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Zhu J, Liu Q, Gilbert RG. The effects of chain-length distributions on starch-related properties in waxy rices. Carbohydr Polym 2024; 339:122264. [PMID: 38823928 DOI: 10.1016/j.carbpol.2024.122264] [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: 02/17/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 06/03/2024]
Abstract
Normal rice starch consists of amylopectin and amylose, whose relative amounts and chain-length distributions (CLDs) are major determinants of the digestibility and rheology of cooked rice, and are related to metabolic health and consumer preference. Here, the mechanism of how molecular structural features of pure amylopectin (waxy) starches affect starch properties was explored. Following debranching, chain-length distributions of seven waxy varieties were measured using size-exclusion chromatography, and parameterized using biosynthesis-based models, which involve breaking up the chain-length distribution into contributions from five enzyme sets covering overlapping ranges of chain length; structure-property correlations involving the fifth set were found to be statistically significant. Digestibility was measured in vitro, and parameters for the slower and longer digestion phase quantified using non-linear least-squares fitting. The coefficient for the significant correlation involving amylopectin fine structure for the fifth set was -0.903, while the amounts of amylopectin short and long chains were found to dominate breakdown viscosity (correlation coefficients 0.801 and - 0.911, respectively). This provides a methodology for finding or developing healthier starch in terms of lower digestion rate, while also having acceptable palatability. As rice breeders can to some extent control CLDs, this can help the development of waxy rices with improved properties.
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Affiliation(s)
- Jihui Zhu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China; The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
| | - Robert G Gilbert
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China; The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia.
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2
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Peng B, Liu Y, Qiu J, Peng J, Sun X, Tian X, Zhang Z, Huang Y, Pang R, Zhou W, Zhao J, Sun Y, Wang Q. OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1436998. [PMID: 39049859 PMCID: PMC11267625 DOI: 10.3389/fpls.2024.1436998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024]
Abstract
Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.
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Affiliation(s)
- Bo Peng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yan Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jing Qiu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jing Peng
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Xiaoyu Sun
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Xiayu Tian
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Zhiguo Zhang
- Henan Lingrui Pharmaceutical Company Limited, Xinyang, China
| | - Yaqin Huang
- School of Pharmacy, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Ruihua Pang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Wei Zhou
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jinhui Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yanfang Sun
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Quanxiu Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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3
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Wu H, Wang S, Wu M. The Waxy Gene Has Pleiotropic Effects on Hot Water-Soluble and -Insoluble Amylose Contents in Rice ( Oryza sativa) Grains. Int J Mol Sci 2024; 25:6561. [PMID: 38928265 PMCID: PMC11203747 DOI: 10.3390/ijms25126561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Rice (Oryza sativa) is a cereal crop with a starchy endosperm. Starch is composed of amylose and amylopectin. Amylose content (AC) is the principal determinant of rice quality, but varieties with similar ACs can still vary substantially in their quality. In this study, we analyzed the total AC (TAC) and its constituent fractions, the hot water-soluble amylose content (SAC) and hot water-insoluble amylose content (IAC), in two sets of related chromosome segment substitution lines of rice with a common genetic background grown in two years. We searched for quantitative trait loci (QTLs) associated with SAC, IAC, and TAC and identified one common QTL (qSAC-6, qIAC-6, and qTAC-6) on chromosome 6. Map-based cloning revealed that the gene underlying the trait associated with this common QTL is Waxy (Wx). An analysis of the colors of soluble and insoluble starch-iodine complexes and their λmax values (wavelengths at the positions of their peak absorbance values) as well as gel permeation chromatography revealed that Wx is responsible for the biosynthesis of amylose, comprising a large proportion of the soluble fractions of the SAC. Wx is also involved in the biosynthesis of long chains of amylopectin, comprising the hot water-insoluble fractions of the IAC. These findings highlight the pleiotropic effects of Wx on the SAC and IAC. This pleiotropy indicates that these traits have a positive genetic correlation. Therefore, further studies of rice quality should use rice varieties with the same Wx genotype to eliminate the pleiotropic effects of this gene, allowing the independent relationship between the SAC or IAC and rice quality to be elucidated through a multiple correlation analysis. These findings are applicable to other valuable cereal crops as well.
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Affiliation(s)
- Hongkai Wu
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China; (S.W.); (M.W.)
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Nie S, Chen L, Zheng M, Dong J, Ma Y, Zhou L, Wang J, Chen J, Hu H, Yang T, Zhao J, Zhang S, Yang W. GWAS and Transcriptomic Analysis Identify OsRING315 as a New Candidate Gene Controlling Amylose Content and Gel Consistency in Rice. RICE (NEW YORK, N.Y.) 2024; 17:38. [PMID: 38849622 PMCID: PMC11161452 DOI: 10.1186/s12284-024-00718-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024]
Abstract
Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice.
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Affiliation(s)
- Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Minhua Zheng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China.
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5
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Sun LQ, Bai Y, Wu J, Fan SJ, Chen SY, Zhang ZY, Xia JQ, Wang SM, Wang YP, Qin P, Li SG, Xu P, Zhao Z, Xiang CB, Zhang ZS. OsNLP3 enhances grain weight and reduces grain chalkiness in rice. PLANT COMMUNICATIONS 2024:100999. [PMID: 38853433 DOI: 10.1016/j.xplc.2024.100999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
Abstract
Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.
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Affiliation(s)
- Liang-Qi Sun
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Yu Bai
- Experimental Center of Engineering and Materials Science, University of Science and Technology of China, Hefei 230027, China
| | - Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Jun Fan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Si-Yan Chen
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zheng-Yi Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Mei Wang
- Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Yu-Ping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shi-Gui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Zhong Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
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6
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Zhu M, Liu Y, Jiao G, Yu J, Zhao R, Lu A, Zhou W, Cao N, Wu J, Hu S, Sheng Z, Wei X, Zhao F, Xie L, Ahmad S, Lin Y, Shao G, Tang S, Hu P. The elite eating quality alleles Wx b and ALK b are regulated by OsDOF18 and coordinately improve head rice yield. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1582-1595. [PMID: 38245899 PMCID: PMC11123401 DOI: 10.1111/pbi.14288] [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: 11/04/2023] [Revised: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
Head rice yield (HRY) measures rice milling quality and determines final grain yield and commercial value. Here, we report that two major quantitative trait loci for milling quality in rice, qMq-1 and qMq-2, represent allelic variants of Waxylv/Waxyb (hereafter Wx) encoding Granule-Bound Starch Synthase I (GBSSI) and Alkali Spreading Value ALKc/ALKb encoding Soluble Starch Synthase IIa (SSIIa), respectively. Complementation and overexpression transgenic lines in indica and japonica backgrounds confirmed that Wx and ALK coordinately regulate HRY by affecting amylose content, the number of amylopectin branches, amyloplast size, and thus grain filling and hardness. The transcription factor OsDOF18 acts upstream of Wx and ALK by activating their transcription. Furthermore, rice accessions with Wxb and ALKb alleles showed improved HRY over those with Wxlv and ALKc. Our study not only reveals the novel molecular mechanism underlying the formation of HRY but also provides a strategy for breeding rice cultivars with improved HRY.
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Affiliation(s)
- Maodi Zhu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Yongqiang Liu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guiai Jiao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Junming Yu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Rumeng Zhao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Ao Lu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Wei Zhou
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Ni Cao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Jiamin Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Shikai Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Fengli Zhao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Lihong Xie
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & AgricultureRiyadhSaudi Arabia
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- Zhejiang LabHangzhouChina
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Peisong Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- Zhejiang LabHangzhouChina
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7
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Yang Y, Zhou L, Feng L, Jiang J, Huang L, Liu Q, Zhang Y, Zhang C, Liu Q. Deciphering the Role of Waxy Gene Mutations in Enhancing Rice Grain Quality. Foods 2024; 13:1624. [PMID: 38890853 PMCID: PMC11171567 DOI: 10.3390/foods13111624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024] Open
Abstract
Amylose content (AC) stands as a pivotal determinant of rice grain quality, primarily governed by the Waxy gene (Wx). The allelic variation within this gene, particularly the presence of the Wxmp allele derived from the ancestral Wxmq allele, significantly influences AC and is prevalent among soft japonica rice varieties in southern China. Although both alleles are associated with lower AC, there remains a paucity of detailed understanding regarding the interplay between specific functional single nucleotide polymorphisms (SNPs) within these alleles and the overarching rice grain quality. To investigate this, we engineered three distinct transgenic rice lines, each harboring the Wxmp, Wxmq, or Wxb-5c alleles in the background of the glutinous rice cultivar Nip(wx). This suite of transgenic rice lines showcased varying degrees of grain transparency inversely correlated to AC, which in turn influenced other physicochemical properties of the rice grains, such as taste value of cooked rice, gel consistency, and starch pasting properties. Additionally, analyses of gene expression and enzyme activity revealed that the functional SNPs, Ex4-53G to A and Ex5-53T to C, lead to a decline in the activity of granule-bound starch synthase I (GBSSI) without altering expression levels.
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Affiliation(s)
- Yong Yang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Lihui Zhou
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Jiangsu High Quality Rice Research and Development Center, Jiangsu Key Laboratory for Agro-Biology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Linhao Feng
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jianying Jiang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Lichun Huang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Qing Liu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Yadong Zhang
- Jiangsu High Quality Rice Research and Development Center, Jiangsu Key Laboratory for Agro-Biology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Changquan Zhang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China; (Y.Y.); (L.Z.); (L.F.); (J.J.); (L.H.); (Q.L.); (Q.L.)
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
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8
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Gaur VS, Sood S, Guzmán C, Olsen KM. Molecular insights on the origin and development of waxy genotypes in major crop plants. Brief Funct Genomics 2024; 23:193-213. [PMID: 38751352 DOI: 10.1093/bfgp/elad035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 06/14/2024] Open
Abstract
Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.
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Affiliation(s)
- Vikram S Gaur
- Raja Bhoj College of Agriculture, Balaghat, JNKVV, Jabalpur, Madhya Pradesh, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla- 171001, Himachal Pradesh, India
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, CeiA3, ES-14071, Córdoba, Spain
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9
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Tang W, Chen H, Zhang S, Tang J, Lin J, Fang X, Chen G, Zhang Y. A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:745. [PMID: 38475591 DOI: 10.3390/plants13050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wxb and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs.
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Affiliation(s)
- Weijie Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Haiyuan Chen
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Suobing Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jun Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jing Lin
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Xianwen Fang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunhui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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10
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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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11
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Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. Multi-model genome-wide association studies for appearance quality in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1304388. [PMID: 38273959 PMCID: PMC10808671 DOI: 10.3389/fpls.2023.1304388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024]
Abstract
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
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Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, International Crop Reseach Institute for Semi Arid Tropics (ICRISAT), Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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12
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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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13
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Jiang J, Song S, Hu C, Jing C, Xu Q, Li X, Zhang M, Hai M, Shen J, Zhang Y, Wang D, Dang X. QTL Detection and Candidate Gene Identification for Eating and Cooking Quality Traits in Rice ( Oryza sativa L.) via a Genome-Wide Association Study. Int J Mol Sci 2024; 25:630. [PMID: 38203801 PMCID: PMC10779416 DOI: 10.3390/ijms25010630] [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: 11/20/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
The eating and cooking quality (ECQ) directly affects the taste of rice, being closely related to factors such as gelatinization temperature (GT), gel consistency (GC) and amylose content (AC). Mining the quantitative trait loci (QTLs), and gene loci controlling ECQ-related traits is vital. A genome-wide association study on ECQ-related traits was conducted, combining 1.2 million single nucleotide polymorphisms (SNPs) with the phenotypic data of 173 rice accessions. Two QTLs for GT, one for GC and five for AC were identified, of which two were found in previously reported genes, and six were newly found. There were 28 positional candidate genes in the region of qAC11. Based on a linkage disequilibrium (LD) analysis, three candidate genes were screened within the LD region associated with AC. There were significant differences between the haplotypes of LOC_Os11g10170, but no significant differences were found for the other two genes. The qRT-PCR results showed that the gene expression levels in the accessions with high ACs were significantly larger than those in the accessions with low ACs at 35d and 42d after flowering. Hap 2 and Hap 3 of LOC_Os11g10170 reduced the AC by 13.09% and 10.77%, respectively. These results provide a theoretical and material basis for improving the ECQ of rice.
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Affiliation(s)
- Jianhua Jiang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shaojie Song
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Changmin Hu
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chunyu Jing
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Qing Xu
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinru Li
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mengyuan Zhang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mei Hai
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jiaming Shen
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Ying Zhang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Dezheng Wang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaojing Dang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
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14
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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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15
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Zhang C, Liu Q, Liu Q. Sake or supper? Breeding rice for culinary excellence and optimal brewing. MOLECULAR PLANT 2023; 16:1879-1881. [PMID: 37853690 DOI: 10.1016/j.molp.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Affiliation(s)
- Changquan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
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16
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Xiong R, Tan X, Yang T, Wang H, Pan X, Zeng Y, Zhang J, Zeng Y. Starch multiscale structure and physicochemical property alterations in high-quality indica rice quality and cooked rice texture under different nitrogen panicle fertilizer applications. Int J Biol Macromol 2023; 252:126455. [PMID: 37633549 DOI: 10.1016/j.ijbiomac.2023.126455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/08/2023] [Accepted: 08/20/2023] [Indexed: 08/28/2023]
Abstract
The starch multiscale structure, physiochemical properties, grain quality and cooked rice texture of high-quality early and late indica were analyzed under nitrogen panicle fertilizer (low panicle fertilizer, LPF; middle panicle fertilizer, MPF; high panicle fertilizer, HPF) treatments and their internal relations were investigated. Compared to the MPF treatment, the starch granules in HPF and LPF had more surface-proteins and irregular voids for high-quality early and late indica rice cultivars, respectively. Nitrogen panicle fertilization application increased amylopectin medium and long chains as well as protein content, resulting in higher relative crystallinity and gelatinization temperatures. Moderate changes in starch multistructures and physicochemical properties such as branching degree, amylopectin medium chain, and pasting viscosities derived from MPF treatment significantly improved processing, appearance qualities and cooked rice texture. Additionally, the decrease in starch branching, gelatinization temperatures, and granule uniformity along with an increase in large granules, breakdown, and △Hgel under MPF treatment were the main reasons for improving rice textural properties.
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Affiliation(s)
- Ruoyu Xiong
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xueming Tan
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Taotao Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Haixia Wang
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaohua Pan
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yongjun Zeng
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanhua Zeng
- Ministry of Education and Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China.
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17
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Duan H, Li J, Sun L, Xiong X, Xu S, Sun Y, Ju X, Xue Z, Gao J, Wang Y, Xie H, Ding D, Zhang X, Tang J. Identification of novel loci associated with starch content in maize kernels by a genome-wide association study using an enlarged SNP panel. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:91. [PMID: 38099287 PMCID: PMC10716104 DOI: 10.1007/s11032-023-01437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
Starch is a major component of cereals, comprising over 70% of dry weight. It serves as a primary carbon source for humans and animals. In addition, starch is an indispensable industrial raw material. While maize (Zea mays) is a key crop and the primary source of starch, the genetic basis for starch content in maize kernels remains poorly understood. In this study, using an enlarged panel, we conducted a genome-wide association study (GWAS) based on best linear unbiased prediction (BLUP) value for starch content of 261 inbred lines across three environments. Compared with previous study, we identified 14 additional significant quantitative trait loci (QTL), encompassed a total of 42 genes, and indicated that increased marker density contributes to improved statistical power. By integrating gene expression profiling, Gene Ontology (GO) enrichment and haplotype analysis, several potential target genes that may play a role in regulating starch content in maize kernels have been identified. Notably, we found that ZmAPC4, associated with the significant SNP chr4.S_175584318, which encodes a WD40 repeat-like superfamily protein and is highly expressed in maize endosperm, might be a crucial regulator of maize kernel starch synthesis. Out of the 261 inbred lines analyzed, they were categorized into four haplotypes. Remarkably, it was observed that the inbred lines harboring hap4 demonstrated the highest starch content compared to the other haplotypes. Additionally, as a significant achievement, we have developed molecular markers that effectively differentiate maize inbred lines based on their starch content. Overall, our study provides valuable insights into the genetic basis of starch content and the molecular markers can be useful in breeding programs aimed at developing maize varieties with high starch content, thereby improving breeding efficiency. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01437-6.
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Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaolong Ju
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhengjie Xue
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Wang
- Zhucheng Mingjue Tender Company Limited, Weifang, China
| | - Huiling Xie
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Department of Agronomy, Henan Agricultural University, Agricultural Road No. 63, Zhengzhou, 450002 China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
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18
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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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19
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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: 2] [Impact Index Per Article: 2.0] [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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20
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Gu Z, Gong J, Zhu Z, Li Z, Feng Q, Wang C, Zhao Y, Zhan Q, Zhou C, Wang A, Huang T, Zhang L, Tian Q, Fan D, Lu Y, Zhao Q, Huang X, Yang S, Han B. Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis. Nat Genet 2023; 55:1745-1756. [PMID: 37679493 PMCID: PMC10562254 DOI: 10.1038/s41588-023-01495-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica-indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica-japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.
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Affiliation(s)
- Zhoulin Gu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zhou Zhu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Li
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Zhan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Congcong Zhou
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ahong Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yiqi Lu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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21
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Praphasanobol P, Purnama PR, Junbuathong S, Chotechuen S, Moung-Ngam P, Kasettranan W, Paliyavuth C, Comai L, Pongpanich M, Buaboocha T, Chadchawan S. Genome-Wide Association Study of Starch Properties in Local Thai Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3290. [PMID: 37765454 PMCID: PMC10535886 DOI: 10.3390/plants12183290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Rice (Oryza sativa L.) is the main source of energy for humans and a staple food of high cultural significance for much of the world's population. Rice with highly resistant starch (RS) is beneficial for health and can reduce the risk of disease, especially type II diabetes. The identification of loci affecting starch properties will facilitate breeding of high-quality and health-supportive rice. A genome-wide association study (GWAS) of 230 rice cultivars was used to identify candidate loci affecting starch properties. The apparent amylose content (AAC) among rice cultivars ranged from 7.04 to 33.06%, and the AAC was positively correlated with RS (R2 = 0.94) and negatively correlated with rapidly available glucose (RAG) (R2 = -0.73). Three loci responsible for starch properties were detected on chromosomes 1, 6, and 11. On chromosome 6, the most significant SNP corresponded to LOC_Os06g04200 which encodes granule-bound starch synthase I (GBSSI) or starch synthase. Two novel loci associated with starch traits were LOC_Os01g65810 and LOC_Os11g01580, which encode an unknown protein and a sodium/calcium exchanger, respectively. The markers associated with GBSSI and LOC_Os11g01580 were tested in two independent sets of rice populations to confirm their effect on starch properties. The identification of genes associated with starch traits will further the understanding of the molecular mechanisms affecting starch in rice and may be useful in the selection of rice varieties with improved starch.
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Affiliation(s)
- Parama Praphasanobol
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Putut Rakhmad Purnama
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supaporn Junbuathong
- Pathum Thani Rice Research Center, Ministry of Agriculture and Cooperatives, Thanyaburi, Pathum Thani 12110, Thailand; (S.J.); (P.M.-N.)
| | - Somsong Chotechuen
- Division of Rice Research and Development, Rice Department, Ministry of Agriculture and Cooperatives, Bangkok 10900, Thailand;
| | - Peerapon Moung-Ngam
- Pathum Thani Rice Research Center, Ministry of Agriculture and Cooperatives, Thanyaburi, Pathum Thani 12110, Thailand; (S.J.); (P.M.-N.)
| | - Waraluk Kasettranan
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (W.K.); (C.P.)
| | - Chanita Paliyavuth
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (W.K.); (C.P.)
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA;
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Teerapong Buaboocha
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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22
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Yoshida H, Okada S, Wang F, Shiota S, Mori M, Kawamura M, Zhao X, Wang Y, Nishigaki N, Kobayashi A, Miura K, Yoshida S, Ikegami M, Ito A, Huang LT, Caroline Hsing YI, Yamagata Y, Morinaka Y, Yamasaki M, Kotake T, Yamamoto E, Sun J, Hirano K, Matsuoka M. Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice. MOLECULAR PLANT 2023; 16:1460-1477. [PMID: 37674315 DOI: 10.1016/j.molp.2023.09.002] [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: 12/11/2022] [Revised: 08/17/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
Improving grain quality is a primary objective in contemporary rice breeding. Japanese modern rice breeding has developed two different types of rice, eating and sake-brewing rice, with different grain characteristics, indicating the selection of variant gene alleles during the breeding process. Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding, we conducted genome scans for divergence, genome-wide association studies, and map-based cloning. Consequently, we successfully identified two genes, OsMnS and OsWOX9D, both contributing to rice grain traits. OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm, a desirable trait for sake brewing but decreases the grain appearance quality. OsWOX9D encodes a grass-specific homeobox-containing transcription factor, which enhances grain width for better sake brewing. Furthermore, haplotype analysis revealed that their defective alleles were selected in East Asia, but not Europe, during modern improvement. In addition, our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection. This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits, based on the concept of "breeding-assisted genomics" in plants.
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Affiliation(s)
- Hideki Yoshida
- Institute of Fermentation Sciences, Fukushima University, Fukushima 960-1248, Japan
| | - Satoshi Okada
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo 675-2103, Japan
| | - Fanmiao Wang
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; Research Center of Genetic Resources, NARO, 2-1-1 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Shohei Shiota
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masaki Mori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mayuko Kawamura
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Xue Zhao
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Yiqiao Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Naho Nishigaki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Asako Kobayashi
- Fukui Agricultural Experiment Station, Fukui 918-8215, Japan
| | - Kotaro Miura
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Shinya Yoshida
- Hyogo Prefectural Research Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan; Research Institute for Food and Agriculture, Ryukoku University, Ootsu, Shiga 520-2194, Japan
| | - Masaru Ikegami
- Hyogo Prefectural Research Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan
| | - Akitoshi Ito
- Food Research Centre, Aichi Centre for Industry and Science Technology, 2-1-1 Shimpukuji-cho, Nagoya, Aichi 451-0083, Japan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, China; Department of Agronomy, National Taiwan University, Taipei, Taiwan, China
| | - Yue-Ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, China; Department of Agronomy, National Taiwan University, Taipei, Taiwan, China
| | - Yoshiyuki Yamagata
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, 744, Motooka, Nishiku, Fukuoka, Japan
| | - Yoichi Morinaka
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo 675-2103, Japan
| | - Toshihisa Kotake
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Makoto Matsuoka
- Institute of Fermentation Sciences, Fukushima University, Fukushima 960-1248, Japan.
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23
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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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24
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Huang L, Liu Q. High-resistant starch crops for human health. Proc Natl Acad Sci U S A 2023; 120:e2305990120. [PMID: 37216520 PMCID: PMC10235962 DOI: 10.1073/pnas.2305990120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Affiliation(s)
- Lichun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou225009, China
- Zhongshan Biological Breeding Laboratory, Nanjing210014, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou225009, China
- Zhongshan Biological Breeding Laboratory, Nanjing210014, China
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25
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Lu Y, Lv D, Zhou L, Yang Y, Hao W, Huang L, Fan X, Zhao D, Li Q, Zhang C, Liu Q. Combined effects of SSII-2RNAi and different Wx alleles on rice grain transparency and physicochemical properties. Carbohydr Polym 2023; 308:120651. [PMID: 36813343 DOI: 10.1016/j.carbpol.2023.120651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Near-isogenic lines Nip(Wxb/SSII-2), Nip(Wxb/ss2-2), Nip(Wxmw/SSII-2), Nip(Wxmw/ss2-2), Nip(Wxmp/SSII-2) and Nip(Wxmp/ss2-2) in the Nipponbare (Nip) background containing the SSII-2RNAi cassette combined with different Waxy (Wx) alleles were investigated in terms of rice grain transparency and quality profiles. Rice lines carrying the SSII-2RNAi cassette displayed downregulation of SSII-2, SSII-3 and Wx genes. Introduction of the SSII-2RNAi cassette decreased apparent amylose content (AAC) in all transgenic lines, but grain transparency differed between low AAC rice lines. Grains from Nip(Wxb/SSII-2) and Nip(Wxb/ss2-2) were transparent, while those of rice were increasingly translucent with decreasing moisture due to cavities within starch granules. Rice grain transparency was positively correlated with grain moisture and AAC, but negatively correlated with cavity area within starch granules. Starch fine structure analysis revealed a marked increase in short amylopectin chains with DP 6-12, but a decrease in intermediate chains with DP 13-24, resulting in decreased gelatinisation temperature. Starch crystalline structure analysis showed that the transgenic rice starches have lower crystallinity and lamellar repeat distance than controls due to differences in starch fine structure. The results highlight the molecular basis underpinning rice grain transparency, and provide strategies for improving rice grain transparency.
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Affiliation(s)
- Yan Lu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Dongjing Lv
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Lian Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yong Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Weizhuo Hao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Lichun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiaolei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Dongsheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, 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/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/State Key Laboratory of Hybrid Rice/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
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26
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Wang A, Jing Y, Cheng Q, Zhou H, Wang L, Gong W, Kou L, Liu G, Meng X, Chen M, Ma H, Shu X, Yu H, Wu D, Li J. Loss of function of SSIIIa and SSIIIb coordinately confers high RS content in cooked rice. Proc Natl Acad Sci U S A 2023; 120:e2220622120. [PMID: 37126676 PMCID: PMC10175802 DOI: 10.1073/pnas.2220622120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/28/2023] [Indexed: 05/03/2023] Open
Abstract
The sedentary lifestyle and refined food consumption significantly lead to obesity, type 2 diabetes, and related complications, which have become one of the major threats to global health. This incidence could be potentially reduced by daily foods rich in resistant starch (RS). However, it remains a challenge to breed high-RS rice varieties. Here, we reported a high-RS mutant rs4 with an RS content of ~10.8% in cooked rice. The genetic study revealed that the loss-of-function SSIIIb and SSIIIa together with a strong Wx allele in the background collaboratively contributed to the high-RS phenotype of the rs4 mutant. The increased RS contents in ssIIIa and ssIIIa ssIIIb mutants were associated with the increased amylose and lipid contents. SSIIIb and SSIIIa proteins were functionally redundant, whereas SSIIIb mainly functioned in leaves and SSIIIa largely in endosperm owing to their divergent tissue-specific expression patterns. Furthermore, we found that SSIII experienced duplication in different cereals, of which one SSIII paralog was mainly expressed in leaves and another in the endosperm. SSII but not SSIV showed a similar evolutionary pattern to SSIII. The copies of endosperm-expressed SSIII and SSII were associated with high total starch contents and low RS levels in the seeds of tested cereals, compared with low starch contents and high RS levels in tested dicots. These results provided critical genetic resources for breeding high-RS rice cultivars, and the evolutionary features of these genes may facilitate to generate high-RS varieties in different cereals.
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Affiliation(s)
- Anqi Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Yanhui Jing
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Qiao Cheng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Hongju Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Lijun Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Wanxin Gong
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou310029, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Haiyan Ma
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Xiaoli Shu
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou310029, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Dianxing Wu
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou310029, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
- Yazhou Bay Laboratory, Sanya572025, China
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27
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Generating waxy rice starch with target type of amylopectin fine structure and gelatinization temperature by waxy gene editing. Carbohydr Polym 2023; 306:120595. [PMID: 36746586 DOI: 10.1016/j.carbpol.2023.120595] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/31/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
Waxy rice, which lacks amylose, is an important variant in rice, and its starches have been widely used. New waxy rice varieties generated via the CRISPR/Cas9 gene-editing system is described. Herein, four waxy rice starches with different physicochemical properties were successfully obtained by the CRISPR/Cas9 editing Waxy (Wx) gene. The results showed that the amylose content (AC) of wx mutant starches ranged from 0.26 to 1.78 %, and CZBwx1 starches had the best gel consistency and highest water solubility among all wx mutants. Mutations of Wxb allele produced more short-chains (degree of chain polymerization (DP) 6-11), and less medium- and long-chains (DP12-70) than that of Wxa, while the AC of Wxa allele mutants was higher than the mutations of Wxb allele. The gelatinization temperature (GT) of wxa mutant starches was higher than that of wxb mutant starches. Moreover, we found that the GT and amylopectin fine structure type of waxy rice starch did not change after Wx gene editing. Based on these findings, it is possible to produce waxy rice starch with different physicochemical properties, containing target GT and chain length distributions of amylopectin.
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28
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Tiozon RJN, Fettke J, Sreenivasulu N, Fernie AR. More than the main structural genes: Regulation of resistant starch formation in rice endosperm and its potential application. JOURNAL OF PLANT PHYSIOLOGY 2023; 285:153980. [PMID: 37086697 DOI: 10.1016/j.jplph.2023.153980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
In the past decade, research on resistant starch has evoked interest due to the prevention and inhibition of chronic human diseases, such as diabetes, cancer, and obesity. Increasing the amylose content (AC) and resistant starch (RS) has been pivotal in improving the nutritional benefit of rice. However, the exact mechanism of RS formation is complex due to interconnected genetic factors regulating amylose-amylopectin variation. In this review, we discussed the regulatory factors influencing the RS formation centered on the transcription, post-transcriptional, and post-translational processes. Furthermore, we described the developments in RS and AC levels in rice compared with other high RS cereals. Briefly, we enumerated potential applications of high RS mutants in health, medical, and other industries. We contest that the information captured herein can be deployed for marker-assisted breeding and precision breeding techniques through genome editing to improve rice varieties with enhanced RS content.
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Affiliation(s)
- Rhowell Jr 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
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Nese Sreenivasulu
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños, 4030, Philippines
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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29
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Hong J, Rosental L, Xu Y, Xu D, Orf I, Wang W, Hu Z, Su S, Bai S, Ashraf M, Hu C, Zhang C, Li Z, Xu J, Liu Q, Zhang H, Zhang F, Luo Z, Chen M, Chen X, Betts N, Fernie A, Liang W, Chen G, Brotman Y, Zhang D, Shi J. Genetic architecture of seed glycerolipids in Asian cultivated rice. PLANT, CELL & ENVIRONMENT 2023; 46:1278-1294. [PMID: 35698268 DOI: 10.1111/pce.14378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. We demonstrated that allelic variation in OsLP1 sequence between indica and japonica results in different enzymatic preference for substrate PC-16:0/16:0 and different saturated TAG levels. Further evidence demonstrated that OsLP1 also affects heading date, and that co-selection of OsLP1 and a flooding-tolerant QTL in Aus results in the abundance of saturated TAGs associated with flooding tolerance. Moreover, we revealed that the sequence polymorphisms in Waxy has pleiotropic effects on lyso-PC and amylose content. We proposed that rice seed glycerolipids have been unintentionally shaped during natural and artificial selection for adaptive or import seed quality traits. Collectively, our findings provide valuable genetic resources for rice improvement and evolutionary insights into seed glycerolipid variations in rice.
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Affiliation(s)
- Jun Hong
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Leah Rosental
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Dawei Xu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Wengsheng Wang
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Hu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Su Su
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoxing Bai
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mohammed Ashraf
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoyang Hu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changquan Zhang
- Department of Agronomy, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Zhikang Li
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Xu
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoquan Liu
- Department of Agronomy, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Hui Zhang
- Department of Plant Science, School of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Fengli Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijing Luo
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingjiao Chen
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Chen
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Natalie Betts
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Alisdair Fernie
- Department of Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wanqi Liang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Dabing Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jianxin Shi
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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30
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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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31
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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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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [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: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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Kumari A, Sharma D, Sharma P, Wang C, Verma V, Patil A, Imran M, Singh MP, Kumar K, Paritosh K, Caragea D, Kapoor S, Chandel G, Grover A, Jagadish SVK, Katiyar-Agarwal S, Agarwal M. Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1133115. [PMID: 36968399 PMCID: PMC10031497 DOI: 10.3389/fpls.2023.1133115] [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: 12/28/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.
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Affiliation(s)
- Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Divya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Sahil
- Department of Botany, University of Delhi, Delhi, India
| | - Chaoxin Wang
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Vibha Verma
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Arun Patil
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Md Imran
- Department of Botany, University of Delhi, Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kuldeep Kumar
- National Institute for Plant Biotechnology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, New Delhi, India
| | - Doina Caragea
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Girish Chandel
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | | | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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Dietary Fibre Impacts the Texture of Cooked Whole Grain Rice. Foods 2023; 12:foods12040899. [PMID: 36832977 PMCID: PMC9957187 DOI: 10.3390/foods12040899] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Consumers' general preference for white rice over whole grain rice stems from the hardness and low palatability of cooked whole grain rice; however, strong links have been found between consuming a large amount of white rice, leading a sedentary lifestyle, and acquiring type 2 diabetes. This led us to formulate a new breeding goal to improve the softness and palatability of whole grain rice while promoting its nutritional value. In this study, the association between dietary fibre profiles (using an enzymatic method combined with high-performance liquid chromatography) and textural properties of whole grain rice (using a texture analyser) was observed. The results showed that a variation in the ratio of soluble dietary fibre (SDF) and insoluble dietary fibre (IDF) influenced the textural characteristics of cooked whole grain rice; found a strong association between SDF to IDF ratio and hardness (r = -0.74, p < 0.01) or gumminess (r = -0.69, p < 0.01) of cooked whole grain rice, and demonstrated that the SDF to IDF ratio was also moderately correlated with cohesiveness (r = -0.45, p < 0.05), chewiness (r = -0.55, p < 0.01), and adhesiveness (r = 0.45, p < 0.05) of cooked whole grain rice. It is suggested that the SDF to IDF ratio can be used as a biomarker for breeding soft and highly palatable whole grain rice of cultivated tropical indica rice to achieve consumer well-being. Lastly, a simple modified method from the alkaline disintegration test was developed for high-throughput screening of dietary fibre profiles in the whole grain indica rice samples.
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35
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Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
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36
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Ma B, Zhang L, He Z. Understanding the regulation of cereal grain filling: The way forward. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:526-547. [PMID: 36648157 DOI: 10.1111/jipb.13456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.
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Affiliation(s)
- Bin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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37
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Fan P, Xu J, Wang Z, Liu G, Zhang Z, Tian J, Wei H, Zhang H. Phenotypic differences in the appearance of soft rice and its endosperm structural basis. FRONTIERS IN PLANT SCIENCE 2023; 14:1074148. [PMID: 36818874 PMCID: PMC9929301 DOI: 10.3389/fpls.2023.1074148] [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: 10/19/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
In view of the significant differences among genotypes in the appearance of soft rice, it is necessary to conduct research on the differences in the appearance quality of soft rice and their mechanisms. It can provide a theoretical basis for the selection and breeding of superior appearance varieties at a later stage. In order to clarify the differences in appearance phenotypes between different soft rice genotypes and structural basis of endosperm structures behind the differences, four soft rice varieties were selected in this study, including two varieties with good-appearance and two varieties with cloudy appearance. The differences in appearance phenotypes and endosperm structure in mature grains of soft rice with different appearance phenotypes were scientifically analyzed. The development process of their endosperm differences at the filling stage was investigated. The results show that the difference in the rice appearance of soft rice varieties mainly lay in the chalk-free seed transparency and chalkiness. These differences were caused by two completely different types of endosperm structure. Fewer and smaller starch grain cavities were responsible for higher chalk-free transparency of soft rice grains, denser starch granules arrangement caused lower chalkiness of soft rice grains. Ten days after flowering, the starch granules in the back and heart of good-appearance soft rice were already significantly fuller and more closely packed than those of cloudy soft rice. At the same time, the number and area of starch granule holes were significantly smaller than those of cloudy soft rice. This difference gradually increased until maturity. Therefore, based on appearance evaluation, soft rice with good-appearance should have higher transparency and lower chalkiness. The endosperm starch granules should be full and tightly arranged. The number of starch grain cavities and the area should be smaller. These differences develop in the early stages of grouting and gradually increase.
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Affiliation(s)
| | | | | | | | | | | | - Haiyan Wei
- *Correspondence: Haiyan Wei, ; Hongcheng Zhang,
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38
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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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39
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Ye J, Zhang M, Yuan X, Hu D, Zhang Y, Xu S, Li Z, Li R, Liu J, Sun Y, Wang S, Feng Y, Xu Q, Yang Y, Wei X. Genomic insight into genetic changes and shaping of major inbred rice cultivars in China. THE NEW PHYTOLOGIST 2022; 236:2311-2326. [PMID: 36114658 DOI: 10.1111/nph.18500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/25/2022] [Indexed: 05/28/2023]
Abstract
The annual planting area of major inbred rice (Oryza sativa) cultivars reach more than half of the total annual planting area of inbred rice cultivars in China. However, how the major inbred rice cultivars changed during decades of genetic improvement and why they can be prevalently cultivated in China remains unclear. Here, we investigated the underlying genetic changes of major inbred cultivars and the contributions of landraces and introduced cultivars during the improvement by resequencing a collection of 439 rice accessions including major inbred cultivars, landraces, and introduced cultivars. The results showed that landraces were the main genetic contribution sources of major inbred Xian (Indica) cultivars, while introduced cultivars were that of major inbred Geng (Japonica) cultivars. Selection scans and haplotype frequency analysis shed light on the reflections of some well-known genes in rice improvement, and breeders had different preferences for the Xian's and Geng's breeding. Six candidate regions associated with agronomic traits were identified by genome-wide association mapping, five of which were under positive selection in rice improvement. Our study provides a comprehensive insight into the development of major inbred rice cultivars and lays the foundation for genomics-based breeding in rice.
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Affiliation(s)
- Junhua Ye
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Mengchen Zhang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaoping Yuan
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dongxiu Hu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yuanyuan Zhang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Siliang Xu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhen Li
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ruosi Li
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Junrong Liu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yanfei Sun
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shan Wang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yue Feng
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qun Xu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yaolong Yang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xinghua Wei
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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40
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Zhang Q, Zhang S, Yu X, Wei X, Huang X, Zhou X. Fine-tuning grain amylose contents by genome editing of Waxy cis-regulatory region in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:72. [PMID: 37313325 PMCID: PMC10248690 DOI: 10.1007/s11032-022-01342-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/12/2022] [Indexed: 06/15/2023]
Abstract
Rice grain amylose contents (ACs) is a key quantitative trait influencing eating and cooking quality. Regulating the expression level of Waxy, a key gene controlling ACs, and in turn fine-tuning the grain ACs, is an ideal approach to improve grain quality of rice varieties. Based on CRISPR/Cas9 genome editing technology, we designed eight targets in the cis-regulatory region of Wxa background, screened phenotypic changes of the transgenic lines and generated eight novel Waxy alleles with altered grain ACs. Among the eight alleles, we found that a 407-bp non-homologous substitution (NHS) in the 5'UTR-intron caused by genome editing regulated Waxy expression and decreased grain ACs by 2.9%. Moreover, embedding the 407-bp NHS into the cis-regulatory region of Wxb allele can also affect gene activity. Our work suggested the effect of 5'UTR-intron on Waxy gene expression regulation, and provided a potentially useful allele in breeding that can finely adjust rice grain ACs.
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Affiliation(s)
- Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Sinan Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xiting Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234 China
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41
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Izawa T. Reloading DNA History in Rice Domestication. PLANT & CELL PHYSIOLOGY 2022; 63:1529-1539. [PMID: 35656860 PMCID: PMC9680854 DOI: 10.1093/pcp/pcac073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Although crop domestication is a prehistoric event, DNA (or genome) sequences of modern cultivars and the accession lines of wild relatives contain information regarding the history of crop domestication and the breeding process. Accordingly, with plentiful genomic data, many new findings have been obtained concerning the crop domestication process, for which various (some controversial) interpretations exist. Since approximately 20 years ago, dozens of quantitative trait genes (QTGs) related to the domestication process have been cloned from several crops including rice, a global staple food. However, the determination of how and when these QTGs were involved in rice domestication requires a precise understanding of the DNA code. In addition to the identification of domestication-related QTGs, large-scale rice genome analysis based on short-read Illumina data (but with shallow depth) including more than 1,000 rice cultivars and hundreds of wild rice (or Oryza rufipogon) lines, along with extensive genome analysis including more than 3,000 cultivars with sufficient Illumina data, has been reported. From these data, the genome-wide changes during rice domestication have been explained. However, these genome-wide changes were not interpreted based on QTG changes for domestication-related traits during rice domestication. In addition, a substantial gap remains between the archeological hypothesis based on ancient relics and findings from DNA variations among current cultivars. Thus, this review reconsiders the present status of rice domestication research from a biologist's perspective.
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42
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Cao R, Zhao S, Jiao G, Duan Y, Ma L, Dong N, Lu F, Zhu M, Shao G, Hu S, Sheng Z, Zhang J, Tang S, Wei X, Hu P. OPAQUE3, encoding a transmembrane bZIP transcription factor, regulates endosperm storage protein and starch biosynthesis in rice. PLANT COMMUNICATIONS 2022; 3:100463. [PMID: 36258666 PMCID: PMC9700205 DOI: 10.1016/j.xplc.2022.100463] [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: 06/08/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 05/11/2023]
Abstract
Starch and storage proteins are the main components of rice (Oryza sativa L.) grains. Despite their importance, the molecular regulatory mechanisms of storage protein and starch biosynthesis remain largely elusive. Here, we identified a rice opaque endosperm mutant, opaque3 (o3), that overaccumulates 57-kDa proglutelins and has significantly lower protein and starch contents than the wild type. The o3 mutant also has abnormal protein body structures and compound starch grains in its endosperm cells. OPAQUE3 (O3) encodes a transmembrane basic leucine zipper (bZIP) transcription factor (OsbZIP60) and is localized in the endoplasmic reticulum (ER) and the nucleus, but it is localized mostly in the nucleus under ER stress. We demonstrated that O3 could activate the expression of several starch synthesis-related genes (GBSSI, AGPL2, SBEI, and ISA2) and storage protein synthesis-related genes (OsGluA2, Prol14, and Glb1). O3 also plays an important role in protein processing and export in the ER by directly binding to the promoters and activating the expression of OsBIP1 and PDIL1-1, two major chaperones that assist with folding of immature secretory proteins in the ER of rice endosperm cells. High-temperature conditions aggravate ER stress and result in more abnormal grain development in o3 mutants. We also revealed that OsbZIP50 can assist O3 in response to ER stress, especially under high-temperature conditions. We thus demonstrate that O3 plays a central role in rice grain development by participating simultaneously in the regulation of storage protein and starch biosynthesis and the maintenance of ER homeostasis in endosperm cells.
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Affiliation(s)
- Ruijie Cao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaolu Zhao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China; Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yingqing Duan
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Liuyang Ma
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Nannan Dong
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Feifei Lu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Mingdong Zhu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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Relation of cooked rice texture to starch structure and physicochemical properties under different nitrogen managements. Carbohydr Polym 2022; 295:119882. [DOI: 10.1016/j.carbpol.2022.119882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 11/20/2022]
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44
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Li Y, Yang Z, Yang C, Liu Z, Shen S, Zhan C, Lyu Y, Zhang F, Li K, Shi Y, Zhou J, Liu X, Fang C, Fernie AR, Li J, Luo J. The NET locus determines the food taste, cooking and nutrition quality of rice. Sci Bull (Beijing) 2022; 67:2045-2049. [PMID: 36546101 DOI: 10.1016/j.scib.2022.09.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/24/2022] [Accepted: 09/13/2022] [Indexed: 01/07/2023]
Affiliation(s)
- Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhuang Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chenkun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Zhenhuan Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Shuangqian Shen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yuanyuan Lyu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Feng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kang Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yuheng Shi
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Junjie Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xianqing Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chuanying Fang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Jie Li
- John Innes Centre, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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45
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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: 9] [Impact Index Per Article: 4.5] [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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Zhao G, Xie S, Zong S, Wang T, Mao C, Shi J, Li J. Mutation of TL1, encoding a novel C 2H 2 zinc finger protein, improves grains eating and cooking quality in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3531-3543. [PMID: 35994056 DOI: 10.1007/s00122-022-04198-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/09/2022] [Indexed: 05/02/2023]
Abstract
The cloning and characterization of a novel C2H2 zinc finger protein that affects rice eating and cooking quality by regulating amylose content and amylopectin chain-length distribution in rice. One of the major objectives in rice breeding aims to increase simultaneously yield and grain quality especially eating and cooking quality (ECQ). Controlling amylose content (AC) and amylopectin chain-length distribution (ACLD) in rice is a major strategy for improving rice ECQ. Previous studies show that some starch synthesis-related genes (SSRGs) are required for normal AC and ACLD, but its underlying regulating network is still unclear. Here, we report the cloning and characterization of a novel C2H2 zinc finger protein TL1 (Translucent endosperm 1) that positively regulates amylose synthesis in rice grains. Loss of TL1 function reduced apparent amylose content (AAC), total starch, gel consistency, and gelatinisation temperature, whereas increased viscosity, total lipid, and ratio of amylopectin A chains with degree of polymerization (DP) 6-12 to B1 chains with DP 13-24, resulting in an enhanced grain ECQ. The improved ECQ was accompanied by altered expression patterns of several tested SSRGs in tl1 mutant grains. Furthermore, knockout of TL1 in the high-yielding rice variety JiaHua NO.1 reduced AAC without obvious side effects on major agronomic traits. These findings expand our understanding of the regulating networks of grain starch metabolism and provide new insights into how rice ECQ quality can be improved via genetic approach.
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Affiliation(s)
- Guochao Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Shuifeng Xie
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Shipeng Zong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Tong Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chanjuan Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianyue Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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47
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Zhang Y, Zhao J, Hu Y, Zhang Y, Ying Y, Xu F, Bao J. Combined Effects of Different Alleles of FLO2, Wx and SSIIa on the Cooking and Eating Quality of Rice. PLANTS 2022; 11:plants11172249. [PMID: 36079631 PMCID: PMC9460582 DOI: 10.3390/plants11172249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/15/2023]
Abstract
The improvement of the cooking and eating quality (CEQ) of rice is one of the major objectives of current rice-breeding programs. A few major genes such as Waxy (Wx) and starch synthase IIa (SSIIa) have been successfully applied in molecular breeding. However, their interactive effects on CEQ have not been fully understood. In this study, a recombinant inbred line (RIL) population was constructed by crossing the white-core mutant GM645 with the transparent phenotype of the japonica rice variety Tainung 67 (TN67). GM645 and TN67 contain different alleles of FLOURY ENDOSPERM2 (FLO2), Wx, and SSIIa. The effects of different allele combinations of FLO2, Wx, and SSIIa on the CEQ of rice were investigated. The inbred lines with the mutation allele flo2 had a significantly lower apparent amylose content (AAC), viscosity characteristics except for setback (SB), and gel texture properties compared to those lines with the FLO2 allele. The allelic combination of FLO2 and Wx significantly affected the AAC, breakdown (BD), and gel textural properties, which could explain most of the variations in those rice quality traits that were correlated with AAC. The allelic combination of FLO2 and SSIIa significantly affected the hot paste viscosity (HPV) and pasting temperature (PT). The Wx × SSIIa interaction had a significant effect on the PT. The interaction of FLO2, Wx and SSIIa significantly affected the AAC, cold paste viscosity (CPV), PT, and consistency viscosity (CS). These results highlight the important roles of these quality-related genes in regulating the CEQ of rice and provide new clues for rice-quality improvement by marker-assisted selection.
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Affiliation(s)
- Yu Zhang
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
| | - Jiajia Zhao
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yaqi Hu
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yanni Zhang
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yining Ying
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Feifei Xu
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
- Correspondence:
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Wang X, Wang W, Tai S, Li M, Gao Q, Hu Z, Hu W, Wu Z, Zhu X, Xie J, Li F, Zhang Z, Zhi L, Zhang F, Ma X, Yang M, Xu J, Li Y, Zhang W, Yang X, Chen Y, Zhao Y, Fu B, Zhao X, Li J, Wang M, Yue Z, Fang X, Zeng W, Yin Y, Zhang G, Xu J, Zhang H, Li Z, Li Z. Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding. J Adv Res 2022; 42:1-16. [PMID: 35988902 PMCID: PMC9788959 DOI: 10.1016/j.jare.2022.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/28/2022] [Accepted: 08/07/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Rice, Oryza sativa L. (Os), is one of the oldest domesticated cereals that has also gone through extensive improvement in modern breeding. OBJECTIVES How rice was domesticated and impacted by modern breeding. METHODS We performed comprehensive analyses of genomic sequences of 504 accessions of Os and 456 accessions of O. rufipogon/O. nivara (Or). RESULTS The natural selection on Or before domestication and the natural and artificial selection during domestication together shaped the well-differentiated genomes of two subspecies, geng(j) (japonica) and xian(i) (indica), while breeding has made apparent genomic imprints between landrace and modern varieties of each subspecies, and also between primary modern and advanced modern varieties of xian(i). Selection during domestication and breeding left genome-wide selective signals covering ∼ 22.8 % and ∼ 8.6 % of the Os genome, significantly reduced within-population genomic diversity by ∼ 22 % in xian(i) and ∼ 53 % in geng(j) plus more pronounced subspecific differentiation. Only ∼ 10 % reduction in the total genomic diversity was observed between the Os and Or populations, indicating domestication did not suffer severe genetic bottleneck. CONCLUSION Our results revealed clear differentiation of the Or accessions into three large populations, two of which correspond to the well-differentiated Os subspecies, geng(j) and xian(i). Improved productivity and common changes in the same suit of adaptive traits in xian(i) and geng(j) during domestication and breeding resulted apparently from compensatory and convergent selections for different genes/alleles acting in the common KEGG terms and/or same gene families, and thus maintaining or even increasing the within population diversity and subspecific differentiation of Os, while more genes/alleles of novel function were selected during domestication than modern breeding. Our results supported the multiple independent domestication of Os in Asia and suggest the more efficient utilization of the rich diversity within Os by exploiting inter-subspecific and among population diversity in future rice improvement.
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Affiliation(s)
- Xueqiang Wang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Institute of Crop Science, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China
| | | | - Min Li
- The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhiqiang Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wushu Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhichao Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jianyin Xie
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fengmei Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhifang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Linran Zhi
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xiaoqian Ma
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yanhong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenzhuo Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiyu Yang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ying Chen
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100193, China
| | - Yan Zhao
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Binying Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Miao Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Wei Zeng
- The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Gengyun Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
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Shim KC, Adeva C, Kang JW, Luong NH, Lee HS, Cho JH, Kim H, Tai TH, Ahn SN. Interaction of starch branching enzyme 3 and granule-bound starch synthase 1 alleles increases amylose content and alters physico-chemical properties in japonica rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:968795. [PMID: 35991424 PMCID: PMC9389286 DOI: 10.3389/fpls.2022.968795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Four near-isogenic lines (NILs) with different allele combinations of the starch branching enzyme 3 (SBE3) and granule-bound starch synthase 1 (GBSS1) were developed by crossing the japonica rice cultivars "Dodamssal" and "Hwayeong." The associations between sequence variations in SBE3 and GBSS1, and starch-related traits were investigated. These sequence variations led to changes in seed morphology, starch structure, starch crystallinity, amylopectin chain length distribution, digestibility, apparent amylose content (AAC), and resistant starch content (RS). SBE3 and GBSS1 showed genetic interaction in regulating AAC and RS. Gene expression profiling of panicle tissues revealed significant differences in expression levels of GBSS1, SBE3, and other starch-related genes among the four NILs, indicating that variations in GBSS1 and SBE3 changed the expression level of starch-related genes. These variations contributed to the changes observed in AAC, RS, and physico-chemical characteristics of the rice starch from the NILs.
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Affiliation(s)
- Kyu-Chan Shim
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Cheryl Adeva
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Ju-Won Kang
- Department of Southern Area Crop Science, Rural Development Administration, Miryang, South Korea
| | - Ngoc Ha Luong
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Hyun-Sook Lee
- Crop Breeding Division, National Institute of Crop Science, Wanju-Gun, South Korea
| | - Jun-Hyeon Cho
- Department of Southern Area Crop Science, Rural Development Administration, Miryang, South Korea
| | | | - Thomas H. Tai
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Sang-Nag Ahn
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
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50
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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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