1
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Matsuba S, Maruyama-Funatsuki W, Umemoto T, Kato H, Kuroki M, Yokogami N, Ikegaya T, Shimizu H, Iriki N. The induced mutant allele flo4-303 confers floury characteristics on the japonica rice cultivar 'Hoshinoko'. BREEDING SCIENCE 2022; 72:383-388. [PMID: 36776444 PMCID: PMC9895802 DOI: 10.1270/jsbbs.22059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
Rice flour is useful as a substitute for wheat flour, however, to obtain fine flour, millers need special milling facilities, which increase the cost of milling. To reduce the milling cost, we developed a floury mutant line by irradiating gamma-rays to dry seeds of the japonica cultivar 'Hoshinoyume'. The line was registered as a new cultivar, 'Hoshinoko'. Genetical analysis of the floury trait was conducted using an F2 population derived from a cross between 'Hoshinoko' and 'Corbetti' (a japonica rice cultivar with normal endosperm), which indicated the involvement of a single recessive gene located near the RM163 marker on the long arm of rice chromosome 5, flanking flo4 identified by Kang et al. (2005). Sequence analysis of flo4 showed a two-bp (CA) insertion in the eighth exon of in 'Hoshinoko' compared to that of 'Hoshinoyume', which led to a frameshift mutation. The CAPS-based genotype of flo4 gene completely correlated to the phenotype of endosperm in two populations. This CAPS marker could be helpful for rice breeders to develop new cultivars harboring floury endosperm of the flo4-303 gene.
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Affiliation(s)
- Shuichi Matsuba
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Wakako Maruyama-Funatsuki
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
- NARO Headquarters, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Takayuki Umemoto
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
- Institute of Food Research, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Hideki Kato
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
- Odawara Research Center, Nippon Soda Co., Ltd., 345 Takada, Odawara, Kanagawa 250-0280, Japan
| | - Makoto Kuroki
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
- Kyushu Okinawa Agricultural Research Center, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Narifumi Yokogami
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
- Tohoku Agricultural Research Center, NARO, 3 Shimo-furumichi, Yotsuya, Daisen, Akita 014-0102, Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Hiroyuki Shimizu
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
- NARO Headquarters, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Norio Iriki
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
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2
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Authentication of carnaroli rice by HRM analysis targeting nucleotide polymorphisms in the Alk and Waxy genes. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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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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4
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Chen MH, Bett-Garber K, Lea J, McClung A, Bergman C. High Resistant Starch Rice: Variation in Starch Related SNPs, and Functional, and Sensory Properties. Foods 2021; 11:foods11010094. [PMID: 35010220 PMCID: PMC8750951 DOI: 10.3390/foods11010094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022] Open
Abstract
Human diets containing greater resistant starch (RS) are associated with superior glycemic control. Although high amylose rice has higher RS (29 g/kg to 44 g/kg) than lower amylose content varieties, sensory and processing properties associated with RS have not been evaluated. This study used variants of Waxy and starch synthase II a (SSIIa) genes to divide high amylose (256 g/kg to 284 g/kg) varieties into three haplotypes to examine their effects on RS, RVA parameters, and 14 cooked rice texture properties. RVA characteristics were influenced by both genes with peak and hotpaste viscosity differentiating the three haplotypes. Setback from hotpaste viscosity was the only RVA parameter correlated with RS content across three haplotypes (r = −0.76 to −0.93). Cooked rice texture attributes were impacted more by Waxy than by SSIIa with initial starch coating, roughness, and intact particles differentiating the three haplotypes. Pairwise correlation (r = 0.46) and PCA analyses suggested that roughness was the only texture attribute associated with RS content; while protein content influenced roughness (r = 0.49) and stickiness between grains (r = 0.45). In conclusion, variation exists among genetic haplotypes with high RS for sensory traits that will appeal to diverse consumers across the globe with limited concern for negatively affecting grain processing quality.
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Affiliation(s)
- Ming-Hsuan Chen
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160, USA;
- Correspondence:
| | - Karen Bett-Garber
- Southern Regional Research Center, USDA-ARS, New Orleans, LA 70124, USA; (K.B.-G.); (J.L.)
| | - Jeanne Lea
- Southern Regional Research Center, USDA-ARS, New Orleans, LA 70124, USA; (K.B.-G.); (J.L.)
| | - Anna McClung
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160, USA;
| | - Christine Bergman
- Food and Beverage Department, University of Nevada Las Vegas, Las Vegas, NV 89154, USA;
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5
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Changes in fried rice batter with increased resistant starch and effects on sensory quality of battered fried onions. Cereal Chem 2021. [DOI: 10.1002/cche.10502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Yu B, Xiang D, Mahfuz H, Patterson N, Bing D. Understanding Starch Metabolism in Pea Seeds towards Tailoring Functionality for Value-Added Utilization. Int J Mol Sci 2021; 22:8972. [PMID: 34445676 PMCID: PMC8396644 DOI: 10.3390/ijms22168972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022] Open
Abstract
Starch is the most abundant storage carbohydrate and a major component in pea seeds, accounting for about 50% of dry seed weight. As a by-product of pea protein processing, current uses for pea starch are limited to low-value, commodity markets. The globally growing demand for pea protein poses a great challenge for the pea fractionation industry to develop new markets for starch valorization. However, there exist gaps in our understanding of the genetic mechanism underlying starch metabolism, and its relationship with physicochemical and functional properties, which is a prerequisite for targeted tailoring functionality and innovative applications of starch. This review outlines the understanding of starch metabolism with a particular focus on peas and highlights the knowledge of pea starch granule structure and its relationship with functional properties, and industrial applications. Using the currently available pea genetics and genomics knowledge and breakthroughs in omics technologies, we discuss the perspectives and possible avenues to advance our understanding of starch metabolism in peas at an unprecedented level, to ultimately enable the molecular design of multi-functional native pea starch and to create value-added utilization.
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Affiliation(s)
- Bianyun Yu
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada; (D.X.); (H.M.); (N.P.)
| | - Daoquan Xiang
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada; (D.X.); (H.M.); (N.P.)
| | - Humaira Mahfuz
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada; (D.X.); (H.M.); (N.P.)
- Department of Biology, Faculty of Science, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Nii Patterson
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada; (D.X.); (H.M.); (N.P.)
| | - Dengjin Bing
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C and E Trail, Lacombe, AB T4L 1W1, Canada;
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7
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Pezzotti G, Zhu W, Chikaguchi H, Marin E, Boschetto F, Masumura T, Sato YI, Nakazaki T. Raman Molecular Fingerprints of Rice Nutritional Quality and the Concept of Raman Barcode. Front Nutr 2021; 8:663569. [PMID: 34249986 PMCID: PMC8260989 DOI: 10.3389/fnut.2021.663569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/25/2021] [Indexed: 12/31/2022] Open
Abstract
The nutritional quality of rice is contingent on a wide spectrum of biochemical characteristics, which essentially depend on rice genome, but are also greatly affected by growing/environmental conditions and aging during storage. The genetic basis and related identification of genes have widely been studied and rationally linked to accumulation of micronutrients in grains. However, genetic classifications cannot catch quality fluctuations arising from interannual, environmental, and storage conditions. Here, we propose a quantitative spectroscopic approach to analyze rice nutritional quality based on Raman spectroscopy, and disclose analytical algorithms for the determination of: (i) amylopectin and amylose concentrations, (ii) aromatic amino acids, (iii) protein content and structure, and (iv) chemical residues. The proposed Raman algorithms directly link to the molecular composition of grains and allow fast/non-destructive determination of key nutritional parameters with minimal sample preparation. Building upon spectroscopic information at the molecular level, we newly propose to represent the nutritional quality of labeled rice products with a barcode specially tailored on the Raman spectrum. The Raman barcode, which can be stored in databases promptly consultable with barcode scanners, could be linked to diet applications (apps) to enable a rapid, factual, and unequivocal product identification based on direct molecular screening.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Orthopedic Surgery, Tokyo Medical University, Tokyo, Japan.,The Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, Japan.,Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
| | - Haruna Chikaguchi
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Francesco Boschetto
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takehiro Masumura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, Kyoto, Japan
| | - Yo-Ichiro Sato
- Research Center for Japanese Food Culture, Kyoto Prefectural University, Kyoto, Japan
| | - Tetsuya Nakazaki
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
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8
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Naseer B, Naik HR, Hussain SZ, Shikari AB, Noor N. Variability in waxy (Wx) allele, in-vitro starch digestibility, glycemic response and textural behaviour of popular Northern Himalayan rice varieties. Sci Rep 2021; 11:12047. [PMID: 34103609 PMCID: PMC8187641 DOI: 10.1038/s41598-021-91537-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/17/2021] [Indexed: 11/29/2022] Open
Abstract
Eight commonly cultivated and consumed rice varieties of Northern Himalayan regions and a popular high amylose rice variety were characterized at Wx locus and evaluated for resistant starch (RS), in-vitro starch digestibility, predicted glycemic index (pGI), glycemic load (GL) and textural parameters. Cytosine and thymine repeats (CT)n at waxy locus (Wx) showed high association with apparent amylose content (AAC). Both pGI and GL varied substantially within the selected varieties. The pGI was relatively lower in high and intermediate amylose Indica varieties compared to low amylose Japonica ones. However, Koshikari despite being a low amylose variety showed relatively lower pGI and GL, due to its higher RS, dietary fiber, protein and fat content. It was thus presumed that in addition to AAC, RS and other grain components also affect the glycemic response. Inherent resistance to enzymatic hydrolysis was also found to be higher in firm textured and less sticky rice varieties. The genotypes-Lalat, Basmati-1509 and Koshikari, in view of their low to moderate pGI and relatively higher RS content, can be explored in future breeding programmes to develop rice varieties whose consumption will help to prevent hyper/hypo glycemic responses in Northern Himalayan regions, where daily staple diet is rice.
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Affiliation(s)
- Bazila Naseer
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, 190025, India
| | - H R Naik
- Department of Food Technology, Islamic University of Science and Technology, Awantipora, 192122, India
| | - Syed Zameer Hussain
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, 190025, India.
| | - Asif Bashir Shikari
- Department of Food Technology, Islamic University of Science and Technology, Awantipora, 192122, India
| | - Nowsheen Noor
- Department of Food Technology, Islamic University of Science and Technology, Awantipora, 192122, India
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9
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Chen M, McClung AM, Rohila JS, Barnaby JY. Effects of alternate wetting and drying irrigation management and air temperature during grainfill on rice grain physicochemical and functionality traits of US inbred varieties. Cereal Chem 2021. [DOI: 10.1002/cche.10440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ming‐Hsuan Chen
- Dale Bumpers National Rice Research Center U.S. Department of Agriculture‐Agricultural Research Service (USDA‐ARS) Stuttgart AR USA
| | - Anna M. McClung
- Dale Bumpers National Rice Research Center U.S. Department of Agriculture‐Agricultural Research Service (USDA‐ARS) Stuttgart AR USA
| | - Jai S. Rohila
- Dale Bumpers National Rice Research Center U.S. Department of Agriculture‐Agricultural Research Service (USDA‐ARS) Stuttgart AR USA
| | - Jinyoung Y. Barnaby
- Dale Bumpers National Rice Research Center U.S. Department of Agriculture‐Agricultural Research Service (USDA‐ARS) Stuttgart AR USA
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10
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You H, Zhang O, Xu L, Liang C, Xiang X. Effects of soluble starch synthase IIa allelic variation on rice grain quality with different Waxy backgrounds. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:5344-5351. [PMID: 32533854 DOI: 10.1002/jsfa.10582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/15/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Soluble starch synthase IIa (ALK, SSII-3) is the major gene regulating gelatinization temperature (GT) and SSII-3 M1 is an effective marker for identifying SSIIa alleles. However, the haplotypes of SSIIa alleles amplified by SSII-3M1 and their allelic effect sunder different Waxy (Wx) background in non-glutinous rice remain unclear. RESULTS By integrating the genetic background analysis and by the identification of the genotypes of Wx and SSIIa, we found that the SSIIa alleles amplified by SSII-3 M1 were haplotype 1 (G/G/GC, indica-type) and 4 (A/G/TT, japonica-type), which had a significant effect on pasting temperature (PaT), hot paste viscosity (HPV), and the alkali spreading value (ASV). There were significant effects of SSIIa alleles on HPV, cool paste viscosity (CPV), and consistency value with different Wx backgrounds. The apparent amylose content (AAC) of samples significantly affected the accuracy of GT, which was represented by the manually determined pasting temperature (PTm). CONCLUSIONS The SSIIa alleles amplified by SSII-3 M1 are indica type and japonica type. Different SSIIa haplotypes significantly affect HPV, CPV, PaT, and ASV. GT, PaT, and PTm are mainly affected by SSIIa alleles. The classification of all samples with different haplotypes of SSIIa indicates that their AAC (Wx genotypes) is essentially. The effects of SSIIa alleles are themselves affected by different Wx alleles. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Hui You
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Ouling Zhang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Liang Xu
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Cheng Liang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
| | - Xunchao Xiang
- Lab of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, Mianyang, China
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11
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Zhang H, Chen J, Shan S, Cao F, Chen G, Zou Y, Huang M, Abou-Elwafa SF. Proteomic profiling reveals differentially expressed proteins associated with amylose accumulation during rice grain filling. BMC Genomics 2020; 21:714. [PMID: 33059592 PMCID: PMC7561244 DOI: 10.1186/s12864-020-07105-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amylose accumulation in rice grains is controlled by genetic and environmental factors. Amylose content is a determinant factor of rice quality in terms of cooking and eating. Great variations in amylose content in indica rice cultivars have been observed. The current study was to identify differentially expressed proteins in starch and sucrose metabolism and glycolysis/gluconeogenesis pathways and their relationships to amylose synthesis using two rice cultivars possess contrasting phenotypes in grain amylose content. RESULTS Synthesis and accumulation of amylose in rice grains significantly affected the variations between rice cultivars in amylose contents. The high amylose content cultivar has three down-regulated differentially expressed proteins, i.e., LOC_Os01g62420.1, LOC_Os02g36600.1, and LOC_Os08g37380.2 in the glycolysis/gluconeogenesis pathway, which limit the glycolytic process and decrease the glucose-1-phosphate consumption. In the starch and sucrose metabolic pathway, an up-regulated protein, i.e., LOC_Os06g04200.1 and two down-regulated proteins, i.e., LOC_Os05g32710.1 and LOC_Os04g43360.1 were identified (Figure 4). Glucose-1-phosphate is one of the first substrates in starch synthesis and glycolysis that are catalyzed to form adenosine diphosphate glucose (ADPG), then the ADPG is catalyzed by granule-bound starch synthase I (GBSS I) to elongate amylose. CONCLUSIONS The results indicate that decreasing the consumption of glucose-1-phosphate in the glycolytic process is essential for the formation of ADPG and UDPG, which are substrates for amylose synthesis. In theory, amylose content in rice can be regulated by controlling the fate of glucose-1-phosphate.
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Affiliation(s)
- Hengdong Zhang
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.,Qianxinan Institute of Karst Regional Development Xingyi, Xingyi, 652400, Guizhou, China
| | - Jiana Chen
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Shuanglü Shan
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Fangbo Cao
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Guanghui Chen
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yingbin Zou
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Min Huang
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
| | - Salah F Abou-Elwafa
- Agronomy Department, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
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12
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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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13
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GWAS for Starch-Related Parameters in Japonica Rice ( Oryza sativa L.). PLANTS 2019; 8:plants8080292. [PMID: 31430915 PMCID: PMC6724095 DOI: 10.3390/plants8080292] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 11/28/2022]
Abstract
Rice quality is mainly related to the following two starch components, apparent amylose content (AAC) and resistant starch (RS). The former affects grain cooking properties, while RS acts as a prebiotic. In the present study, a Genome Wide Association Scan (GWAS) was performed using 115 rice japonica accessions, including tropical and temperate genotypes, with the purpose of expanding the knowledge of the genetic bases affecting RS and AAC. High phenotypic variation was recorded for the two traits, which positively correlated. Moreover, both the parameters correlated with seed length (positive correlation) and seed width (negative correlation). A correlational selection according to human preferences has been hypothesized for the two starch traits and grain size. In addition, human selection has been proposed as the causal agent even for the different phenotypes related to starch and grain size showed by the tropical and temperate japonica accessions utilized in this study. The present GWAS led to the identification of 11 associations for RS on seven chromosomes and five associations for AAC on chromosome 6. Candidate genes and co-positional relationships with quantitative trait loci (QTLs) previously identified as affecting RS and AAC were identified for 6 associations. The candidate genes and the new RS- and/or AAC-associated regions detected provide valuable sources for future functional characterizations and for breeding programs aimed at improving rice grain quality.
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14
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Anacleto R, Badoni S, Parween S, Butardo VM, Misra G, Cuevas RP, Kuhlmann M, Trinidad TP, Mallillin AC, Acuin C, Bird AR, Morell MK, Sreenivasulu N. Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1261-1275. [PMID: 30549178 PMCID: PMC6575982 DOI: 10.1111/pbi.13051] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 11/15/2018] [Accepted: 11/25/2018] [Indexed: 05/19/2023]
Abstract
Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa ) explained the intermediate-to-high GI variation. A SNP (C˃T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.
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Affiliation(s)
| | - Saurabh Badoni
- International Rice Research InstituteLos BañosPhilippines
| | - Sabiha Parween
- International Rice Research InstituteLos BañosPhilippines
| | - Vito M. Butardo
- International Rice Research InstituteLos BañosPhilippines
- Department of Chemistry and BiotechnologyFaculty of Science, Engineering and TechnologySwinburne University of TechnologyHawthornVic.Australia
| | - Gopal Misra
- International Rice Research InstituteLos BañosPhilippines
| | | | - Markus Kuhlmann
- The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | | | - Cecilia Acuin
- International Rice Research InstituteLos BañosPhilippines
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15
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Huggins TD, Chen MH, Fjellstrom RG, Jackson AK, McClung AM, Edwards JD. Association Analysis of Three Diverse Rice ( Oryza sativa L.) Germplasm Collections for Loci Regulating Grain Quality Traits. THE PLANT GENOME 2019; 12:170085. [PMID: 30951092 DOI: 10.3835/plantgenome2017.09.0085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice ( L.) end-use cooking quality is vital for producers and billions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality provides essential information for improved breeding strategies to enhance desirable traits that are stable across variable climatic and environmental conditions. In this study, genome-wide association (GWA) analysis of three rice diversity panels, the USDA rice core subset (1364 accessions), the minicore (MC) (173 accessions after removing non-), and the high density rice array-MC (HDMC) (383 accessions), with simple sequence repeats, single nucleotide polymorphic markers, or both, revealed large- and small-effect loci associated with known genes and previously uncharacterized genomic regions. Clustering of the significant regions in the GWA results suggests that multiple grain quality traits are inherited together. The 11 novel candidate loci for grain quality traits and the seven candidates for grain chalk identified are involved in the starch biosynthesis pathway. This study highlights the intricate pleiotropic relationships that exist in complex genotype-phenotypic associations and gives a greater insight into effective breeding strategies for grain quality improvement.
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Butardo VM, Sreenivasulu N, Juliano BO. Improving Rice Grain Quality: State-of-the-Art and Future Prospects. Methods Mol Biol 2019; 1892:19-55. [PMID: 30397798 DOI: 10.1007/978-1-4939-8914-0_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rice grain quality encompasses complex interrelated traits that cover biochemical composition, cooking, eating, nutritional, and sensory properties. Because rice endosperm is composed mainly of starch, rice grain quality is traditionally defined by characterizing starch structure and composition, which is then subsequently correlated with functional properties of the grain. The current proxy tests routinely used to describe rice grain quality preferences are rather limited to the estimation of apparent amylose content, gelatinization temperature, and gel consistency. Additional tests that characterize starch property, viscoelasticity, grain texture, and aroma are also employed in more advanced laboratories. However, these tests are not routinely applied in breeding programs to distinguish cooking quality classes to reflect evolving consumer preference and market demand. As consumer preferences in Asia and all over the world are diverse due to varied demographics and culture, defining uniform attributes to capture regional grain quality preferences becomes more challenging. Hence, novel and innovative proxy tests are needed to characterize rice grain quality to meet the demand for consumer preferences of commercially-released cultivars. In this chapter, the current methods employed in rice grain quality monitoring are succinctly reviewed. Future prospects for improvement are identified, introducing cutting edge technologies that can facilitate high-throughput screening of rice diversity panels and breeding lines. Aside from addressing the requirements for quality improvement in the traditional inbred rice breeding programs, we also tackled the need to enhance grain quality in the hybrid rice sector.
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Affiliation(s)
- Vito M Butardo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Nese Sreenivasulu
- International Rice Research Institute, Los Baños, Laguna, Philippines.
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17
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Li H, Wen Y, Wang J, Sun B. Relations between chain-length distribution, molecular size, and amylose content of rice starches. Int J Biol Macromol 2018; 120:2017-2025. [DOI: 10.1016/j.ijbiomac.2018.09.204] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/25/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
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18
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Chen MH, Bergman CJ, McClung AM, Everette JD, Tabien RE. Resistant starch: Variation among high amylose rice varieties and its relationship with apparent amylose content, pasting properties and cooking methods. Food Chem 2017; 234:180-189. [DOI: 10.1016/j.foodchem.2017.04.170] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 12/01/2022]
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19
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Wang K, Zhou Q, Liu J, Qiu F, dela Paz MA, Larazo W, Yang Y, Xie F. Genetic Effects of Wx Allele Combinations on Apparent Amylose Content in Tropical Hybrid Rice. Cereal Chem 2017. [DOI: 10.1094/cchem-03-17-0065-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kai Wang
- Yuan Longping High-Tech Agriculture Co., Changsha 410000, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Qunfeng Zhou
- Yuan Longping High-Tech Agriculture Co., Changsha 410000, China
| | - Junyu Liu
- Yuan Longping High-Tech Agriculture Co., Changsha 410000, China
| | - Fulin Qiu
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
- Liaoning Rice Research Institute, Shenyang 110101, Liaoning, China
| | | | - Wenceslao Larazo
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Yuanzhu Yang
- Yuan Longping High-Tech Agriculture Co., Changsha 410000, China
| | - Fangming Xie
- Yuan Longping High-Tech Agriculture Co., Changsha 410000, China
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
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Bett-Garber KL, Bryant RJ, Grimm CC, Chen MH, Lea JM, McClung AM. Physicochemical and Sensory Analysis of U.S. Rice Varieties Developed for the Basmati and Jasmine Markets. Cereal Chem 2017. [DOI: 10.1094/cchem-09-16-0244-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Karen L. Bett-Garber
- Southern Regional Research Center, USDA, ARS, New Orleans, LA, U.S.A. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture
| | - Rolfe J. Bryant
- Dale Bumpers National Rice Research Center, USDA, ARS, Stuttgart, AR, U.S.A
| | - Casey C. Grimm
- Southern Regional Research Center, USDA, ARS, New Orleans, LA, U.S.A. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture
| | - Ming-Hsuan Chen
- Dale Bumpers National Rice Research Center, USDA, ARS, Stuttgart, AR, U.S.A
| | - Jeanne M. Lea
- Southern Regional Research Center, USDA, ARS, New Orleans, LA, U.S.A. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture
| | - Anna M. McClung
- Dale Bumpers National Rice Research Center, USDA, ARS, Stuttgart, AR, U.S.A
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Genotypic diversity and environmental stability of starch physicochemical properties in the USDA rice mini-core collection. Food Chem 2017; 221:1186-1196. [DOI: 10.1016/j.foodchem.2016.11.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 01/28/2023]
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22
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Bao J, Zhou X, Xu F, He Q, Park YJ. Genome-wide association study of the resistant starch content in rice grains. STARCH-STARKE 2017. [DOI: 10.1002/star.201600343] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jinsong Bao
- Department of Plant Resources; College of Industrial Science; Kongju National University; Yesan Republic of Korea
- Institute of Nuclear Agricultural Science; College of Agriculture and Biotechnology; Zhejiang University, Huajiachi Campus; Hangzhou P.R. China
| | - Xin Zhou
- Institute of Nuclear Agricultural Science; College of Agriculture and Biotechnology; Zhejiang University, Huajiachi Campus; Hangzhou P.R. China
| | - Feifei Xu
- Department of Plant Resources; College of Industrial Science; Kongju National University; Yesan Republic of Korea
- Institute of Nuclear Agricultural Science; College of Agriculture and Biotechnology; Zhejiang University, Huajiachi Campus; Hangzhou P.R. China
- Food Science Institute; Zhejiang Academy of Agricultural Sciences; Hangzhou Zhejiang P.R. China
| | - Qiang He
- Department of Plant Resources; College of Industrial Science; Kongju National University; Yesan Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources; College of Industrial Science; Kongju National University; Yesan Republic of Korea
- Center for Crop Genetic Resource and Breeding (CCGRB); Kongju National University; Cheonan Republic of Korea
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23
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Xiang X, Kang C, Xu S, Yang B. Combined effects of Wx and SSIIa haplotypes on rice starch physicochemical properties. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:1229-1234. [PMID: 27312246 DOI: 10.1002/jsfa.7854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Wx and SSIIa are central genes for determining starch physicochemical properties and rice endosperm starch is composed of linear amylose, which is entirely synthesized by granule bound starch synthase I (GBSSI, encoded by Wx) and branched amylopectin. In the present study, different haplotypes of rice were examined to investigate the combined effects of pivotal genes in the metabolic chain of starch, Wx and SSIIa. RESULTS Wx haplotypes differed in terms of apparent amylose content (AAC) and gel consistency (GC). The I-3 [haplotype I (Int1T/Ex10C) of Wx and haplotype 3 (A-G-TT) of SSIIa] and the I-4 combinations of rice had better eating and cooking qualities (ECQs) with lower AAC, lower gelatinization temperature (GT) and softer GC. CONCLUSION The characteristic parameters of Rapid Visco-analyser (RVA) could distinguish differences in AAC and GC but not GT. The I-3 and I-4 haplotype combinations of Wx and SSIIa represent key targets for the production of rice with better ECQs. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Xunchao Xiang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
- Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, 59 Qinglong Road, Mianyang, 621010, China
| | - Cuifang Kang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
| | - Shunju Xu
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
| | - Bowen Yang
- Laboratory of Plant Molecular Genetics and Breeding, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, China
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Mahender A, Anandan A, Pradhan SK, Pandit E. Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches. SPRINGERPLUS 2016; 5:2086. [PMID: 28018794 PMCID: PMC5148756 DOI: 10.1186/s40064-016-3744-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 11/25/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Rice breeding program needs to focus on development of nutrient dense rice for value addition and helping in reducing malnutrition. Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice. RESULTS Genes and QTLs are recently known for the nutritional quality of rice. By comprehensive literature survey and public domain database, we provided a critical review on nutritional aspects like grain protein and amino acid content, vitamins and minerals, glycemic index value, phenolic and flavonoid compounds, phytic acid, zinc and iron content along with QTLs linked to these traits. In addition, achievements through transgenic and advanced genomic approaches have been discussed. The information available on genes and/or QTLs involved in enhancement of micronutrient element and amino acids are summarized with graphical representation. CONCLUSION Compatible QTLs/genes may be combined together to design a desirable genotype with superior in multiple grain quality traits. The comprehensive review will be helpful to develop nutrient dense rice cultivars by integrating molecular markers and transgenic assisted breeding approaches with classical breeding.
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Affiliation(s)
- Anumalla Mahender
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Annamalai Anandan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Elssa Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
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Li H, Prakash S, Nicholson TM, Fitzgerald MA, Gilbert RG. Instrumental measurement of cooked rice texture by dynamic rheological testing and its relation to the fine structure of rice starch. Carbohydr Polym 2016; 146:253-63. [PMID: 27112873 DOI: 10.1016/j.carbpol.2016.03.045] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/08/2016] [Accepted: 03/17/2016] [Indexed: 11/26/2022]
Abstract
Increasing demands for better instrumental methods to evaluate cooked rice texture is driving innovations in rice texture research. This study characterized cooked rice texture by descriptive sensory analysis and two instrumental methods (texture profile analysis (TPA) and dynamic rheological testing) using a set of 18 varieties of rice with a wide range in amylose content (0-30%). The panellists' results indicated that hardness and stickiness were the two most discriminating attributes among 13 tested textural attributes. The consistency coefficient (K(*)) and loss tangent (tan δ) from a dynamic frequency sweep were used to compare with hardness and stickiness tested by TPA and sensory panellists, showing that using K(*) to express hardness, and tan δ to express stickiness, are both statistically and mechanistically meaningful. The instrumental method is rationalized in terms of starch structural differences between rices: a higher proportion of both amylose and long amylopectin branches with DP 70-100 causes a more elastic and less viscous texture, which is readily understood in terms of polymer dynamics in solution.
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Affiliation(s)
- Hongyan Li
- The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane 4072, QLD, Australia
| | - Sangeeta Prakash
- The University of Queensland, School of Agriculture and Food Science, Brisbane 4072, QLD, Australia
| | - Timothy M Nicholson
- The University of Queensland, School of Chemical Engineering, Brisbane 4072, QLD, Australia
| | - Melissa A Fitzgerald
- The University of Queensland, School of Agriculture and Food Science, Brisbane 4072, QLD, Australia
| | - Robert G Gilbert
- The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane 4072, QLD, Australia.
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26
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Cuevas RP, Pede VO, McKinley J, Velarde O, Demont M. Rice Grain Quality and Consumer Preferences: A Case Study of Two Rural Towns in the Philippines. PLoS One 2016; 11:e0150345. [PMID: 26982587 PMCID: PMC4794204 DOI: 10.1371/journal.pone.0150345] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 02/14/2016] [Indexed: 11/18/2022] Open
Abstract
Hedonic pricing analysis is conducted to determine the implicit values of various attributes in the market value of a good. In this study, hedonic pricing analysis was applied to measure the contribution of grain quality search and experience attributes to the price of rice in two rural towns in the Philippines. Rice samples from respondents underwent quantitative routine assessments of grain quality. In particular, gelatinization temperature and chalkiness, two parameters that are normally assessed through visual scores, were evaluated by purely quantitative means (differential scanning calorimetry and by digital image analysis). Results indicate that rice consumed by respondents had mainly similar physical and chemical grain quality attributes. The respondents' revealed preferences were typical of what has been previously reported for Filipino rice consumers. Hedonic regression analyses showed that grain quality characteristics that affected price varied by income class. Some of the traits or socioeconomic factors that affected price were percent broken grains, gel consistency, and household per capita rice consumption. There is an income effect on rice price and the characteristics that affect price vary between income classes.
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Affiliation(s)
- Rosa Paula Cuevas
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO 7777 Metro Manila, Philippines
| | - Valerien O. Pede
- Social Sciences Division, International Rice Research Institute, DAPO 7777 Metro Manila, Philippines
| | - Justin McKinley
- Social Sciences Division, International Rice Research Institute, DAPO 7777 Metro Manila, Philippines
| | - Orlee Velarde
- Social Sciences Division, International Rice Research Institute, DAPO 7777 Metro Manila, Philippines
- Asian Development Bank, 6 ADB Avenue, Mandaluyong City 1550, Metro Manila, Philippines
| | - Matty Demont
- Social Sciences Division, International Rice Research Institute, DAPO 7777 Metro Manila, Philippines
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27
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Zhao X, Zhou L, Ponce K, Ye G. The Usefulness of Known Genes/Qtls for Grain Quality Traits in an Indica Population of Diverse Breeding Lines Tested using Association Analysis. RICE (NEW YORK, N.Y.) 2015; 8:29. [PMID: 26391157 PMCID: PMC4577492 DOI: 10.1186/s12284-015-0064-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/05/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND A number of studies reported major genes/QTLs for rice grain shapes, chalkiness and starch physicochemical properties. For these finely mapped QTLs or cloned genes to make an impact in practical breeding, it is necessary to test their effects in different genetic backgrounds. In this study, two hundred nineteen markers for 20 starch synthesis genes, 41 fine mapped grain shape and related traits QTLs/genes, and 54 chalkiness QTLs/genes plus 15 additional markers and a large indica population of 375 advanced lines were used to identify marker-trait associations under 6 environments that can be used directly in breeding for grain quality traits. RESULTS The significant associations detected by the QK model were used to declare the usefulness of the targeted genes/QTLs. A total of 65 markers were detected associations with grain quality trait at least in one environment. More phenotypic variations could be explained by haplotype than single marker, as exemplified by the starch biosynthesising genes. GBSSI was the major gene for AC and explained up to 55 % of the phenotypic variation, which also affected GC and accounted up to 11.31 % of the phenotypic variation. SSIIa was the major gene for chalkiness and explained up to 17 and 21 % of variation of DEC and PGWC, respectively. In addition, RMw513 and RM18068 were associated with DEC in 6 environments as well. Four markers (RGS1, RM15206, RMw513 and Indel1) tightly linked to GS3, gw5, and qGL7-2 were the most important ones for grain shapes. Allelic combinations between SSIIa and RMw513 revealed more variations in DEC. CONCLUSIONS The validated markers for genes/QTLs with major effects could be directly used in breeding for grain quality via marker-assisted selection. Creating desirable allelic combinations by gene pyramiding might be an effective approach for the development of high quality breeding lines in rice.
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Affiliation(s)
- Xiangqian Zhao
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Lijie Zhou
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
- Present address: Longping Branch, Graduate School of Central South University, Changsha, 410125, Hunan, China
| | - Kimberley Ponce
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Guoyou Ye
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
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28
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Bryant RJ, M. Yeater K, McClung AM. Effect of Nitrogen Rate and the Environment on Physicochemical Properties of Selected High-Amylose Rice Cultivars. Cereal Chem 2015. [DOI: 10.1094/cchem-02-15-0035-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Rolfe J. Bryant
- Retired from U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA
| | | | - Anna M. McClung
- USDA, ARS, Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A
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29
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Birla DS, Malik K, Sainger M, Chaudhary D, Jaiwal R, Jaiwal PK. Progress and challenges in improving the nutritional quality of rice (Oryza sativaL.). Crit Rev Food Sci Nutr 2015; 57:2455-2481. [DOI: 10.1080/10408398.2015.1084992] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Deep Shikha Birla
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Kapil Malik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Manish Sainger
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Darshna Chaudhary
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Ranjana Jaiwal
- Department of Zoology, Maharshi Dayanand University, Rohtak, India
| | - Pawan K. Jaiwal
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
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Li H, Prakash S, Nicholson TM, Fitzgerald MA, Gilbert RG. The importance of amylose and amylopectin fine structure for textural properties of cooked rice grains. Food Chem 2015; 196:702-11. [PMID: 26593544 DOI: 10.1016/j.foodchem.2015.09.112] [Citation(s) in RCA: 288] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/23/2015] [Accepted: 09/29/2015] [Indexed: 10/23/2022]
Abstract
Statistically and causally meaningful relationships are established between starch molecular structure (the molecular distribution of branched starch and the chain length distribution of debranched starch) and texture (hardness and stickiness) of cooked rice grains. The amounts of amylose chains with degree of polymerization (DP) 100-20,000, and of long amylopectin chains, positively correlated with hardness, while amylopectin chains with DP<70 and amylose molecular size both showed negative correlations with hardness (p<0.05). There was also a significant negative correlation between stickiness and the amounts of long amylopectin chains (p<0.01). For rices with similar amylose content, the amount of amylose chains with DP 1000-2000 positively correlated with hardness while size negatively correlated with hardness (p<0.05). This indicates for the first time that, regardless of amylose content, rice varieties with smaller amylose molecular sizes and with higher proportions of long amylose chains have a harder texture after cooking.
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Affiliation(s)
- Hongyan Li
- School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane 4072, QLD, Australia
| | - Sangeeta Prakash
- The University of Queensland, School of Agriculture and Food Science, Brisbane 4072, QLD, Australia
| | - Timothy M Nicholson
- The University of Queensland, School of Chemical Engineering, Brisbane 4072, QLD, Australia
| | - Melissa A Fitzgerald
- The University of Queensland, School of Agriculture and Food Science, Brisbane 4072, QLD, Australia
| | - Robert G Gilbert
- School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane 4072, QLD, Australia.
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31
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Roles of GBSSI and SSIIa in determining amylose fine structure. Carbohydr Polym 2015; 127:264-74. [PMID: 25965483 DOI: 10.1016/j.carbpol.2015.03.081] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 03/27/2015] [Accepted: 03/28/2015] [Indexed: 11/23/2022]
Abstract
This study examines the relationships between genetics (single nucleotide polymorphisms (SNPs) in GBSSI and SSIIa genes), starch structure (amylose and amylopectin fine structures), and starch properties (relating to gelatinization). GBSSI and SSIIa SNPs did not alter the starch content of rice grains. GBSSI SNPs can affect the amylose content, but they are incapable of altering the chain-lengths of amylopectin and amylose. The amounts of both long and short amylose branches changed with the same trend as amylose content, and they appeared to affect starch gelatinization properties. SSIIa synthesizes intermediate single-lamella amylopectin chains (DP 16-21), and consequently impacts the gelatinization temperature. Mathematical modelling suggests that the reduction in SSIIa activity significantly increases the activity of SBEII, resulting in a decreased activity ratio of SS to SBE in the enzyme set governing an appropriate chain-length distribution range. This application of the genetics-structure-property paradigm provides selection strategies to produce rice varieties with improved qualities.
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32
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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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Patindol JA, Siebenmorgen TJ, Wang YJ. Impact of environmental factors on rice starch structure: A review. STARCH-STARKE 2014. [DOI: 10.1002/star.201400174] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- James A. Patindol
- Department of Food Science; University of Arkansas; Fayetteville AR USA
| | | | - Ya-Jane Wang
- Department of Food Science; University of Arkansas; Fayetteville AR USA
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Kaur S, Panesar PS, Bera MB, Kaur V. Simple Sequence Repeat Markers in Genetic Divergence and Marker-Assisted Selection of Rice Cultivars: A Review. Crit Rev Food Sci Nutr 2014; 55:41-9. [DOI: 10.1080/10408398.2011.646363] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hoai TTT, Matsusaka H, Toyosawa Y, Suu TD, Satoh H, Kumamaru T. Influence of single-nucleotide polymorphisms in the gene encoding granule-bound starch synthase I on amylose content in Vietnamese rice cultivars. BREEDING SCIENCE 2014; 64:142-8. [PMID: 24987300 PMCID: PMC4065321 DOI: 10.1270/jsbbs.64.142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 02/23/2014] [Indexed: 05/07/2023]
Abstract
Amylose content is one of the most important factors influencing the physical and chemical properties of starch in rice. Analysis of 352 Vietnamese rice cultivars revealed a wide range of variation in apparent amylose content and the expression level of granule-bound starch synthase. On the basis of single-nucleotide polymorphisms (SNP) at the splicing donor site of the first intron and in the coding region of the granule-bound starch synthase I gene, Waxy gene, alleles can be classified into seven groups that reflect differences in apparent amylose content. The very low and low apparent amylose content levels were tightly associated with a G to T in the first intron whereas intermediate and high amylose was associated with a T genotype at SNP in exon 10. The correlation between the combination of T genotype at SNP in the first intron, C in exon 6, or C in exon 10 was predominant among low amylose rice varieties. Our analysis confirmed the existence of Wx (op) allele in Vietnamese rice germplasm. The results of this study suggest that the low amylose properties of Vietnamese local rice germplasm are attributable to spontaneous mutations at exons, and not at the splicing donor site.
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Affiliation(s)
- Tran Thi Thu Hoai
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University,
Fukuoka 812-8581,
Japan
- Plant Resources Center, Vietnamese Academy of Agricultural Science,
Ankhanh, Hoaiduc, Hanoi,
Vietnam
| | - Hiroaki Matsusaka
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University,
Fukuoka 812-8581,
Japan
| | - Yoshiko Toyosawa
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University,
Fukuoka 812-8581,
Japan
| | - Tran Danh Suu
- Plant Resources Center, Vietnamese Academy of Agricultural Science,
Ankhanh, Hoaiduc, Hanoi,
Vietnam
| | - Hikaru Satoh
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University,
Fukuoka 812-8581,
Japan
| | - Toshihiro Kumamaru
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University,
Fukuoka 812-8581,
Japan
- Corresponding author (e-mail: )
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Cotta MG, Barros LMG, de Almeida JD, de Lamotte F, Barbosa EA, Vieira NG, Alves GSC, Vinecky F, Andrade AC, Marraccini P. Lipid transfer proteins in coffee: isolation of Coffea orthologs, Coffea arabica homeologs, expression during coffee fruit development and promoter analysis in transgenic tobacco plants. PLANT MOLECULAR BIOLOGY 2014; 85:11-31. [PMID: 24469961 DOI: 10.1007/s11103-013-0166-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/06/2013] [Indexed: 06/03/2023]
Abstract
The aim of the present study was to perform a genomic analysis of non-specific lipid-transfer proteins (nsLTPs) in coffee. Several nsLTPs-encoding cDNA and gene sequences were cloned from Coffea arabica and Coffea canephora species. In this work, their analyses revealed that coffee nsLTPs belong to Type II LTP characterized under their mature forms by a molecular weight of around 7.3 kDa, a basic isoelectric points of 8.5 and the presence of typical CXC pattern, with X being an hydrophobic residue facing towards the hydrophobic cavity. Even if several single nucleotide polymorphisms were identified in these nsLTP-coding sequences, 3D predictions showed that they do not have a significant impact on protein functions. Northern blot and RT-qPCR experiments revealed specific expression of Type II nsLTPs-encoding genes in coffee fruits, mainly during the early development of endosperm of both C. arabica and C. canephora. As part of our search for tissue-specific promoters in coffee, an nsLTP promoter region of around 1.2 kb was isolated. It contained several DNA repeats including boxes identified as essential for grain specific expression in other plants. The whole fragment, and a series of 5' deletions, were fused to the reporter gene β-glucuronidase (uidA) and analyzed in transgenic Nicotiana tabacum plants. Histochemical and fluorimetric GUS assays showed that the shorter (345 bp) and medium (827 bp) fragments of nsLTP promoter function as grain-specific promoters in transgenic tobacco plants.
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Affiliation(s)
- Michelle G Cotta
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, CP 02372, Brasília, DF, 70770-917, Brazil
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Calingacion M, Laborte A, Nelson A, Resurreccion A, Concepcion JC, Daygon VD, Mumm R, Reinke R, Dipti S, Bassinello PZ, Manful J, Sophany S, Lara KC, Bao J, Xie L, Loaiza K, El-hissewy A, Gayin J, Sharma N, Rajeswari S, Manonmani S, Rani NS, Kota S, Indrasari SD, Habibi F, Hosseini M, Tavasoli F, Suzuki K, Umemoto T, Boualaphanh C, Lee HH, Hung YP, Ramli A, Aung PP, Ahmad R, Wattoo JI, Bandonill E, Romero M, Brites CM, Hafeel R, Lur HS, Cheaupun K, Jongdee S, Blanco P, Bryant R, Thi Lang N, Hall RD, Fitzgerald M. Diversity of global rice markets and the science required for consumer-targeted rice breeding. PLoS One 2014; 9:e85106. [PMID: 24454799 PMCID: PMC3893639 DOI: 10.1371/journal.pone.0085106] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/22/2013] [Indexed: 11/21/2022] Open
Abstract
With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a 'one size fits all' crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.
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Affiliation(s)
- Mariafe Calingacion
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
- International Network for Quality Rice
| | - Alice Laborte
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Andrew Nelson
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Adoracion Resurreccion
- International Rice Research Institute, Los Baños, Laguna, Philippines
- International Network for Quality Rice
| | | | - Venea Dara Daygon
- International Rice Research Institute, Los Baños, Laguna, Philippines
- International Network for Quality Rice
| | - Roland Mumm
- Plant Research International, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
| | - Russell Reinke
- International Network for Quality Rice
- Yanco Agricultural Institute, NSW Department of Industry and Investment, PMB, Yanco, New South Wales, Australia
| | - Sharifa Dipti
- International Network for Quality Rice
- Grain Quality and Nutrition Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | | | - John Manful
- International Network for Quality Rice
- Africa Rice Center (AfricaRice), Cotonou, Republic of Benin
| | - Sakhan Sophany
- International Network for Quality Rice
- Cambodian Agricultural Research and Development Institute, Phnom Penh, Cambodia
| | - Karla Cordero Lara
- International Network for Quality Rice
- Mejoramiento Genetico de Arroz INIA CRI Quilamapu, Vicente Mendez, Chile
| | - Jinsong Bao
- International Network for Quality Rice
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hua Jiachi Campus, Hangzhou, China
| | - Lihong Xie
- International Network for Quality Rice
- China National Rice Research Institute, Hangzhou, China
| | - Katerine Loaiza
- International Network for Quality Rice
- Laboratorio de Calidad FLAR-CIAT, CIAT, Cali-Palmira, Colombia
| | - Ahmad El-hissewy
- International Network for Quality Rice
- Rice Research Section, Field Crops Research Institute, A.R.C., Rice Research & Training Center, Sakha, Kafr El-Shiekh, Egypt
| | - Joseph Gayin
- International Network for Quality Rice
- CSIR-Food Research Institute, Accra, Ghana
| | - Neerja Sharma
- International Network for Quality Rice
- Rice Section, Department of Plant Breeding and Genetics, Punjab Agricultural University Ludhiana, Ludhiana, India
| | - Sivakami Rajeswari
- International Network for Quality Rice
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University Coimbatore, Tamil Nadu, India
| | - Swaminathan Manonmani
- International Network for Quality Rice
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University Coimbatore, Tamil Nadu, India
| | - N. Shobha Rani
- International Network for Quality Rice
- Crop Improvement Section, Directorate of Rice Research, Rajendra Nagar, Hyderabad, AP, India
| | - Suneetha Kota
- International Network for Quality Rice
- Crop Improvement Section, Directorate of Rice Research, Rajendra Nagar, Hyderabad, AP, India
| | - Siti Dewi Indrasari
- International Network for Quality Rice
- Indonesian Center for Rice Research (ICRR) BB Padi, Sukamandi, Subang Jawa Barat, Indonesia
| | - Fatemeh Habibi
- International Network for Quality Rice
- Rice Research Institute of Iran (RRII), Rasht, I.R. Iran
| | - Maryam Hosseini
- International Network for Quality Rice
- Rice Research Institute of Iran (RRII), Rasht, I.R. Iran
| | - Fatemeh Tavasoli
- International Network for Quality Rice
- Rice Research Institute of Iran (RRII), Rasht, I.R. Iran
| | - Keitaro Suzuki
- International Network for Quality Rice
- NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki, Japan
| | - Takayuki Umemoto
- International Network for Quality Rice
- NARO Hokkaido Agricultural Research Centre, Toyohira, Sapporo, Hokkaido, Japan
| | - Chanthkone Boualaphanh
- International Network for Quality Rice
- Rice and Cash Crop Research Institute, NAFRI, Vientiane, Lao PDR
| | - Huei Hong Lee
- International Network for Quality Rice
- Faculty of Agriculture and Food Science, Universiti Putra Malaysia, Bintulu Sarawak, Malaysia
| | - Yiu Pang Hung
- Faculty of Agriculture and Food Science, Universiti Putra Malaysia, Bintulu Sarawak, Malaysia
| | - Asfaliza Ramli
- International Network for Quality Rice
- Pusat Penyelidikan Padi dan Tanaman Industri, MARDI Seberang Perai Beg Berkunci, Seberang Perai Pulau Penang, Malaysia
| | - Pa Pa Aung
- International Network for Quality Rice
- Plant Biotechnology Center, Myanmar Agriculture Service, Ministry of Agriculture and Irrigation, Yangon, Myanmar
| | - Rauf Ahmad
- International Network for Quality Rice
- Rice Programme, National Agricultural Research Centre, Islamabad, Pakistan
| | - Javed Iqbal Wattoo
- International Network for Quality Rice
- National Institute for Biotechnology and Genetic Engineering, Faislabad, Pakistan
| | - Evelyn Bandonill
- International Network for Quality Rice
- Rice Chemistry and Food Science Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz, Nueva Ecija, Philippines
| | - Marissa Romero
- International Network for Quality Rice
- Rice Chemistry and Food Science Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz, Nueva Ecija, Philippines
| | - Carla Moita Brites
- International Network for Quality Rice
- Instituto Nacional de Investigacao Agraria e Veterinaria, Quinta do Marques, Oeiras, Portugal
| | - Roshni Hafeel
- International Network for Quality Rice
- Rice Research Station, Department of Agriculture, Ambalantota, Sri Lanka
| | - Huu-Sheng Lur
- International Network for Quality Rice
- Department of Agronomy, National Taiwan University, Taiwan
| | - Kunya Cheaupun
- International Network for Quality Rice
- Pathumthani Rice Research Centre, Bureau of Rice Research and Development, Thailand
| | - Supanee Jongdee
- International Network for Quality Rice
- Khon Kaen Rice Research Center, Khon Kaen, Thailand
| | - Pedro Blanco
- International Network for Quality Rice
- Rice Research Program, National Agricultural Research Institute, INIA Treinta y Tres, Treinta y Tres, CP, Uruguay
| | - Rolfe Bryant
- International Network for Quality Rice
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Nguyen Thi Lang
- International Network for Quality Rice
- Genetic & Plant Breeding Division, Cuulong Delta Rice Research Inst., Can Tho, Viet Nam
| | - Robert D. Hall
- International Network for Quality Rice
- Plant Research International, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
| | - Melissa Fitzgerald
- International Rice Research Institute, Los Baños, Laguna, Philippines
- International Network for Quality Rice
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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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Asante MD, Offei SK, Gracen V, Adu-Dapaah H, Danquah EY, Bryant R, McClung A. Starch physicochemical properties of rice accessions and their association with molecular markers. STARCH-STARKE 2013. [DOI: 10.1002/star.201300058] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maxwell Darko Asante
- West African Centre for Crop Improvement; College of Agriculture and Consumer Sciences, University of Ghana; Legon Ghana
- Council for Scientific Industrial Research-Crops Research Institute; Kumasi Ghana
| | - Samuel Kwame Offei
- West African Centre for Crop Improvement; College of Agriculture and Consumer Sciences, University of Ghana; Legon Ghana
| | - Vernon Gracen
- West African Centre for Crop Improvement; College of Agriculture and Consumer Sciences, University of Ghana; Legon Ghana
- Department of Plant Breeding and Genetics; Cornell University; Ithaca NY USA
| | - Hans Adu-Dapaah
- Council for Scientific Industrial Research-Crops Research Institute; Kumasi Ghana
| | - Eric Yirenkyi Danquah
- West African Centre for Crop Improvement; College of Agriculture and Consumer Sciences, University of Ghana; Legon Ghana
| | - Rolfe Bryant
- Dale Bumpers National Rice Research Center; Stuttgart AR USA
| | - Anna McClung
- Dale Bumpers National Rice Research Center; Stuttgart AR USA
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Wambugu PW, Furtado A, Waters DLE, Nyamongo DO, Henry RJ. Conservation and utilization of African Oryza genetic resources. RICE (NEW YORK, N.Y.) 2013; 6:29. [PMID: 24280189 PMCID: PMC4883696 DOI: 10.1186/1939-8433-6-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2013] [Indexed: 05/20/2023]
Abstract
Africa contains a huge diversity of both cultivated and wild rice species. The region has eight species representing six of the ten known genome types. Genetic resources of these species are conserved in various global germplasm repositories but they remain under collected and hence underrepresented in germplasm collections. Moreover, they are under characterized and therefore grossly underutilized. The lack of in situ conservation programs further exposes them to possible genetic erosion or extinction. In order to obtain maximum benefits from these resources, it is imperative that they are collected, efficiently conserved and optimally utilized. High throughput molecular approaches such as genome sequencing could be employed to more precisely study their genetic diversity and value and thereby enhance their use in rice improvement. Oryza sativa was the first crop plant to have its reference genome sequence released marking a major milestone that opened numerous opportunities for functional characterization of the entire rice genome. Studies have however demonstrated that one reference genome sequence is not enough to fully explore the genetic variation in the Oryza genus, hence the need to have reference sequences for other species in the genus. An overview of the state of conservation and utilization of African Oryza is hereby presented. Progress in the release of reference genome sequences for these species is also highlighted.
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Affiliation(s)
- Peterson W Wambugu
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
- />Kenya Agricultural Research Institute, Nairobi, Kenya
| | - Agnelo Furtado
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
| | - Daniel LE Waters
- />Southern Cross Plant Science, Southern Cross University, Lismore, NSW Australia
| | | | - Robert J Henry
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
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Liu DR, Huang WX, Cai XL. Oligomerization of rice granule-bound starch synthase 1 modulates its activity regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:141-50. [PMID: 23849121 DOI: 10.1016/j.plantsci.2013.05.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 05/23/2023]
Abstract
Granule-bound starch synthase 1 (GBSS1) is responsible for amylose synthesis in cereals, and this enzyme is regulated at the transcriptional and post-transcriptional levels. In this study, we show that GBSS1 from Oryza sativa L. (OsGBSS1) can form oligomers in rice endosperm, and oligomerized OsGBSS1 exhibits much higher specific enzymatic activity than the monomer. A monomer-oligomer transition equilibrium for OsGBSS1 occurs in the endosperm during development. Redox potential is a key factor affecting the oligomer percentage as well as the enzymatic activity of OsGBSS1. Adenosine diphosphate glucose, the direct donor of glucose, also impacts OsGBSS1 oligomerization in a concentration-dependent manner. OsGBSS1 oligomerization is influenced by phosphorylation status, which was strongly enhanced by Mitogen-activated protein kinase (MAPK) and ATP treatment and was sharply weakened by protein phosphatase (PPase) treatment. The activity of OsGBSS1 affects the ratio of amylose to amylopectin and therefore the eating quality of rice. Understanding the regulation of OsGBSS1 activity may lead to the improvement of rice eating quality.
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Affiliation(s)
- De-Rui Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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Ficklin SP, Feltus FA. A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PLoS One 2013; 8:e68551. [PMID: 23874666 PMCID: PMC3713027 DOI: 10.1371/journal.pone.0068551] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/30/2013] [Indexed: 12/13/2022] Open
Abstract
Many traits of biological and agronomic significance in plants are controlled in a complex manner where multiple genes and environmental signals affect the expression of the phenotype. In Oryza sativa (rice), thousands of quantitative genetic signals have been mapped to the rice genome. In parallel, thousands of gene expression profiles have been generated across many experimental conditions. Through the discovery of networks with real gene co-expression relationships, it is possible to identify co-localized genetic and gene expression signals that implicate complex genotype-phenotype relationships. In this work, we used a knowledge-independent, systems genetics approach, to discover a high-quality set of co-expression networks, termed Gene Interaction Layers (GILs). Twenty-two GILs were constructed from 1,306 Affymetrix microarray rice expression profiles that were pre-clustered to allow for improved capture of gene co-expression relationships. Functional genomic and genetic data, including over 8,000 QTLs and 766 phenotype-tagged SNPs (p-value < = 0.001) from genome-wide association studies, both covering over 230 different rice traits were integrated with the GILs. An online systems genetics data-mining resource, the GeneNet Engine, was constructed to enable dynamic discovery of gene sets (i.e. network modules) that overlap with genetic traits. GeneNet Engine does not provide the exact set of genes underlying a given complex trait, but through the evidence of gene-marker correspondence, co-expression, and functional enrichment, site visitors can identify genes with potential shared causality for a trait which could then be used for experimental validation. A set of 2 million SNPs was incorporated into the database and serve as a potential set of testable biomarkers for genes in modules that overlap with genetic traits. Herein, we describe two modules found using GeneNet Engine, one with significant overlap with the trait amylose content and another with significant overlap with blast disease resistance.
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Affiliation(s)
- Stephen P Ficklin
- Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
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43
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Chen Y, Wang M, Ouwerkerk PBF. Molecular and environmental factors determining grain quality in rice. Food Energy Secur 2012. [DOI: 10.1002/fes3.11] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Yi Chen
- Sylvius Laboratory Department of Molecular and Developmental Genetics Institute of Biology Leiden University Sylviusweg 72 PO Box 9505 2300 RA Leiden The Netherlands
| | - Mei Wang
- Sylvius Laboratory Department of Molecular and Developmental Genetics Institute of Biology Leiden University Sylviusweg 72 PO Box 9505 2300 RA Leiden The Netherlands
- SU BioMedicine‐TNO Utrechtseweg 48 3704 HE Zeist PO Box 360 3700 AJ Zeist The Netherlands
| | - Pieter B. F. Ouwerkerk
- Sylvius Laboratory Department of Molecular and Developmental Genetics Institute of Biology Leiden University Sylviusweg 72 PO Box 9505 2300 RA Leiden The Netherlands
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Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R, Henry RJ. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci Rep 2012; 2:557. [PMID: 22870386 PMCID: PMC3412280 DOI: 10.1038/srep00557] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/23/2012] [Indexed: 12/25/2022] Open
Abstract
Starch is a major component of human diets. The relative contribution of variation in the genes of starch biosynthesis to the nutritional and functional properties of the rice was evaluated in a rice breeding population. Sequencing 18 genes involved in starch synthesis in a population of 233 rice breeding lines discovered 66 functional SNPs in exonic regions. Five genes, AGPS2b, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Association analysis found 31 of the SNP were associated with differences in pasting and cooking quality properties of the rice lines. Two genes appear to be the major loci controlling traits under human selection in rice, GBSSI (waxy gene) and SSIIa. GBSSI influenced amylose content and retrogradation. Other genes contributing to retrogradation were GPT1, SSI, BEI and SSIIIa. SSIIa explained much of the variation in cooking characteristics. Other genes had relatively small effects.
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Affiliation(s)
| | - Daniel L. E. Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Russell F. Reinke
- International Rice Research Institute, National Institute of Crop Science (NICS) RDA 151 Suin-ro, Gwonsun-gu, Suwon 441-857, Republic of Korea
- EH Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, NSW DPI, Private Mail Bag, Pine Gully Road, Wagga Wagga, New South Wales, 2650, Australia
| | - Rachelle Ward
- Yanco Agricultural Institute, Trunk Road 80, Yanco NSW 2703, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Qld 4072, Australia
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45
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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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Madan P, Jagadish SVK, Craufurd PQ, Fitzgerald M, Lafarge T, Wheeler TR. Effect of elevated CO2 and high temperature on seed-set and grain quality of rice. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3843-52. [PMID: 22438302 PMCID: PMC3388820 DOI: 10.1093/jxb/ers077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 02/13/2012] [Accepted: 02/20/2012] [Indexed: 05/03/2023]
Abstract
Hybrid vigour may help overcome the negative effects of climate change in rice. A popular rice hybrid (IR75217H), a heat-tolerant check (N22), and a mega-variety (IR64) were tested for tolerance of seed-set and grain quality to high-temperature stress at anthesis at ambient and elevated [CO(2)]. Under an ambient air temperature of 29 °C (tissue temperature 28.3 °C), elevated [CO(2)] increased vegetative and reproductive growth, including seed yield in all three genotypes. Seed-set was reduced by high temperature in all three genotypes, with the hybrid and IR64 equally affected and twice as sensitive as the tolerant cultivar N22. No interaction occurred between temperature and [CO(2)] for seed-set. The hybrid had significantly more anthesed spikelets at all temperatures than IR64 and at 29 °C this resulted in a large yield advantage. At 35 °C (tissue temperature 32.9 °C) the hybrid had a higher seed yield than IR64 due to the higher spikelet number, but at 38 °C (tissue temperature 34-35 °C) there was no yield advantage. Grain gel consistency in the hybrid and IR64 was reduced by high temperatures only at elevated [CO(2)], while the percentage of broken grains increased from 10% at 29 °C to 35% at 38 °C in the hybrid. It is concluded that seed-set of hybrids is susceptible to short episodes of high temperature during anthesis, but that at intermediate tissue temperatures of 32.9 °C higher spikelet number (yield potential) of the hybrid can compensate to some extent. If the heat tolerance from N22 or other tolerant donors could be transferred into hybrids, yield could be maintained under the higher temperatures predicted with climate change.
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Affiliation(s)
- P. Madan
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India
- Plant Environment Laboratory, University of Reading, Cutbush Lane, Shinfield, Reading RG2 9AF, UK
| | - S. V. K. Jagadish
- Plant Environment Laboratory, University of Reading, Cutbush Lane, Shinfield, Reading RG2 9AF, UK
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - P. Q. Craufurd
- Plant Environment Laboratory, University of Reading, Cutbush Lane, Shinfield, Reading RG2 9AF, UK
- Resilient Dryland Systems, ICRISAT, Patancheru, AP 502324, India
| | - M. Fitzgerald
- Grain Quality, Nutrition, and Postharvest Center, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - T. Lafarge
- Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- CIRAD, UMR AGAP, F-34398, Montpellier, France
| | - T. R. Wheeler
- Plant Environment Laboratory, University of Reading, Cutbush Lane, Shinfield, Reading RG2 9AF, UK
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47
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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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48
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Juliano BO, Tuaño APP, Monteroso DN, Aoki N, Mestres C, Duldulao JBA, Bergonio KB. Replacement of Acetate with Ammonium Buffer to Determine Apparent Amylose Content of Milled Rice. CEREAL FOOD WORLD 2012. [DOI: 10.1094/cfw-57-1-0014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- B. O. Juliano
- Philippine Rice Research Institute Los Baños, College, Laguna, Philippines
| | - A. P. P. Tuaño
- Philippine Rice Research Institute Los Baños, College, Laguna, Philippines
| | - D. N. Monteroso
- Philippine Rice Research Institute Los Baños, College, Laguna, Philippines
| | - N. Aoki
- National Institute of Crop Science, Tsukuba, Japan
| | - C. Mestres
- Centre International de la Recherche Agronomique pour le Developpement, UMR Qualisud, Montpellier Cedex 5, France
| | - J. B. A. Duldulao
- Philippine Rice Research Institute Central Experiment Station, Muñoz, Nueva Ecija, Philippines
| | - K. B. Bergonio
- Philippine Rice Research Institute Central Experiment Station, Muñoz, Nueva Ecija, Philippines
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49
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Tran NA, Daygon VD, Resurreccion AP, Cuevas RP, Corpuz HM, Fitzgerald MA. A single nucleotide polymorphism in the Waxy gene explains a significant component of gel consistency. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:519-25. [PMID: 21562821 DOI: 10.1007/s00122-011-1604-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 04/26/2011] [Indexed: 05/03/2023]
Abstract
Gel consistency (GC) is a standard assay used in rice improvement programmes to determine whether rice cultivars/breeding lines of high amylose content are soft or firm textured when cooked. In this study, we show that sequence variation in exon 10 of the Waxy (Wx) gene associates with GC using RILs derived from parents with high amylose content that differ in GC. The association was validated using a diverse set of traditional varieties, selected on the basis of amylose content, from the generation challenge programme. Structural investigations to explain how the mutation leads to differences in GC showed a strong association between GC and the proportion of amylose that leaches. It was shown that cooked rices of hard GC do not change in hardness over 24 h, whereas rices of soft GC retrograde significantly over 24 h. This leads to the conclusion that the mutation on exon 10 of the Wx gene affects the proportion of amylose bound to amylopectin and the proportion able to leach, and these structural differences alter the composition of the gel, which affects the amount of time the gel takes to reach a final hardness. The SNP described here completes the set of markers required to genotype for the current traits of cooking quality, but selecting the allele for soft texture has the negative result of also selecting for retrogradation potential.
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Affiliation(s)
- N A Tran
- Grain Quality and Nutrition Centre, International Rice Research Institute, DAPO 7777, Manila, Metro Manila, Philippines
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50
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Development of new markers to genotype the functional SNPs of SSIIa, a gene responsible for gelatinization temperature of rice starch. J Cereal Sci 2010. [DOI: 10.1016/j.jcs.2010.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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