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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) 2024; 13:745. [PMID: 38475591 DOI: 10.3390/plants13050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhang Z, Hu Y, Zhao J, Zhang Y, Ying Y, Xu F, Bao J. The role of different Wx and BEIIb allele combinations on fine structures and functional properties of indica rice starches. Carbohydr Polym 2022; 278:118972. [PMID: 34973786 DOI: 10.1016/j.carbpol.2021.118972] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/21/2021] [Accepted: 11/30/2021] [Indexed: 01/08/2023]
Abstract
This study examined the effects of the combinations of Waxy (Wx) and starch branching enzyme IIb (BEIIb) alleles on starch fine structure and functional properties in indica rice cultivars. The results showed that be2b mutant starches with BEIIb deficiency had higher amylose content, shorter amylose long chains, a higher proportion of amylopectin long chains and molecular order, but a lower proportion of amylopectin short chains and relative crystallinity, resulting in higher gelatinization temperature but lower enthalpy and paste viscosity. Compared with the rice lines carrying Wxb allele, Wxa allele contributed to relatively higher amylose content, longer amylopectin chains, less short-range ordered structure and lower relative crystallinity, leading to a little lower gelatinization enthalpy. This study provides new insight into structure-function relations among rice lines with different allele combinations of starch synthesis related genes, which is a useful strategy for rice quality breeding.
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Feng L, Lu C, Yang Y, Lu Y, Li Q, Huang L, Fan X, Liu Q, Zhang C. The Physicochemical Properties of Starch Are Affected by Wxlv in Indica Rice. Foods 2021; 10:3089. [PMID: 34945643 DOI: 10.3390/foods10123089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Amylose largely determines rice grain quality profiles. The process of rice amylose biosynthesis is mainly driven by the waxy (Wx) gene, which also affects the diversity of amylose content. The present study assessed the grain quality profiles, starch fine structure, and crystallinity characteristics of the near-isogenic lines Q11(Wxlv), NIL(Wxa), and NIL(Wxb) in the indica rice Q11 background containing different Wx alleles. Q11(Wxlv) rice contained a relatively higher amylose level but very soft gel consistency and low starch viscosity, compared with rice lines carrying Wxa and Wxb. In addition, starch fine structure analysis revealed a remarkable decrease in the relative area ratio of the short amylopectin fraction but an increased amylose fraction in Q11(Wxlv) rice. Chain length distribution analysis showed that Q11(Wxlv) rice contained less amylopectin short chains but more intermediate chains, which decreased the crystallinity and lamellar peak intensity, compared with those of NIL(Wxa) and NIL(Wxb) rice. Additionally, the starches in developing grains showed different accumulation profiles among the three rice lines. Moreover, significant differences in starch gelatinization and retrogradation characteristics were observed between near-isogenic lines, which were caused by variation in starch fine structure. These findings revealed the effects of Wxlv on rice grain quality and the fine structure of starch in indica rice.
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Huang X, Su F, Huang S, Mei F, Niu X, Ma C, Zhang H, Zhu X, Zhu JK, Zhang J. Novel Wx alleles generated by base editing for improvement of rice grain quality. J Integr Plant Biol 2021; 63:1632-1638. [PMID: 33847449 DOI: 10.1111/jipb.13098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/12/2021] [Indexed: 05/18/2023]
Abstract
Amylose content (AC), which is regulated by the Waxy (Wx) gene, is a major indicator of eating and cooking quality (ECQ) in rice (Oryza sativa). Thus far, only a limited number of mutations in the N-terminal domain of Wx were found to have a major impact on the AC of rice grains and no mutations with such effects were reported for other regions of the Wx protein. Here, nucleotide substitutions in the middle region of Wx were generated by adenine and cytosine base editors. The nucleotide substitutions led to changes in 15 amino acid residues of Wx, and a series of novel Wx alleles with ACs of 0.3%-29.43% (wild type with AC of 19.87%) were obtained. Importantly, the waxyabe2 allele showed a "soft rice" AC, improved ECQ, favorable appearance, and no undesirable agronomic traits. The transgenes were removed from the waxyabe2 progeny, generating a promising breeding material for improving rice grain quality.
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Affiliation(s)
- Xiaorui Huang
- College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
- Bellagen Biotechnology Co. Ltd, Ji'nan, 250000, China
| | - Fei Su
- College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
- Bellagen Biotechnology Co. Ltd, Ji'nan, 250000, China
| | - Sheng Huang
- College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
- Bellagen Biotechnology Co. Ltd, Ji'nan, 250000, China
| | - Fating Mei
- Bellagen Biotechnology Co. Ltd, Ji'nan, 250000, China
| | - Xiaomu Niu
- Bellagen Biotechnology Co. Ltd, Ji'nan, 250000, China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
| | - Hui Zhang
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China
| | - Xiaoguo Zhu
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jinshan Zhang
- College of Life Sciences, Shandong Normal University, Ji'nan, 250014, China
- Bellagen Biotechnology Co. Ltd, Ji'nan, 250000, China
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Huang L, Gu Z, Chen Z, Yu J, Chu R, Tan H, Zhao D, Fan X, Zhang C, Li Q, Liu Q. Improving rice eating and cooking quality by coordinated expression of the major starch synthesis-related genes, SSII and Wx, in endosperm. Plant Mol Biol 2021; 106:419-432. [PMID: 34129189 DOI: 10.1007/s11103-021-01162-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/07/2021] [Indexed: 05/18/2023]
Abstract
Coordinated regulation of amylose and amylopectin synthesis via manipulation of SSII-2, SSII-3 and Wx expression in endosperm can improve rice eating and cooking quality. With increasing rice consumption worldwide, many researchers are working to increase the yield and improve grain quality, especially eating and cooking quality (ECQ). The rice ECQ is mainly controlled by the expression of starch synthesis-related genes (SSRGs) in endosperm. Although the Wx and SSII-3/SSIIa/ALK genes, two major SSRGs, have been manipulated to improve rice ECQ via various breeding approaches, new methods to further improve ECQ are desired. In our previous study, we enhanced rice ECQ by knocking down SSII-2 expression in the japonica Nipponbare cultivar (carrying the Wxb allele) via RNA interference. Herein, the SSII-2 RNAi was introduced into two Nipponbare-derived near-isogenic lines (NILs), Nip(Wxa) and Nip(wx), carrying Wxa and wx alleles respond for high and no amylose levels, respectively. Analysis of physicochemical properties revealed that the improved grain quality of SSII-2 RNAi transgenic lines was achieved by coordinated downregulating the expression of SSII-2, SSII-3 and Wx. To further confirm this conclusion, we generated ssii-2, ssii-3 and ssii-2ssii-3 mutants via CRISPR/Cas9 technique. The amylopectin structure of the resulting ssii-2sii-3 mutants was similar to that in SSII-2 RNAi transgenic lines, and the absence of SSII-2 decreased the amylose content, gelatinisation temperature and rapid visco-analyser profile, indicating essential roles for SSII-2 in the regulation of amylopectin biosynthesis and amylose content in rice endosperm. The effect of SSII-2 was seen only when the activity of SSII-3 was very low or lacking. Our study provides novel approaches and valuable germplasm resources for improving ECQ via plant breeding.
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Affiliation(s)
- Lichun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Zhengwen Gu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Zhuanzhuan Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Jiawen Yu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Rui Chu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Hongyan Tan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Dongsheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Xiaolei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Changquan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Qianfeng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China.
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China.
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Yang B, Xu S, Xu L, You H, Xiang X. Effects of Wx and Its Interaction With SSIII-2 on Rice Eating and Cooking Qualities. Front Plant Sci 2018; 9:456. [PMID: 29692791 PMCID: PMC5902675 DOI: 10.3389/fpls.2018.00456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/22/2018] [Indexed: 05/13/2023]
Abstract
The Wx gene encodes a granule-bound starch synthase (GBSS) and plays a key role in determining rice eating and cooking qualities (ECQs). SSIII-2 (SSIIIa), a member of the soluble starch synthases, is responsible for the synthesis of long chains of amylopectin. To investigate the effects of Wx and its interaction with SSIII-2 on grain ECQs, a population from a hybrid combination was established as a research material. The genotypes of SSIII-2 and the single nucleotide polymorphisms (SNPs) on intron1, exon6, and exon10 of Wx, and the physicochemical indicators and rapid visco analyzer (RVA) profile characteristics were analyzed. The results revealed various effects of SSIII-2 on rice quality under different backgrounds of Wx alleles. There was no obvious difference between different SSIII-2 alleles under the same background of Wxa , whereas there was a significant diversity under the same background of Wxb . Wxa had a dominant epistasis to SSIII-2 because the effect of SSIII-2 was masked by the massive synthesis of GBSS under Wxa . The apparent amylose content (AAC) was mainly controlled by the In1G/T SNP, and rice gel consistency (GC) was regulated by the Ex10C/T SNP. The combined effects of three SNPs had a significant influence on all ECQs and RVA profile parameters, except for gelatinization temperature. In1T-Ex6A-Ex10C and In1T-Ex6A-Ex10T were classified as being low AAC type. TT-AA-CC and TT-AA-TT had a low AAC and a soft GC. The combined effects of different SNPs of Wx are very important for rice quality breeding.
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Affiliation(s)
- Bowen Yang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Shunju Xu
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Liang Xu
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Hui You
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Xunchao Xiang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang, China
- *Correspondence: Xunchao Xiang
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Muto C, Ishikawa R, Olsen KM, Kawano K, Bounphanousay C, Matoh T, Sato YI. Genetic diversity of the wx flanking region in rice landraces in northern Laos. Breed Sci 2016; 66:580-590. [PMID: 27795683 PMCID: PMC5010311 DOI: 10.1270/jsbbs.16032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8602,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8560,
Japan
- Corresponding author (e-mail: )
| | - Kenneth M. Olsen
- Biology Department, Washington University,
St. Louis 63130-4899,
USA
| | - Kazuaki Kawano
- Institute of Southern Cultural Folklore,
Kirishima, Kagoshima 899-4201,
Japan
| | - Chay Bounphanousay
- Agricultural Research Centre, National Agriculture and Forestry Research Institute,
Nongviengkham, Vientiane 7170,
Lao P.D.R
| | - Toru Matoh
- Graduate School of Agriculture, Kyoto University,
Kyoto 606-8502,
Japan
| | - Yo-Ichiro Sato
- National Institutes for the Humanities,
Minato-ku, Tokyo 105-0001,
Japan
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