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Li C, Yao S, Song B, Zhao L, Hou B, Zhang Y, Zhang F, Qi X. Evaluation of Cooked Rice for Eating Quality and Its Components in Geng Rice. Foods 2023; 12:3267. [PMID: 37685200 PMCID: PMC10486766 DOI: 10.3390/foods12173267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/20/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
At present, ''eating well" is increasingly desired by people instead of merely ''being full". Rice provides the majority of daily caloric needs for half of the global human population. However, eating quality is difficult to objectively evaluate in rice breeding programs. This study was carried out to objectively quantify and predict eating quality in Geng rice. First, eating quality and its components were identified by trained panels. Analysis of variance and broad-sense heritability showed that variation among varieties was significant for all traits except hardness. Among them, viscosity, taste, and appearance were significantly correlated with eating quality. We established an image acquisition and processing system to quantify cooked rice appearance and optimized the process of measuring cooked rice viscosity with a texture analyzer. The results show that yellow areas of the images were significantly correlated with appearance, and adhesiveness was significantly correlated with viscosity. Based on these results, multiple regression analysis was used to predict eating quality: eating quality = 0.37 × adhesiveness - 0.71 × yellow area + 0.89 × taste - 0.34, R2 = 0.85. The correlation coefficient between the predicted and actual values was 0.86. We anticipate that this predictive model will be useful in future breeding programs for high-eating-quality rice.
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Affiliation(s)
- Cui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China; (C.L.); (S.Y.); (B.S.); (B.H.); (F.Z.)
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
- China National Botanical Garden, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Shujun Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China; (C.L.); (S.Y.); (B.S.); (B.H.); (F.Z.)
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
- China National Botanical Garden, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Bo Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China; (C.L.); (S.Y.); (B.S.); (B.H.); (F.Z.)
- China National Botanical Garden, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Lei Zhao
- Tonghua Academy of Agricultural Sciences, Hailong Town, Meihekou 135007, China;
| | - Bingzhu Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China; (C.L.); (S.Y.); (B.S.); (B.H.); (F.Z.)
- China National Botanical Garden, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Yong Zhang
- LUSTER LightTech Co., Ltd., Yard No.13, Cuihu Nanhuan Road, Beijing 100094, China;
| | - Fan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China; (C.L.); (S.Y.); (B.S.); (B.H.); (F.Z.)
- China National Botanical Garden, Nanxincun 20, Fragrant Hill, Beijing 100093, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing 100093, China; (C.L.); (S.Y.); (B.S.); (B.H.); (F.Z.)
- China National Botanical Garden, Nanxincun 20, Fragrant Hill, Beijing 100093, China
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Identification of volatile organic compounds related to the eating quality of cooked japonica rice. Sci Rep 2022; 12:18133. [PMID: 36307468 PMCID: PMC9616908 DOI: 10.1038/s41598-022-21863-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 12/30/2022] Open
Abstract
Eating quality (EQ) of rice has a complex nature composed of physicochemical properties. Nevertheless, breeding programs evaluating EQ through sensory test or taste-evaluation instruments have been laborious, time-consuming and inefficient. EQ is affected by both taste and aroma. However, in actual breeding programs, aroma of cooked rice has been considered the least due to lack of information. Here we identified a total of 41 volatile compounds potentially affecting the EQ of non-aromatic, cooked japonica rice, identified by GC-MS, sensory panel test, and Toyo taste-meter analyses. Partial least squares discriminant analysis demonstrated an outstanding classification effect of the identified volatile compounds on eating-quality discrimination. Several volatile compounds related to lipid oxidation and fatty acid degradation were identified to affect the EQ in japonica rice. Of them, 1-octen-3-ol, 1-ethyl-3,5-dimethylbenzene, 2,6,11-trimethyldodecane, 3-ethyloctane, 2,7,10-trimethyldodecane, methyl salicylate, 2-octanone, and heptanal were selected as important compounds. The discriminant model for the classification of the quality of cultivars was robust and accurate, an r-squared value was 0.91, a q squared value was 0.85, and an accuracy was 1.0. Overall, the results of this study characterize EQ of rice cultivars based on volatile compounds, suggesting the application of metabolite profiling data for rice breeding of high eating quality.
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Lee YK, Lee Y, Jang S, Lee T, Woo MO, Seo J, Kim B, Koh HJ. Sequencing and de novo assembly of the Koshihikari genome and identification of the genomic region related to the eating quality of cooked rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:65. [PMID: 37309489 PMCID: PMC10248671 DOI: 10.1007/s11032-022-01335-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/02/2022] [Indexed: 06/14/2023]
Abstract
The japonica rice (Oryza sativa L.) cultivar Koshihikari is considered an important breeding material with good eating quality (EQ). To effectively utilize Koshihikari in molecular breeding programs, determining its whole genome sequence including cultivar-specific segment is crucial. Here, the Koshihikari genome was sequenced using Nanopore and Illumina platforms, and de novo assembly was performed. A highly contiguous Koshihikari genome sequence was compared with Nipponbare, the reference genome of japonica. Genome-wide synteny was observed, as expected, without large structural variations. However, several gaps in alignment were detected on chromosomes 3, 4, 9, and 11. It was notable that previously identified EQ-related QTLs were found in these gaps. Moreover, sequence variations were identified in chromosome 11 at a region flanking the P5 marker, one of the significant markers of good EQ. The Koshihikari-specific P5 region was found to be transmitted through the lineage. High EQ cultivars derived from Koshihikari possessed P5 sequences; on the other hand, Koshihikari-derived low EQ cultivars didn't contain the P5 region, which implies that the P5 genomic region affects the EQ of Koshihikari progenies. The EQ of near-isogenic lines (NILs) of Samnam (a low EQ cultivar) genetic background harboring the P5 segment was improved compared to that of Samnam in Toyo taste value. The structure of the Koshihikari-specific P5 genomic region associated with good EQ was analyzed, which is expected to facilitate the molecular breeding of rice cultivars with superior EQ. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01335-3.
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Affiliation(s)
- Yoon Kyung Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yunjoo Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Su Jang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Taeyoung Lee
- Bioinformatics Institute, Macrogen Inc, Seoul, 08511 Republic of Korea
| | - Mi-Ok Woo
- Science & Technology Policy Division, Ministry of Agriculture, Food and Rural Affairs, Sejong, South Korea
| | - Jeonghwan Seo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, 55365 Korea
| | - Backki Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Mao T, Zhu M, Ahmad S, Ye G, Sheng Z, Hu S, Jiao G, Xie L, Tang S, Wei X, Hu P, Shao G. Superior japonica rice variety YJ144 with improved rice blast resistance, yield, and quality achieved using molecular design and multiple breeding strategies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:65. [PMID: 34642568 PMCID: PMC8498087 DOI: 10.1007/s11032-021-01259-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 09/30/2021] [Indexed: 05/06/2023]
Abstract
UNLABELLED Yanfeng 47 (YF47) is an elite japonica rice variety cultivated in China on nearly 2 million hectares over the past 20 years. However, YF47 is highly susceptible to rice blast (Magnaporthe oryzae), one of the most destructive rice diseases. In this study, we developed novel TPAP (tetra-primer ARMS-PCR) functional markers for the genes Pita, Pib, and Pid2, all of which afford broad-spectrum resistance to blast. A collection of 91 japonica rice germplasms with similar ecological characteristics to YF47 were screened, and Wuyunjing 27 (WYJ27) with Pita and Pib alleles and P135 with the Pid2 allele were identified. Furthermore, the corresponding positive Pita, Pib, and Pid2 alleles were transferred into YF47 using single, mutual, and backcrosses, together with molecular marker-assisted selection (MAS) and anther culture technology. These genetic materials, carrying one, two, or three functional alleles, were generated within 3 years, and compared to YF47, they all showed improved resistance to naturally inoculated rice blast. Further improved lines (IL) 1 to 5 (all containing Pita, Pib, and Pid2 alleles) were evaluated for yield performance, and when no fungicide was applied, all lines except IL-4 showed increased traits compared with those of YF47. IL-5, renamed Yanjing 144 (YJ144), showed yield increases in the Liaoning province regional variety comparison test and superior appearance quality compared to YF47. Our work provides a molecular design strategy for pyramiding multiple beneficial genes to rapidly improve rice blast resistance, yield, and quality using multiple breeding strategies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11032-021-01259-4.
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Affiliation(s)
- Ting Mao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
- Liaoning Institute of Saline-Alkali and Utilization, Panjin, 124010 China
| | - Mingdong Zhu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
- Hunan Rice Research Institute, Changsha, 410125 China
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
- Maize Research Station, Ayub Agricultural Research Institute, Faisalabad, 38850 Pakistan
| | - Guoyou Ye
- Rice Breeding Innovations Platform, International Rice Research Institute, 1301 Metro Manila, Philippines
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
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Park SG, Park HS, Baek MK, Jeong JM, Cho YC, Lee GM, Lee CM, Suh JP, Kim CS, Kim SM. Improving the Glossiness of Cooked Rice, an Important Component of Visual Rice Grain Quality. RICE (NEW YORK, N.Y.) 2019; 12:87. [PMID: 31776807 PMCID: PMC6881499 DOI: 10.1186/s12284-019-0348-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/06/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rice is one of the few cereals consumed as a whole grain, and therefore the appearance of the final milled product, both before and after cooking, strongly influences the consumer's perception of product quality. Matching consumer preference for rice grain quality is a key component of rice variety development programs, as the quality drives demand, which in turn drives variety adoption, market price, and profitability. The quality of cooked rice is normally evaluated indirectly, through measurement of key elements driving quality as well as more directly by sensory evaluation, but remains a complex trait conditioned by the genetic complexity of factors driving quality, changes wrought by environment, and the complexity of consumer preferences. RESULT In this study, we evaluated 17 traits, including the taste value obtained by glossiness of cooked rice (TV), to explain rice eating quality by statistical methods and identified QTLs associated with TV. To explain the correlation among traits, exploratory factor analysis was performed for 2 years. The overall eating quality (OE) was correlated with TV and protein content loading at the same factor (PA1) in 2017, and there was a relationship between the OE (PA1) and the TV (PA2) in 2018 (PA1:PA2, r = 0.3). In QTL analysis using 174 RILs, three QTLs for TV derived from Wandoaengmi6 were detected on chromosomes 4, 6, and 9. The QTL qTV9 delimited within Id9007180 and 9,851,330 on chromosome 9 was detected in both years, explaining approximately 17% of the variation, on average. Through the use of fine mapping, qTV9 was delimited to an approximately 34-Kbp segment flanked by the DNA markers CTV9_9 and CTV9_13, and nine ORFs were listed in the target region as candidate genes associated with TV. In the evaluation of qTV9's effect on OE, the lines with qTV9 showed a significant increase in correlation coefficiency compared to the negative lines. These data will apply to functional analysis on the glossiness and the MAS breeding program to improve the eating quality of japonica as a donor line. CONCLUSION In this paper we report a number of QTL associated with changes in glossiness of cooked rice, and these may have utility in the development of MAS in breeding programs with a specific focus on cooked grain quality.
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Affiliation(s)
- Seul-Gi Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Man-Kee Baek
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jong-Min Jeong
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Young-Chan Cho
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Gun-Mi Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jung-Pil Suh
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Choon-Song Kim
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Suk-Man Kim
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
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Gull S, Haider Z, Gu H, Raza Khan RA, Miao J, Wenchen T, Uddin S, Ahmad I, Liang G. InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice ( Oryza sativa L.). Int J Mol Sci 2019; 20:E4824. [PMID: 31569360 PMCID: PMC6801599 DOI: 10.3390/ijms20194824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 11/16/2022] Open
Abstract
The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, qPE9~1, GW2, SLG7, GW5, GS3, GS7, GW8, GS5, and GS2, in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (GS3, GS7, GW8, and GS2). GT was also found to be regulated by four different genes (GS3, GS7, GW8, and GS2) out of the nine studied genes. GW was found to be under the control of three studied genes (GW5, GW8, and GS2), whereas TGW was found to be under the influence of four genes (SLG7, GW5, GW8, and GS5) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further.
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Affiliation(s)
- Sadia Gull
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Zulqarnain Haider
- Rice Breeding and Genetics Section, Rice Research Institute, Kala Shah Kaku, Lahore, Pakistan
| | - Houwen Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Rana Ahsan Raza Khan
- Rice Breeding and Genetics Section, Rice Research Institute, Kala Shah Kaku, Lahore, Pakistan
| | - Jun Miao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Tan Wenchen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Saleem Uddin
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding , Beijing Forestry University, Beijing 100083, China
| | - Irshad Ahmad
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
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7
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Zeng D, Tian Z, Rao Y, Dong G, Yang Y, Huang L, Leng Y, Xu J, Sun C, Zhang G, Hu J, Zhu L, Gao Z, Hu X, Guo L, Xiong G, Wang Y, Li J, Qian Q. Rational design of high-yield and superior-quality rice. NATURE PLANTS 2017; 3:17031. [PMID: 28319055 DOI: 10.1038/nplants.2017.31] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/14/2017] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa L.) is a staple food for more than half of the world's population. To meet the ever-increasing demand for food, because of population growth and improved living standards, world rice production needs to double by 20301. The development of new elite rice varieties with high yield and superior quality is challenging for traditional breeding approaches, and new strategies need to be developed. Here, we report the successful development of new elite varieties by pyramiding major genes that significantly contribute to grain quality and yield from three parents over five years. The new varieties exhibit higher yield potential and better grain quality than their parental varieties and the China's leading super-hybrid rice, Liang-you-pai-jiu (LYP9 or Pei-ai 64S/93-11). Our results demonstrate that rational design is a powerful strategy for meeting the challenges of future crop breeding, particularly in pyramiding multiple complex traits.
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Affiliation(s)
- Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuchun Rao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Lichao Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yujia Leng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jie Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Chuan Sun
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Xingming Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Guosheng Xiong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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8
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Pang Y, Ali J, Wang X, Franje NJ, Revilleza JE, Xu J, Li Z. Relationship of Rice Grain Amylose, Gelatinization Temperature and Pasting Properties for Breeding Better Eating and Cooking Quality of Rice Varieties. PLoS One 2016; 11:e0168483. [PMID: 27992591 PMCID: PMC5167365 DOI: 10.1371/journal.pone.0168483] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/30/2016] [Indexed: 11/18/2022] Open
Abstract
A total of 787 non-waxy rice lines– 116 hybrids and 671 inbreds–were used to study the apparent amylose content (AAC), gelatinization temperature (GT), and rapid visco analyzer (RVA) pasting viscosity properties of rice starch to understand their importance in breeding better rice varieties. The investigated traits showed a wide range of diversity for both hybrid (HG) and inbred (IG) groups. The combinations of the different categories of AAC and GT were random in HG but were non-random in IG. For inbred lines, the high level of AAC tended to combine with the low level of GT, the intermediate level of AAC tended to have high or intermediate GT, and the low level of AAC tended to have high or low GT. Some stable correlations of the AAC, GT, and RVA properties may be the results derived from the physicochemical relationships among these traits, which rice breeders could utilize for selection in advanced breeding generations. Through cluster analysis, IG and HG were divided into 52 and 31 sub-clusters, respectively. Identifying the cultivars having AAC, GT, and RVA properties similar to that of popular high-quality rice varieties seems to be an interesting strategy and could be directly used for adaptation trials to breed high-quality rice varieties in targeted areas in a more customized manner.
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Affiliation(s)
- Yunlong Pang
- Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- International Rice Research Institute, Metro Manila, Philippines
| | - Jauhar Ali
- International Rice Research Institute, Metro Manila, Philippines
- * E-mail:
| | - Xiaoqian Wang
- Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- International Rice Research Institute, Metro Manila, Philippines
| | | | | | - Jianlong Xu
- Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
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Lee CM, Park J, Kim B, Seo J, Lee G, Jang S, Koh HJ. Influence of Multi-Gene Allele Combinations on Grain Size of Rice and Development of a Regression Equation Model to Predict Grain Parameters. RICE (NEW YORK, N.Y.) 2015; 8:33. [PMID: 26519289 PMCID: PMC4627975 DOI: 10.1186/s12284-015-0066-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/15/2015] [Indexed: 05/27/2023]
Abstract
BACKGROUND Grain size is one of the key factors determining yield and quality in rice. A large number of genes are involved in the regulation of grain size parameters such as grain length and grain width. Different alleles of these genes have different impacts on the grain size traits under their control. However, the combined influence of multiple alleles of different genes on grain size remains to be investigated. Six key genes known to influence grain size were investigated in this study: GS3, GS5, GS6, GW2, qSW5/GW5, and GW8/OsSPL16. Allele and grain measurement data were used to develop a regression equation model that can be used for molecular breeding of rice with desired grain characteristics. RESULTS A total of 215 diverse rice germplasms, which originated from or were developed in 28 rice-consuming countries, were used in this study. Genotyping analysis demonstrated that a relatively small number of allele combinations were preserved in the diverse population and that these allele combinations were significantly associated with differences in grain size. Furthermore, in several cases, variation at a single gene was sufficient to influence grain size, even when the alleles of other genes remained constant. The data were used to develop a regression equation model for prediction of rice grain size, and this was tested using data from a further 34 germplasms. The model was significantly correlated with three of the four grain size-related traits examined in this study. CONCLUSION Rice grain size is strongly influenced by specific combinations of alleles from six different genes. A regression equation model developed from allele and grain measurement data can be used in rice breeding programs for the development of new rice varieties with desired grain size and shape.
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Affiliation(s)
- Chan-Mi Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.
| | - Jonghwa Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.
| | - Backki Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.
| | - Jeonghwan Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.
| | - Gileung Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.
| | - Su Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.
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10
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Kwak HS, Kim M, Lee Y, Jeong Y. Identification of key sensory attributes for consumer acceptance and instrumental quality of aseptic-packaged cooked rice. Int J Food Sci Technol 2014. [DOI: 10.1111/ijfs.12684] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Han Sub Kwak
- Department of Food Science and Nutrition; Dankook University; Yongin-si 448-701 Korea
- Institute of Global Food Industry; Dankook University; Yongin-si 448-701 Korea
| | - Misook Kim
- Department of Food Science and Nutrition; Dankook University; Yongin-si 448-701 Korea
- Institute of Global Food Industry; Dankook University; Yongin-si 448-701 Korea
| | - Youngseung Lee
- Department of Food Science and Nutrition; Dankook University; Yongin-si 448-701 Korea
- Institute of Global Food Industry; Dankook University; Yongin-si 448-701 Korea
| | - Yoonhwa Jeong
- Department of Food Science and Nutrition; Dankook University; Yongin-si 448-701 Korea
- Institute of Global Food Industry; Dankook University; Yongin-si 448-701 Korea
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11
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Phing Lau WC, Latif MA, Y Rafii M, Ismail MR, Puteh A. Advances to improve the eating and cooking qualities of rice by marker-assisted breeding. Crit Rev Biotechnol 2014; 36:87-98. [PMID: 24937109 DOI: 10.3109/07388551.2014.923987] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The eating and cooking qualities of rice are heavily emphasized in breeding programs because they determine market values and they are the appealing attributes sought by consumers. Conventional breeding has developed traditional varieties with improved eating and cooking qualities. Recently, intensive genetic studies have pinpointed the genes that control eating and cooking quality traits. Advances in genetic studies have developed molecular techniques, thereby allowing marker-assisted breeding (MAB) for improved eating and cooking qualities in rice. MAB has gained the attention of rice breeders for the advantages it can offer that conventional breeding cannot. There have been successful cases of using MAB to improve the eating and cooking qualities in rice over the years. Nevertheless, MAB should be applied cautiously given the intensive effort needed for genotyping. Perspectives from conventional breeding to marker-assisted breeding will be discussed in this review for the advancement of the eating and cooking qualities of fragrance, amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) in rice. These four parameters are associated with eating and cooking qualities in rice. The genetic basis of these four parameters is also included in this review. MAB is another approach to rice variety improvement and development in addition to being an alternative to genetic engineering. The MAB approach shortens the varietal development time, and is therefore able to deliver improved rice varieties to farmers within a shorter period of time.
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Affiliation(s)
- Wendy Chui Phing Lau
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia
| | - Mohammad Abdul Latif
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia .,b Bangladesh Rice Research Institute (BRRI) , Gazipur , Bangladesh , and
| | - Mohd Y Rafii
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia .,c Institute of Tropical Agriculture, Universiti Putra Malaysia , Serdang , Selangor , Malaysia
| | - Mohd Razi Ismail
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia .,c Institute of Tropical Agriculture, Universiti Putra Malaysia , Serdang , Selangor , Malaysia
| | - Adam Puteh
- a Department of Crop Science, Faculty of Agriculture , Universiti Putra Malaysia , Serdang , Selangor , Malaysia
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12
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LESTARI PUJI, REFLINUR, KOH HEEJONG. Prediction of Physicochemical Properties of Indonesian Indica Rice Using Molecular Markers. HAYATI JOURNAL OF BIOSCIENCES 2014. [DOI: 10.4308/hjb.21.2.76] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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13
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Goto H, Asanome N, Suzuki K, Sano T, Saito H, Abe Y, Chuba M, Nishio T. Objective evaluation of whiteness of cooked rice and rice cakes using a portable spectrophotometer. BREEDING SCIENCE 2014; 63:489-94. [PMID: 24757389 PMCID: PMC3949586 DOI: 10.1270/jsbbs.63.489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/03/2013] [Indexed: 05/07/2023]
Abstract
The whiteness of cooked rice and rice cakes was evaluated using a portable spectrophotometer with a whiteness index (WI). Also, by using boiled rice for measurement of Mido values by Mido Meter, it was possible to infer the whiteness of cooked rice without rice cooking. In the analysis of varietal differences of cooked rice, 'Tsuyahime', 'Koshihikari' and 'Koshinokaori' showed high whiteness, while 'Satonoyuki' had inferior whiteness. The whiteness of rice cakes made from 'Koyukimochi' and 'Dewanomochi' was higher than the whiteness of those made from 'Himenomochi' and 'Koganemochi'. While there was a significant correlation (r = 0.84) between WI values and whiteness scores of cooked rice by the sensory test, no correlation was detected between the whiteness scores and Mido values, indicating that the values obtained by a spectrophotometer differ from those obtained by a Mido Meter. Thus, a spectrophotometer may be a novel device for measurement of rice eating quality.
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Affiliation(s)
- Hajime Goto
- Rice Breeding and Crop Science Experiment Station, Yamagata Integrated Agricultural Research Center,
25 Yamanomae, Fujishima, Tsuruoka, Yamagata 999-7601,
Japan
- Graduate School of Agricultural Science, Tohoku University,
1-1 Tsutsumidori-Amamiya, Aoba, Sendai, Miyagi 981-8555,
Japan
| | - Noriyuki Asanome
- Yamagata Integrated Agricultural Research Center,
6060-27 Minorigaoka, Yamagata, Yamagata 990-2372,
Japan
| | - Keitaro Suzuki
- National Institute of Crop Science,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tomoyoshi Sano
- Shonai Area General Branch Administration, Yamagata Prefectural Government,
51 Yamanomae, Fujishima, Tsuruoka, Yamagata 999-7601,
Japan
| | - Hiroshi Saito
- Rice Breeding and Crop Science Experiment Station, Yamagata Integrated Agricultural Research Center,
25 Yamanomae, Fujishima, Tsuruoka, Yamagata 999-7601,
Japan
| | - Yohei Abe
- Rice Breeding and Crop Science Experiment Station, Yamagata Integrated Agricultural Research Center,
25 Yamanomae, Fujishima, Tsuruoka, Yamagata 999-7601,
Japan
| | - Masaru Chuba
- Rice Breeding and Crop Science Experiment Station, Yamagata Integrated Agricultural Research Center,
25 Yamanomae, Fujishima, Tsuruoka, Yamagata 999-7601,
Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University,
1-1 Tsutsumidori-Amamiya, Aoba, Sendai, Miyagi 981-8555,
Japan
- Corresponding author (e-mail: )
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Hsu YC, Tseng MC, Wu YP, Lin MY, Wei FJ, Hwu KK, Hsing YI, Lin YR. Genetic factors responsible for eating and cooking qualities of rice grains in a recombinant inbred population of an inter-subspecific cross. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:655-673. [PMID: 25076839 PMCID: PMC4092229 DOI: 10.1007/s11032-014-0065-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 03/04/2014] [Indexed: 05/07/2023]
Abstract
The eating and cooking qualities of rice grains are the major determinants of consumer preference and, consequently, the economic value of a specific rice variety. These two qualities are largely determined by the physicochemical properties of the starch, i.e. the starch composition, of the rice grain. In our study, we determined the genetic factors responsible for the physicochemical properties of starch in recombinant inbred lines (RILs) of japonica cv. Tainung 78 × indica cv. Taichung Sen 17 (TCS 17) cultivated over two crop seasons by examining palatability characteristics and several Rapid Viscosity Analyzer (RVA) parameters. Thirty-four quantitative trait loci (QTLs), each explaining between 1.2 and 78.1 % phenotypic variation, were mapped in clusters on eight chromosomes in 190 RILs genotyped with 139 markers. Ten pairs of QTLs were detected in the two environments, of which seven were in agreement with previous findings, suggesting that these QTLs may express stable experimental populations across various environments. Waxy (Wx), which controls amylose synthesis, was determined to be a primary gene regulating the physicochemical properties of cooked rice grains, as indicated by the presence of a major QTL cluster on chromosome 6 and by marker regression analysis. Six starch synthesis-related genes (SSRGs) which were located in the QTL intervals significantly differed in terms of gene expression between the two parents during grain-filling and were important genetic factors affecting physicochemical properties. The expression of four genes, PUL, ISA2, GBSSI, and SSII-3, was significantly upregulated in TCS 17, and this expression was positively correlated with six traits. The effects of the six SSRGs and gene interaction depended on genetic background and environment; grain quality may be fine tuned by selecting for SBE4 for japonica and PUL for indica. We provide valuable information for application in the breeding of new rice varieties as daily staple food and for use in industrial manufacturing by marker-assisted selection.
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Affiliation(s)
- Yu-Chia Hsu
- Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Meng-Chun Tseng
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Yong-Pei Wu
- Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Meng-Ying Lin
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Fu-Jin Wei
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Kae-Kang Hwu
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Yue-Ie Hsing
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
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15
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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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16
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Sun MM, Lee HJ, Abdula SE, Jee MG, Cho YG. Overexpression of starch branching enzyme 1 gene improves eating quality in japonica rice. ACTA ACUST UNITED AC 2013. [DOI: 10.5010/jpb.2013.40.2.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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LESTARI PUJI, KOH HEEJONG. Development of New CAPS/dCAPS and SNAP Markers for Rice Eating Quality. HAYATI JOURNAL OF BIOSCIENCES 2013. [DOI: 10.4308/hjb.20.1.15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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18
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Sequence variations in OsAGPase significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.). Genet Res (Camb) 2013; 94:179-89. [PMID: 22950899 DOI: 10.1017/s0016672312000390] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativa L.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. An ADP-glucose pyrophosphorylase small unit 1 (OsAGPS1) SNP (A-G) was significantly associated with increased AC (P<0·001, R(2)=15·6%), while a 12-bp deletion of AGPase large unit 4 (OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (P<0·001, R(2)=16·6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.
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19
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Yoon MR, Rico CW, Koh HJ, Kang MY. A study on the lipid components of rice in relation to palatability and storage. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s13765-012-2050-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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KAUR SHUBHNEET, PANESAR PARMJITS, BERA MANABB. STUDIES ON EVALUATION OF GRAIN QUALITY ATTRIBUTES OF SOME BASMATI AND NON-BASMATI RICE CULTIVARS. J FOOD QUALITY 2011. [DOI: 10.1111/j.1745-4557.2011.00417.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Lestari P, Lee G, Ham TH, Reflinur, Woo MO, Piao R, Jiang W, Chu SH, Lee J, Koh HJ. Single nucleotide polymorphisms and haplotype diversity in rice sucrose synthase 3. ACTA ACUST UNITED AC 2011; 102:735-46. [PMID: 21914668 DOI: 10.1093/jhered/esr094] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rice sucrose synthase 3 (RSUS3) is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening. Because the genetic diversity of this locus is not known yet, the full sequence of RSUS3 from 43 rice varieties was amplified to examine the distribution of DNA polymorphisms. A total of 254 sequence variants, including SNPs and insertion/deletions, were successfully identified in the 7733 bp sequence that comprises the promoter, exons and introns, and 3' downstream nontranscribed region (NTR). Eleven haplotypes were distinguished among the 43 rice varieties based on nucleotide variation in the 3 defined regions (5' NTR, transcript, and 3' NTR). The promoter region showed evidence of a base change on a cis-element that might influence the functional role of the motif in seed-specific expression. The genetic diversity of the RSUS3 gene sequences in the rice germplasm used in this study appears to be the result of nonrandom processes. Analysis of polymorphism sites indicated that at least 11 recombinations have occurred, primarily in the transcribed region. This finding provides insight into the development of a cladistic approach for establishing future genetic association studies of the RSUS3 locus.
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Affiliation(s)
- Puji Lestari
- Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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22
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Kwon SW, Cho YC, Lee JH, Suh JP, Kim JJ, Kim MK, Choi IS, Hwang HG, Koh HJ, Kim YG. Identification of quantitative trait loci associated with rice eating quality traits using a population of recombinant inbred lines derived from a cross between two temperate japonica cultivars. Mol Cells 2011; 31:437-45. [PMID: 21360198 PMCID: PMC3887606 DOI: 10.1007/s10059-011-0289-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 01/29/2011] [Accepted: 02/07/2011] [Indexed: 11/29/2022] Open
Abstract
Improved eating quality is a major breeding target in japonica rice due to market demand. In this study, we performed genetic analysis to identify quantitative trait loci (QTLs) that control rice eating quality traits using 192 recombinant inbred lines (RILs) derived from a cross between two japonica cultivars, 'Suweon365' and 'Chucheongbyeo'. We evaluated the stickiness (ST) and overall evaluation (OE) of cooked rice using a sensory test, the glossiness of cooked rice (GCR) using a Toyo-taste meter, and measured the amylose content (AC), protein content (PC), alkali digestion value (ADV), and days to heading (DH) of the RILs in the years 2006 and 2007. Our analysis revealed 21 QTLs on chromosomes 1, 4, 6, 7, 8, and 11. QTLs on chromosomes 6, 7, and 8 were detected for three traits related to eating quality in both years. QTLs for ST and OE were identified by a sensory test in the same region of the QTLs for AC, PC, ADV, GCR and DH on chromosome 8. QTL effects on the GCR were verified using QTL-NILs (near-isogenic lines) of BC(3)F(4-6) in the Suweon365 background, a low eating quality variety, and some BC(1)F(3) lines. Chucheongbyeo alleles at QTLs on chromosomes 7 and 8 increased the GCR in the NILs and backcrossed lines. The QTLs identified by our analysis will be applicable to future marker-assisted selection (MAS) strategies for improving the eating quality of japonica rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hee-Jong Koh
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea
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Sun MM, Abdula SE, Lee HJ, Cho YC, Han LZ, Koh HJ, Cho YG. Molecular aspect of good eating quality formation in Japonica rice. PLoS One 2011; 6:e18385. [PMID: 21494675 PMCID: PMC3071818 DOI: 10.1371/journal.pone.0018385] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 02/28/2011] [Indexed: 11/18/2022] Open
Abstract
The composition of amylopectin is the determinant of rice eating quality under certain threshold of protein content and the ratio of amylose and amylopectin. In molecular biology level, the fine structure of amylopectin is determined by relative activities of starch branching enzyme (SBE), granule-bound starch synthase (GBSS), and soluble starch synthase (SSS) in rice grain under the same ADP-Glucose level. But the underlying mechanism of eating quality in molecular biology level remains unclear. This paper reports the differences on major parameters such as SNP and insertion-deletion sites, RNA expressions, and enzyme activities associated with eating quality of japonica varieties. Eight japonica rice varieties with significant differences in various eating quality parameters such as palatability and protein content were used in this experiment. Association analysis between nucleotide polymorphism and eating quality showed that S12 and S13 loci in SBE1, S55 in SSS1, S58 in SSS2A were significantly associated with apparent amylose content, alkali digestion value, setback viscosity, consistency viscosity, pasting temperature, which explained most of the variation in apparent amylose content, setback viscosity, and consistency viscosity; and explained almost all variations in alkali digestion value and pasting temperature. Thirty-five SNPs and insertion-deletions from SBE1, SBE3, GBSS1, SSS1, and SSS2A differentiated high or intermediate palatability rice varieties from low palatability rice varieties. Correlation analysis between enzyme activities and eating quality properties revealed that SBE25 and SSS15/W15 were positively correlated with palatability, whereas GBSS10 and GBSS15 were negatively correlated. Gene expressions showed that SBE1 and SBE3 expressions in high palatability varieties tended to be higher than middle and low palatability varieties. Collectively, SBE1, SBE3, SSS1, and SSS2A, especially SBE1 and SBE3 could improve eating quality, but GBSS1 decreased eating quality. The results indicated the possibility of developing high palatability cultivars through modification of key genes related to japonica rice eating quality formation in starch biosynthesis.
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Affiliation(s)
- Ming-Mao Sun
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
| | - Sailila E. Abdula
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
| | - Hye-Jung Lee
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
| | - Young-Chan Cho
- National Institute of Crop Science, Rural Development Administration, Suwon, Korea
| | - Long-Zhi Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hee-Jong Koh
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
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Kang MY, Rico CW, Kim CE, Lee SC. Physicochemical Properties and Eating Qualities of Milled Rice from Different Korean Elite Rice Varieties. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2011. [DOI: 10.1080/10942910903312494] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Jin L, Lu Y, Shao Y, Zhang G, Xiao P, Shen S, Corke H, Bao J. Molecular marker assisted selection for improvement of the eating, cooking and sensory quality of rice (Oryza sativa L.). J Cereal Sci 2010. [DOI: 10.1016/j.jcs.2009.11.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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