1
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Cheng W, Hong C, Zeng F, Liu N, Gao H. Sequence variations affect the 5' splice site selection of plant introns. PLANT PHYSIOLOGY 2023; 193:1281-1296. [PMID: 37394939 DOI: 10.1093/plphys/kiad375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 07/04/2023]
Abstract
Introns are noncoding sequences spliced out of pre-mRNAs by the spliceosome to produce mature mRNAs. The 5' ends of introns mostly begin with GU and have a conserved sequence motif of AG/GUAAGU that could base-pair with the core sequence of U1 snRNA of the spliceosome. Intriguingly, ∼ 1% of introns in various eukaryotic species begin with GC. This occurrence could cause misannotation of genes; however, the underlying splicing mechanism is unclear. We analyzed the sequences around the intron 5' splice site (ss) in Arabidopsis (Arabidopsis thaliana) and found sequences at the GC intron ss are much more stringent than those of GT introns. Mutational analysis at various positions of the intron 5' ss revealed that although mutations impair base pairing, different mutations at the same site can have different effects, suggesting that steric hindrance also affects splicing. Moreover, mutations of 5' ss often activate a hidden ss nearby. Our data suggest that the 5' ss is selected via a competition between the major ss and the nearby minor ss. This work not only provides insights into the splicing mechanism of intron 5' ss but also improves the accuracy of gene annotation and the study of the evolution of intron 5' ss.
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Affiliation(s)
- Wenzhen Cheng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Conghao Hong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Fang Zeng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Nan Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hongbo Gao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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2
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Xia D, Wang Y, Shi Q, Wu B, Yu X, Zhang C, Li Y, Fu P, Li M, Zhang Q, Liu Q, Gao G, Zhou H, He Y. Effects of Wx Genotype, Nitrogen Fertilization, and Temperature on Rice Grain Quality. FRONTIERS IN PLANT SCIENCE 2022; 13:901541. [PMID: 35937336 PMCID: PMC9355397 DOI: 10.3389/fpls.2022.901541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Quality is a complex trait that is not only the key determinant of the market value of the rice grain, but is also a major constraint in rice breeding. It is influenced by both genetic and environmental factors. However, the combined effects of genotypes and environmental factors on rice grain quality remain unclear. In this study, we used a three-factor experimental design to examine the grain quality of different Wx genotypes grown under different nitrogen fertilization and temperature conditions during grain development. We found that the three factors contributed differently to taste, appearance, and nutritional quality. Increased Wx function and nitrogen fertilization significantly reduced eating quality, whereas high temperature (HT) had almost no effect. The main effects of temperature on appearance quality and moderate Wx function at low temperatures (LTs) contributed to better appearance, and higher nitrogen fertilization promoted appearance at HTs. With regard to nutritional quality, Wx alleles promoted amylose content (AC) as well as starch-lipids content (SLC); nitrogen fertilization increased storage protein content (PC); and higher temperature increased lipid content but decreased the PC. This study helps to broaden the understanding of the major factors that affect the quality of rice and provides constructive messages for rice quality improvement and the cultivation of high-quality rice varieties.
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Affiliation(s)
- Duo Xia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yipei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qingyun Shi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaoman Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Pei Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Minqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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3
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Cai Y, Zhang W, Fu Y, Shan Z, Xu J, Wang P, Kong F, Jin J, Yan H, Ge X, Wang Y, You X, Chen J, Li X, Chen W, Chen X, Ma J, Tang X, Zhang J, Bao Y, Jiang L, Wang H, Wan J. Du13 encodes a C 2 H 2 zinc-finger protein that regulates Wx b pre-mRNA splicing and microRNA biogenesis in rice endosperm. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1387-1401. [PMID: 35560858 PMCID: PMC9241381 DOI: 10.1111/pbi.13821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/27/2022] [Accepted: 03/10/2022] [Indexed: 05/07/2023]
Abstract
Amylose content is a crucial physicochemical property responsible for the eating and cooking quality of rice (Oryza sativa L.) grain and is mainly controlled by the Waxy (Wx) gene. Previous studies have identified several Dull genes that modulate the expression of the Wxb allele in japonica rice by affecting the splicing efficiency of the Wxb pre-mRNA. Here, we uncover dual roles for a novel Dull gene in pre-mRNA splicing and microRNA processing. We isolated the dull mutant, du13, with a dull endosperm and low amylose content. Map-based cloning showed that Du13 encodes a C2 H2 zinc-finger protein. Du13 coordinates with the nuclear cap-binding complex to regulate the splicing of Wxb transcripts in rice endosperm. Moreover, Du13 also regulates alternative splicing of other protein-coding transcripts and affects the biogenesis of a subset of microRNAs. Our results reveal an evolutionarily conserved link between pre-mRNA splicing and microRNA biogenesis in rice endosperm. Our findings also provide new insights into the functions of Dull genes in rice and expand our knowledge of microRNA biogenesis in monocots.
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Affiliation(s)
- Yue Cai
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Wenwei Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yushuang Fu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Zhuangzhuang Shan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jiahuan Xu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Peng Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Fei Kong
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jie Jin
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Haigang Yan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xinyuan Ge
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yongxiang Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xiaoman You
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jie Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xin Li
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Weiwei Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xingang Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jing Ma
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xiaojie Tang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jie Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yiqun Bao
- College of Life SciencesNanjing Agricultural UniversityNanjingChina
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
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4
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John D, Sureshkumar S, Raman M. Type‐2 diabetes and identification of major genetic determinants of glycemic index in rice‐ A review. STARCH-STARKE 2022. [DOI: 10.1002/star.202100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Deepa John
- Department of Biotechnology Faculty of Ocean Science and Technology Kerala University of Fisheries and Ocean Studies Cochin Kerala 682506 India
| | - S Sureshkumar
- Faculty of Ocean Science and Technology Kerala University of Fisheries and Ocean Studies Cochin Kerala 682506 India
| | - Maya Raman
- Department of Food Science and Technology Faculty of Ocean Science and Technology Kerala University of Fisheries and Ocean Studies Cochin Kerala 682506 India
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5
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Okpala NE, Aloryi KD, An T, He L, Tang X. The roles of starch branching enzymes and starch synthase in the biosynthesis of amylose in rice. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2021.103393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Wang S, Gao S, Nie J, Tan X, Xie J, Bi X, Sun Y, Luo S, Zhu Q, Geng J, Liu W, Lin Q, Cui P, Hu S, Wu S. Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics. FRONTIERS IN PLANT SCIENCE 2022; 12:769700. [PMID: 35126409 PMCID: PMC8813773 DOI: 10.3389/fpls.2021.769700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/20/2021] [Indexed: 05/28/2023]
Abstract
In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the indica cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the indica cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of waxy make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of Oryza groups in molecular breeding programs.
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Affiliation(s)
- Sen Wang
- 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
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jingyi Nie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junhua Xie
- 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
| | - Xiaochun Bi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sainan Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qianhui Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianing Geng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wanfei Liu
- 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
| | - Qiang Lin
- 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
| | - Peng Cui
- 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
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
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7
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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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8
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Zhu J, Zhang CQ, Xu J, Gilbert RG, Liu Q. Identification of Structure-Controlling Rice Biosynthesis Enzymes. Biomacromolecules 2021; 22:2148-2159. [PMID: 33914519 DOI: 10.1021/acs.biomac.1c00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The main enzymes controlling the chain-length distributions (CLDs) of starches are starch synthases (SSs), starch branching enzymes (SBEs), and debranching enzymes (DBEs), which have various isoforms, denoted as SSI, SSII-1, etc. Different isozymes dominate the CLD in different ranges of degrees of polymerization (DPs). Models have been developed for the CLDs in terms of the activities of isoforms of these enzymes, in terms of two parameters: βi, which is the ratio of the activity of SBE to that of SS in set i, and hi, which is the relative activity of SS in that set. These provide good fits to data but without specifying which isozymes are in set i. Here, CLDs for amylopectin and amylose synthesis in rice endosperm are explored. Molecular weight distributions of the different chains formed in 87 rice varieties were obtained using size-exclusion chromatography following enzymatic debranching (converting a complex branched macromolecule to linear polymers), and fitted by the biosynthesis-based models. The mutants of each isoform among tested rice varieties were identified by amino-acid mutations in coding sequences based on the extraction and analysis of whole gene sequences. The significant differences between mutant groups of different isoforms indicate that SSI, SSII-3, SSIII-1, SSIII-2, and SBEI as well as GBSSI (an isozyme of granule-bound starch synthase) belong to the enzymes sets that control amylose biosynthesis. Further, GBSSI is in the enzyme sets that control amylopectin chains. This enables specification of all isozymes and the DP range, which they dominate, over the entire DP range. As the CLD controls many functional properties of rice, this can help breeders target and develop improved rice species.
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Affiliation(s)
- Jihui Zhu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Jiangsu Key Laboratory of Crop Genetics and Physiology, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 9 100081, China
| | - Robert G Gilbert
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia.,Jiangsu Key Laboratory of Crop Genetics and Physiology, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Jiangsu Key Laboratory of Crop Genetics and Physiology, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou, Jiangsu 225009, China
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9
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Singh N, Wang DR, Ali L, Kim H, Akther KM, Harrington SE, Kang JW, Shakiba E, Shi Y, DeClerck G, Meadows B, Govindaraj V, Ahn SN, Eizenga GC, McCouch SR. A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds. FRONTIERS IN PLANT SCIENCE 2020; 11:564824. [PMID: 33281840 PMCID: PMC7688981 DOI: 10.3389/fpls.2020.564824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/12/2020] [Indexed: 05/27/2023]
Abstract
Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.
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Affiliation(s)
- Namrata Singh
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Diane R. Wang
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Liakat Ali
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR, United States
| | - HyunJung Kim
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Kazi M. Akther
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sandra E. Harrington
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Ju-Won Kang
- Department of Agronomy, Chungnam National University, Daejeon, South Korea
| | - Ehsan Shakiba
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR, United States
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Genevieve DeClerck
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Byron Meadows
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Vishnu Govindaraj
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sang-Nag Ahn
- Department of Agronomy, Chungnam National University, Daejeon, South Korea
| | - Georgia C. Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR, United States
| | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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10
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Roy S, Banerjee A, Basak N, Bagchi TB, Mandal NP, Patra BC, Misra AK, Singh SK, Rathi RS, Pattanayak A. Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity. J Biosci 2020. [DOI: 10.1007/s12038-020-00059-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Development of High Yielding Glutinous Cytoplasmic Male Sterile Rice (Oryza sativa L.) Lines through CRISPR/Cas9 Based Mutagenesis of Wx and TGW6 and Proteomic Analysis of Anther. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8120290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Development of high yielding and more palatable glutinous rice is an important goal in breeding and long-standing cultural interaction in Asia. In this study, the TGW6 and Wx, major genes conferring 1000 grain weight (GW) and amylose content (AC), were edited in a maintainer line by CRISPR/Cas9 technology. Four targets were assembled in pYLCRISPR/Cas9Pubi-H vector and T0 mutant plants were obtained through Agrobacterium mediated transformation with 90% mutation frequency having 28% homozygous mutations without off-target effects in three most likely sites of each target and expression level of target genes in mutant lines was significantly decreased (P < 0.01), the GW and gel consistency (GC) were increased, and the AC and gelatinization temperature (GT) were decreased significantly and grain appearance was opaque, while there was no change in starch content (SC) and other agronomic traits. Mutations were inheritable and some T1 plants were re-edited but T2 generation was completely stable. The pollen fertility status was randomly distributed, and the mutant maintainer lines were hybridized with Cytoplasmic Male Sterile (CMS) line 209A and after subsequent backcrossing the two glutinous CMS lines were obtained in BC2F1. The identified proteins from anthers of CMS and maintainer line were closely associated with transcription, metabolism, signal transduction, and protein biosynthesis. Putative mitochondrial NAD+-dependent malic enzyme was absent in CMS line which caused the pollen sterility because of insufficient energy, while upregulation of putative acetyl-CoA synthetase and Isoamylase in both lines might have strong relationship with CMS and amylose content. High yielding glutinous CMS lines will facilitate hybrid rice breeding and investigations of proteins linked to male sterility will provide the insights to complicated metabolic network in anther development.
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12
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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13
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Inukai T. Differential Regulation of Starch-synthetic Gene Expression in Endosperm Between Indica and Japonica Rice Cultivars. RICE (NEW YORK, N.Y.) 2017; 10:7. [PMID: 28243987 PMCID: PMC5328889 DOI: 10.1186/s12284-017-0146-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/21/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Grain filling rates (GFRs) of indica rice cultivars are often higher than those of japonica cultivars. Although GFR is mainly determined by the starch accumulation rate (SAR) in endosperm, the genetic basis for SAR during the ripening period has not been well studied in rice. To elucidate the factors influencing the differing SARs between typical indica and japonica cultivars, we focused on differences in sink potentials, especially on starch synthesis in the endosperm. RESULTS SAR in indica rice cultivar IR36 was significantly higher than in japonica cultivar T65. Although enzymes for both amylose and amylopectin syntheses had higher activity in IR36, amylopectin synthesis was seemingly more important for accelerating SAR because an elevation of amylose synthesis ability alone in the T65 genetic background did not result in the same level of SAR as IR36. In IR36, most starch-synthetic genes (SSGs) in the endosperm were more highly expressed during ripening than in T65. In panicle culture experiments, the SSGs in rice endosperm were regulated in either sucrose-dependent or -independent manners, or both. All SSGs except SSI and BEIIa were responsive to sucrose in both cultivars, and GBSSI, AGPS2b and PUL were more responsive to sucrose in IR36. Interestingly, the GBSSI gene (Wx a ) in IR36 was highly activated by sucrose, but the GBSSI gene (Wx b ) in T65 was insensitive. In sucrose-independent regulation, AGPL2, SSIIIa, BEI, BEIIb and ISA1 genes in IR36 were upregulated 1.5 to 2 times more than those in T65. Additionally, at least SSI and BEIIa might be regulated by unknown signals; that regulation pathway should be more activated in IR36 than T65. CONCLUSIONS In this study, at least three regulatory pathways seem to be involved in SSG expression in rice endosperm, and all pathways were more active in IR36. One of the factors leading to the high SAR of IR36 seemed to be an increase in the sink potential.
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Affiliation(s)
- Tsuyoshi Inukai
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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Singh N, Singh B, Rai V, Sidhu S, Singh AK, Singh NK. Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:972. [PMID: 28649256 PMCID: PMC5465369 DOI: 10.3389/fpls.2017.00972] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 05/23/2023]
Abstract
The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb). Aus cultivars appear to have the most ancient origin as they shared the maximum number of haplotypes with the wild rice populations, while Indica, Japonica and Aromatic cultivar groups showed varying phylogenetic origins of these genes. Starch synthase genes showed higher variability in cultivated rice than wild rice populations, suggesting diversified selection during and after domestication. O. nivara/O. rufipogon wild rice accessions belonging to different sub-populations shared common haplotypes for all the 10 genes analyzed. Our results support polyphyletic origin of cultivated rice with a complex pattern of migration of domestication alleles from wild to different rice cultivar groups. The findings provide novel insights into evolutionary and domestication history of rice and will help utilization of wild rice germplasm for genetic improvement of rice cultivars.
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Affiliation(s)
- Nisha Singh
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
- Shaheed Udham Singh College of Engineering & Technology, I. K. Gujral Punjab Technical UniversityJalandhar, India
| | - Balwant Singh
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Vandna Rai
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Sukhjeet Sidhu
- Shaheed Udham Singh College of Engineering & Technology, I. K. Gujral Punjab Technical UniversityJalandhar, India
| | - Ashok K. Singh
- Divisions of Genetics, ICAR – Indian Agricultural Research InstituteNew Delhi, India
| | - Nagendra K. Singh
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
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Li K, Bao J, Corke H, Sun M. Association Analysis of Markers Derived from Starch Biosynthesis Related Genes with Starch Physicochemical Properties in the USDA Rice Mini-Core Collection. FRONTIERS IN PLANT SCIENCE 2017; 8:424. [PMID: 28421086 PMCID: PMC5376596 DOI: 10.3389/fpls.2017.00424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/13/2017] [Indexed: 05/05/2023]
Abstract
Rice eating and cooking quality is largely determined by starch physicochemical properties. The diverse accessions in the USDA rice mini-core collection (URMC) facilitate extensive association analysis of starch physicochemical properties with molecular markers specific to starch biosynthesis related genes. To identify significant trait-marker associations that can be utilized in rice breeding programs for improved starch quality, we conducted two association analyses between 26 molecular markers derived from starch biosynthesis related genes and 18 parameters measured of starch physicochemical properties in two sets of the mini-core accessions successfully grown in two environments in China. Many significant trait-marker associations (P < 0.001) were detected in both association analyses. Five markers of Waxy gene, including the (CT)n repeats, the G/T SNP of intron 1, the 23 bp sequence duplication (InDel) of exon 2, the A/C SNP of exon 6, and the C/T SNP of exon 10, were found to be primarily associated with starch traits related to apparent amylose content (AAC), and two markers targeting the 4,329-4,330 bp GC/TT SNPs and 4,198 bp G/A SNP of SSIIa gene were mainly associated with traits related to gelatinization temperature (GT). Two new haplotypes were found in the mini-core collection based on the combinations of the 23 bp InDel and three SNPs (G/T of intron 1, A/C of exon 6, and C/T of exon 10) of Waxy gene. Furthermore, our analyses indicated that the (CT)n polymorphisms of Waxy gene had a non-negligible effect on AAC related traits, as evidenced by significant variation in AAC related traits among rice accessions with the same Waxy SNPs but different (CT) n repeats. As the five Waxy markers and the two SSIIa markers showed consistent major effects on starch quality traits across studies, these markers should have priority for utilization in marker-assisted breeding.
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Affiliation(s)
- Kehu Li
- School of Biological Sciences, University of Hong KongHong Kong, China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Harold Corke
- School of Biological Sciences, University of Hong KongHong Kong, China
- Department of Food Science and Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Mei Sun
- School of Biological Sciences, University of Hong KongHong Kong, China
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Biselli C, Bagnaresi P, Cavalluzzo D, Urso S, Desiderio F, Orasen G, Gianinetti A, Righettini F, Gennaro M, Perrini R, Ben Hassen M, Sacchi GA, Cattivelli L, Valè G. Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits. BMC Genomics 2015; 16:1091. [PMID: 26689934 PMCID: PMC4687084 DOI: 10.1186/s12864-015-2321-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/15/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Rice represents one the most important foods all over the world. In Europe, Italy is the first rice producer and Italian production is driven by tradition and quality. All main rice grain quality traits, like cooking properties, texture, gelatinization temperature, chalkiness and yield, are related to the content and composition of starch and seed-storage proteins in the endosperm and to grain shape. In addition, a number of nutraceutical compounds and allergens are known to have a significant effect on grain quality determination. To investigate the genetic bases underlying the qualitative differences that characterize traditional Italian rice cultivars, a comparative RNA-Seq-based transcriptomic analysis of developing caryopsis was conducted at 14 days after flowering on six popular Italian varieties (Carnaroli, Arborio, Balilla, Vialone Nano, Gigante Vercelli and Volano) phenotypically differing for qualitative grain-related traits. RESULTS Co-regulation analyses of differentially expressed genes showing the same expression patterns in the six genotypes highlighted clusters of loci up or down-regulated in specific varieties, with respect to the others. Among them, we detected loci involved in cell wall biosynthesis, protein metabolism and redox homeostasis, classes of genes affecting in chalkiness determination. Moreover, loci encoding for seed-storage proteins, allergens or involved in the biosynthesis of specific nutraceutical compounds were also present and specifically regulated in the different clusters. A wider investigation of all the DEGs detected in pair-wise comparisons revealed transcriptional variation, among the six genotypes, for quality-related loci involved in starch biosynthesis (e.g. GBSSI, starch synthases and AGPase), genes encoding for transcription factors, additional seed storage proteins, allergens or belonging to additional nutraceutical compounds biosynthetic pathways and loci affecting grain size. Putative functional SNPs associated to amylose content in starch, gelatinization temperature and grain size were also identified. CONCLUSIONS The present work represents a more extended phenotypic characterization of a set of rice accessions that present a wider genetic variability than described nowadays in literature. The results provide the first transcriptional picture for several of the grain quality differences observed among the Italian rice varieties analyzed and reveal that each variety is characterized by the over-expression of a peculiar set of loci affecting grain appearance and quality. A list of candidates and SNPs affecting specific grain properties has been identified offering a starting point for further works aimed to characterize genes and molecular markers for breeding programs.
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Affiliation(s)
- Chiara Biselli
- CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. .,CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy.
| | - Paolo Bagnaresi
- CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy.
| | - Daniela Cavalluzzo
- CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy.
| | - Simona Urso
- CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy.
| | - Francesca Desiderio
- CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy.
| | - Gabriele Orasen
- CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. .,DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy.
| | - Alberto Gianinetti
- CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy.
| | - Federico Righettini
- DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy.
| | - Massimo Gennaro
- CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy.
| | - Rosaria Perrini
- CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy.
| | - Manel Ben Hassen
- CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. .,DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy.
| | - Gian Attilio Sacchi
- DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy.
| | - Luigi Cattivelli
- CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy.
| | - Giampiero Valè
- CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. .,CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy.
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Cai H, Xu D, Zhou L, Cheng J, Zhang Z, Wu J, You A. Development of PCR-based CNP marker of rice Waxy gene with confronting two-pair primers. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Sreenivasulu N, Butardo VM, Misra G, Cuevas RP, Anacleto R, Kavi Kishor PB. Designing climate-resilient rice with ideal grain quality suited for high-temperature stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1737-48. [PMID: 25662847 PMCID: PMC4669556 DOI: 10.1093/jxb/eru544] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 05/18/2023]
Abstract
To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural-functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality.
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Affiliation(s)
- Nese Sreenivasulu
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Vito M Butardo
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Gopal Misra
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Rosa Paula Cuevas
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Roslen Anacleto
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
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Phing Lau WC, Latif MA, Y Rafii M, Ismail MR, Puteh A. Advances to improve the eating and cooking qualities of rice by marker-assisted breeding. Crit Rev Biotechnol 2014; 36:87-98. [PMID: 24937109 DOI: 10.3109/07388551.2014.923987] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The eating and cooking qualities of rice are heavily emphasized in breeding programs because they determine market values and they are the appealing attributes sought by consumers. Conventional breeding has developed traditional varieties with improved eating and cooking qualities. Recently, intensive genetic studies have pinpointed the genes that control eating and cooking quality traits. Advances in genetic studies have developed molecular techniques, thereby allowing marker-assisted breeding (MAB) for improved eating and cooking qualities in rice. MAB has gained the attention of rice breeders for the advantages it can offer that conventional breeding cannot. There have been successful cases of using MAB to improve the eating and cooking qualities in rice over the years. Nevertheless, MAB should be applied cautiously given the intensive effort needed for genotyping. Perspectives from conventional breeding to marker-assisted breeding will be discussed in this review for the advancement of the eating and cooking qualities of fragrance, amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) in rice. These four parameters are associated with eating and cooking qualities in rice. The genetic basis of these four parameters is also included in this review. MAB is another approach to rice variety improvement and development in addition to being an alternative to genetic engineering. The MAB approach shortens the varietal development time, and is therefore able to deliver improved rice varieties to farmers within a shorter period of time.
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Affiliation(s)
- Wendy Chui Phing Lau
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia
| | - Mohammad Abdul Latif
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia .,b Bangladesh Rice Research Institute (BRRI) , Gazipur , Bangladesh , and
| | - Mohd Y Rafii
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia .,c Institute of Tropical Agriculture, Universiti Putra Malaysia , Serdang , Selangor , Malaysia
| | - Mohd Razi Ismail
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia .,c Institute of Tropical Agriculture, Universiti Putra Malaysia , Serdang , Selangor , Malaysia
| | - Adam Puteh
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia
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FASAHAT PARVIZ, RAHMAN SADEQUR, RATNAM WICKNESWARI. Genetic controls on starch amylose content in wheat and rice grains. J Genet 2014; 93:279-92. [DOI: 10.1007/s12041-014-0325-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Rice is a monocot gramineous crop, and one of the most important staple foods. Rice is considered a model species for most gramineous crops. Extensive research on rice has provided critical guidance for other crops, such as maize and wheat. In recent years, climate change and exacerbated soil degradation have resulted in a variety of abiotic stresses, such as greenhouse effects, lower temperatures, drought, floods, soil salinization and heavy metal pollution. As such, there is an extremely high demand for additional research, in order to address these negative factors. Studies have shown that the alternative splicing of many genes in rice is affected by stress conditions, suggesting that manipulation of the alternative splicing of specific genes may be an effective approach for rice to adapt to abiotic stress. With the advancement of microarrays, and more recently, next generation sequencing technology, several studies have shown that more than half of the genes in the rice genome undergo alternative splicing. This mini-review summarizes the latest progress in the research of splicing and alternative splicing in rice, compared to splicing in humans. Furthermore, we discuss how additional studies may change the landscape of investigation of rice functional genomics and genetically improved rice. [BMB Reports 2013; 46(9): 439-447]
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Affiliation(s)
- Zhiguo E
- Nantong University, Nantong 226001, P.R. China ;
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22
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Biselli C, Cavalluzzo D, Perrini R, Gianinetti A, Bagnaresi P, Urso S, Orasen G, Desiderio F, Lupotto E, Cattivelli L, Valè G. Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining. RICE (NEW YORK, N.Y.) 2014; 7:1. [PMID: 26055995 PMCID: PMC3904453 DOI: 10.1186/1939-8433-7-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/26/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. RESULTS In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. CONCLUSIONS The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wxa and Wxb alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.
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Affiliation(s)
- Chiara Biselli
- Rice Research Unit, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, S.S. 11 to Torino, Km 2,5, 13100 Vercelli, Italy
- Genomics Research Centre, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, Piacenza, Italy
| | - Daniela Cavalluzzo
- Rice Research Unit, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, S.S. 11 to Torino, Km 2,5, 13100 Vercelli, Italy
| | - Rosaria Perrini
- Rice Research Unit, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, S.S. 11 to Torino, Km 2,5, 13100 Vercelli, Italy
| | - Alberto Gianinetti
- Genomics Research Centre, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, Piacenza, Italy
| | - Paolo Bagnaresi
- Genomics Research Centre, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, Piacenza, Italy
| | - Simona Urso
- Genomics Research Centre, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, Piacenza, Italy
| | - Gabriele Orasen
- Rice Research Unit, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, S.S. 11 to Torino, Km 2,5, 13100 Vercelli, Italy
| | - Francesca Desiderio
- Genomics Research Centre, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, Piacenza, Italy
| | - Elisabetta Lupotto
- Department of Plant Biology and Crop Production, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Roma, Italy
| | - Luigi Cattivelli
- Genomics Research Centre, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, Piacenza, Italy
| | - Giampiero Valè
- Rice Research Unit, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, S.S. 11 to Torino, Km 2,5, 13100 Vercelli, Italy
- Genomics Research Centre, CRA-Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, Piacenza, Italy
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24
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Bao JS. Toward Understanding the Genetic and Molecular Bases of the Eating and Cooking Qualities of Rice. CEREAL FOOD WORLD 2012. [DOI: 10.1094/cfw-57-4-0148] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- J. S. Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
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Cheng A, Ismail I, Osman M, Hashim H. Simple and rapid molecular techniques for identification of amylose levels in rice varieties. Int J Mol Sci 2012; 13:6156-6166. [PMID: 22754356 PMCID: PMC3382826 DOI: 10.3390/ijms13056156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/03/2012] [Accepted: 05/09/2012] [Indexed: 11/16/2022] Open
Abstract
The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)10, (CT)11, (CT)16, (CT)17, and (CT)18 were identified. Of these, (CT)11 and (CT)17 were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)10 and (CT)11, while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5′-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE.
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Affiliation(s)
- Acga Cheng
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia; E-Mails: (A.C.); (I.I.)
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia; E-Mails: (A.C.); (I.I.)
| | - Mohamad Osman
- Kulliyyah of Science, International Islamic University Malaysia, Jalan Istana, Bandar Indera Mahkota, Kuantan 25200, Pahang Darul Makmur, Malaysia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +609-571-6400; Fax: +609-571-6781
| | - Habibuddin Hashim
- Malaysian Agricultural Research and Development Institute (MARDI), Jalan Paya Keladi/Pinang Tunggal, Pejabat Pos Kepala Batas, Kepala Batas 13200, Pulau Pinang, Malaysia; E-Mail:
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Su Y, Rao Y, Hu S, Yang Y, Gao Z, Zhang G, Liu J, Hu J, Yan M, Dong G, Zhu L, Guo L, Qian Q, Zeng D. Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:859-67. [PMID: 21698394 DOI: 10.1007/s00122-011-1632-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 05/31/2011] [Indexed: 05/04/2023]
Abstract
In this study, one major QTL affecting gel consistency (GC) of japonica/indica cross was identified on chromosome 6 using a DH population. To understand the molecular mechanism that regulates GC in rice grains, the major QTL (qGC-6) was isolated through a map-based cloning approach utilizing chromosome segment substitution lines (CSSLs). Using 64 plants with extremely soft GC that were selected on recombinant break points between two SSR markers, RM540 and RM8200 in a BC4F2 population, qGC-6 was mapped to a 60-kb DNA region between two STS markers, S26 and S27. These two markers were then used to further identify recombination break points. Finally, qGC-6 was delimited in an interval of a 11-kb region. Gene prediction analysis of the 11-kb DNA sequence containing qGC-6 identified only one putative ORF, which encodes granule-bound starch synthesis protein (Wx protein). Results of sequencing analysis and complementation experiment confirmed that this candidate ORF is responsible for rice GC. Genetic evidences revealed that Wx might contribute equally to the grain amylose content-controlling gene as well as gel consistency. This new information is important to breed rice varieties with improved grain quality.
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Affiliation(s)
- Yan Su
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 31006, Hangzhou, China
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Yu G, Olsen KM, Schaal BA. Association between nonsynonymous mutations of starch synthase IIa and starch quality in rice (Oryza sativa). THE NEW PHYTOLOGIST 2011; 189:593-601. [PMID: 20946420 DOI: 10.1111/j.1469-8137.2010.03495.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Starch quality is one of the most important agronomic traits in Asian rice, Oryza sativa. Starch synthase IIa (SsIIa) is a major candidate gene for starch quality variation. Within SsIIa, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in Escherichia coli. To search for the variation in SsIIa that is responsible for starch quality variation in rice, we sequenced the SsIIa exon 8 region and measured starch quality as starch disintegration in alkali for 289 accessions of cultivated rice and 57 accessions of its wild ancestor, Oryza rufipogon. A general linear model and nested clade analysis were used to identify the associations between the three nonsynonymous single nucleotide polymorphisms (SNPs) and starch quality. Among the three nonsynonymous SNPs, we found strong evidence of association at one nucleotide site ('SNP 3'), corresponding to a Leu/Phe replacement at codon 781. A second SNP, corresponding to a Val/Met replacement at codon 737, could potentially show an association with increased sample sizes. Variation in SsIIa enzyme activity is associated with the cohesiveness of rice grains when cooked, and our findings are consistent with selection for more cohesive grains during the domestication of tropical japonica rice.
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Affiliation(s)
- Guoqin Yu
- Department of Biology, Washington University of St. Louis, Missouri, 63130, USA Present address: Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, 20742, USA.
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Yu G, Olsen KM, Schaal BA. Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L. Mol Biol Evol 2010; 28:659-71. [PMID: 20829346 DOI: 10.1093/molbev/msq243] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.
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Affiliation(s)
- Guoqin Yu
- Department of Biology, Washington University, St Louis, Missouri, USA.
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29
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Liu L, Ma X, Liu S, Zhu C, Jiang L, Wang Y, Shen Y, Ren Y, Dong H, Chen L, Liu X, Zhao Z, Zhai H, Wan J. Identification and characterization of a novel Waxy allele from a Yunnan rice landrace. PLANT MOLECULAR BIOLOGY 2009; 71:609-26. [PMID: 19760367 DOI: 10.1007/s11103-009-9544-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 08/24/2009] [Indexed: 05/04/2023]
Abstract
Low amylose content (AC) is a desirable trait for rice (Oryza sativa L.) cooking quality and is selected in soft rice breeding. To gain a better understanding of the molecular mechanism controlling AC formation, we screened 83 Yunnan rice landraces in China and identified a rice variety, Haopi, with low AC. Genetic analyses and transgenic experiments revealed that low AC in Haopi was controlled by a novel allele of the Wx locus, Wx(hp), encoding a granule-bound starch synthase (GBSSI). Sequence comparisons of Wx(hp) and Wx(b) alleles (from Nipponbare) showed several nucleotide changes in the upstream regulatory regions (including the promoter, 5'-untranslated region, and first intron 5' splicing junction site). Interestingly, these changes had no obvious effect on the expression level and splicing efficiency of Wx transcripts. In addition, an examination of the coding region revealed that the Wx(hp) allele carries an A-to-G change at nucleotide position +497 from the start codon, resulting in an Asp(165)/Gly(165) substitution. The amino acid substitution had no detectable effects on GBSSI activity in vitro; however, it notably reduced the binding of GBSSI to starch granules, resulting in a reduction of AC in rice seeds. Moreover, three other Yunnan landraces with low AC also carry a nucleotide substitution identical to Haopi at the +497 position of the Wx gene, suggesting common ancestry. Based on the single-nucleotide polymorphism, we have developed a new derived cleaved amplified polymorphic sequence marker for use in breeding practice to manipulate AC in rice endosperm.
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Affiliation(s)
- Linglong Liu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Weigang 1, 210095 Nanjing, China
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ZHOU LH, LIU QQ, ZHANG CQ, XU Y, TANG SZ, GU MH. Variation and Distribution of Seed Storage Protein Content and Composition among Different Rice Varieties. ZUOWU XUEBAO 2009. [DOI: 10.3724/sp.j.1006.2009.00884] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Prathepha P. An assessment of Wx microsatellite allele, alkali degradation and differentiation of chloroplast DNA in traditional black rice (Oryza sativa L.) from Thailand and Lao PDR. Pak J Biol Sci 2009; 10:261-6. [PMID: 19070026 DOI: 10.3923/pjbs.2007.261.266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Thailand and Lao PDR are the country's rich rice diversity. To contribute a significant knowledge for development new rice varieties, a collection of 142 black rice (Oryza sativa) accessions were determined for variation of physico-chemical properties, Wx microsatellite allele, Wx allele and chloroplast DNA type. The results showed that amylose content of black rice accessions were ranged from 1.9 to 6.8%. All of the alkali disintegration types (high, intermediate and low) was observed in these rice with average of 1.75 on the 1-3 digestibility scale. The unique Wx microsatellite allele (CT)17 was found in these samples and all black rice strains carried Wx(b) allele. In addition, all black rice accessions were found the duplication of the 23 bp sequence motif in the exon 2 of the wx gene. This evidence is a common phenomenon in glutinous rice. Based on two growing condition for black rice, rainfed lowland and rainfed upland, chloroplast DNA type was distinct from each other. All rice strains from rainfed lowland was deletion plastotype, but all other rainfed upland strains were non-deletion types.
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Affiliation(s)
- Preecha Prathepha
- Walai Rukhavej Botanical Research Institute, Mahasarakham University, Khamriang District, Mahasarakham Province, 44150, Thailand
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Abstract
Intron sequences in nuclear pre-mRNAs are excised with either the major U2 snRNA-dependent spliceosomal pathway or the minor U12 snRNA-dependent spliceosomal pathway that exist in most eukaryotic organisms. While the predominant dinucleotides bordering each of these types of introns and the catalytic mechanism used in their excision are conserved in plants and animals, several features aiding in the recognition of plant introns are distinct from those in animals and yeast. Along with their short length, high AU content and high variation in their 5' and 3' splice sites and branchpoint consensus sequences are the most prominent characteristics of plant introns. Detailed surveys of site-directed mutant introns tested in vivo and chemically induced and naturally mutant introns analyzed in planta emphasize the effects of changing individual nucleotides in these splice site consensus sequences and highlight a number of noncanonical dinucleotides that are functional in plant systems.
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Affiliation(s)
- M A Schuler
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA.
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Muth J, Hartje S, Twyman RM, Hofferbert HR, Tacke E, Prüfer D. Precision breeding for novel starch variants in potato. PLANT BIOTECHNOLOGY JOURNAL 2008; 6:576-84. [PMID: 18422889 DOI: 10.1111/j.1467-7652.2008.00340.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Potato can be used as a source of modified starches for culinary and industrial processes, but its allelic diversity and tetraploid genome make the identification of novel alleles a challenge, and breeding such alleles into elite lines is a slow and difficult process. An efficient and reliable strategy has been developed for the rapid introduction and identification of new alleles in elite potato breeding lines, based on the ethylmethanesulphonate mutagenesis of dihaploid seeds. Using the granule-bound starch synthase I gene (waxy) as a model, a series of point mutations that potentially affect gene expression or enzyme function was identified. The most promising loss-of-function allele (waxy(E1100)) carried a mutation in the 5'-splice donor site of intron 1 that caused mis-splicing and protein truncation. This was used to establish elite breeding lineages lacking granule-bound starch synthase I protein activity and producing high-amylopectin starch. This is the first report of rapid and efficient mutation analysis in potato, a genetically complex and vegetatively propagated crop.
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Affiliation(s)
- Jost Muth
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074 Aachen, Germany
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Chen MH, Bergman C, Pinson S, Fjellstrom R. Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection. J Cereal Sci 2008. [DOI: 10.1016/j.jcs.2007.06.013] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Mikami I, Uwatoko N, Ikeda Y, Yamaguchi J, Hirano HY, Suzuki Y, Sano Y. Allelic diversification at the wx locus in landraces of Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:979-89. [PMID: 18305920 DOI: 10.1007/s00122-008-0729-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 02/09/2008] [Indexed: 05/10/2023]
Abstract
To examine continuous variation of amylose levels in Asian rice (Oryza sativa) landraces, the five putative alleles (Wx a, Wx in, Wx b, Wx op, and wx) at the wx locus were investigated in near-isogenic lines (NILs). Apparent amylose levels ranged from 0.5 to 29.9% in the NILs, showing a positive relation with the levels of Wx gene product, granule-bound starch synthase (GBSS) as well as the enzymatic activity per milligram starch granule. Only opaque (Wx op) accessions had an enzymatic activity per GBSS that was reduced to half the level of the others. Nucleotide sequences in the Wx gene were compared among 18 accessions harboring the five different alleles. Each of the Wx alleles had a unique replacement, frame-shift or splice donor site mutation, suggesting that these nucleotide changes could be reflected in phenotype alterations. A molecular phylogenetic tree constructed using the Wx gene indicated that ssp. japonica forms a distinct clade, whereas ssp. indica forms different clades together with the wild progenitor. Unexpectedly, the wx allele of 160 (indica from Taiwan) joined the japonica lineage; however, comparisons using linked genes for two Taiwanese accessions revealed that the wx gene was the product of gene flow from japonica to indica. Therefore, the japonica lineage frequently included Wx in, Wx b and wx, while Wx a and Wx op were found in the other lineages, strongly suggesting that allelic diversification occurred after divergence of the two subspecies. The present results were discussed in relation to the maintenance of agronomically valuable genes in various landraces.
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Affiliation(s)
- I Mikami
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
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36
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Zeng D, Yan M, Wang Y, Liu X, Qian Q, Li J. Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2007; 65:501-9. [PMID: 17579813 DOI: 10.1007/s11103-007-9186-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 05/08/2007] [Indexed: 05/10/2023]
Abstract
Starch is the major component of cereal grains. In rice, starch properties determine the eating and cooking quality. The dull endosperm of rice grains is a classical morphological and agronomical trait that has long been exploited for breeding and genetics study. To understand the molecular mechanism that regulates the starch biosynthesis in rice grains, we characterized a classic rice mutant dull endosperm1 (du1) and isolated Du1 through a map-based cloning approach. Du1, encoding a member of pre-mRNA processing (Prp1) family, is expressed mainly in panicles. Du1 specifically affects the splicing efficiency of Wx(b) and regulates starch biosynthesis by mediating the expression of starch biosynthesis genes. Analysis of du1wx shows that Du1 acts upstream of Wx(b). These results strongly suggest that Du1 may function as a regulator of the starch biosynthesis by affecting the splicing of Wx(b) and the expression of other genes involved in the rice starch biosynthetic pathways.
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Affiliation(s)
- Dali Zeng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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37
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New insights into the history of rice domestication. Trends Genet 2007; 23:578-87. [DOI: 10.1016/j.tig.2007.08.012] [Citation(s) in RCA: 357] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/18/2022]
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38
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Jayamani P, Negrão S, Brites C, Oliveira M. Potential of Waxy gene microsatellite and single-nucleotide polymorphisms to develop japonica varieties with desired amylose levels in rice (Oryza sativa L.). J Cereal Sci 2007. [DOI: 10.1016/j.jcs.2007.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Bao JS, Corke H, Sun M. Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1185-96. [PMID: 16964521 DOI: 10.1007/s00122-006-0394-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Accepted: 08/10/2006] [Indexed: 05/11/2023]
Abstract
Starch characteristics determine the quality of various products of rice, e.g., eating, cooking and processing qualities. Our previous study indicated that molecular markers inside or close to starch synthesizing genes can differentiate the starch properties of 56 waxy rices. Here we report microsatellite (or simple sequence repeat, SSR) polymorphism in the Waxy (Wx) gene, soluble starch synthase I gene (SS1) and starch branching enzyme 1 gene (SBE1), single nucleotide polymorphism (SNP) in Wx and starch branching enzyme 3 gene (SBE3), and a sequence tagged site (STS) in starch branching enzyme 1 gene (SBE1) among 499 nonwaxy rice samples and their relationships with starch physicochemical properties. The nonwaxy rice samples consist of landraces (n = 172) obtained from germplasm centers and cultivars and breeding lines (n = 327) obtained from various breeding programs. Ten (CT)( n ) microsatellite alleles, (CT)(8), (CT)(10), (CT)(11), (CT)(12, )(CT)(17), (CT)(18), (CT)(19), (CT)(20), (CT)(21), and (CT)(22), were found at the Wx locus, of which (CT)(11) was the most frequent, and (CT)(12), (CT)(21) and (CT)(22) were identified for the first time. Four (CT)( n ) microsatellite alleles were found at the SBE1 locus, (CT)(8), (CT)(9), and (CT)(10 )together with an insertion sequence of CTCTCGGGCGA, and (CT)(8) alone without the insertion, of which (CT)(9) and the insertion was a new allele identified in only one rice, IR1552. Multiple microsatellites clustered at the SS1 locus, and in addition to the three alleles previously detected (SSS-A = (AC)(2)...TCC(TC)(11)...(TC)(5)C(ACC)(11), SSS-B = (AC)(3)...TCT(TC)(6)...(TC)(4)C(ACC)(9), and SSS-C = (AC)(3)...TCT(TC)(6)...(TC)(4)C(ACC)(8)), one new allele (SSS-D = (AC)(2)...TCC(TC)(10)...(TC)(4)C(ACC)(9)) was found. Analysis of the starch physicochemical properties of the samples with different microsatellites, SNPs and STS groups indicated that these molecular markers can differentiate almost all the physicochemical properties examined, e.g., apparent amylose content (AAC), pasting viscosity characteristics, and gel textural properties. Wx SSR and Wx SNP alone explained more variations for all physicochemical properties than the other molecular markers. The total six markers could explain 92.2, 81 and 86% of total variation of AAC, gel hardness (HD), and gel cohesiveness (COH), respectively, and they could explain more than 40% of the total variation of hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BD), setback viscosity (SB) and gel adhesiveness (ADH). However, only 29% of the total variation of peak viscosity (PV) and 37% of pasting temperature (PT) could be explained by all the molecular markers. Some of these markers can differentiate the starch physicochemical properties among the rice samples with the same Wx allele, indicating that the variation within Wx allele classes can be explained by other starch synthesizing genes. These SSRs, SNPs and STS are useful in marker-assisted breeding for the improvement of starch quality of rice.
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Affiliation(s)
- J S Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hua Jiachi Campus, Hangzhou, 310029, People's Republic of China.
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Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 2006; 173:975-83. [PMID: 16547098 PMCID: PMC1526538 DOI: 10.1534/genetics.106.056473] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.
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Affiliation(s)
- Kenneth M Olsen
- Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA
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Isshiki M, Tsumoto A, Shimamoto K. The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. THE PLANT CELL 2006; 18:146-58. [PMID: 16339852 PMCID: PMC1323490 DOI: 10.1105/tpc.105.037069] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ser/Arg-rich (SR) proteins play important roles in the constitutive and alternative splicing of pre-mRNA. We isolated 20 rice (Oryza sativa) genes encoding SR proteins, of which six contain plant-specific characteristics. To determine whether SR proteins modulate splicing efficiency and alternative splicing of pre-mRNA in rice, we used transient assays in rice protoplasts by cotransformation of SR protein genes with the rice Waxy(b) (Wx(b))-beta-glucuronidase fusion gene. The results showed that plant-specific RSp29 and RSZp23, an SR protein homologous to human 9G8, enhanced splicing and altered the alternative 5' splice sites of Wx(b) intron 1. The resulting splicing pattern was unique to each SR protein; RSp29 stimulated splicing at the distal site, and RSZp23 enhanced splicing at the proximal site. Results of domain-swapping experiments between plant-specific RSp29 and SCL26, which is a homolog of human SC35, showed the importance of RNA recognition motif 1 and the Arg/Ser-rich (RS) domain for the enhancement of splicing efficiencies. Overexpression of plant-specific RSZ36 and SRp33b, a homolog of human ASF/SF2, in transgenic rice changed the alternative splicing patterns of their own pre-mRNAs and those of other SR proteins. These results show that SR proteins play important roles in constitutive and alternative splicing of rice pre-mRNA.
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Affiliation(s)
- Masayuki Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Ikoma, Japan
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42
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La Rota M, Kantety RV, Yu JK, Sorrells ME. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 2005; 6:23. [PMID: 15720707 PMCID: PMC550658 DOI: 10.1186/1471-2164-6-23] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 02/18/2005] [Indexed: 11/23/2022] Open
Abstract
Background Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags. Results The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice. Conclusion Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals.
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Affiliation(s)
- Mauricio La Rota
- Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Ramesh V Kantety
- Department of Plant & Soil Science, 138 ARC Building, Alabama A&M University, Normal, AL, 35762, USA
| | - Ju-Kyung Yu
- Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, 14853, USA
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Abstract
Glutinous rice is a major type of cultivated rice with long-standing cultural importance in Asia. A mutation in an intron 1 splice donor site of the Waxy gene is responsible for the change in endosperm starch leading to the glutinous phenotype. Here we examine an allele genealogy of the Waxy locus to trace the evolutionary and geographical origins of this phenotype. On the basis of 105 glutinous and nonglutinous landraces from across Asia, we find evidence that the splice donor mutation has a single evolutionary origin and that it probably arose in Southeast Asia. Nucleotide diversity measures indicate that the origin of glutinous rice is associated with reduced genetic variation characteristic of selection at the Waxy locus; comparison with an unlinked locus, RGRC2, confirms that this pattern is specific to Waxy. In addition, we find that many nonglutinous varieties in Northeast Asia also carry the splice donor site mutation, suggesting that partial suppression of this mutation may have played an important role in the development of Northeast Asian nonglutinous rice. This study demonstrates the utility of phylogeographic approaches for understanding trait diversification in crops, and it contributes to growing evidence on the importance of modifier loci in the evolution of domestication traits.
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Affiliation(s)
- Kenneth M Olsen
- Department of Genetics, North Carolina State University, Raleigh 27695, USA.
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Patron NJ, Smith AM, Fahy BF, Hylton CM, Naldrett MJ, Rossnagel BG, Denyer K. The altered pattern of amylose accumulation in the endosperm of low-amylose barley cultivars is attributable to a single mutant allele of granule-bound starch synthase I with a deletion in the 5'-non-coding region. PLANT PHYSIOLOGY 2002; 130:190-8. [PMID: 12226499 PMCID: PMC166552 DOI: 10.1104/pp.005454] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2002] [Revised: 05/02/2002] [Accepted: 05/26/2002] [Indexed: 05/20/2023]
Abstract
Reasons for the variable amylose content of endosperm starch from waxy cultivars of barley (Hordeum vulgare) were investigated. The mature grains of most such cultivars contain some amylose, although amounts are much lower than in wild-type cultivars. In these low-amylose cultivars, amylose synthesis starts relatively late in grain development. Starch granules in the outer cell layers of the endosperm contain more amylose than those in the center. This distribution corresponds to that of granule-bound starch synthase I (GBSSI), which is more severely reduced in amount in the center of the endosperm than in the outer cell layers, relative to wild-type cultivars. A second GBSSI in the barley plant, GBSSIb, is not detectable in the endosperm and cannot account for amylose synthesis in the low-amylose cultivars. The change in the expression of GBSSI in the endosperm of the low-amylose cultivars appears to be due to a 413-bp deletion of part of the promoter and 5'-untranslated region of the gene. Although these cultivars are of diverse geographical origin, all carry this same deletion, suggesting that the low-amylose cultivars have a common waxy ancestor. Records suggest a probable source in China, first recorded in the 16th century. Two further families of waxy cultivars have no detectable amylose in the endosperm starch. These amylose-free cultivars were selected in the 20th century from chemically mutagenized populations of wild-type barley. In both cases, 1-bp alterations in the GBSSI gene completely eliminate GBSSI activity.
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Affiliation(s)
- Nicola J Patron
- John Innes Centre, Norwich Research Park, Colney, Norfolk NR4 7UH, United Kingdom
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Tan Y, Xing Y, Zhang Q, Sun M, Corke H. Quantitative Genetic Basis of Gelatinization Temperature of Rice. Cereal Chem 2001. [DOI: 10.1094/cchem.2001.78.6.666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yifang Tan
- Cereal Science Laboratory, Department of Botany, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- National Key Laboratory for Crop Genetic Improvement, and Department of Agronomy, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory for Crop Genetic Improvement, and Department of Agronomy, Huazhong Agricultural University, Wuhan 430070, China
| | - Qifa Zhang
- National Key Laboratory for Crop Genetic Improvement, and Department of Agronomy, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Sun
- Population Genetics Laboratory, Department of Zoology, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Harold Corke
- Cereal Science Laboratory, Department of Botany, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Corresponding author. E-mail: Fax: +852 2858 3477
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46
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Persans MW, Nieman K, Salt DE. Functional activity and role of cation-efflux family members in Ni hyperaccumulation in Thlaspi goesingense. Proc Natl Acad Sci U S A 2001; 98:9995-10000. [PMID: 11481436 PMCID: PMC55566 DOI: 10.1073/pnas.171039798] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2001] [Indexed: 11/18/2022] Open
Abstract
The ability of Thlaspi goesingense to hyperaccumulate Ni seems to be governed in part by enhanced accumulation of Ni within leaf vacuoles. We have characterized genes from T. goesingense encoding putative vacuolar metal ion transport proteins, termed metal tolerance proteins (TgMTPs). These proteins contain all of the features of cation-efflux family members, and evidence indicates they are derived from a single genomic sequence (TgMTP1) that gives rise to an unspliced (TgMTP1t1) and a spliced (TgMTP1t2) transcript. Heterologous expression of these transcripts in yeast lacking the TgMTP1 orthologues COT1 and ZRC1 complements the metal sensitivity of these yeast strains, suggesting that TgMTP1s are able to transport metal ions into the yeast vacuole in a manner similar to COT1 and ZRC1. The unspliced and spliced TgMTP1 variants differ within a histidine-rich putative metal-binding domain, and these sequence differences are reflected as alterations in the metal specificities of these metal ion transporters. When expressed in yeast, TgMTP1t1 confers the highest level of tolerance to Cd, Co, and Zn, whereas TgMTP1t2 confers the highest tolerance to Ni. TgMTP1 transcripts are highly expressed in T. goesingense compared with orthologues in the nonaccumulators Arabidopsis thaliana, Thlaspi arvense, and Brassica juncea. We propose that the high-level expression of TgMTP1 in T. goesingense accounts for the enhanced ability of this hyperaccumulator to accumulate metal ions within shoot vacuoles.
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Affiliation(s)
- M W Persans
- Department of Chemistry, Northern Arizona University, Flagstaff 86011, USA
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Isshiki M, Yamamoto Y, Satoh H, Shimamoto K. Nonsense-mediated decay of mutant waxy mRNA in rice. PLANT PHYSIOLOGY 2001; 125:1388-95. [PMID: 11244118 PMCID: PMC65617 DOI: 10.1104/pp.125.3.1388] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2000] [Revised: 12/15/2000] [Accepted: 12/19/2000] [Indexed: 05/18/2023]
Abstract
Two rice (Oryza sativa) waxy mutations of the Japonica background were shown to contain approximately 20% of the fully spliced mRNA relative to the wild type. Sequencing analysis of the entire waxy genes of the two mutants revealed the presence of premature translation termination codons in exon 2 and exon 7. These results indicated that the lower accumulation of fully spliced RNA in the mutants was caused by nonsense-mediated decay (NMD), which is an RNA surveillance system universally found in eukaryotes. It is interesting that levels of RNA retaining intron 1 were not changed by premature nonsense codons, suggesting that splicing may be linked with NMD in plants, as previously found in mammalian cells. Measurements of the half-lives of waxy RNAs in transfected rice protoplasts indicated that the half-life of waxy RNA with a premature nonsense codon was 3.3 times shorter than that without a premature nonsense codon. Because the wild-type waxy transcripts, which are derived from the Wx(b) gene predominantly distributed among Japonica rice, have been shown to be less efficiently spliced and their alternative splicing has been documented, we examined whether these splicing properties influenced the efficiency of NMD. However, no effects were observed. These results established that NMD occurs in rice waxy RNA containing a premature nonsense codon.
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Affiliation(s)
- M Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan
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48
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Hirano HY, Sano Y. Comparison of Waxy gene regulation in the endosperm and pollen in Oryza sativa L. Genes Genet Syst 2000; 75:245-9. [PMID: 11245217 DOI: 10.1266/ggs.75.245] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Waxy (Wx) gene controls amylose synthesis in rice (Oryza sativa) and its expression is regulated organ-specifically. The Wx gene is expressed in the endosperm and pollen but not in other organs. In order to know whether Wx gene regulation is the same in the endosperm and pollen, we compared expression patterns of the rice Wx gene in these two organs by immunoblot analysis. We focused on the allelic differences (Wxa and Wxb), cool temperature response and effects of the mutation at the du loci. The results obtained are as follows. First, the quantitative regulation depending on two alleles, Wxa and Wxb, was common to both organs; Wx protein levels from the Wxa allele were about 10-fold higher than those from the Wxb allele in the pollen as well as in the endosperm. Second, in both the endosperm and pollen, expression of the Wxb gene, but not the Wxa gene, was enhanced in response to cool temperature. In contrast to these two types of regulation, analysis of two du mutants, 2035 (du1) and 76-3 (du2), revealed that the pattern of reduction in Wx protein levels in the pollen was distinct from that in the endosperm, suggesting that functions of the two du+ genes differ in these two organs.
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Affiliation(s)
- H Y Hirano
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi, Japan.
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Isshiki M, Nakajima M, Satoh H, Shimamoto K. dull: rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000; 23:451-460. [PMID: 10972871 DOI: 10.1046/j.1365-313x.2000.00803.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the endosperm of japonica rice, du-1 and du-2 mutations cause the reduction of amylose contents. It was previously shown that the Wx(b) allele of rice, which is predominantly distributed in japonica rice, has a mutation in the 5' splice site of intron 1 resulting in the creation of two weak 5' splice sites within exon 1. In du-1 and du-2 mutants, spliced Wx(b) transcripts were highly reduced, whereas the processing of transcripts derived from three other genes highly expressed in endosperm was not apparently influenced. Results of competitive RT-PCR analysis indicate that transcripts spliced at the two newly created 5' splice sites were equally affected in these two mutants. Genetic and molecular analyses of the effects of du-1 and du-2 on Wx(a) pre-mRNA with normal splice sites indicate that these two mutations do not affect the processing of Wx(a) pre-mRNA after splicing, suggesting that du-1 and du-2 are mutations of genes required for the efficient splicing of mutated Wx(b) pre-mRNA. Furthermore, du-1 and du-2 showed differential effects in endosperm and pollen. Although both mutations caused similar effects on the splicing of Wx(a) transcripts in endosperm, du-1 caused higher reduction of Wx(b) mRNA in pollen than in endosperm, while du-2 had a lesser effect in pollen than in endosperm. Based on these results, we propose that the du-1 and du-2 loci of rice encode tissue-specifically regulated splicing factors that are involved in alternative splicing of pre-mRNA in rice.
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Affiliation(s)
- M Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan
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