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Chen P, Lou G, Wang Y, Chen J, Chen W, Fan Z, Liu Q, Sun B, Mao X, Yu H, Jiang L, Zhang J, LV S, Xing J, Pan D, Li C, He Y. The genetic basis of grain protein content in rice by genome-wide association analysis. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:1. [PMID: 37312871 PMCID: PMC10248653 DOI: 10.1007/s11032-022-01347-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/02/2022] [Indexed: 06/15/2023]
Abstract
The grain protein content (GPC) of rice is an important factor that determines its nutritional, cooking, and eating qualities. To date, although a number of genes affecting GPC have been identified in rice, most of them have been cloned using mutants, and only a few genes have been cloned in the natural population. In this study, 135 significant loci were detected in a genome-wide association study (GWAS), many of which could be repeatedly detected across different years and populations. Four minor quantitative trait loci affecting rice GPC at four significant association loci, qPC2.1, qPC7.1, qPC7.2, and qPC1.1, were further identified and validated in near-isogenic line F2 populations (NIL-F2), explaining 9.82, 43.4, 29.2, and 13.6% of the phenotypic variation, respectively. The role of the associated flo5 was evaluated with knockdown mutants, which exhibited both increased grain chalkiness rate and GPC. Three candidate genes in a significant association locus region were analyzed using haplotype and expression profiles. The findings of this study will help elucidate the genetic regulatory network of protein synthesis and accumulation in rice through cloning of GPC genes and provide new insights on dominant alleles for marker-assisted selection in the genetic improvement of rice grain quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01347-z.
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Affiliation(s)
- Pingli Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yufu Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 China
| | - Junxiao Chen
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430070 China
| | - Wengfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Shuwei LV
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Junlian Xing
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
- Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640 China
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Identifying the Genetic Basis of Mineral Elements in Rice Grain Using Genome-Wide Association Mapping. Genes (Basel) 2022; 13:genes13122330. [PMID: 36553597 PMCID: PMC9777918 DOI: 10.3390/genes13122330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mineral malnutrition is a major problem in many rice-consuming countries. It is essential to know the genetic mechanisms of accumulation of mineral elements in the rice grain to provide future solutions for this issue. This study was conducted to identify the genetic basis of six mineral elements (Cu, Fe, K, Mg, Mn, and Zn) by using three models for single-locus and six models for multi-locus analysis of a genome-wide association study (GWAS) using 174 diverse rice accessions and 6565 SNP markers. To declare a SNP as significant, -log10(P) ≥ 3.0 and 15% FDR significance cut-off values were used for single-locus models, while LOD ≥ 3.0 was used for multi-locus models. Using these criteria, 147 SNPs were detected by one or two GWAS methods at -log10(P) ≥ 3.0, 48 of which met the 15% FDR significance cut-off value. Single-locus models outperformed multi-locus models before applying multi-test correction, but once applied, multi-locus models performed better. While 14 (~29%) of the identified quantitative trait loci (QTLs) after multiple test correction co-located with previously reported genes/QTLs and marker associations, another 34 trait-associated SNPs were novel. After mining genes within 250 kb of the 48 significant SNP loci, in silico and gene enrichment analyses were conducted to predict their potential functions. These shortlisted genes with their functions could guide future experimental validation, helping us to understand the complex molecular mechanisms controlling rice grain mineral elements.
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Cruz M, Arbelaez JD, Loaiza K, Cuasquer J, Rosas J, Graterol E. Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean. THE PLANT GENOME 2021; 14:e20134. [PMID: 34510797 DOI: 10.1002/tpg2.20134] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Rice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release. In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from -0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51-75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS. Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.
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Affiliation(s)
- Maribel Cruz
- FLAR (Fondo Latinoamericano para Arroz de Riego), CIAT (International Center for Tropical Agriculture), Kilómetro 17 c, CP, Cali, Valle del Cauca, 763537, Colombia
| | - Juan David Arbelaez
- Dep. of Crop Sciences, Univ. of Illinois, Urbana-Champaign, Turner Hall N-211|1102 S. Goodwin Ave. | 046, Urbana, IL, 61801, USA
| | - Katherine Loaiza
- FLAR (Fondo Latinoamericano para Arroz de Riego), CIAT (International Center for Tropical Agriculture), Kilómetro 17 c, CP, Cali, Valle del Cauca, 763537, Colombia
| | - Juan Cuasquer
- CIAT (International Center for Tropical Agriculture), Kilómetro 17 Recta Cali, Palmira, CP, Cali, Valle del Cauca, 763537, Colombia
| | - Juan Rosas
- INIA (Instituto Nacional de Investigación Agropecuaria), Ruta 8 Km. 281/33000, Treinta y Tres, Uruguay
| | - Eduardo Graterol
- FLAR (Fondo Latinoamericano para Arroz de Riego), CIAT (International Center for Tropical Agriculture), Kilómetro 17 c, CP, Cali, Valle del Cauca, 763537, Colombia
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QTL mapping for starch paste viscosity of rice (Oryza sativa L.) using chromosome segment substitution lines derived from two sequenced cultivars with the same Wx allele. BMC Genomics 2021; 22:596. [PMID: 34353280 PMCID: PMC8340499 DOI: 10.1186/s12864-021-07913-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The eating and cooking qualities (ECQs) of rice (Oryza sativa L.) are key characteristics affecting variety adoption and market value. Starch viscosity profiles tested by a rapid visco analyzer (RVA) offer a direct measure of ECQs and represent the changes in viscosity associated with starch gelatinization. RVA profiles of rice are controlled by a complex genetic system and are also affected by the environment. Although Waxy (Wx) is the major gene controlling amylose content (AC) and ECQs, there are still other unknown genetic factors that affect ECQs. RESULTS Quantitative trait loci (QTLs) for starch paste viscosity in rice were analyzed using chromosome segment substitution lines (CSSLs) developed from the two cultivars 9311 and Nipponbare, which have same Wx-b allele. Thus, the effect of the major locus Wx was eliminated and the other locus associated with the RVA profile could be identified. QTLs for seven parameters of the starch RVA profile were tested over four years in Nanjing, China. A total of 310 QTLs were identified (from 1 to 55 QTLs per trait) and 136 QTLs were identified in more than one year. Among them, 6 QTLs were stalely detected in four years and 26 QTLs were detected in at least three years including 13 pleiotropic loci, controlling 2 to 6 RVA properties simultaneously. These stable QTL hotspots were co-located with several known starch synthesis-related genes (SSRGs). Sequence alignments showed that nucleotide and amino acid sequences of most SSRGs were different between the two parents. Finally, we detected stable QTLs associated with multiple starch viscosity traits near Wx itself, supporting the notion that additional QTLs near Wx control multiple characteristic values of starch viscosity. CONCLUSIONS By eliminating the contribution from the major locus Wx, multiple QTLs associated with the RVA profile of rice were identified, several of which were stably detected over four years. The complexity of the genetic basis of rice starch viscosity traits might be due to their pleiotropic effects and the multiple QTL hot spots. Minor QTLs controlling starch viscosity traits were identified by using the chromosome segment substitution strategy. Allele polymorphism might be the reason that QTLs controlling RVA profile characteristics were detected in some known SSRG regions.
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Song J, Hu Y, Deng G, Dai G, Bao J. The origin of the A/G single nucleotide polymorphism of
starch synthase IIa
in rice and its relation to gelatinization temperature. Cereal Chem 2021. [DOI: 10.1002/cche.10463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jiling Song
- Department of Applied Bioscience College of Agriculture & Biotechnology Zhejiang University Hangzhou China
| | - Yaqi Hu
- Institute of Nuclear Agricultural Sciences College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Guofu Deng
- Rice Research Institute Guangxi Academy of Agricultural Sciences Nanning China
| | - Gaoxing Dai
- Rice Research Institute Guangxi Academy of Agricultural Sciences Nanning China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences College of Agriculture and Biotechnology Zhejiang University Hangzhou China
- Hainan Institute of Zhejiang University Sanya China
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Pereira L, Sapkota M, Alonge M, Zheng Y, Zhang Y, Razifard H, Taitano NK, Schatz MC, Fernie AR, Wang Y, Fei Z, Caicedo AL, Tieman DM, van der Knaap E. Natural Genetic Diversity in Tomato Flavor Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:642828. [PMID: 34149747 PMCID: PMC8212054 DOI: 10.3389/fpls.2021.642828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/23/2021] [Indexed: 05/22/2023]
Abstract
Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5, ALMT9, AAT1, CXE1, and LoxC. The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium, the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum. High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels.
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Affiliation(s)
- Lara Pereira
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, United States
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Hamid Razifard
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Nathan K. Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, United States
- U.S. Department of Agriculture, Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Ana L. Caicedo
- Biology Department, University of Massachusetts Amherst, Amherst, MA, United States
| | - Denise M. Tieman
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
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Hori K, Suzuki K, Ishikawa H, Nonoue Y, Nagata K, Fukuoka S, Tanaka J. Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars. RICE (NEW YORK, N.Y.) 2021; 14:8. [PMID: 33415511 PMCID: PMC7790929 DOI: 10.1186/s12284-020-00447-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/17/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND In temperate rice cultivation regions, japonica rice cultivars are grown preferentially because consumers deem them to have good eating quality, whereas indica rice cultivars have high grain yields and strong heat tolerance but are considered to have poor eating quality. To mitigate the effects of global warming on rice production, it is important to develop novel rice cultivars with both desirable eating quality and resilience to high temperatures. Eating quality and agronomic traits were evaluated in a reciprocal set of chromosome segment substitution lines derived from crosses between a japonica rice cultivar 'Koshihikari' and an indica rice cultivar 'Takanari'. RESULTS We detected 112 QTLs for amylose and protein contents, whiteness, stickiness, hardness and eating quality of cooked rice grains. Almost of 'Koshihikari' chromosome segments consistently improved eating quality. Among detected QTLs, six QTLs on chromosomes 1-5 and 11 were detected that increased whiteness and stickiness of cooked grains or decreased their hardness for 3 years. The QTLs on chromosomes 2-4 were not associated with differences in amylose or protein contents. QTLs on chromosomes 1-5 did not coincide with QTLs for agronomic traits such as heading date, culm length, panicle length, spikelet fertility and grain yield. Genetic effects of the detected QTLs were confirmed in substitution lines carrying chromosome segments from five other indica cultivars in the 'Koshihikari' genetic background. CONCLUSION The detected QTLs were associated with differences in eating quality between indica and japonica rice cultivars. These QTLs appear to be widely distributed among indica cultivars and to be novel genetic factors for eating quality traits because their chromosome regions differed from those of the GBSSI (Wx) and SSIIa (Alk) genes. The detected QTLs would be very useful for improvement of eating quality of indica rice cultivars in breeding programs.
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Affiliation(s)
- Kiyosumi Hori
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Keitaro Suzuki
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Haruka Ishikawa
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazufumi Nagata
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Present address: St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki, Kanagawa, 216-8511, Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Junichi Tanaka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
- Graduate School of Life and Environmental Science, University of Tsukuba, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
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Zhao C, Zhao L, Zhao Q, Chen T, Yao S, Zhu Z, Zhou L, Nadaf AB, Liang W, Lu K, Zhang Y, Wang C. Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping. BMC Genet 2020; 21:119. [PMID: 33054745 PMCID: PMC7556922 DOI: 10.1186/s12863-020-00922-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/29/2020] [Indexed: 12/03/2022] Open
Abstract
Background Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, gelatinization temperature and pasting viscosity are important indices for evaluating rice ECQs. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. Results A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes (SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)n, SSI and SBE1 for indica subpopulation and RM550, Wxmp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and could be selected for further fine mapping. Conclusion This study illustrated the potential for dissecting genetic factors of complex traits in domesticated rice subspecies and provided highly associated markers to facilitate marker-assisted selection for breeding high-quality indica or japonica rice varieties.
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Affiliation(s)
- Chunfang Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Ling Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Tao Chen
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Shu Yao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Zhen Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Lihui Zhou
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | | | - Wenhua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Kai Lu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China.
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu Rice Engineering Research Center, National Center for Rice Improvement (Nanjing), Nanjing, 210014, China.
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Donde R, Mohapatra S, Baksh SKY, Padhy B, Mukherjee M, Roy S, Chattopadhyay K, Anandan A, Swain P, Sahoo KK, Singh ON, Behera L, Dash SK. Identification of QTLs for high grain yield and component traits in new plant types of rice. PLoS One 2020; 15:e0227785. [PMID: 32673318 PMCID: PMC7365460 DOI: 10.1371/journal.pone.0227785] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/11/2020] [Indexed: 11/18/2022] Open
Abstract
A panel of 60 genotypes comprising New Plant Types (NPTs) along with indica, tropical and temperate japonica genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number (qTL-6.1, qTL-11.1, qTL-4.1), panicle length (qPL-1.1, qPL-5.1, qPL-7.1, qPL-8.1), flag leaf length (qFLL-8.1, qFLL-9.1), flag leaf width (qFLW-6.2, qFLW-5.1, qFLW-8.1, qFLW-7.1), total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight (qTGW-a1.1, qTGW-a9.2, qTGW-5.1, qTGW-8.1), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se (qYLD-5.1, qYLD-6.1a, qYLD-11.1).Some of the SSRs were co-localized with more than two traits. The highest co-localization was identified with RM5709 linked to nine traits, followed by RM297 with five traits. Similarly, RM5575, RM204, RM168, RM112, RM26499 and RM22899 were also recorded to be co-localized with more than one trait and could be rated as important for marker-assisted backcross breeding programs, for pyramiding of these QTLs for important yield traits, to produce new-generation rice for prospective increment in yield potentiality and breaking yield ceiling.
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Affiliation(s)
- Ravindra Donde
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Shibani Mohapatra
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - S. K. Yasin Baksh
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Barada Padhy
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Mitadru Mukherjee
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Somnath Roy
- ICAR-NRRI, Regional Research Station (CRURRS), Hazaribagh, Jharkhand
| | | | - A. Anandan
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Padmini Swain
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | | | - Onkar Nath Singh
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
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10
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Tang L, Zhang F, Liu A, Sun J, Mei S, Wang X, Liu Z, Liu W, Lu Q, Chen S. Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice. RICE (NEW YORK, N.Y.) 2019; 12:101. [PMID: 31889226 PMCID: PMC6937365 DOI: 10.1186/s12284-019-0362-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/20/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Carbon (C) and nitrogen (N) are two fundamental components of starch and protein, which are important determinants of grain yield and quality. The food preferences of consumers and the expected end-use of grains in different rice-growing regions require diverse varieties that differ in terms of the grain N content (GNC) and grain C content (GCC) of milled rice. Thus, it is important that quantitative trait loci (QTLs)/genes with large effects on the variation of GNC and GCC are identified in breeding programs. RESULTS To dissect the genetic basis of the variation of GNC and GCC in rice, the Dumas combustion method was used to analyze 751 diverse accessions regarding the GNC, GCC, and C/N ratio of the milled grains. The GCC and GNC differed significantly among the rice subgroups, especially between Xian/Indica (XI) and Geng/Japonica (GJ). Interestingly, in the GJ subgroup, the GNC was significantly lower in modern varieties (MV) than in landraces (LAN). In the XI subgroup, the GCC was significantly higher in MV than in LAN. One, six, and nine QTLs, with 55 suggestively associated single nucleotide polymorphisms, were detected for the GNC, GCC, and C/N ratio in three panels during a single-locus genome-wide association study (GWAS). Three of these QTLs were also identified in a multi-locus GWAS. We screened 113 candidate genes in the 16 QTLs in gene-based haplotype analyses. Among these candidate genes, LOC_Os01g06240 at qNC-1.1, LOC_Os05g33300 at qCC-5.1, LOC_Os01g04360 at qCN-1.1, and LOC_Os05g43880 at qCN-5.2 may partially explain the significant differences between the LAN and MV. These candidate genes should be cloned and may be useful for molecular breeding to rapidly improve the GNC, GCC, and C/N ratio of rice. CONCLUSIONS Our findings represent valuable information regarding the genetic basis of the GNC and GCC and may be relevant for enhancing the application of favorable haplotypes of candidate genes for the molecular breeding of new rice varieties with specific grain N and C contents.
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Affiliation(s)
- Liang Tang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing, 100081, China.
| | - Anjin Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Song Mei
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing, 100081, China
| | - Xin Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhongyuan Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wanying Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qing Lu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shuangjie Chen
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
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11
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Natural variation of OsGluA2 is involved in grain protein content regulation in rice. Nat Commun 2019; 10:1949. [PMID: 31028264 PMCID: PMC6486610 DOI: 10.1038/s41467-019-09919-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/05/2019] [Indexed: 01/09/2023] Open
Abstract
Grain protein content (GPC) affects rice nutrition quality. Here, we identify two stable quantitative trait loci (QTLs), qGPC-1 and qGPC-10, controlling GPC in a mapping population derived from indica and japonica cultivars crossing. Map-based cloning reveals that OsGluA2, encoding a glutelin type-A2 precursor, is the candidate gene underlying qGPC-10. It functions as a positive regulator of GPC and has a pleiotropic effect on rice grain quality. One SNP located in OsGluA2 promoter region is associated with its transcript expression level and GPC diversity. Polymorphisms of this nucleotide can divide all haplotypes into low (OsGluA2LET) and high (OsGluA2HET) expression types. Population genetic and evolutionary analyses reveal that OsGluA2LET, mainly present in japonica accessions, originates from wild rice. However, OsGluA2HET, the dominant type in indica, is acquired through mutation of OsGluA2LET. Our results shed light on the understanding of natural variations of GPC between indica and japonica subspecies. Grain protein content determines rice nutrition quality. Here, the authors show that a single nucleotide polymorphism in the promoter region of OsGluA2, encoding a glutelin type-A2 precursor, is responsible for glutelin content difference between the indica and japonica rice subspecies.
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12
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Wang H, Zhu S, Dang X, Liu E, Hu X, Eltahawy MS, Zaid IU, Hong D. Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping. BMC Genet 2019; 20:34. [PMID: 30890139 PMCID: PMC6423859 DOI: 10.1186/s12863-019-0735-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 03/01/2019] [Indexed: 11/22/2022] Open
Abstract
Background Improving the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) for parental grain eating and cooking qualities (ECQs) are key factors for enhancing average grain ECQs for hybrid japonica rice. Results In this study, a genome-wide association mapping (GWAS) for ECQs was performed on a selected sample of 462 rice accessions in 5 environments using 262 simple sequence repeat markers. We identified 10 loci and 27 favorable alleles for GT, GC and AC, and some of these loci were overlapped with starch synthesis-related genes. Four SSR loci for the GT trait were distributed on chromosomes 3, 5, 8, and 9, of which two SSR loci were novel. Two SSR loci associated with the GC trait were distributed on chromosomes 3 and 6, although only one SSR locus was novel. Four SSR loci associated with the AC trait were distributed on chromosomes 3, 6, 10, and 11, of which three SSR loci were novel. The novel loci RM6712 and RM6327 were simultaneously identified in more than 2 environments and were potentially reliable QTLs for ECQs, with 15 parental combinations being predicted. These QTLs and parental combinations should be used in molecular breeding to improve japonica rice average ECQs. Conclusions Among the 10 SSR loci associated with GT, GC and AC for grain ECQs detected in 27 favorable alleles, the favorable allele RM3600-90bp on chromosome 9 could significantly reduce GT, RM5753-115bp on chromosome 6 could significantly increase GC, and RM6327-230bp on chromosome 11 could significantly reduce AC in hybrid japonica rice mixed rice samples. Electronic supplementary material The online version of this article (10.1186/s12863-019-0735-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Wang
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shangshang Zhu
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaojing Dang
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoxiao Hu
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Moaz Salah Eltahawy
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Imdad Ullah Zaid
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Delin Hong
- Nanjing Agricultural University, Nanjing, 210095, China. .,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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13
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Fiaz S, Ahmad S, Noor MA, Wang X, Younas A, Riaz A, Riaz A, Ali F. Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities. Int J Mol Sci 2019; 20:E888. [PMID: 30791357 PMCID: PMC6412304 DOI: 10.3390/ijms20040888] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/07/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023] Open
Abstract
Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.
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Affiliation(s)
- Sajid Fiaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing 100081, China.
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore 54000, Pakistan.
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Fahad Ali
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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14
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Song JM, Arif M, Zhang M, Sze SH, Zhang HB. Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection. Food Chem 2019; 284:312-322. [PMID: 30744863 DOI: 10.1016/j.foodchem.2019.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/21/2018] [Accepted: 01/03/2019] [Indexed: 12/16/2022]
Abstract
Grain quality is a major breeding objective and paramount to food production. This study was aimed to phenotypically and molecularly dissect the rice grain quality, especially amylose content (AC), grain protein content (GPC) and alkali spreading value (ASV), using the USDA rice mini-core collection representing the world-wide rice germplasm lines. Grain chemical analysis combined with genome-wide association study (GWAS) was used for the study. A wide genetic variation was observed for these grain quality traits in the mini-core collection. Germplasm lines unique in AC, GPC and ASV and desirable for grain quality improvement were identified. The genetic diversity of the collection was re-analyzed using new SNPs, thus providing a more precise genotypic information about the collection. Furthermore, ten loci significantly associated with these grain quality traits were identified through GWAS using 22947 high-quality SNPs. These results, therefore, provide knowledge, resources and molecular tools for efficient rice grain quality improvement.
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Affiliation(s)
- Jian-Min Song
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA; Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Muhammad Arif
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA; Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA.
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA.
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15
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Iijima K, Suzuki K, Hori K, Ebana K, Kimura K, Tsujii Y, Takano K. Endosperm enzyme activity is responsible for texture and eating quality of cooked rice grains in Japanese cultivars. Biosci Biotechnol Biochem 2018; 83:502-510. [PMID: 30458671 DOI: 10.1080/09168451.2018.1547624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Eating quality of cooked rice grains is an important determinant of its market price and consumer acceptance. To comprehensively assess the variation of eating-quality traits in 152 Japanese rice cultivars, we evaluated activities of eight endosperm enzymes related to degradation of starch and cell-wall polysaccharides. Endosperm enzyme activities showed a wide range of variations and were lower in recently developed cultivars than in landraces and old improved cultivars. Activities of most endosperm enzymes correlated significantly with the eating-quality score and surface texture of cooked rice grains. Principal component analysis revealed that rice cultivars with high eating-quality scores had high stickiness of the grain surface and low levels of endosperm enzyme activities. These results suggest that endosperm enzyme activities control texture and eating quality of cooked rice grains in Japanese rice cultivars.
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Affiliation(s)
- Ken Iijima
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Keitaro Suzuki
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Kiyosumi Hori
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Kaworu Ebana
- b Genetic Resources Center , NARO , Tsukuba , Japan
| | - Keiichi Kimura
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
| | - Yoshimasa Tsujii
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
| | - Katsumi Takano
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
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16
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Hori K, Yamamoto T, Yano M. Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars. BREEDING SCIENCE 2017; 67:427-434. [PMID: 29398936 PMCID: PMC5790047 DOI: 10.1270/jsbbs.17053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/11/2017] [Indexed: 05/15/2023]
Abstract
Many quantitative trait loci (QTLs) for agronomically important traits such as grain yield, disease resistance, and stress tolerance of rice (Oryza sativa L.) have been detected by using segregating populations derived from crosses between indica and japonica subspecies or with wild relatives. However, the QTLs involved in the control of natural variation in agronomic traits among closely related cultivars are still unclear. Decoding the whole genome sequences of Nipponbare and other temperate japonica rice cultivars has accelerated the collection of a huge number of single nucleotide polymorphisms (SNPs). These SNPs are good resource for developing polymorphic DNA markers and for detecting QTLs distributed across all rice chromosomes. The temperate japonica rice cultivar Koshihikari has remained the top cultivar for about 40 years since 1979 in Japan. Unraveling the genetic factors in Koshihikari will provide important insights into improving agronomic traits in temperate japonica rice cultivars. Here we describe recent progress in our studies as an example of genetic analysis in closely related cultivars.
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17
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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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