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Singh D, Chaudhary P, Taunk J, Singh CK, Chinnusamy V, Sevanthi AM, Singh VJ, Pal M. Targeting Induced Local Lesions in Genomes (TILLING): advances and opportunities for fast tracking crop breeding. Crit Rev Biotechnol 2024; 44:817-836. [PMID: 37455414 DOI: 10.1080/07388551.2023.2231630] [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: 02/14/2021] [Accepted: 06/01/2023] [Indexed: 07/18/2023]
Abstract
The intensification of food production via conventional crop breeding alone is inadequate to cater for global hunger. The development of precise and expeditious high throughput reverse genetics approaches has hugely benefited modern plant breeding programs. Targeting Induced Local Lesions in Genomes (TILLING) is one such reverse genetics approach which employs chemical/physical mutagenesis to create new genetic sources and identifies superior/novel alleles. Owing to technical limitations and sectional applicability of the original TILLING protocol, it has been timely modified. Successions include: EcoTILLING, Double stranded EcoTILLING (DEcoTILLING), Self-EcoTILLING, Individualized TILLING (iTILLING), Deletion-TILLING (De-TILLING), PolyTILLING, and VeggieTILLING. This has widened its application to a variety of crops and needs. They can characterize mutations in coding as well as non-coding regions and can overcome complexities associated with the large genomes. Combining next generation sequencing tools with the existing TILLING protocols has enabled screening of huge germplasm collections and mutant populations for the target genes. In silico TILLING platforms have transformed TILLING into an exciting breeding approach. The present review outlines these multifarious TILLING modifications for precise mutation detection and their application in advance breeding programmes together with relevant case studies. Appropriate use of these protocols will open up new avenues for crop improvement in the twenty first century.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Dong W, Li D, Zhang L, Tao P, Zhang Y. Flowering-associated gene expression and metabolic characteristics in adzuki bean ( Vigna angularis L.) with different short-day induction periods. PeerJ 2024; 12:e17716. [PMID: 39035158 PMCID: PMC11260412 DOI: 10.7717/peerj.17716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/18/2024] [Indexed: 07/23/2024] Open
Abstract
Background The adzuki bean is a typical short-day plant and an important grain crop that is widely used due to its high nutritional and medicinal value. The adzuki bean flowering time is affected by multiple environmental factors, particularly the photoperiod. Adjusting the day length can induce flower synchronization in adzuki bean and accelerate the breeding process. In this study, we used RNA sequencing analysis to determine the effects of different day lengths on gene expression and metabolic characteristics related to adzuki bean flowering time. Methods 'Tangshan hong xiao dou' was used as the experimental material in this study and field experiments were conducted in 2022 using a randomized block design with three treatments: short-day induction periods of 5 d (SD-5d), 10 d (SD-10d), and 15 d (SD-15d). Results A total of 5,939 differentially expressed genes (DEGs) were identified, of which 38.09% were up-regulated and 23.81% were down-regulated. Gene ontology enrichment analysis was performed on the target genes to identify common functions related to photosystems I and II. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified two pathways involved in the antenna protein and circadian rhythm. Furthermore, florescence was promoted by down-regulating genes in the circadian rhythm pathway through the blue light metabolic pathway; whereas, antenna proteins promoted flowering by enhancing the reception of light signals and accelerating electron transport. In these two metabolic pathways, the number of DEGs was the greatest between the SD-5d VS SD-15d groups. Real-time reverse transcription‒quantitative polymerase chain reaction analysis results of eight DEGs were consistent with the sequencing results. Thus, the sequencing results were accurate and reliable and eight genes were identified as candidates for the regulation of short-day induction at the adzuki bean seedling stage. Conclusions Short-day induction was able to down-regulate the expression of genes related to flowering according to the circadian rhythm and up-regulate the expression of certain genes in the antenna protein pathway. The results provide a theoretical reference for the molecular mechanism of short-day induction and multi-level information for future functional studies to verify the key genes regulating adzuki bean flowering.
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Affiliation(s)
- Weixin Dong
- College of Agronomy and Medical, Hebei Open University, Shijiazhuang, Hebei, China
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Dongxiao Li
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Lei Zhang
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong, China
| | - Peijun Tao
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Yuechen Zhang
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
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Khalifa AM, Safhi FA, Elsherif DE. Green synthesis of a dual-functional sulfur nanofertilizer to promote growth and enhance salt stress resilience in faba bean. BMC PLANT BIOLOGY 2024; 24:607. [PMID: 38926889 PMCID: PMC11202339 DOI: 10.1186/s12870-024-05270-7] [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: 01/30/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Salinity is a major abiotic stress, and the use of saline water in the agricultural sector will incur greater demand under the current and future climate changing scenarios. The objective of this study was to develop a dual-functional nanofertilizer capable of releasing a micronutrient that nourishes plant growth while enhancing salt stress resilience in faba bean (Vicia faba L.). RESULTS Moringa oleifera leaf extract was used to synthesize sulfur nanoparticles (SNPs), which were applied as a foliar spray at different concentrations (0, 25, 50, and 100 mg/l) to mitigate the negative effects of salt stress (150 mM NaCl) on faba bean plants. The SNPs were characterized and found to be spherical in shape with an average size of 10.98 ± 2.91 nm. The results showed that salt stress had detrimental effects on the growth and photosynthetic performance (Fv/Fm) of faba bean compared with control, while foliar spraying with SNPs improved these parameters under salinity stress. SNPs application also increased the levels of osmolytes (soluble sugars, amino acids, proline, and glycine betaine) and nonenzymatic antioxidants, while reducing the levels of oxidative stress biomarkers (MDA and H2O2). Moreover, SNPs treatment under salinity stress stimulated the activity of antioxidant enzymes (ascorbate peroxidase (APX), and peroxidase (POD), polyphenol oxidase (PPO)) and upregulated the expression of stress-responsive genes: chlorophyll a-b binding protein of LHCII type 1-like (Lhcb1), ribulose bisphosphate carboxylase large chain-like (RbcL), cell wall invertase I (CWINV1), ornithine aminotransferase (OAT), and ethylene-responsive transcription factor 1 (ERF1), with the greatest upregulation observed at 50 mg/l SNPs. CONCLUSION Overall, foliar application of sulfur nanofertilizers in agriculture could improve productivity while minimizing the deleterious effects of salt stress on plants. Therefore, this study provides a strong foundation for future research focused on evaluating the replacement of conventional sulfur-containing fertilizers with their nanoforms to reduce the harmful effects of salinity stress and enhance the productivity of faba beans.
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Affiliation(s)
- Asmaa M Khalifa
- Botany and Microbiology Department, Faculty of Science, Al Azhar University (Girls Branch), Cairo, Egypt
| | - Fatmah A Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Doaa E Elsherif
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
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da Paschoa RP, Pinto VB, Pereira JP, Cavatte PC, Garbin ML, Godinho T, Xavier LR, Carrijo TT, Silveira V. Proteomic and physiological signatures of altitude adaptation in a Myrsine coriacea population under common garden conditions. J Proteomics 2024; 299:105156. [PMID: 38467267 DOI: 10.1016/j.jprot.2024.105156] [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: 12/23/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
Plants exhibit phenotypic plasticity in response to environmental variations, which can lead to stable genetic and physiological adaptations if exposure to specific conditions is prolonged. Myrsine coriacea demonstrates this through its ability to thrive in diverse environments. The objective of the article is to investigate potential differences in protein accumulation and physiological responses of M. coriacea by cultivating plants from seeds collected from four populations at different altitudes in a common garden experiment. Additionally, we aim to evaluate whether these differences exhibit genetic fixation. Through integrated physiological and proteomic analyses, we identified 170 differentially accumulated proteins and observed significant physiological differences among the populations. The high-altitude population (POP1) exhibited a unique proteomic profile with significant down-regulation of proteins involved in carbon fixation and energy metabolism, suggesting a potential reduction in photosynthetic efficiency. Physiological analyses showed lower leaf nitrogen content, net CO2 assimilation rate, specific leaf area, and relative growth rate in stem height for POP1, alongside higher leaf carbon isotopic composition (δ13C) and leaf carbon (C) content. These findings provide insight into the complex interplay between proteomic and physiological adaptations in M. coriacea and underscore the importance of local adaptations. SIGNIFICANCE: We investigate the adaptive responses of M. coriacea, a shrub with a broad phenotypic range, by cultivating plants from seeds collected at four different altitudes in a common garden experiment. These findings provide insight into the complex interplay between proteomic and physiological adaptations in M. coriacea and underscore the importance of local adaptations in the face of climate change. This study contributes to advancing our understanding of the influence of altitude-specific selection pressures on the molecular biology and physiology of plants in natural populations. Our findings provide valuable insights that enhance our ability to predict and comprehend how plants respond to climate change.
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Affiliation(s)
- Roberta Pena da Paschoa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil
| | | | - Jéssica Priscilla Pereira
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Paulo Cezar Cavatte
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Mário Luís Garbin
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Tiago Godinho
- Reserva Natural Vale, Rodovia BR 101, km 122 s/n Zona Rural, Linhares, ES 29900-111, Brazil
| | - Lucas Rodrigues Xavier
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil
| | - Tatiana Tavares Carrijo
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil.
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil.
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Huang X, Gao F, Zhou P, Ma C, Tan W, Ma Y, Li M, Ni Z, Shi T, Hayat F, Li Y, Gao Z. Allelic variation of PmCBF03 contributes to the altitude and temperature adaptability in Japanese apricot (Prunus mume Sieb. et Zucc.). PLANT, CELL & ENVIRONMENT 2024; 47:1379-1396. [PMID: 38221869 DOI: 10.1111/pce.14813] [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: 08/04/2023] [Revised: 12/26/2023] [Accepted: 12/31/2023] [Indexed: 01/16/2024]
Abstract
Japanese apricot is an important subtropical deciduous fruit tree in China, widely distributed in different altitude areas. How does it adapt to the different temperature environments in these areas? In this study, we identified a low-temperature transcription factor PmCBF03 on chromosome 7 through adaptive analysis of populations at different altitudes, which has an early termination single nucleotide polymorphism mutation. There were two different types of variation, PmCBF03A type in high-altitude areas and PmCBF03T type in low-altitude areas. PmCBF03A gene increased the survival rate, Fv/Fm values, antioxidant enzyme activity, and expression levels of antioxidant enzyme genes, and reducing electrolyte leakage and accumulation of reactive oxygen species in transgenic Arabidopsis under low temperature and freezing stress. Simultaneously, PmCBF03A gene promoted the dormancy of transgenic Arabidopsis seeds than wild-type. Biochemical analysis demonstrated that PmCBF03A directly bound to the DRE/CRT element in the promoters of the PmCOR413, PmDAM6 and PmABI5 genes, promoting their transcription and enhanced the cold resistance and dormancy of the overexpressing PmCBF03A lines. While PmCBF03T gene is unable to bind to the promoters of PmDAM6 and PmABI5 genes, leading to early release of dormancy to adapt to the problem of insufficient chilling requirement in low-altitude areas.
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Affiliation(s)
- Xiao Huang
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Feng Gao
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Pengyu Zhou
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chengdong Ma
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Tan
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yufan Ma
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Minglu Li
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhaojun Ni
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ting Shi
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Faisal Hayat
- Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Yongping Li
- Department of Special Fruit Tree Germplasm Resources, Yunnan Green Food Development Center, Kunming, Yunnan, China
| | - Zhihong Gao
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Han X, Han S, Li Y, Li K, Yang L, Ma D, Fang Z, Yin J, Zhu Y, Gong S. Double roles of light-harvesting chlorophyll a/b binding protein TaLhc2 in wheat stress tolerance and photosynthesis. Int J Biol Macromol 2023; 253:127215. [PMID: 37793527 DOI: 10.1016/j.ijbiomac.2023.127215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/23/2023] [Accepted: 10/01/2023] [Indexed: 10/06/2023]
Abstract
Light-harvesting chlorophyll a/b binding proteins are encoded by nucleus genes and widely involve in capturing light energy, transferring energy, and responding to various stresses. However, their roles in wheat photosynthesis and stress tolerance are largely unknown. Here, Triticum aestivumlight-harvesting chlorophyll a/b binding protein TaLhc2 was identified. It showed subcellular localization in chloroplast, contained light responsive cis-elements, and highly expressed in green tissues and down-regulated by multiple stresses. TaLhc2 promoted the colonization of hemi-biotrophic pathogen; further analysis showed that TaLhc2 strengthened BAX-induced cell death, enhanced the ROS accumulation, and up-regulated pathogenesis-related genes; those results suggested that TaLhc2 has adverse influence on host immunity and function as a susceptible gene, thus host decreased its expression when faced with pathogen infection. RT-qPCR results showed that TaLhc2 was down-regulated by drought and salt stresses, while TaLhc2 improved the ROS accumulation under the two stresses, suggesting TaLhc2 may participate in wheat responding to abiotic stress. Additionally, TaLhc2 can increase the content of total chlorophyll and carotenoid by 1.3 % and 2.9 %, increase the net photosynthetic rate by 18 %, thus promote plant photosynthesis. Conclusively, we preliminarily deciphered the function of TaLhc2 in biotic/abiotic stresses and photosynthesis, which laid foundation for its usage in wheat breeding.
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Affiliation(s)
- Xiaowen Han
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Shuo Han
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Yiting Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Keke Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Lijun Yang
- Key Laboratory of Integrated Pest Management of Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds Control, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Dongfang Ma
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Zhengwu Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
| | - Junliang Yin
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Yongxing Zhu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Shuangjun Gong
- Key Laboratory of Integrated Pest Management of Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds Control, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China.
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Li X, Jiang Z, Zhang C, Cai K, Wang H, Pan W, Sun X, Gao Y, Xu K. Comparative genomics analysis provide insights into evolution and stress responses of Lhcb genes in Rosaceae fruit crops. BMC PLANT BIOLOGY 2023; 23:484. [PMID: 37817059 PMCID: PMC10566169 DOI: 10.1186/s12870-023-04438-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023]
Abstract
BACKGROUND Light-harvesting chlorophyll a/b b evelopment of higher plants and in response to abiotic stress. Previous works has demonstrated that that Lhcb genes were involved in the phytochrome regulation and responded to the different light and temperature conditions in Poaceae (such as maize). However, the evolution and functions of Lhcb genes remains poorly characterized in important Rosaceae species. RESULTS In this investigation, we conducted a genome-wide analysis and identified a total of 212 Lhcb genes across nine Rosaceae species. Specifically, we found 23 Lhcb genes in Fragaria vesca, 20 in Prunus armeniaca, 33 in Malus domestica 'Gala', 21 in Prunus persica, 33 in Rosa chinensis, 29 in Pyrus bretschneideri, 18 in Rubus occidentalis, 20 in Prunus mume, and 15 in Prunus salicina. Phylogenetic analysis revealed that the Lhcb gene family could be classified into seven major subfamilies, with members of each subfamily sharing similar conserved motifs. And, the functions of each subfamily was predicted based on the previous reports from other species. The Lhcb proteins were highly conserved within their respective subfamilies, suggesting similar functions. Interestingly, we observed similar peaks in Ks values (0.1-0.2) for Lhcb genes in apple and pear, indicating a recent whole genome duplication event (about 30 to 45 million years ago). Additionally, a few Lhcb genes underwent tandem duplication and were located across all chromosomes of nine species of Rosaceae. Furthermore, the analysis of the cis-acting elements in the 2000 bp promoter region upstream of the pear Lhcb gene revealed four main categories: light response correlation, stress response correlation, hormone response correlation, and plant growth. Quantitative expression analysis demonstrated that Lhcb genes exhibited tissue-specific expression patterns and responded differently to low-temperature stress in Rosaceae species. CONCLUSIONS These findings shed light on the evolution and phylogeny of Lhcb genes in Rosaceae and highlight the critical role of Lhcb in pear's response to low temperatures. The results obtained provide valuable insights for further investigations into the functions of Lhcb genes in Rosaceae, and these functional genes will be used for further fruit tree breeding and improvement to cope with the current climate changes.
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Affiliation(s)
- Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Zeyu Jiang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Chaofan Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kefan Cai
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Hui Wang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Weiyi Pan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xuepeng Sun
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Yongbin Gao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Kai Xu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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Wang L, Wei J, Shi X, Qian W, Mehmood J, Yin Y, Jia H. Identification of the Light-Harvesting Chlorophyll a/b Binding Protein Gene Family in Peach ( Prunus persica L.) and Their Expression under Drought Stress. Genes (Basel) 2023; 14:1475. [PMID: 37510379 PMCID: PMC10378835 DOI: 10.3390/genes14071475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
In higher plants, light-harvesting chlorophyll a/b binding (Lhc) proteins play a vital role in photosynthetic processes and are widely involved in the regulation of plant growth, development, and response to abiotic stress. However, the Lhc gene family has not been well identified in peaches (Prunus persica L.). In this study, 19 PpLhc genes were identified in the peach genome database, which were unevenly distributed on all chromosomes. Phylogenetic analysis demonstrated that PpLhc proteins could be divided into three major subfamilies, each of whose members had different exon-intron structures but shared similar conserved motifs. A total of 17 different kinds of cis-regulatory elements were identified in the promoter regions of all PpLhc genes, which could be classified into three categories: plant growth and development, stress response, and phytohormone response. In addition, transcriptomic data analysis and RT-qPCR results revealed that the expression profiles of some PpLhc genes changed under drought treatment, suggesting the crucial roles of Lhc genes in the regulation of plant tolerance to drought stress. Taken together, these findings will provide valuable information for future functional studies of PpLhc genes, especially in response to drought stress.
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Affiliation(s)
- Li Wang
- Huzhou Academy of Agricultural Sciences, Huzhou 313000, China
| | - Jia Wei
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xingyun Shi
- Huzhou Academy of Agricultural Sciences, Huzhou 313000, China
| | - Weihong Qian
- Huzhou Academy of Agricultural Sciences, Huzhou 313000, China
| | - Jan Mehmood
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yiming Yin
- Huzhou Academy of Agricultural Sciences, Huzhou 313000, China
| | - Huijuan Jia
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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Benton M, Furr M, Govind Kumar V, Polasa A, Gao F, Heyes CD, Suresh Kumar TK, Moradi M. cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach. J Chem Inf Model 2023. [PMID: 37336508 DOI: 10.1021/acs.jcim.3c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. In this study, we explore the structural stability and flexibility of cpSRP43 using a combination of computational and experimental techniques and find that this protein is concurrently highly stable and flexible. In addition to microsecond-level unbiased molecular dynamics (MD), biased MD simulations based on system-specific collective variables are used along with biophysical experimentation to explain the basis of the flexibility and stability of cpSRP43, showing that the free and cpSRP54-bound cpSRP43 has substantially different conformations and conformational dynamics.
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Affiliation(s)
- Mitchell Benton
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Mercede Furr
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Feng Gao
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Colin David Heyes
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | | | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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Chen L, Yang W, Liu S, Meng Y, Zhu Z, Liang R, Cao K, Xie Y, Li X. Genome-wide analysis and identification of light-harvesting chlorophyll a/b binding (LHC) gene family and BSMV-VIGS silencing TaLHC86 reduced salt tolerance in wheat. Int J Biol Macromol 2023; 242:124930. [PMID: 37236564 DOI: 10.1016/j.ijbiomac.2023.124930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/24/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023]
Abstract
The discovery and identification of gene families by using wide-genome and public databases is an effective way to gain initial insight into gene function, which also is one of the current hot spots of research. Chlorophyll ab-binding proteins (LHC) are important for photosynthesis and widely involved in plant adversity stress. However, the study in wheat has not been reported. In this study, we identified 127 TaLHC members from common wheat which were unevenly distributed on all chromosomes except 3B and 3D. All members divided into three subfamilies, LHC a, LHC b and the LHC t which was only discovered in wheat. All of them had maximum expression in leaves and contained multiple light-responsive cis-acting element, which were evidence of the extensive involvement of LHC families in photosynthesis. In addition, we also analyzed their collinear relationship, targeting relationship with miRNA and their responses under different stresses. Based on these analyses, it was found that TaLHC86 was an excellent candidate gene for stress resistance. The full-length ORF of TaLHC86 was 792 bp and was localized on the chloroplasts. The salt tolerance of wheat was reduced when BSMV-VIGS silenced TaLHC86, and the photosynthetic rate and electron transport were also seriously affected. This study made a comprehensive analysis of the TaLHC family and found that TaLHC86 was a good gene for salt tolerance.
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Affiliation(s)
- Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weibing Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shuqing Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhanhua Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiyan Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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11
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Yu X, Wei P, Zhao S, Chen Z, Li X, Zhang W, Liu C, Yang Y, Li X, Liu X. Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau. PLANT CELL REPORTS 2023; 42:879-893. [PMID: 36973418 DOI: 10.1007/s00299-023-03005-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: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Shuqi Zhao
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Zhuyifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xinzhong Li
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Wencai Zhang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Yujiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan, 430072, Hubei, China.
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China.
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12
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Yan S, Gong S, Sun K, Li J, Zhang H, Fan J, Gong Z, Zhang Z, Yan C. Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return. FRONTIERS IN PLANT SCIENCE 2022; 13:997557. [PMID: 36176680 PMCID: PMC9514043 DOI: 10.3389/fpls.2022.997557] [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: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Straw return is crucial for the sustainable development of rice planting, but no consistent results were observed for the effect of straw return on rice growth. To investigate the response of rice leaves to rice straw return in Northeast China, two treatments were set, no straw return (S0) and rice straw return (SR). We analyzed the physiological index of rice leaves and measured differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with the S0 treatment, the SR treatment significantly decreased the dry weight of rice plants and non-structural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves of SR treatment, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs were mainly involved in photosynthesis and oxidative phosphorylation, and DEMs were mainly involved in alpha-linolenic acid metabolism, galactose metabolism, glycerophospholipid metabolism, pentose and gluconic acid metabolism, and other metabolic pathways. Rice straw return promoted the accumulation of scavenging substances of active oxygen and osmotic adjustment substances, such as glutathione, organic acids, amino acids, and other substances. The SR treatment reduced the photosynthetic capacity and energy production of carbon metabolism, inhibiting the growth of rice plants, while the increase of metabolites involved in defense against abiotic stress enhanced the adaptability of rice plants to straw return stress.
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Affiliation(s)
- Shuangshuang Yan
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Shengdan Gong
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Kexin Sun
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jinwang Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongming Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jinsheng Fan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhenping Gong
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhongxue Zhang
- College of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, China
| | - Chao Yan
- College of Agriculture, Northeast Agricultural University, Harbin, China
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13
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Gonin M, Jeong K, Coudert Y, Lavarenne J, Hoang GT, Bes M, To HTM, Thiaw MN, Do TV, Moukouanga D, Guyomarc'h S, Bellande K, Brossier J, Parizot B, Nguyen HT, Beeckman T, Bergougnoux V, Rouster J, Sallaud C, Laplaze L, Champion A, Gantet P. CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:546-566. [PMID: 35596715 PMCID: PMC9542200 DOI: 10.1111/tpj.15838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
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Affiliation(s)
- Mathieu Gonin
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kwanho Jeong
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyon69007France
| | - Jeremy Lavarenne
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Martine Bes
- CIRAD, UMR AGAPF‐34398MontpellierFrance
- UMR AGAPUniversité de Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, LMIRICE2Vietnam Academy of Science and Technology11300HanoiVietnam
| | - Marie‐Rose Ndella Thiaw
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Toan Van Do
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Daniel Moukouanga
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Soazig Guyomarc'h
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kevin Bellande
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Jean‐Rémy Brossier
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Boris Parizot
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Hieu Trang Nguyen
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Tom Beeckman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Jacques Rouster
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Christophe Sallaud
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Laurent Laplaze
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Antony Champion
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Pascal Gantet
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
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14
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Dong W, Li D, Zhang L, Yin B, Zhang Y. Transcriptome Analysis of Short-Day Photoperiod Inducement in Adzuki Bean ( Vigna angularis L.) Based on RNA-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:893245. [PMID: 35845693 PMCID: PMC9280645 DOI: 10.3389/fpls.2022.893245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
The flowering characteristics of adzuki bean are influenced by several environmental factors. Light is an important ecological factor that induces flowering in adzuki bean, but to date, there have been few reports on the transcriptomic features of photoperiodic regulation of adzuki bean flowering. This study is based on RNA sequencing (RNA-seq) techniques to elucidate the expression of light-related regulatory genes under short-day photoperiod inducement of adzuki bean flowering, providing an important theoretical basis for its accelerated breeding. Short-day photoperiod inducement of 10 h was conducted for 5 day, 10 day, and 15 day periods on "Tang shan hong xiao dou" varieties, which are more sensitive to short-day photoperiod conditions than the other varieties. Plants grown under natural light (14.5 h) for 5 days, 10 days, and 15 days were used as controls to compare the progress of flower bud differentiation and flowering characteristics. The topmost unfolded functional leaves were selected for transcriptome sequencing and bioinformatics analysis. The short-day photoperiod inducement promoted flower bud differentiation and advanced flowering time in adzuki bean. Transcriptomic analysis revealed 5,608 differentially expressed genes (DEGs) for the combination of CK-5d vs. SD-5d, CK-10d vs. SD-10d, and CK-15d vs. SD-15d. The three groups of the DEGs were analyzed using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genomes and Genomes (KEGG) databases; the DEGs were associated with flowering, photosystem, and the circadian rhythm and were mainly concentrated in the hormone signaling and metabolism, circadian rhythm, and antenna protein pathways; So, 13 light-related genes across the three pathways were screened for differential and expression characteristics. Through the functional annotations of orthologs, these genes were related to flowering, which were supposed to be good candidate genes in adzuki bean. The findings provide a deep understanding of the molecular mechanisms of adzuki bean flowering in response to short-day photoperiod inducement, which laid a foundation for the functional verification of genes in the next step, and provide an important reference for the molecular breeding of adzuki bean.
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Affiliation(s)
- Weixin Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
- Hebei Open University, Shijiazhuang, China
| | - Dongxiao Li
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Lei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Baozhong Yin
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yuechen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
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15
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Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
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16
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Feng Y, Zhao Y, Li Y, Zhou J, Li Y, Shi H. Physiological and transcriptome analysis reveals the differences in nitrate content between lamina and midrib of flue-cured tobacco. Sci Rep 2022; 12:2932. [PMID: 35190651 PMCID: PMC8861034 DOI: 10.1038/s41598-022-07011-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 02/07/2022] [Indexed: 11/09/2022] Open
Abstract
Nitrate is an important precursor of tobacco-specific nitrosamines (TSNAs) and a remarkable difference in nitrate accumulation between lamina and midrib of flue-cured tobacco has long been observed. However, the physiological and molecular mechanisms underpinning this difference remain poorly understood. In this study, physiological and genetic factors impacting nitrate accumulation were identified in pot experiments using flue-cured tobacco K326 with contrasting nitrate content between lamina and midrib. The results showed that three times higher NO3-N content was observed in midrib than that in the lamina, along with lower pigment, NH4-N content, nitrate reductase activity (NRA), sucrose synthetase activity (SSA), and glutamine synthetase activity (GSA) in midrib. Transcriptome analysis revealed that expression of genes involved in porphyrin and chlorophyll metabolism, carotenoid biosynthesis, photosynthesis-antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, starch and sucrose metabolism, nitrogen metabolism, and biosynthesis of amino acids were significantly lower in midrib than in lamina. qRT-PCR results showed that the expression level of nitrate transporter genes LOC107782967, LOC107806749, LOC107775674, LOC107829632, LOC107799198, LOC107768465 decreased by 2.74, 1.81, 49.5, 3.5, 2.64 and 2.96-folds while LOC107789301 increased by 8.23-folds in midrib but not in lamina. Reduced chlorophyll content might result in low carbohydrate formation which is the source of energy and carbon skeleton supply, then the low capacity of nitrogen reduction, assimilation and transportation, and the poor ability of nitrate reallocation but the high capacity of accumulation might lead to nitrate accumulation in midrib. The results laid the foundation for reducing nitrate content and TSNA formation in tobacco midribs and their products.
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Affiliation(s)
- Yuqing Feng
- National Tobacco Cultivation & Physiology & Biochemistry Research Center, Tobacco Harm Reduction Research Center of China Tobacco, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuanyuan Zhao
- National Tobacco Cultivation & Physiology & Biochemistry Research Center, Tobacco Harm Reduction Research Center of China Tobacco, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yafei Li
- National Tobacco Cultivation & Physiology & Biochemistry Research Center, Tobacco Harm Reduction Research Center of China Tobacco, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Zhou
- Beijing Cigarette Factory, Shanghai Tobacco Group Co., Ltd., Beijing, 100024, China
| | - Yujing Li
- National Tobacco Cultivation & Physiology & Biochemistry Research Center, Tobacco Harm Reduction Research Center of China Tobacco, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongzhi Shi
- National Tobacco Cultivation & Physiology & Biochemistry Research Center, Tobacco Harm Reduction Research Center of China Tobacco, Henan Agricultural University, Zhengzhou, 450002, China.
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17
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Ma C, Rehman A, Li HG, Zhao ZB, Sun G, Du XM. Mapping of dwarfing QTL of Ari1327, a semi-dwarf mutant of upland cotton. BMC PLANT BIOLOGY 2022; 22:5. [PMID: 34979924 PMCID: PMC8722190 DOI: 10.1186/s12870-021-03359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Upland Cotton (Gossypium hirsutum L.) has few cotton varieties suitable for mechanical harvesting. The plant height of the cultivar is one of the key features that need to modify. Hence, this study was planned to locate the QTL for plant height in a 60Co γ treated upland cotton semi-dwarf mutant Ari1327. RESULTS Interestingly, bulk segregant analysis (BSA) and genotyping by sequencing (GBS) methods exhibited that candidate QTL was co-located in the region of 5.80-9.66 Mb at D01 chromosome in two F2 populations. Using three InDel markers to genotype a population of 1241 individuals confirmed that the offspring's phenotype is consistent with the genotype. Comparative analysis of RNA-seq between the mutant and wild variety exhibited that Gh_D01G0592 was identified as the source of dwarfness from 200 genes. In addition, it was also revealed that the appropriate use of partial separation markers in QTL mapping can escalate linkage information. CONCLUSIONS Overwhelmingly, the results will provide the basis to reveal the function of candidate genes and the utilization of excellent dwarf genetic resources in the future.
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Affiliation(s)
- Chenhui Ma
- State Key Laboratory of cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 66000, Pakistan
| | - Hong Ge Li
- State Key Laboratory of cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zi Bo Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Gaofei Sun
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Anyang, China
| | - Xiong Ming Du
- State Key Laboratory of cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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18
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Quero G, Bonnecarrère V, Simondi S, Santos J, Fernández S, Gutierrez L, Garaycochea S, Borsani O. Genetic architecture of photosynthesis energy partitioning as revealed by a genome-wide association approach. PHOTOSYNTHESIS RESEARCH 2021; 150:97-115. [PMID: 32072456 DOI: 10.1007/s11120-020-00721-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The photosynthesis process is determined by the intensity level and spectral quality of the light; therefore, leaves need to adapt to a changing environment. The incident energy absorbed can exceed the sink capability of the photosystems, and, in this context, photoinhibition may occur in both photosystem II (PSII) and photosystem I (PSI). Quantum yield parameters analyses reveal how the energy is managed. These parameters are genotype-dependent, and this genotypic variability is a good opportunity to apply mapping association strategies to identify genomic regions associated with photosynthesis energy partitioning. An experimental and mathematical approach is proposed for the determination of an index which estimates the energy per photon flux for each spectral bandwidth (Δλ) of the light incident (QI index). Based on the QI, the spectral quality of the plant growth, environmental lighting, and the actinic light of PAM were quantitatively very similar which allowed an accurate phenotyping strategy of a rice population. A total of 143 genomic single regions associated with at least one trait of chlorophyll fluorescence were identified. Moreover, chromosome 5 gathers most of these regions indicating the importance of this chromosome in the genetic regulation of the photochemistry process. Through a GWAS strategy, 32 genes of rice genome associated with the main parameters of the photochemistry process of photosynthesis in rice were identified. Association between light-harvesting complexes and the potential quantum yield of PSII, as well as the relationship between coding regions for PSI-linked proteins in energy distribution during the photochemical process of photosynthesis is analyzed.
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Affiliation(s)
- Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay.
| | - Victoria Bonnecarrère
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Sebastián Simondi
- Área de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Jorge Santos
- Área de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Sebastián Fernández
- Facultad de Ingeniería, Instituto de Ingeniería Eléctrica, Universidad de La República, Julio Herrera y Reissig 565, Montevideo, Uruguay
| | - Lucía Gutierrez
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr., Madison, WI, 53706, USA
- Departamento de Biometría, Estadística y Cómputos, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, Uruguay
| | - Silvia Garaycochea
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Omar Borsani
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay
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19
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Chen P, Liu P, Zhang Q, Bu C, Lu C, Srivastava S, Zhang D, Song Y. Gene Coexpression Network Analysis Indicates that Hub Genes Related to Photosynthesis and Starch Synthesis Modulate Salt Stress Tolerance in Ulmus pumila. Int J Mol Sci 2021; 22:4410. [PMID: 33922506 PMCID: PMC8122946 DOI: 10.3390/ijms22094410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 01/20/2023] Open
Abstract
Ulmus pumila L. is an excellent afforestation and biofuel tree that produces high-quality wood, rich in starch. In addition, U. pumila is highly adaptable to adverse environmental conditions, which is conducive to its utilization for vegetating saline soils. However, little is known about the physiological responses and transcriptional regulatory network of U. pumila under salt stress. In this study, we exposed five main cultivars in saline-alkali land (Upu2, 5, 8, 11, and 12) to NaCl stress. Of the five cultivars assessed, Upu11 exhibited the highest salt resistance. Growth and biomass accumulation in Upu11 were promoted under low salt concentrations (<150 mM). However, after 3 months of continuous treatment with 150 mM NaCl, growth was inhibited, and photosynthesis declined. A transcriptome analysis conducted after 3 months of treatment detected 7009 differentially expressed unigenes (DEGs). The gene annotation indicated that these DEGs were mainly related to photosynthesis and carbon metabolism. Furthermore, PHOTOSYNTHETIC ELECTRON TRANSFERH (UpPETH), an important electron transporter in the photosynthetic electron transport chain, and UpWAXY, a key gene controlling amylose synthesis in the starch synthesis pathway, were identified as hub genes in the gene coexpression network. We identified 25 and 62 unigenes that may interact with PETH and WAXY, respectively. Overexpression of UpPETH and UpWAXY significantly increased the survival rates, net photosynthetic rates, biomass, and starch content of transgenic Arabidopsis plants under salt stress. Our findings clarify the physiological and transcriptional regulators that promote or inhibit growth under environmental stress. The identification of salt-responsive hub genes directly responsible for photosynthesis and starch synthesis or metabolism will provide targets for future genetic improvements.
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Affiliation(s)
- Panfei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (P.C.); (P.L.); (C.B.); (C.L.); (S.S.); (D.Z.)
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Peng Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (P.C.); (P.L.); (C.B.); (C.L.); (S.S.); (D.Z.)
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Quanfeng Zhang
- Hebei Academy of Forestry and Grassland Sicences, No. 75, Xuefu Road, Shijiazhuang 050061, China;
| | - Chenhao Bu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (P.C.); (P.L.); (C.B.); (C.L.); (S.S.); (D.Z.)
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Chunhao Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (P.C.); (P.L.); (C.B.); (C.L.); (S.S.); (D.Z.)
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Sudhakar Srivastava
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (P.C.); (P.L.); (C.B.); (C.L.); (S.S.); (D.Z.)
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (P.C.); (P.L.); (C.B.); (C.L.); (S.S.); (D.Z.)
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Yuepeng Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (P.C.); (P.L.); (C.B.); (C.L.); (S.S.); (D.Z.)
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
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20
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Jin H, Yu X, Yang Q, Fu X, Yuan F. Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants. Sci Rep 2021; 11:8740. [PMID: 33888781 PMCID: PMC8062490 DOI: 10.1038/s41598-021-88055-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Phytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3-InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.
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Affiliation(s)
- Hangxia Jin
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaomin Yu
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Qinghua Yang
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xujun Fu
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Fengjie Yuan
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
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21
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Zhao S, Gao H, Luo J, Wang H, Dong Q, Wang Y, Yang K, Mao K, Ma F. Genome-wide analysis of the light-harvesting chlorophyll a/b-binding gene family in apple (Malus domestica) and functional characterization of MdLhcb4.3, which confers tolerance to drought and osmotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:517-529. [PMID: 32688296 DOI: 10.1016/j.plaphy.2020.06.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 05/27/2023]
Abstract
In higher plants, the light-harvesting chlorophyll a/b-binding (Lhc) proteins function in multiple processes that are critical to plant growth, development, and abiotic stress response. However, the Lhc gene family has not been well characterized in the important fruit crop, apple (Malus × domestica Borkh.). In this study, we identified 27 Lhc genes in the apple genome. Phylogenetic analysis showed that the Lhc gene family could be classified into three major subfamilies, each of whose members shared similar conserved motifs. Evolutionary analysis indicated that duplicated MdLhc genes were primarily under purifying selection. MdLhcs were expressed at varying levels in all tissues examined and showed different expression patterns under drought stress. The overexpression of MdLhcb4.3 in transgenic Arabidopsis and apple callus enhanced their tolerance to drought and osmotic stress. Taken together, these results demonstrate the important role of Lhc proteins in the regulation of plant resistance to drought and osmotic stress and provide valuable information for further study of Lhc functions in apple.
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Affiliation(s)
- Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
| | - Hanbing Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
| | - Jiawei Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
| | - Haibo Wang
- Shandong Institute of Pomology, Tai'an, 271000, China.
| | - Qinglong Dong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
| | - Yanpeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
| | - Kaiyan Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
| | - Ke Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
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22
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Liu X, Li L, Zhang B, Zeng L, Li L. AhHDA1-mediated AhGLK1 promoted chlorophyll synthesis and photosynthesis regulates recovery growth of peanut leaves after water stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110461. [PMID: 32234234 DOI: 10.1016/j.plantsci.2020.110461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/04/2020] [Accepted: 02/24/2020] [Indexed: 06/11/2023]
Abstract
Peanut (Arachis hypogaea L.) is an important crop that is adversely affected by drought. Post-drought growth is essential for improving peanut productivity and quality. Previous studies demonstrated that AhGLK1 (Arachis hypogaea L. Golden2-like 1) activates the expression of AhPORA to stimulate chlorophyll biosynthesis, and that AhGLK1 physically interacts with AhHDA1 (Arachis hypogaea L. histone deacetylase 1). However, the roles of the AhGLK1/AhHDA1 interaction in post-drought recovery remain to be elucidated. Herein, we report that AhHDA1 binds to AhGLK1 promoter and alters histone deacetylation levels to inhibit AhGLK1 expression. RNA-seq confirms that chlorophyll synthesis and photosynthesis-related genes are induced in AhGLK1-overexpressing, but reduced in AhGLK1 RNAi hairy roots. Furthermore, ChIP-seq shows that AhCAB (Arachis hypogaea L. chlorophyll A/B binding protein) is a target of both AhHDA1 and AhGLK1. Transactivation assays reveal that AhGLK1 activates AhCAB expression, while AhHDA1 inhibits the effect of AhGLK1 on AhCAB and AhPORA transcription. ChIP-qPCR shows that AhHDA1 and AhGLK1 bind to the promoters of AhCAB and AhPORA to regulate their expression during water stress and recovery. We propose that AhHDA1 and AhGLK1 consist of an ON/OFF switch for AhCAB and AhPORA expression during water stress and recovery. AhGLK1 activates, whereas AhHDA1 suppresses the expression of AhCAB and AhPORA.
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Affiliation(s)
- Xing Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China; Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Limei Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Baihong Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Lidan Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ling Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.
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23
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Cloning and characterization of two chlorophyll A/B binding protein genes and analysis of their gene family in Camellia sinensis. Sci Rep 2020; 10:4602. [PMID: 32165676 PMCID: PMC7067855 DOI: 10.1038/s41598-020-61317-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/21/2020] [Indexed: 12/16/2022] Open
Abstract
In this study, two chlorophyll A/B binding protein (CAB) genes (CsCP1 and CsCP2) in tea plant were cloned. The proteins encoded by these genes belong to the external or internal antenna proteins of PS II, respectively. They may be the targets of physiological regulation for tea leaf cell PS II because they all contain multiple functional domains and modifiable sites. The CAB gene family in the tea genome consists of 25 homologous genes. We measured the expression patterns of ten genes in the CsCP1 and CsCP2 subfamily under six different stresses. CsCP1 expression was inhibited in response to 6 kinds of stress; CsCP2 expression was slightly upregulated only after cold stress and ABA treatment. However, the expression levels of CSA016997 and CSA030476 were upregulated significantly in the six stresses. The results suggested that the 10 CAB genes may have different functions in tea leaves. Moreover, changes in the expression of the 10 genes under stress appear to be related to ABA- and MeJA-dependent signalling pathways, and their responses to MeJA treatment is faster than those to ABA. In addition, we introduced our experiences for cloning the genes in the context of complex genomes.
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24
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Wang MQ, Zeng QH, Huang QX, Lin P, Li Y, Liu QL, Zhang L. Transcriptomic Analysis of Verbena bonariensis Leaves Under Low-Temperature Stress. DNA Cell Biol 2019; 38:1233-1248. [PMID: 31532241 DOI: 10.1089/dna.2019.4707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Verbena bonariensis is a valuable plant for both ornament and flower border. As a major constraint, low temperature affects the growing development and survival of V. bonariensis. However, there are few systematic studies in terms of molecular mechanism on the tolerance of low temperature in V. bonariensis. In this study, Illumina sequencing technology was applied to analyze the cold resistance mechanism of plants. Six cDNA libraries were obtained from two samples of two groups, the cold-treated group and the control group. A total of 271,920 unigenes were produced from 406,641 assembled transcripts. Among these, 19,003 differentially expressed genes (DEGs) (corrected p-value <0.01, |log2(fold change) | >3) were obtained, including 9852 upregulated and 9151 downregulated genes. The antioxidant enzyme system, photosynthesis, plant hormone signal transduction, fatty acid metabolism, starch and sucrose metabolism pathway, and transcription factors were analyzed. Based on these results, series of candidate genes related to cold stress were screened out and discussed. The physiological indexes related to response mechanism of low temperature were tested. Eleven upregulated DEGs were validated by Quantitative Real-time PCR. In this study, we provided the transcriptome sequence resource of V. bonariensis and used these data to realize its molecular mechanism under cold stress. The results contributed to valuable clues for genetic studies and helped to screen candidate genes for cold-resistance breeding.
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Affiliation(s)
- Meng-Qi Wang
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qin-Han Zeng
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qiu-Xiang Huang
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ping Lin
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, China
| | - Qing-Lin Liu
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, Chengdu, China
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Irshad A, Guo H, Zhang S, Gu J, Zhao L, Xie Y, Xiong H, Zhao S, Ding Y, Ma Y, Liu L. EcoTILLING Reveals Natural Allelic Variations in Starch Synthesis Key Gene TaSSIV and Its Haplotypes Associated with Higher Thousand Grain Weight. Genes (Basel) 2019; 10:genes10040307. [PMID: 31003564 PMCID: PMC6523294 DOI: 10.3390/genes10040307] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 01/18/2023] Open
Abstract
Wheat is a staple food commodity grown worldwide, and wheat starch is a valuable source of energy and carbon that constitutes 80% of the grain weight. Manipulation of genes involved in starch synthesis significantly affects wheat grain weight and yield. TaSSIV plays an important role in starch synthesis and its main function is granule formation. To mine and stack more favorable alleles, single nucleotide polymorphisms (SNPs) of TaSSIV-A, B, and D were investigated across 362 wheat accessions by Ecotype-Targeting Induced Local Lesions IN Genome (EcoTILLING). As a result, a total of 38 SNPs in the amplified regions of three TaSSIV genes were identified, of which 10, 15, and 13 were in TaSSIV-A, B, and D, respectively. These 38 SNPs were evaluated by using KASP and six SNPs showed an allele frequency >5% whereas the rest were <5%, i.e., considered to be minor alleles. In the Chinese mini core collection, three haplotypes were detected for TaSSIV–A and three for TaSSIV–B. The results of an association study in the Chinese mini core collection with thousand grain weight (TGW) and spike length (SPL) showed that Hap-2-1A was significantly associated with TGW and Hap-3-1B with SPL. Allelic frequency and geographic distribution indicated that the favored haplotype (Hap-2-1A) has been positively selected in Chinese wheat breeding. These results suggested that the Kompetitive Allele Specific PCR (KASP) markers can be applied in starch improvement to ultimately improve wheat yield by marker assisted selection in wheat breeding.
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Affiliation(s)
- Ahsan Irshad
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Shunlin Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Yuping Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
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26
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Diurnal biomarkers reveal key photosynthetic genes associated with increased oil palm yield. PLoS One 2019; 14:e0213591. [PMID: 30856213 PMCID: PMC6411157 DOI: 10.1371/journal.pone.0213591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/25/2019] [Indexed: 01/07/2023] Open
Abstract
To investigate limiters of photosynthate assimilation in the carbon-source limited crop, oil palm (Elaeis guineensis Jacq.), we measured differential metabolite, gene expression and the gas exchange in leaves in an open field for palms with distinct mesocarp oil content. We observed higher concentrations of glucose 1-phosphate, glucose 6-phosphate, sucrose 6-phosphate, and sucrose in high-oil content palms with the greatest difference being at 11:00 (p-value ≤0.05) immediately after the period of low morning light intensity. Three important photosynthetic genes were identified using differentially expressed gene analysis (DEGs) and were found to be significantly enriched through Gene Ontology (GO) and pathway enrichment: chlorophyll a-b binding protein (CAB-13), photosystem I (PSI), and Ferredoxin-NADP reductase (FNR), particularly for sampling points at non-peak light (11:00 and 19:00), ranging from 3.3-fold (PSI) and 5.6-fold (FNR) to 10.3-fold (CAB-13). Subsequent gas exchange measurements further supported increased carbon assimilation through higher level of internal CO2 concentration (Ci), stomatal conductance (gs) and transpiration rate (E) in high-oil content palms. The selection for higher expression of key photosynthesis genes together with CO2 assimilation under low light is likely to be important for crop improvement, in particular at full maturity and under high density planting regimes where light competition exists between palms.
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Basu U, Bajaj D, Sharma A, Malik N, Daware A, Narnoliya L, Thakro V, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK. Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea. PLANT, CELL & ENVIRONMENT 2019; 42:158-173. [PMID: 29676051 DOI: 10.1111/pce.13319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, quantitative trait loci (QTL) mapping, and expression profiling. This identified 16 potential single nucleotide polymorphism loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association and in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding (CAB) protein-coding gene and its interacting gene, Timing of CAB Expression 1 (TOC1), which appear to be most promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.
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Affiliation(s)
- Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akash Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajendra Kumar
- U.P. Council of Agricultural Research, Gomati Nagar, Lucknow, 226010, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Ranwez V, Serra A, Pot D, Chantret N. Domestication reduces alternative splicing expression variations in sorghum. PLoS One 2017; 12:e0183454. [PMID: 28886042 PMCID: PMC5590825 DOI: 10.1371/journal.pone.0183454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/06/2017] [Indexed: 01/09/2023] Open
Abstract
Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
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Affiliation(s)
| | - Audrey Serra
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
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Genetic variations of HvP5CS1 and their association with drought tolerance related traits in barley (Hordeum vulgare L.). Sci Rep 2017; 7:7870. [PMID: 28801593 PMCID: PMC5554244 DOI: 10.1038/s41598-017-08393-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/10/2017] [Indexed: 11/21/2022] Open
Abstract
Delta-1-pyrroline-5-carboxylate synthase gene1 (P5CS1) is the key gene involved in the biosynthesis of proline and is significantly induced by drought stress. The exploration of genetic variation in HvP5CS1 may facilitate a better understanding of the mechanism of drought adaptation in barley. In the current study, 41 polymorphisms including 16 single nucleotide polymorphisms (SNPs) and 25 insertions/deletions (indels) were detected in HvP5CS1 among 287 barley (Hordeum vulgare L.) accessions collected worldwide, with 13 distinct haplotypes identified in the barley collection. Five polymorphisms in HvP5CS1 were significantly (P < 0.001) associated with drought tolerance related traits in barley. The phenotypic variation of a given trait explained by each associated polymorphism ranged from 4.43% to 9.81%. Two sequence variations that were significantly (P < 0.0001) associated with grain yield had marginally significant positive Tajima’s D values in the sliding window, so they might have been selected for environmental adaptation. Meanwhile, two haplotypes HvP5CS1_H1 and HvP5CS1_H4, which contained desired alleles of the two variations mentioned above, were significantly (P < 0.001) associated with drought tolerance related traits, and explained 5.00~11.89% of the phenotypic variations. These variations associated with drought tolerance related traits can be used as potential markers for improving drought tolerance in barley.
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Chanroj V, Rattanawong R, Phumichai T, Tangphatsornruang S, Ukoskit K. Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone. Genomics 2017; 109:475-484. [PMID: 28751185 DOI: 10.1016/j.ygeno.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/07/2017] [Accepted: 07/21/2017] [Indexed: 12/29/2022]
Abstract
Latex yield and growth are the key complex traits in commercial rubber production. The present study is the first to report genome-wide association mapping of latex yield and girth, for 170 Amazonian accessions grown in a suboptimal area characterized by limited rainfall and a lengthy dry season. Targeted sequence enrichment to capture gene transcripts generated 14,155 high quality filtered single nucleotide polymorphisms (SNPs) of which 94.3% resided in coding regions. The rapid decay of linkage disequilibrium over physical and genetic distance found in the accessions was comparable to those previously reported for several outcrossing species. A mixed linear model detected three significant SNPs in three candidate genes involved in plant adaptation to drought stress, individually explaining 12.7-15.7% of the phenotypic variance. The SNPs identified in the study will help to extend understanding, and to support genetic improvement of rubber trees grown in drought-affected regions.
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Affiliation(s)
- Vipavee Chanroj
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Ratchanee Rattanawong
- Nong Khai Rubber Research Center, Rubber Research Institute of Thailand, Rattanawapi District, Nong Khai, 43120, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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Zeng YD, Sun JL, Bu SH, Deng KS, Tao T, Zhang YM, Zhang TZ, Du XM, Zhou BL. EcoTILLING revealed SNPs in GhSus genes that are associated with fiber- and seed-related traits in upland cotton. Sci Rep 2016; 6:29250. [PMID: 27385639 PMCID: PMC4935865 DOI: 10.1038/srep29250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/14/2016] [Indexed: 12/16/2022] Open
Abstract
Cotton is the most important textile crop in the world due to its cellulose-enriched fibers. Sucrose synthase genes (Sus) play pivotal roles in cotton fiber and seed development. To mine and pyramid more favorable alleles for cotton molecular breeding, single nucleotide polymorphisms (SNPs) of GhSus family genes were investigated across 277 upland cotton accessions by EcoTILLING. As a result, a total of 24 SNPs in the amplified regions of eight GhSus genes were identified. These SNPs were significantly associated with at least one fiber- or seed-related trait measured in Nanjing, Anyang and Kuche in 2007-2009. Four main-effect quantitative trait nucleotides (QTNs) and five epistatic QTNs, with 0.76-3.56% of phenotypic variances explained by each QTN (PVE), were found to be associated with yield-related traits; six epistatic QTNs, with the 0.43-3.48% PVE, were found to be associated with fiber quality-related traits; and one main-effect QTN and one epistatic QTN, with the PVE of 1.96% and 2.53%, were found to be associated with seed oil content and protein content, respectively. Therefore, this study provides new information for molecular breeding in cotton.
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Affiliation(s)
- Yan-Da Zeng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun-Ling Sun
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Su-Hong Bu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kang-Sheng Deng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Tao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan-Ming Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian-Zhen Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiong-Ming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Bao-Liang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Bajaj D, Srivastava R, Nath M, Tripathi S, Bharadwaj C, Upadhyaya HD, Tyagi AK, Parida SK. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:450. [PMID: 27148286 PMCID: PMC4835497 DOI: 10.3389/fpls.2016.00450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/22/2016] [Indexed: 05/22/2023]
Abstract
The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.
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Affiliation(s)
- Deepak Bajaj
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Rishi Srivastava
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Manoj Nath
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Akhilesh K. Tyagi
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
| | - Swarup K. Parida
- Govt. of India, Plant Genomics and Molecular Breeding Lab, Department of Biotechnology, National Institute of Plant Genome ResearchNew Delhi, India
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Zhou Q, Sun W, Lai Z. Differential expression of genes in purple-shoot tea tender leaves and mature leaves during leaf growth. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:1982-9. [PMID: 26084622 DOI: 10.1002/jsfa.7308] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 05/28/2015] [Accepted: 06/13/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND Tea (Camellia sinensis L.), contains high levels of secondary metabolic products with both commercial and medicinal value. At present, most cultivated tea plant have green leaves; although tea plants with purple leaves exist, their supply is inadequate. During leaf growth and maturation, the content of secondary metabolic compounds decreases, resulting in higher content in tender purple leaves (TPL), and lower content in mature green leaves (MGL). The aim of this study was to analyze the differential expression of genes in these two tissues, with a cDNA-AFLP (amplified fragment length polymorphism) approach and biochemical analysis. RESULTS Compared to MGL samples, TPL samples had higher content of anthocyanin, total polyphenols and total catechins, a higher carotenoid-to-chlorophyll ratio and lower content of soluble sugars (glucose, fructose and sucrose). TPL samples showed a lower photosynthetic ability, demonstrated by a lower CO2 assimilation and carbohydrate accumulation rate. Using cDNA-AFLP with 256 primer combinations, differential transcript profiling generated 148 matched transcript-derived fragments (TDFs). Among these TDFs, 77 genes were upregulated and 71 were downregulated. These were grouped into 11 functional categories which are important for final tea quality parameters. CONCLUSIONS Our data presented the first effort to elucidate the molecular basis of differential accumulation of key metabolites during tea leaf maturation. Our findings also provided a theoretical molecular explanation for the color change during leaf growth.
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Affiliation(s)
- Qiongqiong Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Weijiang Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Han P, Lu X, Mi F, Dong J, Xue C, Li J, Han B, Zhang X. Proteomic analysis of heterosis in the leaves of sorghum-sudangrass hybrids. Acta Biochim Biophys Sin (Shanghai) 2016; 48:161-73. [PMID: 26792642 DOI: 10.1093/abbs/gmv126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/08/2015] [Indexed: 01/15/2023] Open
Abstract
Sorghum-sudangrass hybrids are widely used for forage and silage in the animal husbandry industry due to their hardiness. The heterozygous first generation of sorghum-sudangrass hybrids displays performance superior to their homozygous, parental inbred lines. In order to study the molecular details underlying its heterosis, the leaves of sorghum-sudangrass hybrids and their parents were compared using mass spectrometry-based proteomics. Results showed that among the 996 proteins that were identified, 32 proteins showed 'additive accumulation expression patterns', indicating that the protein abundance in sorghum-sudangrass hybrids showed no significant difference from the average of their parents. Additionally, 74 proteins showed 'nonadditive accumulation expression patterns' (the proteins abundance in the hybrids showed significant difference from the average of their parents). Both additive and nonadditive proteins were mainly involved in photosynthesis and carbohydrate metabolism. More upregulated additive and nonadditive proteins were in the hybrids than in their parents, suggesting that additive and nonadditive proteins are essential to the vigor of sorghum-sudangrass hybrids. The nonadditive proteins were enriched in photosynthesis, carbohydrate metabolism, and protein oligomerization, but the additive proteins were not enriched in any pathway, which indicated that the nonadditive proteins could be greater contributors to heterosis than additive proteins. Furthermore, the highly activated photosynthetic pathway in nonadditive proteins implies that photosynthesis in hybrids is heightened to assimilate more organic matter, resulting in an increased yield. Our results provide a proof-of-concept that reveals the molecular components of heterosis in sorghum-sudangrass hybrid leaves and serves as an important step for future genetic manipulation of specific proteins to improve the performance of hybrids.
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Affiliation(s)
- Pingan Han
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Xiaoping Lu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Fugui Mi
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Jing Dong
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Chunlei Xue
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Jianke Li
- Chinese Academy of Agricultural Science, Institute of Apicultural Research, Beijing 100093, China
| | - Bin Han
- Chinese Academy of Agricultural Science, Institute of Apicultural Research, Beijing 100093, China
| | - Xiaoyu Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
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Li Y, Xu H, Han F, Mu J, Chen D, Feng B, Zeng H. Regulation of lipid metabolism in the green microalga Chlorella protothecoides by heterotrophy-photoinduction cultivation regime. BIORESOURCE TECHNOLOGY 2015; 192:781-91. [PMID: 25127016 DOI: 10.1016/j.biortech.2014.07.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 07/01/2014] [Accepted: 07/04/2014] [Indexed: 05/09/2023]
Abstract
Proteomics in conjunction with biochemical strategy was employed to unravel regulation of lipid metabolism in the green microalga Chlorella protothecoides by heterotrophy-photoinduction cultivation regime (HPC). Interestingly, HPC triggered transiently synthesis of starch followed by substantial lipid accumulation. And a marked decrease in intracellular protein and chlorophyll contents was also observed after 12h of photo-induction. The highest lipid content of 50.5% was achieved upon the photo-induction stage, which represented 69.3% higher than that of the end of heterotrophic cultivation. Results suggested that turnover of carbon-nitrogen-rich compounds such as starch, protein, and chlorophyll might provide carbon or energy for lipid accumulation. The proteomics analysis indicated that several pathways including glycolysis, TCA cycle, β-oxidation of fatty acids, Calvin cycle, photosynthesis, energy and transport, protein biosynthesis, regulate and defense were involved in the lipid biosynthesis. Malate dehydrogenase and acyl-CoA dehydrogenase were suggested as key regulatory factors in enhancing lipid accumulation.
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Affiliation(s)
- Yuqin Li
- School of Chemical Engineering, Xiangtan University, Xiangtan, China.
| | - Hua Xu
- School of Chemical Engineering, Xiangtan University, Xiangtan, China
| | - Fangxin Han
- School of Chemical Engineering, Xiangtan University, Xiangtan, China
| | - Jinxiu Mu
- School of Chemical Engineering, Xiangtan University, Xiangtan, China
| | - Di Chen
- School of Chemical Engineering, Xiangtan University, Xiangtan, China
| | - Bo Feng
- School of Chemical Engineering, Xiangtan University, Xiangtan, China
| | - Hongyan Zeng
- School of Chemical Engineering, Xiangtan University, Xiangtan, China
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Sehgal D, Skot L, Singh R, Srivastava RK, Das SP, Taunk J, Sharma PC, Pal R, Raj B, Hash CT, Yadav RS. Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits. PLoS One 2015; 10:e0122165. [PMID: 25970600 PMCID: PMC4430295 DOI: 10.1371/journal.pone.0122165] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/07/2015] [Indexed: 11/19/2022] Open
Abstract
A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance.
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Affiliation(s)
- Deepmala Sehgal
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Leif Skot
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Richa Singh
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Department of Molecular Biology and Biotechnology, Hisar, Haryana, India
| | - Rakesh Kumar Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | - Sankar Prasad Das
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, India
| | - Jyoti Taunk
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Department of Molecular Biology and Biotechnology, Hisar, Haryana, India
| | - Parbodh C. Sharma
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- Central Soil Salinity Research Institute (CSSRI), Karnal, India
| | - Ram Pal
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- National Research Centre for Orchids, Darjeeling Campus, Darjeeling, India
| | - Bhasker Raj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | | | - Rattan S. Yadav
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
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Wang L, Wang X, Jin X, Jia R, Huang Q, Tan Y, Guo A. Comparative proteomics of Bt-transgenic and non-transgenic cotton leaves. Proteome Sci 2015; 13:15. [PMID: 25949214 PMCID: PMC4422549 DOI: 10.1186/s12953-015-0071-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/03/2015] [Indexed: 01/05/2023] Open
Abstract
Background As the rapid growth of the commercialized acreage in genetically modified (GM) crops, the unintended effects of GM crops’ biosafety assessment have been given much attention. To investigate whether transgenic events cause unintended effects, comparative proteomics of cotton leaves between the commercial transgenic Bt + CpTI cotton SGK321 (BT) clone and its non-transgenic parental counterpart SY321 wild type (WT) was performed. Results Using enzyme linked immunosorbent assay (ELISA), Cry1Ac toxin protein was detected in the BT leaves, while its content was only 0.31 pg/g. By 2-DE, 58 differentially expressed proteins (DEPs) were detected. Among them 35 were identified by MS. These identified DEPs were mainly involved in carbohydrate transport and metabolism, chaperones related to post-translational modification and energy production. Pathway analysis revealed that most of the DEPs were implicated in carbon fixation and photosynthesis, glyoxylate and dicarboxylate metabolism, and oxidative pentose phosphate pathway. Thirteen identified proteins were involved in protein-protein interaction. The protein interactions were mainly involved in photosynthesis and energy metabolite pathway. Conclusions Our study demonstrated that exogenous DNA in a host cotton genome can affect the plant growth and photosynthesis. Although some unintended variations of proteins were found between BT and WT cotton, no toxic proteins or allergens were detected. This study verified genetically modified operation did not sharply alter cotton leaf proteome, and the target proteins were hardly checked by traditional proteomic analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0071-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Limin Wang
- Chinese Academy of Tropical Agricultural Sciences, The Institute of Tropical Biosciences and Biotechnology, Haikou, Hainan 571101 China ; Chinese Academy of Agricultural Sciences, The Oilcrops Research Institute, Wuhan, 430062 China
| | - Xuchu Wang
- Chinese Academy of Tropical Agricultural Sciences, The Institute of Tropical Biosciences and Biotechnology, Haikou, Hainan 571101 China
| | - Xiang Jin
- Chinese Academy of Tropical Agricultural Sciences, The Institute of Tropical Biosciences and Biotechnology, Haikou, Hainan 571101 China
| | - Ruizong Jia
- Chinese Academy of Tropical Agricultural Sciences, The Institute of Tropical Biosciences and Biotechnology, Haikou, Hainan 571101 China
| | - Qixing Huang
- Chinese Academy of Tropical Agricultural Sciences, The Institute of Tropical Biosciences and Biotechnology, Haikou, Hainan 571101 China
| | - Yanhua Tan
- Chinese Academy of Tropical Agricultural Sciences, The Institute of Tropical Biosciences and Biotechnology, Haikou, Hainan 571101 China
| | - Anping Guo
- Chinese Academy of Tropical Agricultural Sciences, The Institute of Tropical Biosciences and Biotechnology, Haikou, Hainan 571101 China
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Dawson IK, Russell J, Powell W, Steffenson B, Thomas WTB, Waugh R. Barley: a translational model for adaptation to climate change. THE NEW PHYTOLOGIST 2015; 206:913-931. [PMID: 25605349 DOI: 10.1111/nph.13266] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes - including examples that are indicative of the complexities involved in designing appropriate responses - are presented, and key developments for the future highlighted.
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Affiliation(s)
- Ian K Dawson
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Joanne Russell
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Wayne Powell
- CGIAR Consortium Office, Montpellier Cedex 5, France
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - William T B Thomas
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, College of Life Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
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Xie L, He X, Shang S, Zheng W, Liu W, Zhang G, Wu F. Comparative proteomic analysis of two tobacco (Nicotiana tabacum) genotypes differing in Cd tolerance. Biometals 2014; 27:1277-89. [PMID: 25173101 DOI: 10.1007/s10534-014-9789-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/22/2014] [Indexed: 12/18/2022]
Abstract
Tobacco can easily accumulate cadmium (Cd) in leaves and thus poses a potential threat to human health. Cd-stress-hydroponic-experiments were performed, and the proteomic and transcriptional features of two contrasting tobacco genotypes Yun-yan2 (Cd-tolerant) and Guiyan1 (Cd-sensitive) were compared. We identified 18 Cd-tolerance-associated proteins in leaves, using 2-dimensional gel electrophoresis coupled with mass spectrometry, whose expression were significantly induced in Yunyan2 leaves but down-regulated/unchanged in Guiyan1, or unchanged in Yunyan2 but down-regulated in Guiyan1 under 50 µM Cd stress. They are including epoxide hydrolase, enoyl-acyl-carrier-protein reductase, NPALDP1, chlorophyll a-b binding protein 25, heat shock protein 70 and 14-3-3 proteins. They categorized as 8 groups of their functions: metabolism, photosynthesis, stress response, signal transduction, protein synthesis, protein processing, transport and cell structure. Furthermore, the expression patterns of three Cd-responsive proteins were validated by quantitative real-time PCR. Our findings provide an insight into proteomic basis for Cd-detoxification in tobacco which offers molecular resource for Cd-tolerance.
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Affiliation(s)
- Lupeng Xie
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
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Mapping-by-sequencing identifies HvPHYTOCHROME C as a candidate gene for the early maturity 5 locus modulating the circadian clock and photoperiodic flowering in barley. Genetics 2014; 198:383-96. [PMID: 24996910 PMCID: PMC4174949 DOI: 10.1534/genetics.114.165613] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phytochromes play an important role in light signaling and photoperiodic control of flowering time in plants. Here we propose that the red/far-red light photoreceptor HvPHYTOCHROME C (HvPHYC), carrying a mutation in a conserved region of the GAF domain, is a candidate underlying the early maturity 5 locus in barley (Hordeum vulgare L.). We fine mapped the gene using a mapping-by-sequencing approach applied on the whole-exome capture data from bulked early flowering segregants derived from a backcross of the Bowman(eam5) introgression line. We demonstrate that eam5 disrupts circadian expression of clock genes. Moreover, it interacts with the major photoperiod response gene Ppd-H1 to accelerate flowering under noninductive short days. Our results suggest that HvPHYC participates in transmission of light signals to the circadian clock and thus modulates light-dependent processes such as photoperiodic regulation of flowering.
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Silva CC, Mantello CC, Campos T, Souza LM, Gonçalves PS, Souza AP. Leaf-, panel- and latex-expressed sequenced tags from the rubber tree ( Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:1035-1053. [PMID: 25242886 PMCID: PMC4162974 DOI: 10.1007/s11032-014-0095-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/17/2014] [Indexed: 05/10/2023]
Abstract
Hevea brasiliensis is a native species of the Amazon Basin of South America and the primary source of natural rubber worldwide. Due to the occurrence of South American Leaf Blight disease in this area, rubber plantations have been extended to suboptimal regions. Rubber tree breeding is time-consuming and expensive, but molecular markers can serve as a tool for early evaluation, thus reducing time and costs. In this work, we constructed six different cDNA libraries with the aim of developing gene-targeted molecular markers for the rubber tree. A total of 8,263 reads were assembled, generating 5,025 unigenes that were analyzed; 912 expressed sequence tags (ESTs) represented new transcripts, and two sequences were highly up-regulated by cold stress. These unigenes were scanned for microsatellite (SSR) regions and single nucleotide polymorphisms (SNPs). In total, 169 novel EST-SSR markers were developed; 138 loci were polymorphic in the rubber tree, and 98 % presented transferability to six other Hevea species. Locus duplication was observed in H. brasiliensis and other species. Additionally, 43 SNP markers in 13 sequences that showed similarity to proteins involved in stress response, latex biosynthesis and developmental processes were characterized. cDNA libraries are a rich source of SSR and SNP markers and enable the identification of new transcripts. The new markers developed here will be a valuable resource for linkage mapping, QTL identification and other studies in the rubber tree and can also be used to evaluate the genetic variability of other Hevea species, which are valuable assets in rubber tree breeding.
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Affiliation(s)
- Carla C. Silva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
| | - Camila C. Mantello
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
| | - Tatiana Campos
- Centro de Pesquisa Agroflorestal do Acre (CPAFAC), Embrapa, Rodovia BR-364, km 14, CP 321, Rio Branco, AC CEP 69900-970 Brazil
| | - Livia M. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
| | - Paulo S. Gonçalves
- Instituto Agronômico de Campinas (IAC), CP 28, Campinas, SP CEP 13012-970 Brazil
| | - Anete P. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6109, Campinas, SP CEP 13083-970 Brazil
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Xia Y, Li R, Ning Z, Bai G, Siddique KHM, Yan G, Baum M, Varshney RK, Guo P. Single nucleotide polymorphisms in HSP17.8 and their association with agronomic traits in barley. PLoS One 2013; 8:e56816. [PMID: 23418603 PMCID: PMC3572059 DOI: 10.1371/journal.pone.0056816] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 01/15/2013] [Indexed: 11/19/2022] Open
Abstract
Small heat shock protein 17.8 (HSP17.8) is produced abundantly in plant cells under heat and other stress conditions and may play an important role in plant tolerance to stress environments. However, HSP17.8 may be differentially expressed in different accessions of a crop species exposed to identical stress conditions. The ability of different genotypes to adapt to various stress conditions resides in their genetic diversity. Allelic variations are the most common forms of genetic variation in natural populations. In this study, single nucleotide polymorphisms (SNPs) of the HSP17.8 gene were investigated across 210 barley accessions collected from 30 countries using EcoTILLING technology. Eleven SNPs including 10 from the coding region of HSP17.8 were detected, which form nine distinguishable haplotypes in the barley collection. Among the 10 SNPs in the coding region, six are missense mutations and four are synonymous nucleotide changes. Five of the six missense changes are predicted to be deleterious to HSP17.8 function. The accessions from Middle East Asia showed the higher nucleotide diversity of HSP17.8 than those from other regions and wild barley (H. spontaneum) accessions exhibited greater diversity than the cultivated barley (H. vulgare) accessions. Four SNPs in HSP17.8 were found associated with at least one of the agronomic traits evaluated except for spike length, namely number of grains per spike, thousand kernel weight, plant height, flag leaf area and leaf color. The association between SNP and these agronomic traits may provide new insight for study of the gene's potential contribution to drought tolerance of barley.
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Affiliation(s)
- Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhengxiang Ning
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Kadambot H. M. Siddique
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Guijun Yan
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Aleppo, Syria
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Greater Hyderabad, India
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012. [PMID: 23161406 DOI: 10.1007/s10142‐012‐0300‐5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012; 12:573-83. [PMID: 23161406 PMCID: PMC3508266 DOI: 10.1007/s10142-012-0300-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/26/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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