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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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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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3
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Sharma V, Jahan K, Kumar P, Puri A, Sharma VK, Mishra A, Bharatam PV, Sharma D, Rishi V, Roy J. Mechanistic insights into granule-bound starch synthase I (GBSSI.L539P) allele in high amylose starch biosynthesis in wheat (Triticum aestivum L.). Funct Integr Genomics 2022; 23:20. [PMID: 36564499 DOI: 10.1007/s10142-022-00923-y] [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: 07/18/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
Amylose fraction of grain starch is correlated with a type of resistant starch with better nutritional quality. Granule-bound starch synthase I (GBSSI) is the known starch synthase, responsible for elongation of linear amylose chains. GBSSI expression, activity, and binding to starch and other proteins are the key factors that can affect amylose content. Previously, a QTL, qhams7A.1 carrying GBSSI mutant allele, was identified through QTL mapping using F2 population of the high amylose mutant line, 'TAC 75'. This high amylose mutant line has >2-fold higher amylose content than wild variety 'C 306'. In this study, we characterized this novel mutant allele, GBSSI.L539P. In vitro starch synthase activity of GBSSI.L539P showed improved activity than the wild type (GBSSI-wt). When expressed in yeast glycogen synthase mutants (Δgsy1gsy2), GBSSI-wt and GBSSI.L539P partially complemented the glycogen synthase (gsy1gsy2) activity in yeast. Structural analysis by circular dichroism (CD) and homology modelling showed no significant structural distortion in the mutant enzyme. Molecular docking studies suggested that the residue Leu539 is distant from the catalytic active site (ADP binding pocket) and had no detectable conformational changes in active site. Both wild and mutant enzymes were assayed for starch binding in vitro, and demonstrating higher affinity of the GBSSI.L539P mutant for starch than the wild type. The present study indicated that distant residue (L539P) influenced GBSSI activity by affecting its starch-binding ability. Therefore, it may be a potential molecular target for enhanced amylose content in grain.
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Affiliation(s)
- Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education & Research (IISER) Mohali, SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Prashant Kumar
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Anuradhika Puri
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Vishnu K Sharma
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - P V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Deepak Sharma
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India.
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4
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Zhou L, Zhang C, Zhang Y, Wang C, Liu Q. Genetic manipulation of endosperm amylose for designing superior quality rice to meet the demands in the 21st century. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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5
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KHARSHIING GAYLE, CHRUNGOO NIKHILK. Wx alleles in rice: relationship with apparent amylose content of starch and a possible role in rice domestication. J Genet 2021. [DOI: 10.1007/s12041-021-01311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Maung TZ, Yoo JM, Chu SH, Kim KW, Chung IM, Park YJ. Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:707237. [PMID: 34504507 PMCID: PMC8421862 DOI: 10.3389/fpls.2021.707237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by F ST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Ji-Min Yoo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Kyu-Won Kim
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Ill-Min Chung
- Department of Applied Life Science, Konkuk University, Seoul, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
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Zhou H, Xia D, Zhao D, Li Y, Li P, Wu B, Gao G, Zhang Q, Wang G, Xiao J, Li X, Yu S, Lian X, He Y. The origin of Wx la provides new insights into the improvement of grain quality in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:878-888. [PMID: 32886450 PMCID: PMC8252478 DOI: 10.1111/jipb.13011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/03/2020] [Indexed: 05/23/2023]
Abstract
Appearance and taste are important factors in rice (Oryza sativa) grain quality. Here, we investigated the taste scores and related eating-quality traits of 533 diverse cultivars to assess the relationships between-and genetic basis of-rice taste and eating-quality. A genome-wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy (Wx) allele, Wxla , which combined two mutations from Wxb and Wxin , exhibited a unique phenotype. Reduced GBSSI activity conferred Wxla rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wxla was derived from intragenic recombination. In fact, the recombination rate at the Wx locus was estimated to be 3.34 kb/cM, which was about 75-fold higher than the genome-wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.
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Affiliation(s)
- Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Da Zhao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhan 430070China
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Zhang C, Yang Y, Chen S, Liu X, Zhu J, Zhou L, Lu Y, Li Q, Fan X, Tang S, Gu M, Liu Q. A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:889-901. [PMID: 32886440 PMCID: PMC8246539 DOI: 10.1111/jipb.13010] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/02/2020] [Indexed: 05/18/2023]
Abstract
In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wxmw , which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wxmw may have derived from recombination between two important natural Wx alleles, Wxin and Wxb . We validated the effects of Wxmw on rice grain quality using both transgenic lines and near-isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wxmw resulted in a moderate AC that was intermediate between that of NILs carrying the Wxb allele and NILs with the Wxmp allele. Notably, mature grains of NILs fixed for Wxmw had an improved transparent endosperm relative to soft rice. Further, we introduced Wxmw into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wxmw is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Yong Yang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
| | - Shengjie Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Xueju Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Jihui Zhu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Lihui Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Yan Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Qianfeng Li
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Xiaolei Fan
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Shuzhu Tang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Minghong Gu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
| | - Qiaoquan Liu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid RiceYangzhou UniversityYangzhou225009China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu ProvinceYangzhou UniversityYangzhou225009China
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9
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Zhang C, Zhu J, Chen S, Fan X, Li Q, Lu Y, Wang M, Yu H, Yi C, Tang S, Gu M, Liu Q. Wx lv, the Ancestral Allele of Rice Waxy Gene. MOLECULAR PLANT 2019; 12:1157-1166. [PMID: 31181338 DOI: 10.1016/j.molp.2019.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 05/28/2019] [Indexed: 05/07/2023]
Abstract
In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. The effects of several Wx alleles on amylose content and the taste of cooked rice have been elucidated. However, the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain unclear. Here we report the identification of an ancestral allele, Wxlv, which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jihui Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Shengjie Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiaolei Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yan Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Min Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Chuandeng Yi
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Shuzhu Tang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China.
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Crofts N, Itoh A, Abe M, Miura S, Oitome NF, Bao J, Fujita N. Three Major Nucleotide Polymorphisms in the Waxy Gene Correlated with the Amounts of Extra-long Chains of Amylopectin in Rice Cultivars with S or L-type Amylopectin. J Appl Glycosci (1999) 2019; 66:37-46. [PMID: 34354518 PMCID: PMC8056923 DOI: 10.5458/jag.jag.jag-2018_005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/03/2018] [Indexed: 11/19/2022] Open
Abstract
Extra-long chains (ELC) of amylopectin in rice endosperm are synthesized by granule-bound starch synthase I encoded by the Waxy (Wx) gene, which primarily synthesizes amylose. Previous studies showed that single nucleotide polymorphisms (SNP) in intron 1 and exon 6 of the Wx gene influences ELC amount. However, whether these SNPs are conserved among rice cultivars and if any other SNPs are present in the Wx gene remained unknown. Here, we sequenced the Wx gene from 17 rice cultivars with S or L-type amylopectin, including those with known ELC content and those originating in China with unique starch properties, as well as typical japonica and indica cultivars. In addition to the two SNPs described above, an additional SNP correlating with ELC content was found in exon 10. Low ELC cultivars (<3.0 %) had thymine at the splicing donor site of intron 1, Tyr224 in exon 6, and Pro415 in exon 10. Cultivars with moderate ELC content (4.1–6.9 %) had guanine at the splicing donor site of intron 1, Ser224 in exon 6, and Pro415 in exon 10. Cultivars with high ELC content (7.7–13.9 %) had guanine at the splicing donor site of intron 1, Tyr224 in exon 6, and Ser415 in exon 10. The chain length distribution pattern of amylopectin was correlated with the amounts of SSIIa found in starch granules and gelatinization temperature, but not with ELC content. The combinations of SNPs in the Wx gene found in this study may provide useful information for screening specific cultivars with different ELC content.
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Affiliation(s)
- Naoko Crofts
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Ayaka Itoh
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Misato Abe
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Satoko Miura
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Naoko F Oitome
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Jinsong Bao
- 2 Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University
| | - Naoko Fujita
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
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