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Li Y, Ai Z, Mu Y, Zhao T, Zhang Y, Li L, Huang Z, Nie L, Khan MN. Rice yield penalty and quality deterioration is associated with failure of nitrogen uptake from regreening to panicle initiation stage under salinity. FRONTIERS IN PLANT SCIENCE 2023; 14:1120755. [PMID: 37025146 PMCID: PMC10071828 DOI: 10.3389/fpls.2023.1120755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
In recent years, the development and utilization of saline land for rice cultivation have effectively expanded grain productivity. Rice is a salt-sensitive crop, and the increasing salinity problem threatens rice yield and quality. Therefore, we conducted open field experiments to study the effect of salinity on different growth stages of rice. Irrigating saline treatment was conducted at three different growth stages: irrigating saline from the regreening stage to the panicle initiation stage (S1), irrigating saline from the panicle initiation stage to the flowering stage (S2), and irrigating saline from the flowering stage to the maturity stage (S3). Each treatment period lasted for about 30 days. At the same time, irrigating saline water from the regreening stage to the maturity stage (S4) treatment was added in 2022 to explore the performance of salt stress during the whole growth period of rice. Based on the treatment of these different saline irrigation growth periods, three saline concentrations were incorporated, including salinity 0‰ (T1), 3‰ (T2), and 6‰ (T3) concentrations. No irrigating saline during the whole growth period was also used as a control (CK). The results indicated that rice grain yield and quality were most sensitive to saline treatment during S1 among the three stress periods. At the S1 stage, salinity mainly reduced the nitrogen uptake, resulting in stunted plant growth, reducing tillering, yield, and yield components, and deteriorating the rice quality. Compared to the control, IEN (grain yield over the total amount of N uptake in plants at maturity) was more sensitive at the S1 stage than S2 and S3 stages under salinity. Furthermore, the findings of our study suggest that under salinity, rice growth is not only directly affected by the higher sodium (Na+) content in plants, but the higher concentration of Na+ reduced the ability of plants to uptake nitrogen. Thus, more attention should be paid to the field management of the S1 stage, the most sensitive stage during rice cultivation in salinized areas. It is necessary to avoid salt damage to rice during this period and ensure irrigation with precious freshwater resources.
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Affiliation(s)
- Yusheng Li
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhiyong Ai
- National Innovation Center of Saline−Alkali Tolerant Rice in Sanya, Sanya, China
- Hunan Hybrid Rice Research Center, Changsha, China
| | - Yixue Mu
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Tingcheng Zhao
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yicheng Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Lin Li
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zheng Huang
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Lixiao Nie
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
- National Innovation Center of Saline−Alkali Tolerant Rice in Sanya, Sanya, China
| | - Mohammad Nauman Khan
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
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Wang N, Chen H, Qian Y, Liang Z, Zheng G, Xiang J, Feng T, Li M, Zeng W, Bao Y, Liu E, Zhang C, Xu J, Shi Y. Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions. PLANTS (BASEL, SWITZERLAND) 2023; 12:419. [PMID: 36771503 PMCID: PMC9919668 DOI: 10.3390/plants12030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Rice (Oryza sativa L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (qTGW4.1, qTGW4.2, qGL4.1, qGL12.1, qGL12.2, qGW2.1, qGW4.1, qGW6.1, qGW8.1, qGW8.2, qGW9.1, qGW11.1, qGLWR2.1, qGLWR2.2, qGLWR4.2, qPGWC5.1 and qDEC6.1) were identified for haplotype analysis. Among these QTLs, two (qTGW4.2 and qGW6.1), were overlapped with FLO19 and OsbZIP47, respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction.
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Affiliation(s)
- Nansheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Huguang Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingzhi Qian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhaojie Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Guiqiang Zheng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jun Xiang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wei Zeng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yaling Bao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chaopu Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
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Chen H, Zhai L, Chen K, Shen C, Zhu S, Qu P, Tang J, Liu J, He H, Xu J. Genetic background- and environment-independent QTL and candidate gene identification of appearance quality in three MAGIC populations of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1074106. [PMID: 36438096 PMCID: PMC9697191 DOI: 10.3389/fpls.2022.1074106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/28/2022] [Indexed: 06/01/2023]
Abstract
Many QTL have been identified for grain appearance quality by linkage analysis (LA) in bi-parental mapping populations and by genome-wide association study (GWAS) in natural populations in rice. However, few of the well characterized genes/QTL have been successfully applied in molecular rice breeding due to genetic background (GB) and environment effects on QTL expression and deficiency of favorable alleles. In this study, GWAS and LA were performed to identify QTL for five grain appearance quality-related traits using three multi-parent advanced generation inter-cross (MAGIC) populations. A total of 22 QTL on chromosomes 1-3, 5-8 were identified by GWAS for five traits in DC1, DC2 and 8way, and four combined populations DC12 (DC1+DC2), DC18 (DC1+8way), DC28 (DC2+8way) and DC128 (DC1+DC2+8way). And a total of 42 QTL were identified on all 12 chromosomes except 10 by LA in the three single populations. Among 20 QTL identified by GWAS in DC1, DC2 and 8way, 10, four and three QTL were commonly detected in DC18, DC28, and DC128, respectively. Similarly, among 42 QTL detected by LA in the three populations, four, one and two QTL were commonly detected in DC18, DC28, and DC128, respectively. There was no QTL mapped together in DC12 by both two mapping methods, indicating that GB could greatly affect the mapping results, and it was easier to map the common QTL among populations with similar GB. The 8way population was more powerful for QTL mapping than the DC1, DC2 and various combined populations. Compared with GWAS, LA can not only identify large-effect QTL, but also identify minor-effect ones. Among 11 QTL simultaneously detected by the two methods in different GBs and environments, eight QTL corresponded to known genes, including AqGL3b and AqGLWR3a for GL and GLWR, AqGW5a, AqGLWR5, AqDEC5 and AqPGWC5 for GW, GLWR, DEC and PGWC, and AqDEC6b and AqPGWC6b for DEC and PGWC, respectively. AqGL7, AqGL3c/AqGLWR3b, AqDEC6a/AqPGWC6a, and AqPGWC7 were newly identified and their candidate genes were analyzed and inferred. It was discussed to further improve grain appearance quality through designed QTL pyramiding strategy based on the stable QTL identified in the MAGIC populations.
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Affiliation(s)
- Huizhen Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Pingxiang Center for Agricultural Sciences and Technology Research, Pingxiang, Jiangxi, China
| | - Laiyuan Zhai
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Congcong Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuangbing Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Pingping Qu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Tang
- Pingxiang Center for Agricultural Sciences and Technology Research, Pingxiang, Jiangxi, China
| | - Jianping Liu
- Pingxiang Center for Agricultural Sciences and Technology Research, Pingxiang, Jiangxi, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jianlong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhao D, Zhang C, Li Q, Liu Q. Genetic control of grain appearance quality in rice. Biotechnol Adv 2022; 60:108014. [PMID: 35777622 DOI: 10.1016/j.biotechadv.2022.108014] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/27/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023]
Abstract
Grain appearance, one of the key determinants of rice quality, reflects the ability to attract consumers, and is characterized by four major properties: grain shape, chalkiness, transparency, and color. Mining of valuable genes, genetic mechanisms, and breeding cultivars with improved grain appearance are essential research areas in rice biology. However, grain appearance is a complex and comprehensive trait, making it challenging to understand the molecular details, and therefore, achieve precise improvement. This review highlights the current findings of grain appearance control, including a detailed description of the key genes involved in the formation of grain appearance, and the major environmental factors affecting chalkiness. We also discuss the integration of current knowledge on valuable genes to enable accurate breeding strategies for generation of rice grains with superior appearance quality.
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Affiliation(s)
- Dongsheng Zhao
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, 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
| | - Changquan Zhang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Functional Genomics of the Ministry of Education, 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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Wang X, Wang K, Yin T, Zhao Y, Liu W, Shen Y, Ding Y, Tang S. Nitrogen Fertilizer Regulated Grain Storage Protein Synthesis and Reduced Chalkiness of Rice Under Actual Field Warming. FRONTIERS IN PLANT SCIENCE 2021; 12:715436. [PMID: 34527011 PMCID: PMC8435852 DOI: 10.3389/fpls.2021.715436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/05/2021] [Indexed: 06/02/2023]
Abstract
Our previous study has shown that nitrogen plays an important role in dealing with significantly increased chalkiness caused by elevated temperature. However, the role of nitrogen metabolites has not been given sufficient attention, and its regulatory mechanism is not clear. This study investigated the effects of high temperature and nitrogen fertilizer on the synthesis of grain storage protein and further explored the quality mechanism under the actual scenario of field warming. Results showed that increased temperature and nitrogen fertilizer could affect the activities of nitrogen metabolism enzymes, namely, glutamate synthetase, glutamine synthetase, glutamic pyruvic transaminase, and glutamic oxaloacetic transaminase, and the expressions of storage protein synthesis factor genes, namely, GluA and GluB, and subfamily genes, namely, pro14, BiP1, and PDIL1, which co-induced the changes of storage protein synthesis in rice grains. Furthermore, the increased temperature changed the balance of grain storage substances which may lead to the significantly increased chalky rate (197.67%) and chalkiness (532.92%). Moreover, there was a significant negative correlation between prolamin content and chalkiness, indicating that nitrogen fertilizer might regulate the formation of chalkiness by affecting the synthesis of prolamin. Results suggested that nitrogen application could regulate the related core factors involved in nitrogen metabolism pathways, which, in turn, affects the changes in the storage protein components in the grain and further affects quality. Therefore, as a conventional cultivation measure, nitrogen application would have a certain value in future rice production in response to climate warming.
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Affiliation(s)
- Xueqin Wang
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Kailu Wang
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Tongyang Yin
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Yufei Zhao
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Wenzhe Liu
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Yingying Shen
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - She Tang
- College of Agronomy, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
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Park JR, Kim EG, Jang YH, Kim KM. Screening and identification of genes affecting grain quality and spikelet fertility during high-temperature treatment in grain filling stage of rice. BMC PLANT BIOLOGY 2021; 21:263. [PMID: 34098898 PMCID: PMC8186072 DOI: 10.1186/s12870-021-03056-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/17/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Recent temperature increases due to rapid climate change have negatively affected rice yield and grain quality. Particularly, high temperatures during right after the flowering stage reduce spikelet fertility, while interfering with sugar energy transport, and cause severe damage to grain quality by forming chalkiness grains. The effect of high-temperature on spikelet fertility and grain quality during grain filling stage was evaluated using a double haploid line derived from another culture of F1 by crossing Cheongcheong and Nagdong cultivars. Quantitative trait locus (QTL) mapping identifies candidate genes significantly associated with spikelet fertility and grain quality at high temperatures. RESULTS Our analysis screened OsSFq3 that contributes to spikelet fertility and grain quality at high-temperature. OsSFq3 was fine-mapped in the region RM15749-RM15689 on chromosome 3, wherein four candidate genes related to the synthesis and decomposition of amylose, a starch component, were predicted. Four major candidate genes, including OsSFq3, and 10 different genes involved in the synthesis and decomposition of amylose and amylopectin, which are starch constituents, together with relative expression levels were analyzed. OsSFq3 was highly expressed during the initial stage of high-temperature treatment. It exhibited high homology with FLOURY ENDOSPERM 6 in Gramineae plants and is therefore expected to function similarly. CONCLUSION The QTL, major candidate genes, and OsSFq3 identified herein could be effectively used in breeding rice varieties to improve grain quality, while tolerating high temperatures, to cope with climate changes. Furthermore, linked markers can aid in marker-assisted selection of high-quality and -yield rice varieties tolerant to high temperatures.
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Affiliation(s)
- Jae-Ryoung Park
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, 41566 Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Eun-Gyeong Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Yoon-Hee Jang
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, 41566 Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu, 41566 Republic of Korea
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