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Moon HS, Thiruvengadam M, Chi HY, Kim B, Prabhu S, Chung IM, Kim SH. Comparative study for metabolomics, antioxidant activity, and molecular docking simulation of the newly bred Korean red rice accessions. Food Chem 2024; 458:140277. [PMID: 38970957 DOI: 10.1016/j.foodchem.2024.140277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024]
Abstract
This study analyzed the metabolite profiles and antioxidant capacities of two waxy and non-waxy Korean red rice accessions newly bred. Fifteen phenolic compounds were detected in the rice samples. Accession1 had high fatty acids, phytosterols, and vitamin E; accession3 had high vitamin E and phytosterol; and accession4 had a high total flavonoid. The correlation analysis findings from this study validated the positive association between all the metabolites and antioxidant activity. in silico results revealed that protocatechuic acid had a docking score of -9.541, followed by luteolin, quercetin, and caffeic acid, all of which had significant docking scores and a significant number of contacts. Similarly, molecular dynamics simulations showed that phytochemicals had root mean square deviation values of <2.8 Å with Keap 1, indicating better stability. This study provides valuable insights into potential directions for future investigations and improvements in the functional qualities of other colored rice varieties.
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Affiliation(s)
- Hee-Sung Moon
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Hee-Youn Chi
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Backki Kim
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
| | - Srinivasan Prabhu
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683104, Kerala, India
| | - Ill-Min Chung
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Republic of Korea.
| | - Seung-Hyun Kim
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Republic of Korea.
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Wang F, Xi Z, Wang M, Wang L, Wang J. Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2331-2348. [PMID: 38976378 DOI: 10.1111/tpj.16920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/21/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter-subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype-specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR-related genes with maternal Z04A-bias allele-specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015-bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter-subspecific hybrid rice.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zengde Xi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengyao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Linyou Wang
- Zhejiang Academy of Agricultural Sciences, Institute of Crop and Nuclear Technology Utilization, Hangzhou, 310021, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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3
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Muzaffar A, Chen Y, Lee H, Wu C, Le TT, Liang J, Lu C, Balasubramaniam H, Lo S, Yu L, Chan C, Chen K, Lee M, Hsing Y, Ho TD, Yu S. A newly evolved rice-specific gene JAUP1 regulates jasmonate biosynthesis and signalling to promote root development and multi-stress tolerance. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1417-1432. [PMID: 38193234 PMCID: PMC11022792 DOI: 10.1111/pbi.14276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 12/01/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024]
Abstract
Root architecture and function are critical for plants to secure water and nutrient supply from the soil, but environmental stresses alter root development. The phytohormone jasmonic acid (JA) regulates plant growth and responses to wounding and other stresses, but its role in root development for adaptation to environmental challenges had not been well investigated. We discovered a novel JA Upregulated Protein 1 gene (JAUP1) that has recently evolved in rice and is specific to modern rice accessions. JAUP1 regulates a self-perpetuating feed-forward loop to activate the expression of genes involved in JA biosynthesis and signalling that confers tolerance to abiotic stresses and regulates auxin-dependent root development. Ectopic expression of JAUP1 alleviates abscisic acid- and salt-mediated suppression of lateral root (LR) growth. JAUP1 is primarily expressed in the root cap and epidermal cells (EPCs) that protect the meristematic stem cells and emerging LRs. Wound-activated JA/JAUP1 signalling promotes crosstalk between the root cap of LR and parental root EPCs, as well as induces cell wall remodelling in EPCs overlaying the emerging LR, thereby facilitating LR emergence even under ABA-suppressive conditions. Elevated expression of JAUP1 in transgenic rice or natural rice accessions enhances abiotic stress tolerance and reduces grain yield loss under a limited water supply. We reveal a hitherto unappreciated role for wound-induced JA in LR development under abiotic stress and suggest that JAUP1 can be used in biotechnology and as a molecular marker for breeding rice adapted to extreme environmental challenges and for the conservation of water resources.
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Affiliation(s)
- Adnan Muzaffar
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Life SciencesNational Defense Medical CenterTaipeiTaiwan, ROC
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Yi‐Shih Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Hsiang‐Ting Lee
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Life SciencesNational Defense Medical CenterTaipeiTaiwan, ROC
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Cheng‐Chieh Wu
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Trang Thi Le
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Jin‐Zhang Liang
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Department of Agricultural ChemistryNational Taiwan UniversityTaipeiTaiwan, ROC
| | - Chun‐Hsien Lu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Genome and Systems Biology Degree ProgramNational Taiwan University and Academia SinicaTaipeiTaiwan, ROC
| | - Hariharan Balasubramaniam
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan, ROC
| | - Shuen‐Fang Lo
- International Bachelor Program of AgribusinessNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Lin‐Chih Yu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Chien‐Hao Chan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Ku‐Ting Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Miin‐Huey Lee
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Yue‐Ie Hsing
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Tuan‐Hua David Ho
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan, ROC
| | - Su‐May Yu
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Life SciencesNational Defense Medical CenterTaipeiTaiwan, ROC
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
- Genome and Systems Biology Degree ProgramNational Taiwan University and Academia SinicaTaipeiTaiwan, ROC
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate ProgramAcademia Sinica and National Chung Hsing UniversityTaipeiTaiwan, ROC
- Department of Plant PathologyNational Chung Hsing UniversityTaichungTaiwan, ROC
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Yang X, Yu S, Yan S, Wang H, Fang W, Chen Y, Ma X, Han L. Progress in Rice Breeding Based on Genomic Research. Genes (Basel) 2024; 15:564. [PMID: 38790193 PMCID: PMC11121554 DOI: 10.3390/genes15050564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.
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Affiliation(s)
- Xingye Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Shicong Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Shen Yan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Hao Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Wei Fang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Yanqing Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Xiaoding Ma
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Longzhi Han
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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5
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He L, Sui Y, Che Y, Liu L, Liu S, Wang X, Cao G. New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS. Int J Mol Sci 2024; 25:4667. [PMID: 38731885 PMCID: PMC11083390 DOI: 10.3390/ijms25094667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Lysine is an essential amino acid that cannot be synthesized in humans. Rice is a global staple food for humans but has a rather low lysine content. Identification of the quantitative trait nucleotides (QTNs) and genes underlying lysine content is crucial to increase lysine accumulation. In this study, five grain and three leaf lysine content datasets and 4,630,367 single nucleotide polymorphisms (SNPs) of 387 rice accessions were used to perform a genome-wide association study (GWAS) by ten statistical models. A total of 248 and 71 common QTNs associated with grain/leaf lysine content were identified. The accuracy of genomic selection/prediction RR-BLUP models was up to 0.85, and the significant correlation between the number of favorable alleles per accession and lysine content was up to 0.71, which validated the reliability and additive effects of these QTNs. Several key genes were uncovered for fine-tuning lysine accumulation. Additionally, 20 and 30 QTN-by-environment interactions (QEIs) were detected in grains/leaves. The QEI-sf0111954416 candidate gene LOC_Os01g21380 putatively accounted for gene-by-environment interaction was identified in grains. These findings suggested the application of multi-model GWAS facilitates a better understanding of lysine accumulation in rice. The identified QTNs and genes hold the potential for lysine-rich rice with a normal phenotype.
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Affiliation(s)
- Liqiang He
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yao Sui
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yanru Che
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Lihua Liu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Shuo Liu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Xiaobing Wang
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Guangping Cao
- Hainan Key Laboratory of Crop Genetics and Breeding, Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou 571100, China
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Keil R, de Oliveira Neves L, da Silva LCO, Lamb TI, Berghahn E, Pita FM, Johann L, Wang Y, Feng Z, Wang G, Zuo S, Sperotto RA. Osmotin1 is involved in rice resistance to Schizotetranychus oryzae (Acari: Tetranychidae) infestation. PEST MANAGEMENT SCIENCE 2024; 80:2154-2161. [PMID: 38153938 DOI: 10.1002/ps.7955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Rice is one of the most consumed cereals in the world. Productivity losses are caused by different biotic stresses. One of the most common is the phytophagous mite Schizotetranychus oryzae Rossi de Simons (Acari: Tetranychidae), which inhibits plant development and seed production. The identification of plant defense proteins is important for a better understanding of the mite-plant interaction. We previously detected a high expression of Osmotin1 protein in mite-resistant rice cultivars, under infested conditions, suggesting it could be involved in plant defense against mite attack. We therefore aimed to evaluate the responses of three rice lines overexpressing Osmotin1 (OSM1-OE) and three lines lacking the Osmotin1 gene (osm1-ko) to mite attack. RESULTS The numbers of individuals (adults, immature stages, and eggs) were significantly lower in OSM1-OE lines than those in wild-type (WT) plants. On the other hand, the osm1-ko lines showed larger numbers of mites per leaf than WT plants. When plants reached the full maturity stage, two out of the three infested OSM1-OE lines presented lower plant height than WT, while the three osm1-ko lines (infested or not) presented higher plant height than WT. The reduction in seed number caused by mite infestation was lower in OSM1-OE lines (12-19%) than in WT plants (34%), while osm1-ko lines presented higher reduction (24-54%) in seed number than WT plants (13%). CONCLUSION These data suggest that Osmotin1 is involved in rice resistance to S. oryzae infestation. This is the first work showing increased plant resistance to herbivory overexpressing an Osmotin gene. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Rosana Keil
- Life Sciences Area, University of Vale do Taquari - Univates, Lajeado, Brazil
| | | | | | - Thainá Inês Lamb
- Graduate Program in Biotechnology, University of Vale do Taquari - Univates, Lajeado, Brazil
| | - Emílio Berghahn
- Graduate Program in Biotechnology, University of Vale do Taquari - Univates, Lajeado, Brazil
| | | | - Liana Johann
- Life Sciences Area, University of Vale do Taquari - Univates, Lajeado, Brazil
- Graduate Program in Biotechnology, University of Vale do Taquari - Univates, Lajeado, Brazil
- Graduate Program in Sustainable Environmental Systems, University of Vale do Taquari - Univates, Lajeado, Brazil
| | - Yu Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zhiming Feng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Guanda Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Shimin Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Zhongshan Biological Breeding Laboratory, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Raul Antonio Sperotto
- Life Sciences Area, University of Vale do Taquari - Univates, Lajeado, Brazil
- Graduate Program in Biotechnology, University of Vale do Taquari - Univates, Lajeado, Brazil
- Graduate Program in Plant Physiology, Federal University of Pelotas, Pelotas, Brazil
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Wu W, Zhang TT, You LL, Wang ZY, Du SQ, Song HY, Wang ZH, Huang YJ, Liao JL. The QTL and Candidate Genes Regulating the Early Tillering Vigor Traits of Late-Season Rice in Double-Cropping Systems. Int J Mol Sci 2024; 25:1497. [PMID: 38338776 PMCID: PMC10855346 DOI: 10.3390/ijms25031497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Rice effective panicle is a major trait for grain yield and is affected by both the genetic tiller numbers and the early tillering vigor (ETV) traits to survive environmental adversities. The mechanism behind tiller bud formation has been well described, while the genes and the molecular mechanism underlying rice-regulating ETV traits are unclear. In this study, the candidate genes in regulating ETV traits have been sought by quantitative trait locus (QTL) mapping and bulk-segregation analysis by resequencing method (BSA-seq) conjoint analysis using rice backcross inbred line (BIL) populations, which were cultivated as late-season rice of double-cropping rice systems. By QTL mapping, seven QTLs were detected on chromosomes 1, 3, 4, and 9, with the logarithm of the odds (LOD) values ranging from 3.52 to 7.57 and explained 3.23% to 12.98% of the observed phenotypic variance. By BSA-seq analysis, seven QTLs on chromosomes 1, 2, 4, 5, 7, and 9 were identified using single-nucleotide polymorphism (SNP) and insertions/deletions (InDel) index algorithm and Euclidean distance (ED) algorithm. The overlapping QTL resulting from QTL mapping and BSA-seq analysis was shown in a 1.39 Mb interval on chromosome 4. In the overlap interval, six genes, including the functional unknown genes Os04g0455650, Os04g0470901, Os04g0500600, and ethylene-insensitive 3 (Os04g0456900), sialyltransferase family domain containing protein (Os04g0506800), and ATOZI1 (Os04g0497300), showed the differential expression between ETV rice lines and late tillering vigor (LTV) rice lines and have a missense base mutation in the genomic DNA sequences of the parents. We speculate that the six genes are the candidate genes regulating the ETV trait in rice, which provides a research basis for revealing the molecular mechanism behind the ETV traits in rice.
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Affiliation(s)
- Wei Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
| | - Tian-Tian Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
| | - Li-Li You
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
| | - Zi-Yi Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
| | - Si-Qi Du
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
| | - Hai-Yan Song
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
- Key Laboratory of Agriculture Responding to Climate Change, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zao-Hai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
- Key Laboratory of Agriculture Responding to Climate Change, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ying-Jin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
- Key Laboratory of Agriculture Responding to Climate Change, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jiang-Lin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China; (W.W.); (H.-Y.S.)
- Key Laboratory of Agriculture Responding to Climate Change, Jiangxi Agricultural University, Nanchang 330045, China
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8
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Zhao B, Wang JW. Perenniality: From model plants to applications in agriculture. MOLECULAR PLANT 2024; 17:141-157. [PMID: 38115580 DOI: 10.1016/j.molp.2023.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; New Cornerstone Science Laboratory, Shanghai 200032, China.
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9
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Sui Y, Che Y, Zhong Y, He L. Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains. PLANTS (BASEL, SWITZERLAND) 2023; 12:2970. [PMID: 37631180 PMCID: PMC10459631 DOI: 10.3390/plants12162970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.
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Affiliation(s)
| | | | | | - Liqiang He
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou 570228, China
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Li R, Huang Y, Yang X, Su M, Xiong H, Dai Y, Wu W, Pei X, Yuan Q. Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:2876. [PMID: 37571029 PMCID: PMC10421310 DOI: 10.3390/plants12152876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/15/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.
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Affiliation(s)
- Rongju Li
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Yinling Huang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinsen Yang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Meng Su
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Huaiyang Xiong
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Yang Dai
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Wei Wu
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qianhua Yuan
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
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