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Alam M, Lou G, Abbas W, Osti R, Ahmad A, Bista S, Ahiakpa JK, He Y. Improving Rice Grain Quality Through Ecotype Breeding for Enhancing Food and Nutritional Security in Asia-Pacific Region. RICE (NEW YORK, N.Y.) 2024; 17:47. [PMID: 39102064 DOI: 10.1186/s12284-024-00725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/28/2024] [Indexed: 08/06/2024]
Abstract
Rice grain is widely consumed as a staple food, providing essential nutrition for households, particularly marginalized families. It plays a crucial role in ensuring food security, promoting human nutrition, supporting good health, and contributing to global food and nutritional security. Addressing the diverse quality demands of emerging diverse and climate-risked population dietary needs requires the development of a single variety of rice grain that can meet the various dietary and nutritional requirements. However, there is a lack of concrete definition for rice grain quality, making it challenging to cater to the different demands. The lack of sufficient genetic study and development in improving rice grain quality has resulted in widespread malnutrition, hidden hunger, and micronutrient deficiencies affecting a significant portion of the global population. Therefore, it is crucial to identify genetically evolved varieties with marked qualities that can help address these issues. Various factors account for the declining quality of rice grain and requires further study to improve their quality for healthier diets. We characterized rice grain quality using Lancastrians descriptor and a multitude of intrinsic and extrinsic quality traits. Next, we examined various components of rice grain quality favored in the Asia-Pacific region. This includes preferences by different communities, rice industry stakeholders, and value chain actors. We also explored the biological aspects of rice grain quality in the region, as well as specific genetic improvements that have been made in these traits. Additionally, we evaluated the factors that can influence rice grain quality and discussed the future directions for ensuring food and nutritional security and meeting consumer demands for grain quality. We explored the diverse consumer bases and their varied preferences in Asian-Pacific countries including India, China, Nepal, Bhutan, Vietnam, Sri Lanka, Pakistan, Thailand, Cambodia, Philippines, Bangladesh, Indonesia, Korea, Myanmar and Japan. The quality preferences encompassed a range of factors, including rice head recovery, grain shape, uniform size before cooking, gelatinization, chalkiness, texture, amylose content, aroma, red-coloration of grain, soft and shine when cooked, unbroken when cooked, gelatinization, less water required for cooking, gelatinization temperature (less cooking time), aged rice, firm and dry when cooked (gel consistency), extreme white, soft when chewed, easy-to-cook rice (parboiled rice), vitamins, and minerals. These preferences were evaluated across high, low, and medium categories. A comprehensive analysis is provided on the enhancement of grain quality traits, including brown rice recovery, recovery rate of milled rice, head rice recovery, as well as morphological traits such as grain length, grain width, grain length-width ratio, and grain chalkiness. We also explored the characteristics of amylose, gel consistency, gelatinization temperature, viscosity, as well as the nutritional qualities of rice grains such as starch, protein, lipids, vitamins, minerals, phytochemicals, and bio-fortification potential. The various factors that impact the quality of rice grains, including pre-harvest, post-harvest, and genotype considerations were explored. Additionally, we discussed the future direction and genetic strategies to effectively tackle these challenges. These qualitative characteristics represent the fundamental focus of regional and national breeding strategies employed by different countries to meet consumer preference. Given the significance of rice as a staple food in Asia-Pacific countries, it is primarily consumed domestically, with only a small portion being exported internationally. All the important attributes must be clearly defined within specific parameters. It is crucial for geneticists and breeders to develop a rice variety that can meet the diverse demands of consumers worldwide by incorporating multiple desirable traits. Thus, the goal of addressing global food and nutritional security, and human healthy can be achieved.
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Affiliation(s)
- Mufid Alam
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Waseem Abbas
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rajani Osti
- College of Humanities and Social Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Aqeel Ahmad
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Science and Natural Resource Research, Chinese Academy of Science (CAS), Beijing, China
| | - Sunita Bista
- Sichuan Agricultural University, Chengdu, Sichuan, China
| | - John K Ahiakpa
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Hu S, Zhou L, Wang J, Mawia AM, Hui S, Xu B, Jiao G, Sheng Z, Shao G, Wei X, Wang L, Xie L, Zhao F, Tang S, Hu P. Production of grains with ultra-low heavy metal accumulation by pyramiding novel Alleles of OsNramp5 and OsLsi2 in two-line hybrid rice. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38898780 DOI: 10.1111/pbi.14414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
Ensuring rice yield and grain safety quality are vital for human health. In this study, we developed two-line hybrid rice (TLHR) with ultra-low grain cadmium (Cd) and arsenic (As) accumulation by pyramiding novel alleles of OsNramp5 and OsLsi2. We first generated low Cd accumulation restorer (R) lines by editing OsNramp5, OsLCD, and OsLCT in japonica and indica. After confirming that OsNramp5 was most efficient in reducing Cd, we edited this gene in C815S, a genic male sterile line (GMSL), and screened it for alleles with low Cd accumulation. Next, we generated R and GMSL lines with low As accumulation by editing OsLsi2 in a series of YK17 and C815S lines. When cultivated in soils that were heavily polluted with Cd and As, the edited R, GMSL, and TLHR plants showed significantly reduced heavy metal accumulation, while maintaining a relatively stable yield potential. This study provides an effective scheme for the safe production of grains in As- and/or Cd-polluted paddy fields.
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Affiliation(s)
- Shikai Hu
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Liang Zhou
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Jingxin Wang
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Amos Musyoki Mawia
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Suozhen Hui
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Bo Xu
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Ling Wang
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Lihong Xie
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Fengli Zhao
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
| | - Peisong Hu
- State Key Laboratory of Rice Biology Breeding, China National Rice Research Institute, Hangzhou, People's Republic of China
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Nie S, Chen L, Zheng M, Dong J, Ma Y, Zhou L, Wang J, Chen J, Hu H, Yang T, Zhao J, Zhang S, Yang W. GWAS and Transcriptomic Analysis Identify OsRING315 as a New Candidate Gene Controlling Amylose Content and Gel Consistency in Rice. RICE (NEW YORK, N.Y.) 2024; 17:38. [PMID: 38849622 PMCID: PMC11161452 DOI: 10.1186/s12284-024-00718-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024]
Abstract
Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice.
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Affiliation(s)
- Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Minhua Zheng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China
| | - Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, P.R. China.
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Chen Y, Shi H, Yang G, Liang X, Lin X, Tan S, Guo T, Wang H. OsCRLK2, a Receptor-Like Kinase Identified by QTL Analysis, is Involved in the Regulation of Rice Quality. RICE (NEW YORK, N.Y.) 2024; 17:24. [PMID: 38587574 PMCID: PMC11001810 DOI: 10.1186/s12284-024-00702-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024]
Abstract
The quality of rice (Oryza sativa L) is determined by a combination of appearance, flavor, aroma, texture, storage characteristics, and nutritional composition. Rice quality directly influences acceptance by consumers and commercial value. The genetic mechanism underlying rice quality is highly complex, and is influenced by genotype, environment, and chemical factors such as starch type, protein content, and amino acid composition. Minor variations in these chemical components may lead to substantial differences in rice quality. Among these components, starch is the most crucial and influential factor in determining rice quality. In this study, quantitative trait loci (QTLs) associated with eight physicochemical properties related to the rapid viscosity analysis (RVA) profile were identified using a high-density sequence map constructed using recombinant inbred lines (RILs). Fifty-nine QTLs were identified across three environments, among which qGT6.4 was a novel locus co-located across all three environments. By integrating RNA-seq data, we identified the differentially expressed candidate gene OsCRLK2 within the qGT6.4 interval. osclrk2 mutants exhibited decreased gelatinization temperature (GT), apparent amylose content (AAC) and viscosity, and increased chalkiness. Furthermore, osclrk2 mutants exhibited downregulated expression of the majority of starch biosynthesis-related genes compared to wild type (WT) plants. In summary, OsCRLK2, which encodes a receptor-like protein kinase, appears to consistently influence rice quality across different environments. This discovery provides a new genetic resource for use in the molecular breeding of rice cultivars with improved quality.
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Affiliation(s)
- Ying Chen
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Hanfeng Shi
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Guili Yang
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Xueyu Liang
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Xiaolian Lin
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Siping Tan
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China.
| | - Hui Wang
- National Engineering Research Center of Plant Aerospace-mutation Breeding, South China Agricultural University, 510642, Guangzhou, China.
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Wang Q, Gao H, Liu K, Wang H, Zhang F, Wei L, Lu K, Li M, Shi Y, Zhao J, Zhou W, Peng B, Yuan H. CRISPR/Cas9-mediated enhancement of semi-dwarf glutinous traits in elite Xiangdaowan rice ( Oryza sativa L.): targeting SD1 and Wx genes for yield and quality improvement. FRONTIERS IN PLANT SCIENCE 2024; 15:1333191. [PMID: 38434426 PMCID: PMC10904601 DOI: 10.3389/fpls.2024.1333191] [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: 11/04/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
In rice cultivation, the traits of semi-dwarfism and glutinous texture are pivotal for optimizing yield potential and grain quality, respectively. Xiangdaowan (XDW) rice, renowned for its exceptional aromatic properties, has faced challenges due to its tall stature and high amylose content, resulting in poor lodging resistance and suboptimal culinary attributes. To address these issues, we employed CRISPR/Cas9 technology to precisely edit the SD1 and Wx genes in XDW rice, leading to the development of stable genetically homozygous lines with desired semi-dwarf and glutinous characteristics. The sd1-wx mutant lines exhibited reduced gibberellin content, plant height, and amylose content, while maintaining hardly changed germination rate and other key agronomic traits. Importantly, our study demonstrated that exogenous GA3 application effectively promoted growth by compensating for the deficiency of endogenous gibberellin. Based on this, a semi-dwarf glutinous elite rice (Oryza sativa L.) Lines was developed without too much effect on most agronomic traits. Furthermore, a comparative transcriptome analysis unveiled that differentially expressed genes (DEGs) were primarily associated with the anchored component of the membrane, hydrogen peroxide catabolic process, peroxidase activity, terpene synthase activity, and apoplast. Additionally, terpene synthase genes involved in catalyzing the biosynthesis of diterpenoids to gibberellins were enriched and significantly down-regulated. This comprehensive study provides an efficient method for simultaneously enhancing rice plant height and quality, paving the way for the development of lodging-resistant and high-quality rice varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Hongyu Yuan
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
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Hao Y, Huang F, Gao Z, Xu J, Zhu Y, Li C. Starch Properties and Morphology of Eight Floury Endosperm Mutants in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3541. [PMID: 37896005 PMCID: PMC10610063 DOI: 10.3390/plants12203541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Besides increasing grain yield, improving rice (Oryza sativa L.) quality has been paid more and more attention recently. Cooking and eating quality (CEQ) is an important indicator of rice quality. Since CEQs are quantitative traits and challenging for measurement, efforts have mainly focused on two major genes, Wx and SSIIa. Chalkiness and floury endosperm significantly affect the eating quality of rice, leading to noticeable changes in CEQ. Due to the easily observable phenotype of floury endosperm, cloning single gene mutations that cause floury endosperm and evaluating changes in CEQs indirectly facilitate the exploration of the minor genes controlling CEQ. In this study, eight mutants with different degrees of floury endosperm, generated through ethylmethane sulfonate (EMS) mutagenesis, were analyzed. These mutants exhibited wide variation in starch morphology and CEQs. Particularly, the z2 mutant showed spherical starch granules significantly increased rapid visco analyzer (RVA) indexes and urea swelling, while the z4 mutant displayed extremely sharp starch granules and significantly decreased RVA indexes and urea swelling compared to the wild type. Additionally, these mutants still maintained correlations with certain RVA profiles, suggesting that the genes PUL, which affect these indexes, may not undergo mutation. Cloning these mutated genes in the future, especially in z2 and z4, will enhance the genetic network of rice eating quality and hold significant importance for molecular marker-assisted breeding to improve rice quality.
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Affiliation(s)
- Yuanyuan Hao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.H.); (F.H.); (Z.G.)
| | - Fudeng Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.H.); (F.H.); (Z.G.)
| | - Zhennan Gao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.H.); (F.H.); (Z.G.)
| | - Junfeng Xu
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China;
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Hangzhou 310021, China
| | - Chunshou Li
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.H.); (F.H.); (Z.G.)
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Zheng Y, Thi KM, Lin L, Xie X, Khine EE, Nyein EE, Lin MHW, New WW, Aye SS, Wu W. Genome-wide association study of cooking-caused grain expansion in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1250854. [PMID: 37711286 PMCID: PMC10498926 DOI: 10.3389/fpls.2023.1250854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.
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Affiliation(s)
- Yan Zheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Khin Mar Thi
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lihui Lin
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ei Ei Khine
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ei Ei Nyein
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Min Htay Wai Lin
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - Win Win New
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - San San Aye
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - Weiren Wu
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Wang Q, Chen P, Wang H, Chao S, Guo W, Zhang Y, Miao C, Yuan H, Peng B. Physiological and transcriptomic analysis of OsLHCB3 knockdown lines in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:38. [PMID: 37312752 PMCID: PMC10248686 DOI: 10.1007/s11032-023-01387-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: 11/02/2022] [Accepted: 04/18/2023] [Indexed: 06/15/2023]
Abstract
The photosystem II (PSII) outer antenna LHCB3 protein plays critical roles in distributing the excitation energy and modulating the rate of state transition for photosynthesis. Here, OsLHCB3 knockdown mutants were produced using the RNAi system. Phenotypic analyses showed that OsLHCB3 knockdown led to pale green leaves and lower chlorophyll contents at both tillering and heading stages. In addition, mutant lines exhibited decreased non-photochemical quenching (NPQ) capacity and net photosynthetic rate (Pn) by downregulating the expression of PSII-related genes. Moreover, RNA-seq experiments were performed at both tillering and heading stages. The differentially expressed genes (DEGs) mainly involved in chlorophyll binding response to abscisic acid, photosystem II, response to chitin, and DNA-binding transcription factor. Besides, our transcriptomic and physiological data indicated that OsLHCB3 was essential for binding chlorophyll, but not for the metabolism of chlorophyll in rice. OsLHCB3 RNAi knockdown plants affected the expression of PS II-related genes, but not PS I-related genes. Overall, these results suggest that OsLHCB3 also plays vital roles in regulating photosynthesis and antenna proteins in rice as well as responses to environment stresses. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01387-z.
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Affiliation(s)
- Quanxiu Wang
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Pingli Chen
- Guangdong Key Laboratory of New Technology in Rice Breeding, The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Honglin Wang
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Shuangshuang Chao
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Wenru Guo
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Yuxue Zhang
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Chenglin Miao
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Hongyu Yuan
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Bo Peng
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
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9
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Lu Z, Fang Z, Liu W, Lu D, Wang X, Wang S, Xue J, He X. Grain quality characteristics analysis and application on breeding of Yuenongsimiao, a high-yielding and disease-resistant rice variety. Sci Rep 2023; 13:6335. [PMID: 37072409 PMCID: PMC10113224 DOI: 10.1038/s41598-022-21030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/21/2022] [Indexed: 05/03/2023] Open
Abstract
Rice quality is one of the main targets of rice breeding and is a complex trait that involves grain appearance, milling, cooking, eating and nutritional quality. For many years, rice breeding has contended with imbalances in rice yield, quality, and disease and lodging resistance. Here, the milling and appearance quality, cooking quality, starch rapid viscosity analyzer (RVA) profile, and nutritional quality of grains of Yuenongsimiao (YNSM), an indica rice variety with high yield, high quality and disease resistance, were determined. YNSM had excellent appearance and quality, with low amylose contents and high gel consistency, and these characteristics exhibited significant correlations with the RVA profile such as hot paste viscosity, cool paste viscosity, setback viscosity, and consistency. Moreover, 5 genes related to length-to-width ratio (LWR) as well as the Wx gene were used to detect the main quality genotype of YNSM. The results showed that YNSM is a semilong-grain rice with a relatively high brown rice rate, milled rice rate and head rice yield and low chalkiness. The results indicated that the LWR and food quality of YNSM might be related to gs3, gw7 and Wxb. This study also reports the quality characteristics of hybrid rice developed using YNSM as a restorer line. The quality characteristics and the genotype for grain quality determined through gene analysis in YNSM may facilitate the breeding of new rice varieties that achieve a balance of grain yield, resistance and quality.
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Affiliation(s)
- Zhanhua Lu
- 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
| | - Zhiqiang Fang
- 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
| | - Wei 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
| | - Dongbai Lu
- 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
| | - Xiaofei Wang
- 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
| | - Shiguang Wang
- 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
| | - Jiao Xue
- 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
| | - Xiuying He
- 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.
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10
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Zhang C, Yun P, Xia J, Zhou K, Wang L, Zhang J, Zhao B, Yin D, Fu Z, Wang Y, Ma T, Li Z, Wu D. CRISPR/Cas9-mediated editing of Wx and BADH2 genes created glutinous and aromatic two-line hybrid rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:24. [PMID: 37313522 PMCID: PMC10248662 DOI: 10.1007/s11032-023-01368-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/02/2023] [Indexed: 06/15/2023]
Abstract
Amylose content (AC) is one of the physicochemical indexes of rice quality, which is largely determined by the Waxy (Wx) gene. Fragrance in rice is favored because it adds good flavor and a faint scent. Loss of function of the BADH2 (FGR) gene promotes the biosynthesis of 2-acetyl-1-pyrroline (2AP), which is the main compound responsible for aroma in rice. Here, we used a CRISPR/Cas9 system to simultaneously knock out Wx and FGR genes in 1892S and M858, which are the parents of an indica two-line hybrid rice, Huiliangyou 858 (HLY858). Four T-DNA-free homozygous mutants (1892Swxfgr-1, 1892Swxfgr-2, M858wxfgr-1, and M858wxfgr-2) were obtained. The 1892Swxfgr and M858wxfgr were crossed to generate double mutant hybrid lines HLY858wxfgr-1 and HLY858wxfgr-2. Size-exclusion chromatography (SEC) data indicated that true AC of the wx mutant starches ranged from 0.22 to 1.63%, much lower than those of the wild types (12.93 to 13.76%). However, the gelatinization temperature (GT) of the wx mutants in backgrounds of 1892S, M858, and HLY858 were still high, and showed no significant differences with the wild type controls. The aroma compounds 2AP content in grains of HLY858wxfgr-1 and HLY858wxfgr-2 were 153.0 μg/kg and 151.0 μg/kg, respectively. In contrast, 2AP was not detected in grains of HLY858. There were no significant differences in major agronomic traits between the mutants and HLY858. This study provides guidelines for cultivation of ideal glutinous and aromatic hybrid rice by gene editing.
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Affiliation(s)
- Caijuan Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Peng Yun
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Jiafa Xia
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Kunneng Zhou
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Lili Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Jingwen Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Bo Zhao
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Daokun Yin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Zhe Fu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Yuanlei Wang
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Tingchen Ma
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Zefu Li
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
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11
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Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
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12
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Sun Y, Zhao H, Chen Z, Chen H, Li B, Wang C, Lin X, Cai Y, Zhou D, Ouyang L, Zhu C, He H, Peng X. Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:156. [PMID: 36616286 PMCID: PMC9824520 DOI: 10.3390/plants12010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either CRY1C gene on chromosome 11 or CRY2A gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits. Using 512 microsatellite markers, the three transgenic lines inherited 2.9-4.3% of the Minghui 63 donor genome and 96.3-97.1% of the CH891 recurrent parent genome. As compared with the recurrent parent, the number of upregulated and down-regulated proteins in the three transgenic lines varied from 169 to 239 and from 131 to 199, respectively. Most DEPs were associated with the secondary metabolites biosynthesis transport and catabolism, carbohydrate transport and metabolism, post-translational modification, and signal transduction mechanisms. Although several differentially expressed proteins were observed between transgenic rice and its recurrent parent, the differences may not have been associated with grain yield and most other phenotypic traits in transgenic rice.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huan Zhao
- Jiangxi Biotech Vocational College, JAU, Nanchang 330200, China
| | - Zhongkai Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huizhen Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Bai Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Chunlei Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaoli Lin
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Yicong Cai
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
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13
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Sreenivasulu N, Zhang C, Tiozon RN, Liu Q. Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century. PLANT COMMUNICATIONS 2022; 3:100271. [PMID: 35576153 PMCID: PMC9251384 DOI: 10.1016/j.xplc.2021.100271] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 05/14/2023]
Abstract
The eating and cooking quality (ECQ) of rice is critical for determining its economic value in the marketplace and promoting consumer acceptance. It has therefore been of paramount importance in rice breeding programs. Here, we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in rice. Innovations in gene- and genome-editing techniques have enabled improvements in rice ECQ. Significant genes and quantitative trait loci (QTLs) have been shown to regulate starch composition, thereby affecting amylose content and thermal and pasting properties. A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and aroma. Marker-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ properties. The post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.
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Affiliation(s)
- Nese Sreenivasulu
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños 4030, Philippines.
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Rhowell N Tiozon
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños 4030, Philippines; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China.
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14
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Omics: a tool for resilient rice genetic improvement strategies. Mol Biol Rep 2022; 49:5075-5088. [PMID: 35298758 DOI: 10.1007/s11033-022-07189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/24/2022] [Indexed: 10/18/2022]
Abstract
Rice is pivotal pyramid of about half of the world population. Bearing small genome size and worldwide utmost food crop rice has been known as ideal cereal crop for genome research. Currently, decreasing water table and soil fatigue are big challenges and intense consequences in changing climate. Whole sequenced genome of rice sized 389 Mb of which 95% is covered with excellent mapping order. Sequenced rice genome helps in molecular biology and transcriptomics of cereals as it provides whole genome sequence of indica and japonica sub species. Through rice genome sequencing and functional genomics, QTLs or genes, genetic variability and halophyte blocks for agronomic characters were identified which have proved much more useful in molecular breeding and direct selection. There are different numbers of genes or QTLs identified for yield related traits i.e., 6 QTLs/genes for plant architecture, 6 for panicle characteristics, 4 for grain number, 1 gene/QTL for tiller, HGW, grain filling and shattering. QTLS/genes for grain quality, biotic stresses and for abiotic stresses are 7, 23 and 13 respectively. Low yield, inferior quality and susceptibility to biotic and abiotic stresses of a crop is due to narrow genetic background of new evolving rice verities. Wild rice provides genetic resources for improvement of these characters, molecular and genomics tool at different stages can overcome these stresses and improve yield and quality of rice crop.
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15
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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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Huang L, Gu Z, Chen Z, Yu J, Chu R, Tan H, Zhao D, Fan X, Zhang C, Li Q, Liu Q. Improving rice eating and cooking quality by coordinated expression of the major starch synthesis-related genes, SSII and Wx, in endosperm. PLANT MOLECULAR BIOLOGY 2021; 106:419-432. [PMID: 34129189 DOI: 10.1007/s11103-021-01162-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/07/2021] [Indexed: 05/18/2023]
Abstract
Coordinated regulation of amylose and amylopectin synthesis via manipulation of SSII-2, SSII-3 and Wx expression in endosperm can improve rice eating and cooking quality. With increasing rice consumption worldwide, many researchers are working to increase the yield and improve grain quality, especially eating and cooking quality (ECQ). The rice ECQ is mainly controlled by the expression of starch synthesis-related genes (SSRGs) in endosperm. Although the Wx and SSII-3/SSIIa/ALK genes, two major SSRGs, have been manipulated to improve rice ECQ via various breeding approaches, new methods to further improve ECQ are desired. In our previous study, we enhanced rice ECQ by knocking down SSII-2 expression in the japonica Nipponbare cultivar (carrying the Wxb allele) via RNA interference. Herein, the SSII-2 RNAi was introduced into two Nipponbare-derived near-isogenic lines (NILs), Nip(Wxa) and Nip(wx), carrying Wxa and wx alleles respond for high and no amylose levels, respectively. Analysis of physicochemical properties revealed that the improved grain quality of SSII-2 RNAi transgenic lines was achieved by coordinated downregulating the expression of SSII-2, SSII-3 and Wx. To further confirm this conclusion, we generated ssii-2, ssii-3 and ssii-2ssii-3 mutants via CRISPR/Cas9 technique. The amylopectin structure of the resulting ssii-2sii-3 mutants was similar to that in SSII-2 RNAi transgenic lines, and the absence of SSII-2 decreased the amylose content, gelatinisation temperature and rapid visco-analyser profile, indicating essential roles for SSII-2 in the regulation of amylopectin biosynthesis and amylose content in rice endosperm. The effect of SSII-2 was seen only when the activity of SSII-3 was very low or lacking. Our study provides novel approaches and valuable germplasm resources for improving ECQ via plant breeding.
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Affiliation(s)
- Lichun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Zhengwen Gu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Zhuanzhuan Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Jiawen Yu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Rui Chu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Hongyan Tan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Dongsheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Xiaolei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Changquan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
| | - Qianfeng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China.
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China.
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Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice. PLANTS 2021; 10:plants10061154. [PMID: 34204124 PMCID: PMC8227427 DOI: 10.3390/plants10061154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022]
Abstract
Starch is a major ingredient in rice, and the amylose content of starch significantly impacts rice quality. OsSS (starch synthase) is a gene family related to the synthesis of amylose and amylopectin, and 10 members have been reported. In the present study, a synteny analysis of a novel family member belonging to the OsSSIV subfamily that contained a starch synthase catalytic domain showed that three segmental duplications and multiple duplications were identified in rice and other species. Expression data showed that the OsSS gene family is involved in diverse expression patterns. The prediction of miRNA targets suggested that OsSS are possibly widely regulated by miRNA functions, with miR156s targeted to OsSSII-3, especially. Haplotype analysis exhibited the relationship between amylose content and diverse genotypes. These results give new insight and a theoretical basis for the improved amylose content and eating quality of rice.
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18
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Pang H, Chen Q, Li Y, Wang Z, Wu L, Yang Q, Zheng X. Comparative analysis of the transcriptomes of two rice subspecies during domestication. Sci Rep 2021; 11:3660. [PMID: 33574456 PMCID: PMC7878495 DOI: 10.1038/s41598-021-83162-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/28/2021] [Indexed: 11/11/2022] Open
Abstract
Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5'flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.
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Affiliation(s)
- Hongbo Pang
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Qiang Chen
- Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Yueying Li
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Ze Wang
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Longkun Wu
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Qingwen Yang
- Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoming Zheng
- Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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19
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Liang Y, Nan W, Qin X, Zhang H. Field performance on grain yield and quality and genetic diversity of overwintering cultivated rice (Oryza sativa L.) in southwest China. Sci Rep 2021; 11:1846. [PMID: 33469098 PMCID: PMC7815827 DOI: 10.1038/s41598-021-81291-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/04/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding the field performance on grain yield and quality and the genetic diversity of overwintering (OW) cultivated rice (Oryza sativa L.) across main crop (MC) and ratooning crop (RC) is the premise to make strategies for the future OW rice variety improvement in rice production. The present field experiments were conducted in RC of 2016, in MC of both 2017 and 2018, and RC in 2019 to identify genotypes OW rice that perform stable in terms of grain yield and quality across different climate conditions. The grain yield plant-1 (GYP) and its components in six genotypes of OW rice exhibited significant difference across the 4 years (P ≤ 0.05), the maximum GYP in OW6 rice was harvested (60.28 g) in MC of 2017, but the minimum GYP in OW1 rice was harvested (33.01 g) in MC of 2018. Within six genotypes of OW rice, four grain shape traits displayed a relative small significant difference, four grain quality traits exhibited a relative small significant difference except for chalkiness rate (CR), there 226 pairs of significant PCC values between GYP and its components were calculated in all tested rice and varied from six in OW6 to eleven in OW1, there 130 pairs of significant PCC values among the four grain shape traits were calculated and ranged from twenty-one in OW1, 3, 5 to twenty-three in OW2, there 118 pairs of significant PCC values among the four grain quality traits were calculated and ranged from seventeen in OW2 to twenty-three in OW1. The numbers, directions, and size of PCC values for the grain yield and quality characters in all tested rice displayed a series of irregular variations. Six genotypes of OW rice were apparently distinguished by employing 196 pairs of simple-sequence repeats (SSRs) markers and exhibited abundant genetic diversity at the DNA level. Data from this study provide an extensive archive for the future exploration and innovation of overwintering cultivated rice variety.
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Affiliation(s)
- Yongshu Liang
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing, 401331, China.
| | - Wenbin Nan
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing, 401331, China
| | - Xiaojian Qin
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing, 401331, China
| | - Hanma Zhang
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing, 401331, China
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20
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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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21
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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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22
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Zhang A, Gao Y, Li Y, Ruan B, Yang S, Liu C, Zhang B, Jiang H, Fang G, Ding S, Jahan N, Xie L, Dong G, Xu Z, Gao Z, Guo L, Qian Q. Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency. FRONTIERS IN PLANT SCIENCE 2020; 11:342. [PMID: 32265976 PMCID: PMC7105826 DOI: 10.3389/fpls.2020.00342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/06/2020] [Indexed: 05/27/2023]
Abstract
Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world's population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC4F2 population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.
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Affiliation(s)
- Anpeng Zhang
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shenglong Yang
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guonan Fang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Noushin Jahan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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23
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Liang Y, Yan C, Qin X, Nan W, Zhang H. Construction of three half-sib SSR linkage maps derived from overwintering cultivated rice and segregation distortion loci mapping. Genome 2020; 63:239-251. [PMID: 32053407 DOI: 10.1139/gen-2019-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Segregation distortion is a common phenomenon that has been observed in genetics and plant breeding; however, the mechanism of segregation distortion is unknown. In the present study, three half-sib F2 populations derived from three japonica overwinter (perennial) rice varieties (W1, W2, and W3) crossed to the indica rice variety Minghui725 (MH725) were developed to construct three half-sib linkage maps. We established linkage map lengths of 2032.8, 2317.4, and 2108.7 cM with average intervals of 20.1, 20.5, and 19.7 cM using 101, 113, and 107 SSR markers in W1/MH725, W2/MH725, and W3/MH725, respectively. Discrepancies in marker order and genetic linkage distance occurred in the three half-sib linkage maps due to segregation distortion. A total of 88 markers exhibited segregation distortion across the three linkage maps at P < 0.01 level, 42 segregation distortion loci (SDLs) were detected across the three half-sib populations and exhibited variable LOD value that ranged from 3.2 (SDL2f) to 30.1 (SDL5d), and 13 of the 42 SDLs were repeatedly located at the same chromosomal regions of the previously published hybrid sterility quantitative trait loci. Data from this study provide an extensive archive for investigating the genetic characteristic of overwintering cultivated rice and the future exploration and innovation of overwintering rice breeding.
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Affiliation(s)
- Yongshu Liang
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Chao Yan
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Xiaojian Qin
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Wenbin Nan
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Hanma Zhang
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
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24
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Leng Y, Gao Y, Chen L, Yang Y, Huang L, Dai L, Ren D, Xu Q, Zhang Y, Ponce K, Hu J, Shen L, Zhang G, Chen G, Dong G, Gao Z, Guo L, Ye G, Qian Q, Zhu L, Zeng D. Using Heading date 1 preponderant alleles from indica cultivars to breed high-yield, high-quality japonica rice varieties for cultivation in south China. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:119-128. [PMID: 31141272 PMCID: PMC6920332 DOI: 10.1111/pbi.13177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/22/2023]
Abstract
Heading date 1 (Hd1) is an important gene for the regulation of flowering in rice, but its variation in major cultivated rice varieties, and the effect of this variation on yield and quality, remains unknown. In this study, we selected 123 major rice varieties cultivated in China from 1936 to 2009 to analyse the relationship between the Hd1 alleles and yield-related traits. Among these varieties, 19 haplotypes were detected in Hd1, including two major haplotypes (H8 and H13) in the japonica group and three major haplotypes (H14, H15 and H16) in the indica group. Analysis of allele frequencies showed that the secondary branch number was the major aimed for Chinese indica breeding. In the five major haplotypes, SNP316 (C-T) was the only difference between the two major japonica haplotypes, and SNP495 (C-G) and SNP614 (G-A) are the major SNPs in the three indica haplotypes. Association analysis showed that H16 is the most preponderant allele in modern cultivated Chinese indica varieties. Backcrossing this allele into the japonica variety Chunjiang06 improved yield without decreasing grain quality. Therefore, our analysis offers a new strategy for utilizing these preponderant alleles to improve yield and quality of japonica varieties for cultivation in the southern areas of China.
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Affiliation(s)
- Yujia Leng
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yihong Gao
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Long Chen
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yaolong Yang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Lichao Huang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Liping Dai
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Deyong Ren
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Qiankun Xu
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Ya Zhang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Kimberly Ponce
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jiang Hu
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Lan Shen
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guangheng Zhang
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guang Chen
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guojun Dong
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Zhenyu Gao
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Longbiao Guo
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Guoyou Ye
- CAAS‐IRRI Joint Laboratory for Genomics‐assisted Germplasm Enhancement, Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Qian Qian
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Li Zhu
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Dali Zeng
- State Key Laboratory for Rice BiologyChina National Rice Research InstituteHangzhouChina
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25
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Ren D, Cui Y, Hu H, Xu Q, Rao Y, Yu X, Zhang Y, Wang Y, Peng Y, Zeng D, Hu J, Zhang G, Gao Z, Zhu L, Chen G, Shen L, Zhang Q, Guo L, Qian Q. AH2 encodes a MYB domain protein that determines hull fate and affects grain yield and quality in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:813-824. [PMID: 31357245 DOI: 10.1111/tpj.14481] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/03/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
The palea and lemma (hull) are grass-specific organs, and determine grain size and quality. In the study, AH2 encodes a MYB domain protein, and functions in the development of hull and grain. Mutation of AH2 produces smaller grains and alters grain quality including decreased amylose content and gel consistency, and increased protein content. Meantime, part of the hull lost the outer silicified cells, and induces a transformation of the outer rough epidermis to inner smooth epidermis cells, and the body of the palea was reduced in the ah2 mutant. We confirmed the function of AH2 by complementation, CRISPR-Cas9, and cytological and molecular tests. Additionally, AH2, as a repressor, repress transcription of the downstream genes. Our results revealed that AH2 plays an important role in the determination of hull epidermis development, palea identity, and grain size.
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Affiliation(s)
- Deyong Ren
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yuanjiang Cui
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Haitao Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Qiankun Xu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yuchun Rao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, People's Republic of China
| | - Xiaoqi Yu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yu Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Yuexing Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Youlin Peng
- Rice Research Institute, Southwest University of Science and Technology, Mianyang, 621010, People's Republic of China
| | - Dali Zeng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Jiang Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Guangheng Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Zhenyu Gao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Li Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Guang Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Lan Shen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qiang Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Longbiao Guo
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
| | - Qian Qian
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, People's Republic of China
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Yang X, Xia X, Zeng Y, Nong B, Zhang Z, Wu Y, Xiong F, Zhang Y, Liang H, Deng G, Li D. Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing. PLoS One 2018; 13:e0196690. [PMID: 29746484 PMCID: PMC5944943 DOI: 10.1371/journal.pone.0196690] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/17/2018] [Indexed: 11/18/2022] Open
Abstract
Rice is an important cereal in the world. The study of the genetic basis of important agronomic traits in rice landraces and identification of genes will facilitate the breed improvement. Gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC) are important indices of rice cooking and eating quality evaluation and potential nutritional importance, which attract wide attentions in the application of genetic and breeding. To dissect the genetic basis of GT, GC and PC, a total of 419 rice landraces core germplasm collections consisting of 330 indica lines, 78 japonica lines and 11 uncertain varieties were planted, collected, then GT, GC, PC were measured for two years, and sequenced using specific-locus amplified fragment sequencing (SLAF-seq) technology. In this study, 261,385,070 clean reads and 56,768 polymorphic SLAF tags were obtained, which a total of 211,818 single nucleotide polymorphisms (SNPs) were discovered. With 208,993 SNPs meeting the criterion of minor allele frequency (MAF) > 0.05 and integrity> 0.5, the phylogenetic tree and population structure analysis were performed for all 419 rice landraces, and the whole panel mainly separated into six subpopulations based on population structure analysis. Genome-wide association study (GWAS) was carried out for the whole panel, indica subpanel and japonica subpanel with subset SNPs respectively. One quantitative trait locus (QTL) on chromosome 6 for GT was detected in the whole panel and indica subpanel, and one QTL associated with GC was located on chromosome 6 in the whole panel and indica subpanel. For the PC trait, 8 QTLs were detected in the whole panel on chromosome 1, 3, 4, 7, 8, 10 and 11, and 7 QTLs in the indica subpanel on chromosome 3, 4, 7, 8, 10 and 11. For the three traits, no QTL was detected in japonica subpanel, probably because of the polymorphism repartition between the subpanel, or small population size of japonica subpanel. This paper provides new gene resources and insights into the molecular mechanisms of important agricultural trait of rice phenotypic variation and genetic improvement of rice quality variety breeding.
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Affiliation(s)
- Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Xiuzhong Xia
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Yu Zeng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Baoxuan Nong
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Zongqiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Yanyan Wu
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Yuexiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- * E-mail:
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Zhang C, Chen S, Ren X, Lu Y, Liu D, Cai X, Li Q, Gao J, Liu Q. Molecular Structure and Physicochemical Properties of Starches from Rice with Different Amylose Contents Resulting from Modification of OsGBSSI Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2222-2232. [PMID: 28241110 DOI: 10.1021/acs.jafc.6b05448] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
OsGBSSI, encoded by the Waxy (Wx) gene, is the key enzyme in the synthesis of amylose chains. Transgenic rice lines with various GBSSI activities were previously developed via site-directed mutagenesis of the Wx gene in the glutinous cultivar Guanglingxiangnuo (GLXN). In this study, grain morphology, molecular structure, and physicochemical properties were investigated in four transgenic lines with modified OsGBSSI activity and differences in amylose content. A milky opaque appearance was observed in low- and non-amylose rice grains due to air spaces in the starch granules. Gel permeation chromatography (GPC) and high-performance anion-exchange chromatography (HPAEC) analyses showed that although OsGBSSI can synthesize intermediate and extra-long amylopectin chains, it is mainly responsible for the longer amylose chains. Amylose content was positively correlated with trough viscosity, final viscosity, setback viscosity, pasting time, pasting temperature, and gelatinization temperature and negatively with gel consistency, breakdown viscosity, gelatinization enthalpy, and crystallinity. Overall, the findings suggest that OsGBSSI may be also involved in amylopectin biosynthesis, in turn affecting grain appearance, thermal and pasting properties, and the crystalline structure of starches in the rice endosperm.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
| | - Shengjie Chen
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
| | - Xinyu Ren
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
| | - Yan Lu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
| | - Derui Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032, China
| | - Xiuling Cai
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
| | - Jiping Gao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University , Yangzhou 225009, China
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Ren D, Rao Y, Huang L, Leng Y, Hu J, Lu M, Zhang G, Zhu L, Gao Z, Dong G, Guo L, Qian Q, Zeng D. Fine Mapping Identifies a New QTL for Brown Rice Rate in Rice (Oryza Sativa L.). RICE (NEW YORK, N.Y.) 2016; 9:4. [PMID: 26847792 PMCID: PMC4742455 DOI: 10.1186/s12284-016-0076-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 01/25/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND High yield and quality determine the commercial potential of rice variety. Brown rice rate (BRR) is a key factor ensuring grain yield and quality in rice. So far, there were few reports about the genes that directly controlled the BRR in rice. Therefore, dissecting the genetic mechanism of the BRR genes can facilitate improving effective rice supply or edible grain yield. RESULTS A double haploid population derived from the cross between Taichung Native 1 (TN1) (an indica variety) and Chunjiang 06 (CJ06) (a japonica variety) was used to investigate the genetic basis of grain milling and appearance traits affecting the BRR. By using a constructed molecular linkage map, four quantitative trait loci (QTLs) for the BRR were detected on chromosomes 1, 8, 9, and 10, respectively. In addition, three QTLs for appearance traits, including grain weight and grain length/width ratio, were detected on chromosomes 6, 9 and 10, respectively. Chromosome segment substitution lines (CSSLs) were established at the qBRR-10 locus. Finally, the qBRR-10 was narrowed to a 39.5 kb region on chromosome 10. In this region, two candidate genes, LOC_Os10g32124 and LOC_Os10g32190, showed significantly differential expression in TN1 and CSSL1-2 compared with CJ06. Histocytological analysis suggested that cell size and hull thickness may be important factors for the BRR. CONCLUSION In the study, the qBRR-10 affected the BRR and was finally located to a region between two markers, P13 and P14. Two candidate genes were selected based on the expression difference between two parents, which facilitated the further cloning of the qBRR-10 gene and largely contributed to improve the grain yield and quality in rice.
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Affiliation(s)
- Deyong Ren
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yuchun Rao
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, P. R. China
| | - Lichao Huang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yujia Leng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Jiang Hu
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Mei Lu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, P. R. China
| | - Guangheng Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Li Zhu
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhenyu Gao
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guojun Dong
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China.
| | - Dali Zeng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China.
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Yang Y, Xu J, Huang L, Leng Y, Dai L, Rao Y, Chen L, Wang Y, Tu Z, Hu J, Ren D, Zhang G, Zhu L, Guo L, Qian Q, Zeng D. PGL, encoding chlorophyllide a oxygenase 1, impacts leaf senescence and indirectly affects grain yield and quality in rice. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1297-310. [PMID: 26709310 PMCID: PMC4762379 DOI: 10.1093/jxb/erv529] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Chlorophyll (Chl) b is a ubiquitous accessory pigment in land plants, green algae, and prochlorophytes. This pigment is synthesized from Chl a by chlorophyllide a oxygenase and plays a key role in adaptation to various environments. This study characterizes a rice mutant, pale green leaf (pgl), and isolates the gene PGL by using a map-based cloning approach. PGL, encoding chlorophyllide a oxygenase 1, is mainly expressed in the chlorenchyma and activated in the light-dependent Chl synthesis process. Compared with wild-type plants, pgl exhibits a lower Chl content with a reduced and disorderly thylakoid ultrastructure, which decreases the photosynthesis rate and results in reduced grain yield and quality. In addition, pgl exhibits premature senescence in both natural and dark-induced conditions and more severe Chl degradation and reactive oxygen species accumulation than does the wild-type. Moreover, pgl is sensitive to heat stress.
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Affiliation(s)
- Yaolong Yang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China
| | - Jie Xu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China
| | - Lichao Huang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Yujia Leng
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Liping Dai
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Yuchun Rao
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Long Chen
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Yuqiong Wang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Zhengjun Tu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Jiang Hu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Deyong Ren
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Guangheng Zhang
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Li Zhu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
| | - Dali Zeng
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
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30
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Ren D, Rao Y, Leng Y, Li Z, Xu Q, Wu L, Qiu Z, Xue D, Zeng D, Hu J, Zhang G, Zhu L, Gao Z, Chen G, Dong G, Guo L, Qian Q. Regulatory Role of OsMADS34 in the Determination of Glumes Fate, Grain Yield, and Quality in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1853. [PMID: 28018389 PMCID: PMC5156729 DOI: 10.3389/fpls.2016.01853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/23/2016] [Indexed: 05/07/2023]
Abstract
Grasses produce seeds on spikelets, a unique type of inflorescence. Despite the importance of grass crops for food, the genetic mechanisms that control spikelet development remain poorly understood. In this study, we used m34-z, a new mutant allele of the rice (Oryza sativa) E-class gene OsMADS34, to examine OsMADS34 function in determining the identities of glumes (rudimentary glume and sterile lemma) and grain size. In the m34-z mutant, both the rudimentary glume and sterile lemma were homeotically converted to the lemma-like organ and acquired the lemma identity, suggesting that OsMADS34 plays important roles in the development of glumes. In the m34-z mutant, most of the grains from the secondary panicle branches (spb) were decreased in size, compared with grains from wild-type, but no differences were observed in the grains from the primary panicle branches. The amylose content and gel consistency, and a seed-setting rate from the spb were reduced in the m34-z mutant. Interesting, transcriptional activity analysis revealed that OsMADS34 protein was a transcription repressor and it may influence grain yield by suppressing the expressions of BG1, GW8, GW2, and GL7 in the m34-z mutant. These findings revealed that OsMADS34 largely affects grain yield by affecting the size of grains from the secondary branches.
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Affiliation(s)
- Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Yuchun Rao
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
- College of Chemistry and Life Sciences, Zhejiang Normal UniversityZhejiang, China
| | - Yujia Leng
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Zizhuang Li
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
- College of Life and Environmental Sciences, Hangzhou Normal UniversityZhejiang, China
| | - Qiankun Xu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Liwen Wu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Zhennan Qiu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal UniversityZhejiang, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
- *Correspondence: Qian Qian, Longbiao Guo,
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research InstituteZhejiang, China
- *Correspondence: Qian Qian, Longbiao Guo,
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31
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Lau WCP, Rafii MY, Ismail MR, Puteh A, Latif MA, Ramli A. Review of functional markers for improving cooking, eating, and the nutritional qualities of rice. FRONTIERS IN PLANT SCIENCE 2015; 6:832. [PMID: 26528304 PMCID: PMC4604308 DOI: 10.3389/fpls.2015.00832] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/22/2015] [Indexed: 05/16/2023]
Abstract
After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers' preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated.
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Affiliation(s)
- Wendy C. P. Lau
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohd Y. Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohd R. Ismail
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Adam Puteh
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | | | - Asfaliza Ramli
- Rice and Industrial Crops Research Centre, Malaysian Agricultural Research and Development InstituteSeberang Perai, Malaysia
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32
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Anacleto R, Cuevas RP, Jimenez R, Llorente C, Nissila E, Henry R, Sreenivasulu N. Prospects of breeding high-quality rice using post-genomic tools. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1449-66. [PMID: 25993897 DOI: 10.1007/s00122-015-2537-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 05/08/2015] [Indexed: 05/15/2023]
Abstract
The holistic understanding derived from integrating grain quality and sensory research outcomes in breeding high-quality rice in the light of post-genomics resources has been synthesized. Acceptance of new rice genotypes by producers and consumers hinges not only on their potential for higher yield but recent emphasis has also been on premium-value genotypes that have the ability to satisfy consumer preferences for grain quality. This review article provides insights into how to link grain quality attributes and sensory perception to support breeding superior rice varieties. Recent advances in quality profiling and omics technologies have provided efficient approaches to identify the key genes and biochemical markers involved in rice quality traits. Emphasis has been given to the upcoming area of holistic understanding of grain quality and attributes derived from sensory evaluation to leverage integrative gene discovery strategies that enable breeding programs to efficiently tap the huge genetic diversity in rice for novel genes that enhance rice food quality.
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Affiliation(s)
- Roslen Anacleto
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines,
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33
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Bargsten JW, Nap JP, Sanchez-Perez GF, van Dijk ADJ. Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. BMC PLANT BIOLOGY 2014; 14:330. [PMID: 25492368 PMCID: PMC4274756 DOI: 10.1186/s12870-014-0330-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/10/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Elucidation of genotype-to-phenotype relationships is a major challenge in biology. In plants, it is the basis for molecular breeding. Quantitative Trait Locus (QTL) mapping enables to link variation at the trait level to variation at the genomic level. However, QTL regions typically contain tens to hundreds of genes. In order to prioritize such candidate genes, we show that we can identify potentially causal genes for a trait based on overrepresentation of biological processes (gene functions) for the candidate genes in the QTL regions of that trait. RESULTS The prioritization method was applied to rice QTL data, using gene functions predicted on the basis of sequence- and expression-information. The average reduction of the number of genes was over ten-fold. Comparison with various types of experimental datasets (including QTL fine-mapping and Genome Wide Association Study results) indicated both statistical significance and biological relevance of the obtained connections between genes and traits. A detailed analysis of flowering time QTLs illustrates that genes with completely unknown function are likely to play a role in this important trait. CONCLUSIONS Our approach can guide further experimentation and validation of causal genes for quantitative traits. This way it capitalizes on QTL data to uncover how individual genes influence trait variation.
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Affiliation(s)
- Joachim W Bargsten
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
- />Laboratory for Plant Breeding, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Jan-Peter Nap
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Gabino F Sanchez-Perez
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Aalt DJ van Dijk
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
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34
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Luo Y, Zakaria S, Basyah B, Ma T, Li Z, Yang J, Yin Z. Marker-assisted breeding of Indonesia local rice variety Siputeh for semi-dwarf phonetype, good grain quality and disease resistance to bacterial blight. RICE (NEW YORK, N.Y.) 2014; 7:33. [PMID: 26224562 PMCID: PMC4884010 DOI: 10.1186/s12284-014-0033-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rice is one of the most important staple food crops in Asia. Since the first green revolution beginning in 1960s, high-yield semidwarf modern rice varieties have been widely planted; however, traditional rice varieties with tall plant type are still grown in many countries due to their good grain quality and adaptation to local climate and environment. Siputeh, a local rice variety mainly planted in Java and Sumatra islands of Indonesia, produces long grain rice with good cooking and eating quality. However, the variety has low yield with tall plant type and long growth duration and is highly susceptible to biotic and abiotic stress. RESULTS Siputeh as the recurrent female was crossed with the donor line WH421, an elite paternal line of hybrid rice containing the sd1, Wx (b), Xa4 and Xa21 genes, followed by backcrossing and self-pollination. TS4, a BC3F4 line derived from the breeding program, was obtained through marker-assisted selection for the sd1, Wx (b), Xa4 and Xa21 loci. TS4 has semi-dwarf phenotype and short growth duration. TS4 conferred disease resistance to multiple Xanthomonas oryzae pv. oryzae (Xoo) strains collected from different countries around the world. TS4 achieved higher grain yield than Siputeh in two field trials conducted in Banda Aceh, Indonesia and Lingshui, China, respectively. Finally, TS4 has better grain quality than Siputeh in terms of degree of chalkiness and amylose content. CONCLUSION An improved rice line, designed as TS4, has been developed to contain semi-dwarf gene sd1, low amylase content gene Wx (b) and bacterial light resistance genes Xa4 and Xa21 through marker-assisted selection. TS4 has semi-dwarf phenotype with reduced growth duration, produces high yield with good grain quality and provides broad-spectrum resistance to Xoo strains. The development of TS4 enriches the diversity of local rice varieties with high yield potential and good grain quality.
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Affiliation(s)
- Yanchang Luo
- />Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604 Republic of Singapore
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Sabaruddin Zakaria
- />Department of Agrotechnology, Agriculture Faculty, Syiah Kuala University, Darussalam-Banda, 23111 Aceh, Indonesia
| | - Bakhtiar Basyah
- />Department of Agrotechnology, Agriculture Faculty, Syiah Kuala University, Darussalam-Banda, 23111 Aceh, Indonesia
| | - Tingchen Ma
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Zefu Li
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Jianbo Yang
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Zhongchao Yin
- />Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604 Republic of Singapore
- />Department of Biological Sciences, 14 Science Drive, National University of Singapore, Singapore 117543 Republic of Singapore
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Kaur S, Panesar PS, Bera MB, Kaur V. Simple Sequence Repeat Markers in Genetic Divergence and Marker-Assisted Selection of Rice Cultivars: A Review. Crit Rev Food Sci Nutr 2014; 55:41-9. [DOI: 10.1080/10408398.2011.646363] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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Rao Y, Li Y, Qian Q. Recent progress on molecular breeding of rice in China. PLANT CELL REPORTS 2014; 33:551-64. [PMID: 24442397 PMCID: PMC3976512 DOI: 10.1007/s00299-013-1551-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 05/22/2023]
Abstract
Molecular breeding of rice for high yield, superior grain quality, and strong environmental adaptability is crucial for feeding the world's rapidly growing population. The increasingly cloned quantitative trait loci and genes, genome variations, and haplotype blocks related to agronomically important traits in rice have provided a solid foundation for direct selection and molecular breeding, and a number of genes have been successfully introgressed into mega varieties of rice. Here we summarize China's great achievements in molecular breeding of rice in the following five traits: high yield, biotic stress resistance, abiotic stress resistance, quality and physiology. Further, the prospect of rice breeding by molecular design is discussed.
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Affiliation(s)
- Yuchun Rao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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Zhang H, Duan L, Dai JS, Zhang CQ, Li J, Gu MH, Liu QQ, Zhu Y. Major QTLs reduce the deleterious effects of high temperature on rice amylose content by increasing splicing efficiency of Wx pre-mRNA. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:273-82. [PMID: 24162153 DOI: 10.1007/s00122-013-2216-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/14/2013] [Indexed: 05/12/2023]
Abstract
We discovered four QTLs that maintain proper rice amylose content at high temperature by increasing the splicing efficiency of Wx gene. Amylose content mainly controlled by Wx gene is a key physicochemical property for eating and cooking quality in rice. During the grain filling stage, high temperature can harm rice grain quality by significantly reducing the amylose content in many rice varieties. Here, we provide genetic evidences between Wx gene expression and rice amylose content at high temperature, and identified several quantitative trait loci (QTLs) in this pathway. We performed a genome-wide survey on a set of chromosome segment substitution lines (CSSLs) which carried chromosomal segments from the heat resistant indica 9311 in the heat-sensitive japonica Nipponbare background. Four QTLs, qHAC4, qHAC8a, qHAC8b and qHAC10, which can reduce the deleterious effects of amylose content at high temperature, were identified and mapped to chromosome 4, 8, 8 and 10, respectively. The major QTL qHAC8a, with the highest LOD score of 6.196, was physically mapped to a small chromosome segment (~300 kb). The CSSLs carrying the qHAC8a, qHAC8b and/or qHAC4 from 9311 have the high pre-mRNA splicing efficiency of Wx gene and likely lead to stable amylose content at high temperature. Thus, increasing pre-mRNA processing efficiency of Wx gene could be an important regulation mechanism for maintaining stable amylose content in rice seeds at high temperature. In addition, our results provide a theoretical basis for breeding heat-stable grain in rice.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Gene identification using rice genome sequences. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci U S A 2012; 109:21534-9. [PMID: 23236132 DOI: 10.1073/pnas.1219776110] [Citation(s) in RCA: 264] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Grain size and shape are important components determining rice grain yield, and they are controlled by quantitative trait loci (QTLs). Here, we report the cloning and functional characterization of a major grain length QTL, qGL3, which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of the qgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties, due to its favorable effect on grain length, filling, and weight.
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Bao JS. Toward Understanding the Genetic and Molecular Bases of the Eating and Cooking Qualities of Rice. CEREAL FOOD WORLD 2012. [DOI: 10.1094/cfw-57-4-0148] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- J. S. Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
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