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Prodhan ZH, Samonte SOPB, Sanchez DL, Talukder SK. Profiling and Improvement of Grain Quality Traits for Consumer Preferable Basmati Rice in the United States. PLANTS (BASEL, SWITZERLAND) 2024; 13:2326. [PMID: 39204762 PMCID: PMC11359321 DOI: 10.3390/plants13162326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/10/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Basmati rice is a premium aromatic rice that consumers choose primarily because of its distinct aroma and excellent grain quality. The grain quality of Basmati rice (GQBR) reflects the perspectives of producers, processors, sellers, and consumers related to the production, processing, marketing, and consumption of Basmati rice. Consumers, an invaluable part of the production demand and value chain of the Basmati rice industry, have the freedom to choose from different types of aromatic rice. Consumers expect their preferred Basmati rice to possess all superior rice grain qualities, including the physical, biochemical, and physiological properties. Gene functional analysis explained that a 10-base pair deletion in the promoter region of the OsSPL16 gene causes the slender grains in Basmati rice, whereas an 8-base-pair deletion in exon 7 of the OsBadh2 gene (located in the fgr region on rice chromosome 8) results in the distinct aroma. Furthermore, a combination of the genetic characteristics of the gw8 and gs3 genes has led to the creation of a long-grain Basmati-type rice cultivar. It has also been demonstrated that agricultural, genetic, and environmental conditions significantly influence GQBR. Hence, research on improving GQBR requires a multidimensional approach and sophisticated elements due to the complexity of its nature and preference diversity. This review covers the basic definitions of grain quality traits, consumer preference criteria, influencing factors, and strategies for producing superior-quality Basmati rice in the United States. This knowledge will be useful in improving the grain quality of Basmati and Basmati-type rice, as well as developing appropriate breeding programs that will meet the preferences of different countries and cultures.
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Affiliation(s)
- Zakaria Hossain Prodhan
- Texas A&M AgriLife Research Center, 1509 Aggie Drive, Beaumont, TX 77713, USA; (D.L.S.); (S.K.T.)
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2
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Fan G, Jiang J, Long Y, Wang R, Liang F, Liu H, Xu J, Qiu X, Li Z. Generation of Two-Line Restorer Line with Low Chalkiness Using Knockout of Chalk5 through CRISPR/Cas9 Editing. BIOLOGY 2024; 13:617. [PMID: 39194555 DOI: 10.3390/biology13080617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 08/06/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024]
Abstract
Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H+-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both PGEC and DEC. In this study, the first exon of Chalk5 was edited in the elite restorer line 9311 using the CRISPR/Cas9 system and two knockout mutants were obtained, one of which did not contain the exogenous Cas9 cassette. PGWC and DEC were both significantly reduced in both mutants, while the seed setting ratio (SSR) was also significantly decreased. Staggered sowing experiments showed that the chalkiness of the mutants was insensitive to temperature during the grain-filling stage, and the head milled rice rate (HMRR) could be improved even under high-temperature conditions. Finally, in the hybrid background, the mutants showed significantly reduced PGWC and DEC without changes in other agronomic traits. The results provide important germplasm and allele resources for breeding high-yield rice varieties with superior quality, especially for high-yield indica hybrid rice varieties with superior quality in high-temperature conditions.
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Affiliation(s)
- Gucheng Fan
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Jiefeng Jiang
- Ningbo Academy of Agricultural Science, Ningbo 315101, China
| | - Yu Long
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Run Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Famao Liang
- Yichang Academy of Agricultural Sciences, Yichang 443004, China
| | - Haiyang Liu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Junying Xu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Xianjin Qiu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Zhixin Li
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434025, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
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3
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Shi H, Yun P, Zhu Y, Wang L, Wang Y, Li P, Zhou H, Cheng S, Liu R, Gao G, Zhang Q, Xiao J, Li Y, Xiong L, You A, He Y. Natural variation of WBR7 confers rice high yield and quality by modulating sucrose supply in sink organs. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38943653 DOI: 10.1111/pbi.14420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/17/2024] [Accepted: 06/09/2024] [Indexed: 07/01/2024]
Abstract
Grain chalkiness is an undesirable trait that negatively regulates grain yield and quality in rice. However, the regulatory mechanism underlying chalkiness is complex and remains unclear. We identified a positive regulator of white-belly rate (WBR). The WBR7 gene encodes sucrose synthase 3 (SUS3). A weak functional allele of WBR7 is beneficial in increasing grain yield and quality. During the domestication of indica rice, a functional G/A variation in the coding region of WBR7 resulted in an E541K amino acid substitution in the GT-4 glycosyltransferase domain, leading to a significant decrease in decomposition activity of WBR7A (allele in cultivar Jin23B) compared with WBR7G (allele in cultivar Beilu130). The NIL(J23B) and knockout line NIL(BL130)KO exhibited lower WBR7 decomposition activity than that of NIL(BL130) and NIL(J23B)COM, resulting in less sucrose decomposition and metabolism in the conducting organs. This caused more sucrose transportation to the endosperm, enhancing the synthesis of storage components in the endosperm and leading to decreased WBR. More sucrose was also transported to the anthers, providing sufficient substrate and energy supply for pollen maturation and germination, ultimately leading to an increase rate of seed setting and increased grain yield. Our findings elucidate a mechanism for enhancing rice yield and quality by modulating sucrose metabolism and allocation, and provides a valuable allele for improved rice quality.
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Affiliation(s)
- Huan Shi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Peng Yun
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yun Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lu Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yipei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Pingbo Li
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hao Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shiyuan Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Aiqing You
- Institute of Food Crop, Hubei Academy of Agricultural Science, Wuhan, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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4
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Sun LQ, Bai Y, Wu J, Fan SJ, Chen SY, Zhang ZY, Xia JQ, Wang SM, Wang YP, Qin P, Li SG, Xu P, Zhao Z, Xiang CB, Zhang ZS. OsNLP3 enhances grain weight and reduces grain chalkiness in rice. PLANT COMMUNICATIONS 2024:100999. [PMID: 38853433 DOI: 10.1016/j.xplc.2024.100999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
Abstract
Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.
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Affiliation(s)
- Liang-Qi Sun
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Yu Bai
- Experimental Center of Engineering and Materials Science, University of Science and Technology of China, Hefei 230027, China
| | - Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Jun Fan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Si-Yan Chen
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zheng-Yi Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Mei Wang
- Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Yu-Ping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shi-Gui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Zhong Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
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5
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Peng B, Zhang Q, Liu Y, Zhao Q, Zhao J, Zhang Z, Sun X, Peng J, Sun Y, Song X, Guo G, Huang Y, Pang R, Zhou W, Wang Q. OsAAP8 mutation leads to significant improvement in the nutritional quality and appearance of rice grains. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:34. [PMID: 38725797 PMCID: PMC11076445 DOI: 10.1007/s11032-024-01473-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
Members of the permease gene family are responsible for important biological functions in the growth and development of rice. Here, we show that OsAAP8 is a constitutive expression gene, and its translated protein is localized on the cell membrane. Mutation of the OsAAP8 can promote the expression of genes related to protein and amylopectin synthesis, and also promote the enlargement of protein bodies in its endosperm, leading to an increase in the protein, amylopectin, and total amino acid content of grains in OsAAP8 mutants. Seeds produced by the OsAAP8 mutant were larger, and the chalkiness traits of the OsAAP8 mutants were significantly reduced, thereby improving the nutritional quality and appearance of rice grains. The OsAAP8 protein is involved in the transport of various amino acids; OsAAP8 mutation significantly enhanced the root absorption of a range of amino acids and might affect the distribution of various amino acids. Therefore, OsAAP8 is an important quality trait gene with multiple biological functions, which provides important clues for the molecular design of breeding strategies for developing new high-quality varieties of rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01473-w.
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Affiliation(s)
- Bo Peng
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Qingxi Zhang
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Yan Liu
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Qiang Zhao
- Henan Scientific Research Platform Service Center, Zhengzhou, 450003 China
| | - Jinhui Zhao
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Zhiguo Zhang
- Henan Lingrui Pharmaceutical Company Limited, Xinyang, 464000 China
| | - Xiaoyu Sun
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Juan Peng
- Xinyang Station of Plant Protection and Inspection, Xinyang, 464000 China
| | - Yanfang Sun
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Xiaohua Song
- Xinyang Academy of Agricultural Science, Xinyang, 464000 China
| | - Guiying Guo
- Xinyang Academy of Agricultural Science, Xinyang, 464000 China
| | - Yaqin Huang
- College of Biological and Pharmaceutical Engineering, Xinyang Agriculture and Forestry University, Xinyang, 464000 China
| | - Ruihua Pang
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Wei Zhou
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
| | - Quanxiu Wang
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000 China
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6
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Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. Multi-model genome-wide association studies for appearance quality in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1304388. [PMID: 38273959 PMCID: PMC10808671 DOI: 10.3389/fpls.2023.1304388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024]
Abstract
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
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Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, International Crop Reseach Institute for Semi Arid Tropics (ICRISAT), Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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7
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Yang W, Chen S, Hao Q, Zhu H, Tan Q, Lin S, Chen G, Li Z, Bu S, Liu Z, Liu G, Wang S, Zhang G. Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness. RICE (NEW YORK, N.Y.) 2024; 17:4. [PMID: 38185771 PMCID: PMC10772014 DOI: 10.1186/s12284-023-00680-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we identified six QTLs for the percentage of grain chalkiness (PGC), named qPGC5, qPGC6, qPGC8.1, qPGC8.2, qPGC9 and qPGC11, using single-segment substitution lines (SSSLs) with genetic background of Huajingxian 74 (HJX74). In this study, we utilized the six low chalkiness QTLs to develop 17 pyramiding lines with 2-4 QTLs. The results showed that the PGC decreased with the increase of QTLs in the pyramiding lines. The pyramiding lines with 4 QTLs significantly reduced the chalkiness of rice and reached the best quality level. Among the six QTLs, qPGC5 and qPGC6 showed greater additive effects and were classified as Group A, while the other four QTLs showed smaller additive effects and were classified as Group B. In pyramiding lines, although the presence of epistasis, additivity remained the main component of QTL effects. qPGC5 and qPGC6 showed stronger ability to reduce rice chalkiness, particularly in the environment of high temperature (HT) in the first cropping season (FCS). Our research demonstrates that by pyramiding low chalkiness QTLs, it is feasible to develop the high-quality rice varieties with low chalkiness at the best quality level even in the HT environment of FCS.
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Affiliation(s)
- Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Songliang Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Qingwen Hao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Guodong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhan Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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8
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Kumar A, Thomas J, Gill N, Dwiningsih Y, Ruiz C, Famoso A, Pereira A. Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress. Sci Rep 2023; 13:4880. [PMID: 36966148 PMCID: PMC10039871 DOI: 10.1038/s41598-023-31399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from - 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from - 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.
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Affiliation(s)
- Anuj Kumar
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Julie Thomas
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Yheni Dwiningsih
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Charles Ruiz
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Rayne, LA, 70578, USA
| | - Andy Pereira
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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9
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Li J, Zhang C, Luo X, Zhang T, Zhang X, Liu P, Yang W, Lei Y, Tang S, Kang L, Huang L, Li T, Wang Y, Chen W, Yuan H, Qin P, Li S, Ma B, Tu B. Fine mapping of the grain chalkiness quantitative trait locus qCGP6 reveals the involvement of Wx in grain chalkiness formation. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad112. [PMID: 36964899 DOI: 10.1093/jxb/erad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Indexed: 06/18/2023]
Abstract
Grain chalkiness is an important index of rice appearance quality and is negatively associated with rice processing and eating qualities. However, the genetic mechanism underlying chalkiness formation is largely unknown. To identify the genetic basis of chalkiness, 410 recombinant inbred lines (RILs) derived from two representative indica rice varieties, Shuhui498 (R498) and Yihui3551 (R3551), were used to discover quantitative trait loci (QTL). The two parental lines and RILs were grown in three locations in China under three controlled fertilizer application level. Analyses indicated that chalkiness was significantly affected by genotype, the environment, and the interaction between the two, and that heritability was high. Several QTLs were isolated, including the two stable QTLs, i.e., qCGP6 and qCGP8. Fine mapping and candidate gene verification of qCGP6 showed that Wx may play a key role in chalkiness formation. Chromosomal segment substitution lines (CSSLs) and near-isogenic lines (NILs) carrying the Wxa or Wxin allele produced more chalky grain than the R498 parent. A similar result was also observed in the 3611 background. Notably, the effect of the Wx genotype on rice chalkiness was shown to be dependent on environmental conditions and Wx alleles exhibited different sensitivities to shading treatment. Using CRISPR/Cas9, the Wxa promoter region was successfully edited, down-regulating Wx alleviates chalkiness formation in NILR498-Wxa. This study developed a new strategy for synergistic improvement of eating and appearance qualities in rice, and created a novel Wx allele with great potential in breeding applications.
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Affiliation(s)
- Jialian Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang, Liaoning 110101, China
| | - Xia Luo
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyu Zhang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Pin Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Wen Yang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yuekun Lei
- Chengdu Juannong Intelligent Agriculture Technology Development Co., Ltd
| | - Siwen Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Liangzhu Kang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Weilan Chen
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Peng Qin
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Bingtian Ma
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
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10
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Wu M, Cai M, Zhai R, Ye J, Zhu G, Yu F, Ye S, Zhang X. A mitochondrion-associated PPR protein, WBG1, regulates grain chalkiness in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1136849. [PMID: 36968383 PMCID: PMC10033517 DOI: 10.3389/fpls.2023.1136849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Rice kernel quality has vital commercial value. Grain chalkiness deteriorates rice's appearance and palatability. However, the molecular mechanisms that govern grain chalkiness remain unclear and may be regulated by many factors. In this study, we identified a stable hereditary mutant, white belly grain 1 (wbg1), which has a white belly in its mature grains. The grain filling rate of wbg1 was lower than that of the wild type across the whole filling period, and the starch granules in the chalky part were oval or round and loosely arranged. Map-based cloning showed that wbg1 was an allelic mutant of FLO10, which encodes a mitochondrion-targeted P-type pentatricopeptide repeat protein. Amino acid sequence analysis found that two PPR motifs present in the C-terminal of WBG1 were lost in wbg1. This deletion reduced the splicing efficiency of nad1 intron 1 to approximately 50% in wbg1, thereby partially reducing the activity of complex I and affecting ATP production in wbg1 grains. Furthermore, haplotype analysis showed that WBG1 was associated with grain width between indica and japonica rice varieties. These results suggested that WBG1 influences rice grain chalkiness and grain width by regulating the splicing efficiency of nad1 intron 1. This deepens understanding of the molecular mechanisms governing rice grain quality and provides theoretical support for molecular breeding to improve rice quality.
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Affiliation(s)
- Mingming Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Maohong Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jing Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guofu Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Faming Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shenghai Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoming Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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11
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Kumari A, Sharma D, Sharma P, Wang C, Verma V, Patil A, Imran M, Singh MP, Kumar K, Paritosh K, Caragea D, Kapoor S, Chandel G, Grover A, Jagadish SVK, Katiyar-Agarwal S, Agarwal M. Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1133115. [PMID: 36968399 PMCID: PMC10031497 DOI: 10.3389/fpls.2023.1133115] [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: 12/28/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.
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Affiliation(s)
- Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Divya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Sahil
- Department of Botany, University of Delhi, Delhi, India
| | - Chaoxin Wang
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Vibha Verma
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Arun Patil
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Md Imran
- Department of Botany, University of Delhi, Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kuldeep Kumar
- National Institute for Plant Biotechnology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, New Delhi, India
| | - Doina Caragea
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Girish Chandel
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | | | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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12
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Jin SK, Xu LN, Yang QQ, Zhang MQ, Wang SL, Wang RA, Tao T, Hong LM, Guo QQ, Jia SW, Song T, Leng YJ, Cai XL, Gao JP. High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing. FRONTIERS IN PLANT SCIENCE 2023; 13:1050882. [PMID: 36714703 PMCID: PMC9878556 DOI: 10.3389/fpls.2022.1050882] [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: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Rice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice quality breeding and improvement. In the present study, we performed high-resolution QTL mapping for rice grain quality traits using a genotyping-by-sequencing approach. An F2 population derived from a cross between an elite japonica variety, Koshihikari, and an indica variety, Nona Bokra, was used to construct a high-density genetic map. A total of 3,830 single nucleotide polymorphism markers were mapped to 12 linkage groups spanning a total length of 2,456.4 cM, with an average genetic distance of 0.82 cM. Seven grain quality traits-the percentage of whole grain, percentage of head rice, percentage of area of head rice, transparency, percentage of chalky rice, percentage of chalkiness area, and degree of chalkiness-of the F2 population were investigated. In total, 15 QTLs with logarithm of the odds (LOD) scores >4 were identified, which mapped to chromosomes 6, 7, and 9. These loci include four QTLs for transparency, four for percentage of chalky rice, four for percentage of chalkiness area, and three for degree of chalkiness, accounting for 0.01%-61.64% of the total phenotypic variation. Of these QTLs, only one overlapped with previously reported QTLs, and the others were novel. By comparing the major QTL regions in the rice genome, several key candidate genes reported to play crucial roles in grain quality traits were identified. These findings will expedite the fine mapping of these QTLs and QTL pyramiding, which will facilitate the genetic improvement of rice grain quality.
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Affiliation(s)
- Su-Kui Jin
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Na Xu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qing-Qing Yang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Ming-Qiu Zhang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Shui-Lian Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ruo-An Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Tao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Lian-Min Hong
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qian-Qian Guo
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Shu-Wen Jia
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Song
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Jia Leng
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Xiu-Ling Cai
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ji-Ping Gao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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13
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Zhang Y, Qin Y, Li D, Wang W, Gao X, Hao C, Feng H, Wang Y, Li T. Fine mapping and cloning of a novel BrSCC1 gene for seed coat color in Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:11. [PMID: 36658295 DOI: 10.1007/s00122-023-04287-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
A novel BrSCC1 gene for seed coat color was fine mapped within a 41.1-kb interval on chromosome A03 in Brassica rapa and functionally validated by ectopic expression analysis. Yellow seed is a valuable breeding trait that can be potentiality applied for improving seed quality and oil productivity in oilseed Brassica crops. However, only few genes for yellow seed have been identified in B. rapa. We previously identified a minor quantitative trait locus (QTL), qSC3.1, for seed coat color on chromosome A03 in B. rapa. In order to isolate the seed coat color gene, a brown-seeded chromosome segment substitution line, CSSL-38, harboring the qSC3.1, was selected and crossed with the yellow-seeded recurrent parent, a rapid cycling inbred line of B. rapa (RcBr), to construct the secondary F2 population. Metabolite identification suggested that seed coat coloration in CSSL-38 was independent of proanthocyanidins (PAs) accumulation. Genetic analysis revealed that yellow seed was controlled by a single recessive gene, Seed Coat Color 1 (BrSCC1). Utilizing bulked segregant analysis (BSA)-seq and secondary F2 and F2:3 recombinants analysis, BrSCC1 was fine mapped within a 41.1-kb interval. By integrating gene expression profiling, genome sequence comparison, metabolite analysis, and functional validation through ectopic expression in Arabidopsis, the BraA03g040800.3C gene was confirmed to be BrSCC1, which positively correlated with the seed coat coloration. Our study provides a novel gene resource for the genetic improvement of yellow seeds in oilseed B. rapa.
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Affiliation(s)
- Yinghuan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yao Qin
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Dongxiao Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xu Gao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Chunming Hao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, People's Republic of China.
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, People's Republic of China
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14
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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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15
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Chen F, Lu Y, Pan L, Fan X, Li Q, Huang L, Zhao D, Zhang C, Liu Q. The Underlying Physicochemical Properties and Starch Structures of indica Rice Grains with Translucent Endosperms under Low-Moisture Conditions. Foods 2022; 11:foods11101378. [PMID: 35626949 PMCID: PMC9141583 DOI: 10.3390/foods11101378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 01/27/2023] Open
Abstract
Rice grain quality is a complex trait that includes processing, appearance, eating, cooking, and nutrition components. The amylose content (AC) in the rice endosperm affects the eating and cooking quality along with the appearance of milled rice. In this study, four indica rice varieties with different ACs were used to study the factors affecting endosperm transparency along with the physical and chemical characteristics and eating quality of translucent endosperm varieties. Endosperm transparency was positively correlated with water content and negatively correlated with the cumulative area of cavities within starch granules. The indica landrace 28Zhan had a translucent endosperm and exhibited good taste. Based on starch fine structure analysis, long-chain amylopectin and the B2 chain of amylopectin might be major contributors to the good taste and relatively slow digestion of this landrace.
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Affiliation(s)
- Fei Chen
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
| | - Yan Lu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
| | - Lixu Pan
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
| | - Xiaolei Fan
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
| | - Qianfeng Li
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
| | - Lichun Huang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
| | - Dongsheng Zhao
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
| | - Changquan Zhang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, State Key Laboratory of Hybrid Rice, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.C.); (Y.L.); (L.P.); (X.F.); (Q.L.); (L.H.); (D.Z.); (C.Z.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, State Key Laboratory of Hybrid Rice, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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16
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Wu B, Yun P, Zhou H, Xia D, Gu Y, Li P, Yao J, Zhou Z, Chen J, Liu R, Cheng S, Zhang H, Zheng Y, Lou G, Chen P, Wan S, Zhou M, Li Y, Gao G, Zhang Q, Li X, Lian X, He Y. Natural variation in WHITE-CORE RATE 1 regulates redox homeostasis in rice endosperm to affect grain quality. THE PLANT CELL 2022; 34:1912-1932. [PMID: 35171272 PMCID: PMC9048946 DOI: 10.1093/plcell/koac057] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/09/2022] [Indexed: 05/11/2023]
Abstract
Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.
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Affiliation(s)
- Bian Wu
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Peng Yun
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuan Gu
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jialing Yao
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhuqing Zhou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianxian Chen
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shiyuan Cheng
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hao Zhang
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuanyuan Zheng
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Pingli Chen
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shanshan Wan
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingsong Zhou
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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17
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Fang J, Liu C, Law CL, Mujumdar AS, Xiao HW, Zhang C. Superheated steam processing: An emerging technology to improve food quality and safety. Crit Rev Food Sci Nutr 2022; 63:8720-8736. [PMID: 35389273 DOI: 10.1080/10408398.2022.2059440] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Heat processing is one of the most efficient strategies used in food industry to improve quality and prolong shelf life. However, conventional processing methods such as microwave heating, burning charcoal treatment, boiling, and frying are energy-inefficient and often lead to inferior product quality. Superheated steam (SHS) is an innovative technology that offers many potential benefits to industry and is increasingly used in food industry. Compared to conventional processing methods, SHS holds higher heat transfer coefficients, which can reduce microorganisms on surface of foodstuffs efficiently. Additionally, SHS generates a low oxygen environment, which prevents lipid oxidation and harmful compounds generation. Furthermore, SHS can facilitate development of desired product quality, such as protein denaturation with functional characteristics, proper starch gelatinization, and can also reduce nutrient loss, and improve the physicochemical properties of foodstuffs. The current work provides a comprehensive review of the impact of SHS on the nutritional, physicochemical, and safety properties of various foodstuffs including meat, fruits, and vegetables, cereals, etc. Additionally, it also provides food manufacturers and researchers with basic knowledge and practical techniques for SHS processing of foodstuffs, which may improve the current scope of SHS and transfer current food systems to a healthy and sustainable one.
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Affiliation(s)
- Jiajia Fang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China)
| | - Chongxin Liu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China)
| | - Chung-Lim Law
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Selangor, Malaysia
| | - Arun S Mujumdar
- Department of Bioresource Engineering, McGill University, Quebec, Canada
| | - Hong-Wei Xiao
- College of Engineering, China Agricultural University, Beijing, China
| | - Chunjiang Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China)
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18
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Okpala NE, Aloryi KD, An T, He L, Tang X. The roles of starch branching enzymes and starch synthase in the biosynthesis of amylose in rice. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2021.103393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Jiang L, Zhong H, Jiang X, Zhang J, Huang R, Liao F, Deng Y, Liu Q, Huang Y, Wang H, Tao Y, Zheng J. Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape. FRONTIERS IN PLANT SCIENCE 2022; 12:814928. [PMID: 35126437 PMCID: PMC8810533 DOI: 10.3389/fpls.2021.814928] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/20/2021] [Indexed: 05/31/2023]
Abstract
Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes have been cloned to date. In this study, the candidate gene GSE5 of a major quantitative trait locus (QTL) for rice chalkiness, qDEC5, was identified by map-based cloning. Phenotyping and haplotype analysis of proActin:GSE5 transgenic line, gse5-cr mutant, and 69 rice varieties further confirmed that GSE5 had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed GSE5 was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to GSE5 was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that GSE5 played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by GSE5 to affect the formation of chalkiness, including some newly discovered genes, such as OsCESA9, OsHSP70, OsTPS8, OsPFK04, OsSTA1, OsERdj3A, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly; OsDjC10 and OsSUS3 were upregulated at 6 and 12 DAP, respectively, and OsGSTL2 was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of qDEC5 dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.
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Affiliation(s)
- Liangrong Jiang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hui Zhong
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xianbin Jiang
- Guangxi Rice Genetics and Breeding Key Laboratory, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jiaoping Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Rongyu Huang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Furong Liao
- Xiamen Entry-Exit Inspection and Quarantine Bureau, Xiamen, China
| | - Yaqin Deng
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingqing Liu
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yumin Huang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Houcong Wang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yi Tao
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jingsheng Zheng
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, China
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20
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Wu B, Xia D, Zhou H, Cheng S, Wang Y, Li M, Gao G, Zhang Q, Li X, He Y. Fine mapping of qWCR7, a grain chalkiness QTL in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:68. [PMID: 37309362 PMCID: PMC10236040 DOI: 10.1007/s11032-021-01260-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Abstract
Chalkiness is one of the key determinants of rice quality and is a highly undesirable trait for breeding and marketing. In this study, qWCR7, a major quantitative trait locus (QTL) of white-core rate (WCR), was genetically validated using a BC3F2 segregation population and further fine mapped using a near isogenic line (NIL) population, of which both were derived from a cross between the donor parent DL208 and the recurrent parent ZS97. qWCR7 was finally narrowed to a genomic interval of ~ 68 kb, containing seven annotated genes. Among those, two genes displayed markedly different expression levels in endosperm of NILs. Transcriptome analysis showed that the synthesis and accumulation of metabolites played a key role in chalkiness formation. The contents of storage components and expression levels of related genes were detected, suggesting that starch and storage protein were closely related to white-core trait. Our findings have laid the foundation of map-based cloning of qWCR7, which may have potential value in quality improvement during rice breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01260-x.
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Affiliation(s)
- Bian Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Shiyuan Cheng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yipei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Minqi Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
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21
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Cruz M, Arbelaez JD, Loaiza K, Cuasquer J, Rosas J, Graterol E. Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean. THE PLANT GENOME 2021; 14:e20134. [PMID: 34510797 DOI: 10.1002/tpg2.20134] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Rice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release. In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from -0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51-75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS. Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.
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Affiliation(s)
- Maribel Cruz
- FLAR (Fondo Latinoamericano para Arroz de Riego), CIAT (International Center for Tropical Agriculture), Kilómetro 17 c, CP, Cali, Valle del Cauca, 763537, Colombia
| | - Juan David Arbelaez
- Dep. of Crop Sciences, Univ. of Illinois, Urbana-Champaign, Turner Hall N-211|1102 S. Goodwin Ave. | 046, Urbana, IL, 61801, USA
| | - Katherine Loaiza
- FLAR (Fondo Latinoamericano para Arroz de Riego), CIAT (International Center for Tropical Agriculture), Kilómetro 17 c, CP, Cali, Valle del Cauca, 763537, Colombia
| | - Juan Cuasquer
- CIAT (International Center for Tropical Agriculture), Kilómetro 17 Recta Cali, Palmira, CP, Cali, Valle del Cauca, 763537, Colombia
| | - Juan Rosas
- INIA (Instituto Nacional de Investigación Agropecuaria), Ruta 8 Km. 281/33000, Treinta y Tres, Uruguay
| | - Eduardo Graterol
- FLAR (Fondo Latinoamericano para Arroz de Riego), CIAT (International Center for Tropical Agriculture), Kilómetro 17 c, CP, Cali, Valle del Cauca, 763537, Colombia
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22
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Yang W, Xiong L, Liang J, Hao Q, Luan X, Tan Q, Lin S, Zhu H, Liu G, Liu Z, Bu S, Wang S, Zhang G. Substitution Mapping of Two Closely Linked QTLs on Chromosome 8 Controlling Grain Chalkiness in Rice. RICE (NEW YORK, N.Y.) 2021; 14:85. [PMID: 34601659 PMCID: PMC8487414 DOI: 10.1186/s12284-021-00526-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/18/2021] [Indexed: 05/27/2023]
Abstract
Rice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness, grain length and width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by higher temperature. Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to higher temperature.
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Affiliation(s)
- Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Xiong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jiayan Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Qingwen Hao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Luan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shiwan Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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23
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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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Selvaraj R, Singh AK, Singh VK, Abbai R, Habde SV, Singh UM, Kumar A. Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 2021; 11:10082. [PMID: 33980871 PMCID: PMC8115083 DOI: 10.1038/s41598-021-87964-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/19/2021] [Indexed: 02/03/2023] Open
Abstract
Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.
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Affiliation(s)
- Ramchander Selvaraj
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Arun Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Vikas Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Sonali Vijay Habde
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Uma Maheshwar Singh
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Arvind Kumar
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India.
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India.
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Yang W, Liang J, Hao Q, Luan X, Tan Q, Lin S, Zhu H, Liu G, Liu Z, Bu S, Wang S, Zhang G. Fine mapping of two grain chalkiness QTLs sensitive to high temperature in rice. RICE (NEW YORK, N.Y.) 2021; 14:33. [PMID: 33792792 PMCID: PMC8017073 DOI: 10.1186/s12284-021-00476-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/23/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Grain chalkiness is one of important factors affected rice grain quality. It is known that chalkiness is affected by the high temperature during the seed filling period. Although a larger of QTLs for chalkiness were reported across all 12 chromosomes, only a few of the QTLs were fine mapped or cloned up to now. Here, we fine map two QTLs for chalkiness in two single-segment substitution lines (SSSLs), 11-09 with substitution segment from O. sativa and HP67-11 with substitution segment from O. glaberrima. RESULTS The grain chalkiness of SSSLs 11-09 and HP67-11 was significantly lower than that in the recipient Huajingxian 74 (HJX74) in consecutive 8 cropping seasons. The regression correlation analysis showed that percentage of chalky grain (PCG) and percentage of chalky area (PCA) were significantly and positively correlated with percentage of grain chalkiness (PGC). Two QTLs for grain chalkiness were located on two chromosomes by substitution mapping. qPGC9 was mapped on chromosome 9 with an estimated interval of 345.6 kb. qPGC11 was located on chromosome 11 and delimited to a 432.1 kb interval in the O. sativa genome and a 332.9 kb interval in the O. glaberrima genome. qPGC11 is a QTL for grain chalkiness from O. glaberrima and was mapped in a new region of chromosome 11. The effect of two QTLs was incomplete dominance. The additive effects of two QTLs on chalkiness in second cropping season (SCS) were significantly greater than that in first cropping season (FCS). CONCLUSIONS qPGC11 is a new QTL for grain chalkiness. The two QTLs were fine mapped. The donor alleles of qPGC9 and qPGC11 were sensitive to the high temperature of FCS.
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Affiliation(s)
- Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jiayan Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Qingwen Hao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Luan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shiwan Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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Ayaad M, Han Z, Zheng K, Hu G, Abo-Yousef M, Sobeih SES, Xing Y. Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice. J Adv Res 2020; 28:183-194. [PMID: 33364055 PMCID: PMC7753235 DOI: 10.1016/j.jare.2020.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/19/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022] Open
Abstract
4-way Multiparental population covered the limitations of the biparental structure. The combination of SNP and bin-GWAS showed a powerful tool for QTL mapping. qPGWC8.2 harbored a novel predicted gene for rice chalkiness quality.
Introduction The multiparental population provides us the chance to identify superior alleles controlling a trait for genetic improvement. Genome wide association studies at bin level (bin-GWAS) are expected to be more power in QTL mapping than GWAS at SNP level (SNP-GWAS). Objectives This study is to estimate genetic effects of QTL conferring grain appearance quality in rice by SNP-GWAS and bin-GWAS, compare their power in QTL mapping and identify the superior alleles of all detected QTL from 4 parents for genetic improvement. Methods A 4-way MAGIC population and its four founders were cultivated in two environments to dissect the genetic basis of rice grain appearance quality. Both SNP-GWAS and bin-GWAS were conducted for QTL mapping. Multiple comparison among 4 parental bin/alleles was used to identify the superior alleles. Results A total of 16 and 20 QTL associated with grain appearance quality were identified by SNP- and bin-GWAS, respectively. A minor chalkiness QTL qPGWC8.2/qDEC8 was assigned to a 30-kb genomic region, in which OsMH_08T0121900 is the potential candidate gene because its encoded protein, glucan endo-1,3-beta-glucosidase precursor is involved in the starch and sucrose metabolism pathway. The superior parental alleles for GS3, GL3.1, GW5, GW7, and Chalk5 and two QTLs were almost carried by the high-quality parents Cypress and Yuejingsimiao (YJSM), while the poor-quality parent Guichao-2 (GC2) always carried the inferior alleles. The top five recombinant inbred lines with the highest quality of grain shape and chalkiness traits all carried gene combinations of superior alleles. Conclusions Both SNP- and bin-GWAS methods are encouraged for joint QTL mapping with MAGIC population. qPGWC8.2/qDEC8 is a novel candidate gene strongly associated with chalkiness. The superior alleles of GS3, GW5, GL3.1, GW7, Chalk5 and qPGWC8.2 were identified, and the pyramiding of these superior alleles is helpful to improve rice appearance quality.
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Affiliation(s)
- Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China.,Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal 13759, Egypt
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Kou Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Gang Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Mahmoud Abo-Yousef
- Rice Research and Training Center, Agriculture Research Center, Sakha 33717, Egypt
| | - Sobeih El S Sobeih
- Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal 13759, Egypt
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
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Zhang L, Zhao L, Zhang J, Cai X, Liu Q, Wei C. Relationships between transparency, amylose content, starch cavity, and moisture of brown rice kernels. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.102854] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Abstract
Increasing paddy yield in rice does not directly translate to enhancing food security because significant decrease in grain yield can happen during postharvest processing of the rice paddy. In parallel with enhancing paddy yield, improving the milling quality of rice is essential in ensuring food security by mitigating the impact of significant losses during the postharvest processing of rice grains. From an industrial standpoint, maximizing the milling recovery of whole grain polished rice is crucial in fetching higher revenues to rice farmers. Significant advances in rice postharvest processing technology have been achieved which are geared toward reducing the incidence of fissures and chalkiness to increase head rice yield (HRY) in rice. The genetic bases of kernel development and grain dimension are also characterized. In addition to these advancements, an integrated phenotyping suite to simultaneously characterize phenotypes related to milling quality will help in screening for breeding lines with high HRY. Toward this goal, modern imaging tools and computer algorithms are currently being developed for high-throughput characterization of rice milling quality. With the availability of more sophisticated, affordable, automated, and nondestructive phenotyping methods of milling quality, it is envisioned that significant improvement in HRY will be made possible to ensure rice food security in the future.
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Cheng C, Ali A, Shi Q, Zeng Y, Tan X, Shang Q, Huang S, Xie X, Zeng Y. Response of chalkiness in high-quality rice (Oryza sativa L.) to temperature across different ecological regions. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.02.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Fiaz S, Ahmad S, Noor MA, Wang X, Younas A, Riaz A, Riaz A, Ali F. Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities. Int J Mol Sci 2019; 20:E888. [PMID: 30791357 PMCID: PMC6412304 DOI: 10.3390/ijms20040888] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/07/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023] Open
Abstract
Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.
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Affiliation(s)
- Sajid Fiaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing 100081, China.
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore 54000, Pakistan.
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Fahad Ali
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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31
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Zhu A, Zhang Y, Zhang Z, Wang B, Xue P, Cao Y, Chen Y, Li Z, Liu Q, Cheng S, Cao L. Genetic Dissection of qPCG1 for a Quantitative Trait Locus for Percentage of Chalky Grain in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1173. [PMID: 30147703 PMCID: PMC6095994 DOI: 10.3389/fpls.2018.01173] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/23/2018] [Indexed: 05/18/2023]
Abstract
Rice is a pivotal cereal crop that provides the staple food for more than half of the world's population. Along with improvements in the standard of living, people not only pay attention to the grain yield but also to the grain quality. Chalkiness is one of the most important index of grain quality. In this study, qPCG1, a QTL for percentage of chalky grain, was mapped in an interval with a physical distance about 139 kb on chromosome 1 by residual heterozygous line (RHL) method. qPCG1 was incomplete dominant and the additive effect plays a major role and explained 6.8-21.9% of phenotypic variance within the heterogeneous region on chromosome 1. The effect of allele from Zhonghui9308 was decreasing the percentage of chalky grains (PCG). Microscope observation results indicated that there are great differences in the shape, structure and arrangement of starch granule between the chalky part and transparent part. Analysis of starch physicochemical properties showed that the total starch content, amylose content and chain length distribution of amylopectin changed while the protein contents were not apparently affected with the changed chalkiness. qPCG1 had little influence on main agronomic traits and it might be useful in rice breeding for it did not bring negative effect on grain yield while reducing the chalkiness.
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Affiliation(s)
- Aike Zhu
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Nanchong Academy of Agricultural Sciences, Nanchong, China
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenhua Zhang
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Beifang Wang
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Pao Xue
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yongrun Cao
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Crop Genetic Breeding Department, Henan Agricultural University, Zhengzhou, China
| | - Yuyu Chen
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zihe Li
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qunen Liu
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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Nevame AYM, Emon RM, Malek MA, Hasan MM, Alam MA, Muharam FM, Aslani F, Rafii MY, Ismail MR. Relationship between High Temperature and Formation of Chalkiness and Their Effects on Quality of Rice. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1653721. [PMID: 30065932 PMCID: PMC6051336 DOI: 10.1155/2018/1653721] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/24/2018] [Indexed: 12/18/2022]
Abstract
Occurrence of chalkiness in rice is attributed to genetic and environmental factors, especially high temperature (HT). The HT induces heat stress, which in turn compromises many grain qualities, especially transparency. Chalkiness in rice is commonly studied together with other quality traits such as amylose content, gel consistency, and protein storage. In addition to the fundamental QTLs, some other QTLs have been identified which accelerate chalkiness occurrence under HT condition. In this review, some of the relatively stable chalkiness, amylose content, and gel consistency related QTLs have been presented well. Genetically, HT effect on chalkiness is explained by the location of certain chalkiness gene in the vicinity of high-temperature-responsive genes. With regard to stable QTL distribution and availability of potential material resources, there is still feasibility to find out novel stable QTLs related to chalkiness under HT condition. A better understanding of those achievements is essential to develop new rice varieties with a reduced chalky grain percentage. Therefore, we propose the pyramiding of relatively stable and nonallelic QTLs controlling low chalkiness endosperm into adaptable rice varieties as pragmatic approach to mitigate HT effect.
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Affiliation(s)
- A. Y. M. Nevame
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - R. M. Emon
- Bangladesh Institute of Nuclear Agriculture, BAU Campus, Mymensingh 2202, Bangladesh
| | - M. A. Malek
- Bangladesh Institute of Nuclear Agriculture, BAU Campus, Mymensingh 2202, Bangladesh
| | - M. M. Hasan
- Bangladesh Institute of Nuclear Agriculture, BAU Campus, Mymensingh 2202, Bangladesh
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
| | - Md. Amirul Alam
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200 Besut, Terengganu, Malaysia
| | - Farrah Melissa Muharam
- Laboratory of Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
| | - Farzad Aslani
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
| | - M. Y. Rafii
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
| | - M. R. Ismail
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
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Qiu X, Chen K, Lv W, Ou X, Zhu Y, Xing D, Yang L, Fan F, Yang J, Xu J, Zheng T, Li Z. Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:951-967. [PMID: 28299373 PMCID: PMC5395602 DOI: 10.1007/s00122-017-2862-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 01/17/2017] [Indexed: 05/04/2023]
Abstract
A novel QTL cluster for appearance quality on Chr07 was identified using reciprocal introgression populations in different locations in China. Two secondary F 2 populations validated QTL with significant effect on appearance quality. Appearance quality (AQ) is the main determinants of market value of rice. Identification of QTL affecting AQ is the prerequisite for efficient improvement of AQ through marker-assisted selection (MAS). Two sets of reciprocal introgression lines derived from indica Minghui 63 and japonica 02428 were used to dissect the stability of QTL affecting five AQ traits, including grain length, grain width, length to width ratio, percentage of grains with chalkiness, and degree of endosperm chalkiness using 4568 bin genotype produced from 58,000 SNPs across five different environments. A total of 41 and 30 main-effect QTL were identified in MH63 and 02428 backgrounds, respectively. Among them, 9 background-independent QTL (BI-QTL) were found. There were also 13 and 10 stable-expressed QTL (SE-QTL) across at least two environments in MH63 and 02428 backgrounds, respectively. Two important BI- and SE-QTL regions (BISERs) including BISER-I harboring qPGWC5, qDEC5, qGW5.1, and qLWR5 on chromosome 5 and BISER-II harboring qGL7, qLWR7, qPGWC7, and qDEC7 on chromosome 7 were identified. The BISER-II was newly reported and validated by two secondary F2 populations in the reciprocal backgrounds. Among 59 epistatic QTL (E-QTL) detected in this study, there were only four SE- but no BI-E-QTL detected in different environments, indicating that genetic background has stronger effect on AQ traits than the environmental factors, especially for percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) with lower heritability. BISER-I and BISER-II harboring many BI- and SE-QTL with favorable alleles from slender grain rice are much important for improvement of rice AQ by MAS.
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Affiliation(s)
- Xianjin Qiu
- Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Kai Chen
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wenkai Lv
- Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Xiaoxue Ou
- Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yajun Zhu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Danying Xing
- Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Longwei Yang
- Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Fangjun Fan
- Institute of Food Crops, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jie Yang
- Institute of Food Crops, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jianlong Xu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
- Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Tianqing Zheng
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhikang Li
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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Gao Y, Liu C, Li Y, Zhang A, Dong G, Xie L, Zhang B, Ruan B, Hong K, Xue D, Zeng D, Guo L, Qian Q, Gao Z. QTL analysis for chalkiness of rice and fine mapping of a candidate gene for qACE9. RICE (NEW YORK, N.Y.) 2016; 9:41. [PMID: 27549111 PMCID: PMC4993740 DOI: 10.1186/s12284-016-0114-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/12/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND An ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Therefore, clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. Although a number of QTLs related to chalkiness were mapped, few of them have been cloned so far. RESULTS In this study, using recombinant inbred lines (RILs) of PA64s and 9311, we identified 19 QTLs associated with chalkiness on chromosomes 1, 4, 6, 7, 9 and 12, which accounted for 5.1 to 30.6 % of phenotypic variations. A novel major QTL qACE9 for the area of chalky endosperm (ACE) was detected in Hainan and Hangzhou, both mapped in the overlapping region on chromosome 9. It was further fine mapped to an interval of 22 kb between two insertion-deletion (InDel) markers IND9-4 and IND9-5 using a BC4F2 population. Gene prediction analysis identified five putative genes, among which only one gene (OsAPS1), whose product involved in starch synthesis, was detected two nucleotide substitutions causing amino acid change between the parents. Significant difference was found in apparent amylose content (AAC) between NILqACE9 and 9311. And starch granules were round and loosely packed in NILqACE9 compared with 9311 by scanning electron microscopy (SEM) analysis. CONCLUSIONS OsAPS1 was selected as a novel candidate gene for fine-mapped qACE9. The candidate gene not only plays a critical role during starch synthesis in endosperm, but also determines the area of chalky endosperm in rice. Further cloning of the QTL will facilitate the improvement of quality in hybrid rice.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Anpeng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Kai Hong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- 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
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Chen L, Gao W, Chen S, Wang L, Zou J, Liu Y, Wang H, Chen Z, Guo T. High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. RICE (NEW YORK, N.Y.) 2016; 9:48. [PMID: 27659284 PMCID: PMC5033801 DOI: 10.1186/s12284-016-0121-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/14/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study. RESULTS A RIL population derived from an inter-subspecific cross between indica rice PYZX and japonica rice P02428 was generated, based on the significant variations for the grain morphology and cytological structure between these two parents. Using the Genotyping-By-Sequencing (GBS) approach, 2711 recombination bin markers with an average physical length of 137.68 kb were obtained, and a high-density genetic map was constructed. Global genetic mapping of QTLs affecting grain shape and chalkiness traits was performed across four environments and the newly identified stable loci were obtained. Twelve important QTL clusters were detected, four of which were coincident with the genomic regions of cloned genes or fine mapped QTL reported. Eight novel QTL clusters (including six for grain shape, one for chalkiness, and one for both grain shape and chalkiness) were firstly obtained and highlighted the value and reliability of the QTL analysis. The important QTL cluster on chromosome 5 affects multiple traits including circularity (CS), grain width (GW), area size of grain (AS), percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), indicating some potentially pleiotropic effects. The transcriptome analysis demonstrated an available gene expression profile responsible for the development of chalkiness, and several DEGs (differentially expressed genes) were co-located nearby the three chalkiness-related QTL regions on chromosomes 5, 7, and 8. Candidate genes were extrapolated, which were suitable for functional validation and breeding utilization. CONCLUSION QTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers. The important differentially expressed genes (DEGs) were co-located in the QTL cluster regions on chromosomes 5, 7 and 8 affecting PGWC and DEC parameters. Our research provides a crucial insight into the genetic architecture of rice grain shape and chalkiness, and acquired potential candidate loci for molecular cloning and grain quality improvement.
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Affiliation(s)
- Likai Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Weiwei Gao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Siping Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Liping Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jiyong Zou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Agricultural Technology Extension, Guangzhou, 510520, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
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Zhao X, Daygon VD, McNally KL, Hamilton RS, Xie F, Reinke RF, Fitzgerald MA. Identification of stable QTLs causing chalk in rice grains in nine environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:141-53. [PMID: 26498441 DOI: 10.1007/s00122-015-2616-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/05/2015] [Indexed: 05/18/2023]
Abstract
A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10% of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) population using joined analysis across all environments, respectively. Six major QTLs clusters were found on five chromosomes: 1, 2, 4, 5 and 11. The biggest cluster at id4007289-RM252 on Chr04 was a novelty, including 16 and 4 QTLs detected by single environment analysis and joint mapping across all environments, respectively. The detected digenic epistatic QTLs explained up to 13% of phenotypic variation, suggesting that epistasis play an important role in the genetic control of chalkiness in rice. QTL NILs showed that each QTL cluster had a significant effect on chalk. These chromosomal regions could be targets for MAS, fine mapping and map-based cloning for low chalkiness breeding.
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Zhao X, Zhou L, Ponce K, Ye G. The Usefulness of Known Genes/Qtls for Grain Quality Traits in an Indica Population of Diverse Breeding Lines Tested using Association Analysis. RICE (NEW YORK, N.Y.) 2015; 8:29. [PMID: 26391157 PMCID: PMC4577492 DOI: 10.1186/s12284-015-0064-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/05/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND A number of studies reported major genes/QTLs for rice grain shapes, chalkiness and starch physicochemical properties. For these finely mapped QTLs or cloned genes to make an impact in practical breeding, it is necessary to test their effects in different genetic backgrounds. In this study, two hundred nineteen markers for 20 starch synthesis genes, 41 fine mapped grain shape and related traits QTLs/genes, and 54 chalkiness QTLs/genes plus 15 additional markers and a large indica population of 375 advanced lines were used to identify marker-trait associations under 6 environments that can be used directly in breeding for grain quality traits. RESULTS The significant associations detected by the QK model were used to declare the usefulness of the targeted genes/QTLs. A total of 65 markers were detected associations with grain quality trait at least in one environment. More phenotypic variations could be explained by haplotype than single marker, as exemplified by the starch biosynthesising genes. GBSSI was the major gene for AC and explained up to 55 % of the phenotypic variation, which also affected GC and accounted up to 11.31 % of the phenotypic variation. SSIIa was the major gene for chalkiness and explained up to 17 and 21 % of variation of DEC and PGWC, respectively. In addition, RMw513 and RM18068 were associated with DEC in 6 environments as well. Four markers (RGS1, RM15206, RMw513 and Indel1) tightly linked to GS3, gw5, and qGL7-2 were the most important ones for grain shapes. Allelic combinations between SSIIa and RMw513 revealed more variations in DEC. CONCLUSIONS The validated markers for genes/QTLs with major effects could be directly used in breeding for grain quality via marker-assisted selection. Creating desirable allelic combinations by gene pyramiding might be an effective approach for the development of high quality breeding lines in rice.
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Affiliation(s)
- Xiangqian Zhao
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Lijie Zhou
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
- Present address: Longping Branch, Graduate School of Central South University, Changsha, 410125, Hunan, China
| | - Kimberley Ponce
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Guoyou Ye
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
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Sun W, Zhou Q, Yao Y, Qiu X, Xie K, Yu S. Identification of genomic regions and the isoamylase gene for reduced grain chalkiness in rice. PLoS One 2015; 10:e0122013. [PMID: 25790260 PMCID: PMC4366167 DOI: 10.1371/journal.pone.0122013] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
Grain chalkiness is an important grain quality related to starch granules in the endosperm. A high percentage of grain chalkiness is a major problem because it diminishes grain quality in rice. Here, we report quantitative trait loci identification for grain chalkiness using high-throughput single nucleotide polymorphism genotyping of a chromosomal segment substitution line population in which each line carried one or a few introduced japonica cultivar Nipponbare segments in the genetic background of the indica cultivar ZS97. Ten quantitative trait loci regions were commonly identified for the percentage of grain chalkiness and the degree of endosperm chalkiness. The allelic effects at nine of these quantitative trait loci reduced grain chalkiness. Furthermore, a quantitative trait locus (qPGC8-2) on chromosome 8 was validated in a chromosomal segment substitution line-derived segregation population, and had a stable effect on chalkiness in a multiple-environment evaluation of the near-isogenic lines. Residing on the qPGC8-2 region, the isoamylase gene (ISA1) was preferentially expressed in the endosperm and revealed some nucleotide polymorphisms between two varieties, Nipponbare and ZS97. Transgenic lines with suppression of ISA1 by RNA interference produced grains with 20% more chalkiness than the control. The results support that the gene may underlie qPGC8-2 for grain chalkiness. The multiple-environment trials of the near-isogenic lines also show that combination of the favorable alleles such as the ISA1 gene for low chalkiness and the GS3 gene for long grains considerably improved grain quality of ZS97, which proves useful for grain quality improvement in rice breeding programs.
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Affiliation(s)
- Wenqian Sun
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoling Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yue Yao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kun Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Sun L, Li X, Fu Y, Zhu Z, Tan L, Liu F, Sun X, Sun X, Sun C. GS6, a member of the GRAS gene family, negatively regulates grain size in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:938-49. [PMID: 23650998 DOI: 10.1111/jipb.12062] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/01/2013] [Indexed: 05/07/2023]
Abstract
Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today's cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the +348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a "ggc" repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield.
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Affiliation(s)
- Lianjun Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Beijing 100193, China; Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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40
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QTL Analysis of Rice Ratooning Ability and Related Agronomic Traits by. ACTA AGRONOMICA SINICA 2013. [DOI: 10.3724/sp.j.1006.2012.01240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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QTL mapping and correlation analysis for 1000-grain weight and percentage of grains with chalkiness in rice. J Genet 2013; 92:281-7. [DOI: 10.1007/s12041-013-0267-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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42
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Knockout of the VPS22 component of the ESCRT-II complex in rice (Oryza sativa L.) causes chalky endosperm and early seedling lethality. Mol Biol Rep 2012; 40:3475-81. [PMID: 23275199 DOI: 10.1007/s11033-012-2422-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
In both yeast and mammals, the major constituent of the endosomal sorting complex required for transport-II (ESCRT-II) is the VPS22/EAP30 protein, which plays an important role in ubiquitin-mediated degradation of membrane proteins through the multivesicular body pathway. However, the functions of ESCRT-II subunits in plants are largely unknown. In this work, we report the genetic analysis and phenotypic characterization of mutants in OsVPS22 gene, which encodes a functional VPS22 homolog in rice. On the basis of a collection of T-DNA lines, we identified a T-DNA insertion mutant, which showed abnormal segregation ratios; we then found that the T-DNA insertion is located within the sixth intron of the OsVPS22 gene. Compared with the wild type, this vps22 mutant exhibited seedling lethality and severe reduction in shoot and root growth. In addition, the vps22 mutant had a chalky endosperm in the grain. In summary, our data suggest that OsVPS22 may be required for seedling viability and grain filling in rice, thus providing a valuable resource for further exploration of the functions of the ESCRTing machinery in plants.
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Cui J, He P, Liu F, Tan J, Chen L, Fenn J. 60 years of development of the journal of integrative plant biology. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:682-702. [PMID: 22966769 DOI: 10.1111/j.1744-7909.2012.01163.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In celebration of JIPB's 60(th) anniversary, this paper summarizes and reviews the development process of the journal. To start, we offer our heartfelt thanks to JIPB's pioneer Editors-in-Chief who helped get the journal off the ground and make it successful. Academic achievement is the soul of academic journals, and this paper summarizes JIPB's course of academic development by analyzing it in four stages: the first two stages are mostly qualitative analyses, and the latter two stages are dedicated to quantitative analyses. Most-cited papers were statistically analyzed. Improvements in editing, publication, distribution and online accessibility--which are detailed in this paper--contribute to JIPB's sustainable development. In addition, JIPB's evaluation index and awards are provided with accompanying pictures. At the end of the paper, JIPB's milestones are listed chronologically. We believe that JIPB's development, from a national journal to an international one, parallels the development of the Chinese plant sciences.
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Bai X, Wu B, Xing Y. Yield-related QTLs and their applications in rice genetic improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:300-11. [PMID: 22463712 DOI: 10.1111/j.1744-7909.2012.01117.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Grain yield is one of the most important indexes in rice breeding, which is governed by quantitative trait loci (QTLs). Different mapping populations have been used to explore the QTLs controlling yield related traits. Primary populations such as F(2) and recombinant inbred line populations have been widely used to discover QTLs in rice genome-wide, with hundreds of yield-related QTLs detected. Advanced populations such as near isogenic lines (NILs) are efficient to further fine-map and clone target QTLs. NILs for primarily identified QTLs have been proposed and confirmed to be the ideal population for map-based cloning. To date, 20 QTLs directly affecting rice grain yield and its components have been cloned with NIL-F(2) populations, and 14 new grain yield QTLs have been validated in the NILs. The molecular mechanisms of a continuously increasing number of genes are being unveiled, which aids in the understanding of the formation of grain yield. Favorable alleles for rice breeding have been 'mined' from natural cultivars and wild rice by association analysis of known functional genes with target trait performance. Reasonable combination of favorable alleles has the potential to increase grain yield via use of functional marker assisted selection.
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Affiliation(s)
- Xufeng Bai
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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45
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Li J, Zhang W, Wu H, Guo T, Liu X, Wan X, Jin J, Hanh TTT, Thoa NTN, Chen M, Liu S, Chen L, Liu X, Wang J, Zhai H, Wan J. Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments. BREEDING SCIENCE 2011; 61:338-46. [PMID: 23136470 PMCID: PMC3406775 DOI: 10.1270/jsbbs.61.338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 08/05/2011] [Indexed: 05/26/2023]
Abstract
Amylose content (AC) and viscosity profile are primary indices for evaluating eating and cooking qualities of rice grain. Using chromosome segment substitution lines (CSSLs), previous studies identified a QTL cluster of genes for rice eating and cooking quality in the interval R727-G1149 on chromosome 8. In this study we report two QTLs for viscosity parameters, respectively controlling setback viscosity (SBV) and consistency viscosity (CSV), located in the same interval using rapid viscosity analyzer (RVA) profile as an indicator of eating quality. Previously reported QTL for AC was dissected into two components with opposite genetic effects. Of four QTLs, qCSV-8 and qAC-8-2 had stable genetic effects across three and four environments, respectively. qSBV-8, qCSV-8 and qAC-8-1 partly overlapped, but were separated from qAC-8-2. Based on data from an Affymetrix rice GeneChip, two genes related to starch biosynthesis at the qAC-8-2 locus were chosen for further quantitative expression analysis. Both genes showed enhanced expression in sub-CSSLs carrying the target qAC-8-2 allele, but not in sub-CSSLs without the target qAC-8-2 allele, indicating their possible role in rice quality determination. Molecular markers closely linked to the two stable QTL provide the opportunity for marker-assisted selection (MAS) in breeding high quality rice.
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Affiliation(s)
- Jingjing Li
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Wenwei Zhang
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Hongkai Wu
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Tao Guo
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xiaolu Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangyuan Wan
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
| | - Jiansheng Jin
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Than Thi Thu Hanh
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Nguyen Thi Nhu Thoa
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Mingjiang Chen
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Shijia Liu
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Liangming Chen
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xi Liu
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huqu Zhai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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