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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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Fiaz S, Sheng Z, Zeb A, Barman HN, Shar T, Ali U, Tang S. Analysis of genomic regions for crude protein and fractions of protein using a recombinant inbred population in Rice ( Oryza sativa L.). JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.1991733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sajid Fiaz
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
- Department of Plant Breeding and Genetics, University of Haripur, Haripur, Pakistan
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Aqib Zeb
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Hirendra Nath Barman
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Tahmina Shar
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Umed Ali
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Centre for Rice Improvement, China National Rice Research Institute, Hangzhou, People’s Republic of China
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Chen P, Shen Z, Ming L, Li Y, Dan W, Lou G, Peng B, Wu B, Li Y, Zhao D, Gao G, Zhang Q, Xiao J, Li X, Wang G, He Y. Genetic Basis of Variation in Rice Seed Storage Protein (Albumin, Globulin, Prolamin, and Glutelin) Content Revealed by Genome-Wide Association Analysis. FRONTIERS IN PLANT SCIENCE 2018; 9:612. [PMID: 29868069 PMCID: PMC5954490 DOI: 10.3389/fpls.2018.00612] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/18/2018] [Indexed: 05/18/2023]
Abstract
Rice seed storage protein (SSP) is an important source of nutrition and energy. Understanding the genetic basis of SSP content and mining favorable alleles that control it will be helpful for breeding new improved cultivars. An association analysis for SSP content was performed to identify underlying genes using 527 diverse Oryza sativa accessions grown in two environments. We identified more than 107 associations for five different traits, including the contents of albumin (Alb), globulin (Glo), prolamin (Pro), glutelin (Glu), and total SSP (Total). A total of 28 associations were located at previously reported QTLs or intervals. A lead SNP sf0709447538, associated for Glu content in the indica subpopulation in 2015, was further validated in near isogenic lines NIL(Zhenshan97) and NIL(Delong208), and the Glu phenotype had significantly difference between two NILs. The association region could be target for map-based cloning of the candidate genes. There were 13 associations in regions close to grain-quality-related genes; five lead single nucleotide polymorphisms (SNPs) were located less than 20 kb upstream from grain-quality-related genes (PG5a, Wx, AGPS2a, RP6, and, RM1). Several starch-metabolism-related genes (AGPS2a, OsACS6, PUL, GBSSII, and ISA2) were also associated with SSP content. We identified favorable alleles of functional candidate genes, such as RP6, RM1, Wx, and other four candidate genes by haplotype analysis and expression pattern. Genotypes of RP6 and RM1 with higher Pro were not identified in japonica and exhibited much higher expression levels in indica group. The lead SNP sf0601764762, repeatedly detected for Alb content in 2 years in the whole association population, was located in the Wx locus that controls the synthesis of amylose. And Alb content was significantly and negatively correlated with amylose content and the level of 2.3 kb Wx pre-mRNA examined in this study. The associations or candidate genes identified would provide new insights into the genetic basis of SSP content that will help in developing rice cultivars with improved grain nutritional quality through marker-assisted breeding.
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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, China
| | - Zhikang Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Luchang Ming
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Wenhan Dan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bo Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yanhua Li
- Life Science and Technology Center, China National Seed Group Co., Ltd., Wuhan, China
| | - Da Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
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Morita R, Kusaba M, Iida S, Yamaguchi H, Nishio T, Nishimura M. Molecular characterization of mutations induced by gamma irradiation in rice. Genes Genet Syst 2010; 84:361-70. [PMID: 20154423 DOI: 10.1266/ggs.84.361] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In order to analyze mutations induced by gamma irradiation in higher plants, we irradiated rice with gamma rays and screened for mutations expressing phenotypes of glutinous endosperm (wx), chlorophyll b deficiency, endosperm protein deficiency, gibberellin-related dwarfism, and shortened plastochron-in order to clarify types of mutations. Nucleotide sequence analysis showed that the most frequent mutation induced by gamma rays was deletion, particularly small deletion. Of the 24 mutations, 15 were small deletions (1-16 bp), four were large deletions (9.4-129.7 kbp), three were single-base substitutions, and two were inversions. Deletions 100 bp-8 kbp in length were not found, suggesting that gamma irradiation is unlikely to induce deletions of 100 bp to 8 kbp but is more likely to induce deletions between 1 and several ten bp or those of around 10 kbp or more. Based on the results, reverse genetics applications may be possible for gamma irradiation-induced deletions in rice by mismatch cleavage analysis used in Targeting Induced Local Lesions IN Genomes (TILLING) to detect small deletions and base substitutions or by using array comparative genomic hybridization (aCGH) to detect large deletions.
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Affiliation(s)
- Ryouhei Morita
- Institute of Radiation Breeding, National Institute of Agrobiological Sciences, 2425 Kamimurata, Hitachi-ohmiya, Ibaraki 319-2293, Japan.
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