants was 13 cm × 30 cm), and low nitrogen and high density (LNHD; low nitrogen: 270 kg·hm−2, high density: the row spacing of rice plants was 10 cm × 30 cm). The rice quality indexes, including the processing quality, amylose content, and taste value, were compared under different treatments, and we analyzed their relationship with the metabolites. The results show that the milled rice rate of HNLD was 13.85% and was 1.89% higher than that of LNHD and MNMD, respectively. The head milled rice rate of HNLD was 32.45% and 6.39% higher than that of LNHD and MNMD, respectively. The milled rice rate and head milled rice rate of HNLD and MNMD were significantly higher than those of LNHD. This study identified 22 differential metabolites (DMs) in HNLD and LNHD, 38 DMs in HNLD and MNMD, and 23 DMs in LNHD and MNMD. Most of the identified differential metabolites were lipid metabolites, which were mainly enriched in the lipid metabolic pathways and amino acid metabolic pathways. The correlation analysis showed that the lipid metabolite physapubescin was significantly negatively correlated with the taste value. The lipid metabolites 2-undecen-1-ol, lucidenic acid F, and 8-deoxy-11,13-dihydroxygrosheimin were significantly positively correlated with the taste value. Lipids may be important substances that lead to differences in taste under different nitrogen fertilizer and density treatments.
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Shen L, Li J, Li Y. Resistant starch formation in rice: Genetic regulation and beyond. PLANT COMMUNICATIONS 2022; 3:100329. [PMID: 35576157 PMCID: PMC9251435 DOI: 10.1016/j.xplc.2022.100329] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/09/2022] [Accepted: 04/18/2022] [Indexed: 05/07/2023]
Abstract
Resistant starch (RS), a healthy dietary fiber, is a particular type of starch that has attracted much research attention in recent years. RS has important roles in reducing glycemic index, postprandial blood glucose levels, and serum cholesterol levels, thereby improving and preventing many diseases, such as diabetes, obesity, and cardiovascular disease. The formation of RS is influenced by intrinsic properties of starch (e.g., starch granule structure, starch crystal structure, and amylose-to-amylopectin ratio) and non-starch components (e.g., proteins, lipids, and sugars), as well as storage and processing conditions. Recent studies have revealed that several starch-synthesis-related genes (SSRGs) are crucial for the formation of RS during seed development. Several transcription factors and mRNA splicing factors have been shown to affect the expression or splicing of SSRGs that regulate RS content, suggesting their potential roles in RS formation. This review focuses mainly on recent research progress on the genetic regulation of RS content and discusses the emerging genetic and molecular mechanisms of RS formation in rice.
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Affiliation(s)
- Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Science, Beijing 100039, China.
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Science, Beijing 100039, China.
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Sreenivasulu N, Zhang C, Tiozon RN, Liu Q. Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century. PLANT COMMUNICATIONS 2022; 3:100271. [PMID: 35576153 PMCID: PMC9251384 DOI: 10.1016/j.xplc.2021.100271] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 05/14/2023]
Abstract
The eating and cooking quality (ECQ) of rice is critical for determining its economic value in the marketplace and promoting consumer acceptance. It has therefore been of paramount importance in rice breeding programs. Here, we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in rice. Innovations in gene- and genome-editing techniques have enabled improvements in rice ECQ. Significant genes and quantitative trait loci (QTLs) have been shown to regulate starch composition, thereby affecting amylose content and thermal and pasting properties. A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and aroma. Marker-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ properties. The post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.
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Affiliation(s)
- Nese Sreenivasulu
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños 4030, Philippines.
| | - Changquan Zhang
- 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 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Rhowell N Tiozon
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños 4030, Philippines; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - 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 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China.
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Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
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Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
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Zhou L, Zhang C, Zhang Y, Wang C, Liu Q. Genetic manipulation of endosperm amylose for designing superior quality rice to meet the demands in the 21st century. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Li P, Chen YH, Lu J, Zhang CQ, Liu QQ, Li QF. Genes and Their Molecular Functions Determining Seed Structure, Components, and Quality of Rice. RICE (NEW YORK, N.Y.) 2022; 15:18. [PMID: 35303197 PMCID: PMC8933604 DOI: 10.1186/s12284-022-00562-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/01/2022] [Indexed: 05/14/2023]
Abstract
With the improvement of people's living standards and rice trade worldwide, the demand for high-quality rice is increasing. Therefore, breeding high quality rice is critical to meet the market demand. However, progress in improving rice grain quality lags far behind that of rice yield. This might be because of the complexity of rice grain quality research, and the lack of consensus definition and evaluation standards for high quality rice. In general, the main components of rice grain quality are milling quality (MQ), appearance quality (AQ), eating and cooking quality (ECQ), and nutritional quality (NQ). Importantly, all these quality traits are determined directly or indirectly by the structure and composition of the rice seeds. Structurally, rice seeds mainly comprise the spikelet hull, seed coat, aleurone layer, embryo, and endosperm. Among them, the size of spikelet hull is the key determinant of rice grain size, which usually affects rice AQ, MQ, and ECQ. The endosperm, mainly composed of starch and protein, is the major edible part of the rice seed. Therefore, the content, constitution, and physicochemical properties of starch and protein are crucial for multiple rice grain quality traits. Moreover, the other substances, such as lipids, minerals, vitamins, and phytochemicals, included in different parts of the rice seed, also contribute significantly to rice grain quality, especially the NQ. Rice seed growth and development are precisely controlled by many genes; therefore, cloning and dissecting these quality-related genes will enhance our knowledge of rice grain quality and will assist with the breeding of high quality rice. This review focuses on summarizing the recent progress on cloning key genes and their functions in regulating rice seed structure and composition, and their corresponding contributions to rice grain quality. This information will facilitate and advance future high quality rice breeding programs.
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Affiliation(s)
- Pei Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yu-Hao Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jun Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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Liu X, Ding Q, Wang W, Pan Y, Tan C, Qiu Y, Chen Y, Li H, Li Y, Ye N, Xu N, Wu X, Ye R, Liu J, Ma C. Targeted Deletion of the First Intron of the Wx b Allele via CRISPR/Cas9 Significantly Increases Grain Amylose Content in Rice. RICE (NEW YORK, N.Y.) 2022; 15:1. [PMID: 34982277 PMCID: PMC8727654 DOI: 10.1186/s12284-021-00548-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 12/28/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND The rice Waxy (Wx) gene plays a major role in seed amylose synthesis and consequently controls grain amylose content. Wx gene expression is highly regulated at the post-transcriptional level. In particular, the GT/TT polymorphism at the 5'splicing site of its 1st intron greatly affects this intron's splicing efficiency and defines two predominant Wx alleles, Wxa and Wxb. Wxa rice often harbours intermediate to high amylose contents, whereas Wxb rice exhibits low to intermediate amylose contents. By deleting the Wx 1st intron using CRISPR/Cas9 technology, we generate a completely novel Wx allele and further investigate how intron removal affects Wx gene expression and rice grain amylose content. RESULTS CRISPR/Cas9-mediated targeted deletion of the Wx 1st intron was performed on 4 rice inbred lines: KY131 (Wxb), X32 (Wxb), X35 (Wxa) and X55 (Wxlv). Deletion of the 1st intron occurred in 8.6-11.8% of the primary transformants of these 4 inbred lines. Compared to wild-type plants, amylose content was significantly increased from 13.0% to approximately 24.0% in KY131 and X32 mutant lines, which both carried the Wxb allele. However, no significant difference in amylose content was observed between wild-type plants and X35 and X55 mutant lines, which carried the Wxa and Wxlv alleles, respectively. Wx gene expression analysis of wild-type plants and mutants yielded results that were highly consistent with amylose content results. KY131 and X32 mutants accumulated increased levels of steady mRNA transcripts compared with wild-type plants, whereas steady mRNA levels were not altered in X35 and X55 mutants compared with wild-type plants. Grain quality, including appearance quality and eating and cooking quality, which are tightly associated with amylose content, was also assessed in wild-type and mutant plants, and data were presented and analysed. CONCLUSIONS This study presents a novel and rapid strategy to increase amylose content in inbred rice carrying a Wxb allele. Our data strongly suggest that the 1st intron of the Wx gene regulates Wx gene expression mainly at the post-transcriptional level in rice. This finding is in contrast to a previous hypothesis suggesting that it influences Wx gene transcription. In addition, removal of the first intron generates a completely novel Wx allele. Further studies on this new Wx allele will provide invaluable insights into the regulation of Wx gene expression, which will help researchers engineer new Wx alleles to facilitate the breeding of rice cultivars with better eating and cooking quality.
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Affiliation(s)
- Xingdan Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Ding
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Wenshu Wang
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yanling Pan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Chao Tan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yingbo Qiu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Ya Chen
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Hongjing Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yinlong Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Naizhong Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Nian Xu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Xiao Wu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Rongjian Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Jianfeng Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
| | - Chonglie Ma
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
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Zhang H, Xu H, Jiang Y, Zhang H, Wang S, Wang F, Zhu Y. Genetic Control and High Temperature Effects on Starch Biosynthesis and Grain Quality in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:757997. [PMID: 34975940 PMCID: PMC8718882 DOI: 10.3389/fpls.2021.757997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/23/2021] [Indexed: 05/29/2023]
Abstract
Grain quality is one of the key targets to be improved for rice breeders and covers cooking, eating, nutritional, appearance, milling, and sensory properties. Cooking and eating quality are mostly of concern to consumers and mainly determined by starch structure and composition. Although many starch synthesis enzymes have been identified and starch synthesis system has been established for a long time, novel functions of some starch synthesis genes have continually been found, and many important regulatory factors for seed development and grain quality control have recently been identified. Here, we summarize the progress in this field as comprehensively as possible and hopefully reveal some underlying molecular mechanisms controlling eating quality in rice. The regulatory network of amylose content (AC) determination is emphasized, as AC is the most important index for rice eating quality (REQ). Moreover, the regulatory mechanism of REQ, especially AC influenced by high temperature which is concerned as a most harmful environmental factor during grain filling is highlighted in this review.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Heng Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Yingying Jiang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Shiyu Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Fulin Wang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
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The Physicochemical Properties of Starch Are Affected by Wxlv in Indica Rice. Foods 2021; 10:foods10123089. [PMID: 34945643 PMCID: PMC8701004 DOI: 10.3390/foods10123089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Amylose largely determines rice grain quality profiles. The process of rice amylose biosynthesis is mainly driven by the waxy (Wx) gene, which also affects the diversity of amylose content. The present study assessed the grain quality profiles, starch fine structure, and crystallinity characteristics of the near-isogenic lines Q11(Wxlv), NIL(Wxa), and NIL(Wxb) in the indica rice Q11 background containing different Wx alleles. Q11(Wxlv) rice contained a relatively higher amylose level but very soft gel consistency and low starch viscosity, compared with rice lines carrying Wxa and Wxb. In addition, starch fine structure analysis revealed a remarkable decrease in the relative area ratio of the short amylopectin fraction but an increased amylose fraction in Q11(Wxlv) rice. Chain length distribution analysis showed that Q11(Wxlv) rice contained less amylopectin short chains but more intermediate chains, which decreased the crystallinity and lamellar peak intensity, compared with those of NIL(Wxa) and NIL(Wxb) rice. Additionally, the starches in developing grains showed different accumulation profiles among the three rice lines. Moreover, significant differences in starch gelatinization and retrogradation characteristics were observed between near-isogenic lines, which were caused by variation in starch fine structure. These findings revealed the effects of Wxlv on rice grain quality and the fine structure of starch in indica rice.
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Maung TZ, Chu SH, Park YJ. Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II ( GBSSII) Gene in Korean Rice Accessions (KRICE_CORE). Foods 2021; 10:2359. [PMID: 34681408 PMCID: PMC8535093 DOI: 10.3390/foods10102359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022] Open
Abstract
Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1-C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima's D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima's D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
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Huang L, Tan H, Zhang C, Li Q, Liu Q. Starch biosynthesis in cereal endosperms: An updated review over the last decade. PLANT COMMUNICATIONS 2021; 2:100237. [PMID: 34746765 PMCID: PMC8554040 DOI: 10.1016/j.xplc.2021.100237] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/08/2021] [Accepted: 08/27/2021] [Indexed: 05/13/2023]
Abstract
Starch is a vital energy source for living organisms and is a key raw material and additive in the food and non-food industries. Starch has received continuous attention in multiple research fields. The endosperm of cereals (e.g., rice, corn, wheat, and barley) is the most important site for the synthesis of storage starch. Around 2010, several excellent reviews summarized key progress in various fields of starch research, serving as important references for subsequent research. In the past 10 years, many achievements have been made in the study of starch synthesis and regulation in cereals. The present review provides an update on research progress in starch synthesis of cereal endosperms over the past decade, focusing on new enzymes and non-enzymatic proteins involved in starch synthesis, regulatory networks of starch synthesis, and the use of elite alleles of starch synthesis-related genes in cereal breeding programs. We also provide perspectives on future research directions that will further our understanding of cereal starch biosynthesis and regulation to support the rational design of ideal quality grain.
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Affiliation(s)
- Lichun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Tan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Changquan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
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29
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Maung TZ, Yoo JM, Chu SH, Kim KW, Chung IM, Park YJ. Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:707237. [PMID: 34504507 PMCID: PMC8421862 DOI: 10.3389/fpls.2021.707237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by F ST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Ji-Min Yoo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Kyu-Won Kim
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Ill-Min Chung
- Department of Applied Life Science, Konkuk University, Seoul, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
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30
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Lou G, Chen P, Zhou H, Li P, Xiong J, Wan S, Zheng Y, Alam M, Liu R, Zhou Y, Yang H, Tian Y, Bai J, Rao W, Tan X, Gao H, Li Y, Gao G, Zhang Q, Li X, Liu C, He Y. FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:36. [PMID: 37309330 PMCID: PMC10236042 DOI: 10.1007/s11032-021-01226-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/27/2021] [Indexed: 06/14/2023]
Abstract
As a staple food for more than half of the world's population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to their unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on floury endosperm in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential floury genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performances of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01226-z.
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Affiliation(s)
- Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Pingli Chen
- Guangdong Key Laboratory of New Technology in Rice Breeding, The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jiawang Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Shanshan Wan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yuanyuan Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Mufid Alam
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yin Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yahong Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Bai
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Wenting Rao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xuan Tan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Haozhou Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Chuanguang Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
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31
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Hori K, Suzuki K, Ishikawa H, Nonoue Y, Nagata K, Fukuoka S, Tanaka J. Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars. RICE (NEW YORK, N.Y.) 2021; 14:8. [PMID: 33415511 PMCID: PMC7790929 DOI: 10.1186/s12284-020-00447-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/17/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND In temperate rice cultivation regions, japonica rice cultivars are grown preferentially because consumers deem them to have good eating quality, whereas indica rice cultivars have high grain yields and strong heat tolerance but are considered to have poor eating quality. To mitigate the effects of global warming on rice production, it is important to develop novel rice cultivars with both desirable eating quality and resilience to high temperatures. Eating quality and agronomic traits were evaluated in a reciprocal set of chromosome segment substitution lines derived from crosses between a japonica rice cultivar 'Koshihikari' and an indica rice cultivar 'Takanari'. RESULTS We detected 112 QTLs for amylose and protein contents, whiteness, stickiness, hardness and eating quality of cooked rice grains. Almost of 'Koshihikari' chromosome segments consistently improved eating quality. Among detected QTLs, six QTLs on chromosomes 1-5 and 11 were detected that increased whiteness and stickiness of cooked grains or decreased their hardness for 3 years. The QTLs on chromosomes 2-4 were not associated with differences in amylose or protein contents. QTLs on chromosomes 1-5 did not coincide with QTLs for agronomic traits such as heading date, culm length, panicle length, spikelet fertility and grain yield. Genetic effects of the detected QTLs were confirmed in substitution lines carrying chromosome segments from five other indica cultivars in the 'Koshihikari' genetic background. CONCLUSION The detected QTLs were associated with differences in eating quality between indica and japonica rice cultivars. These QTLs appear to be widely distributed among indica cultivars and to be novel genetic factors for eating quality traits because their chromosome regions differed from those of the GBSSI (Wx) and SSIIa (Alk) genes. The detected QTLs would be very useful for improvement of eating quality of indica rice cultivars in breeding programs.
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Affiliation(s)
- Kiyosumi Hori
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Keitaro Suzuki
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Haruka Ishikawa
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazufumi Nagata
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Present address: St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki, Kanagawa, 216-8511, Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Junichi Tanaka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
- Graduate School of Life and Environmental Science, University of Tsukuba, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
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