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Ma M, Zhong W, Zhang Q, Deng L, Wen J, Yi B, Tu J, Fu T, Zhao L, Shen J. Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid. FRONTIERS IN PLANT SCIENCE 2023; 14:1123729. [PMID: 36778699 PMCID: PMC9911877 DOI: 10.3389/fpls.2023.1123729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.
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Liu Z, Wang J, Qiu B, Ma Z, Lu T, Kang X, Yang J. Induction and Characterization of Tetraploid Through Zygotic Chromosome Doubling in Eucalyptus urophylla. FRONTIERS IN PLANT SCIENCE 2022; 13:870698. [PMID: 35574074 PMCID: PMC9094141 DOI: 10.3389/fpls.2022.870698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Improvements in plant growth can bring great benefits to the forest industry. Eucalyptus urophylla is an important plantation species worldwide, and given that ploidy increases are often associated with plant phenotype changes, it was reasoned that its polyploidization may have good prospects and great significance toward its cultivation. In this study, the zygotic development period of E. urophylla was observed through paraffin sections, and a correlation between the development time of flower buds after pollination and the zygotic development period was established. On this basis, it was determined that the 25th day after pollination was the appropriate time for a high temperature to induce zygotic chromosome doubling. Then tetraploid E. urophylla was successfully obtained for the first time through zygotic chromosome doubling induced by high temperature, and the appropriate conditions were treating flower branches at 44°C for 6 h. The characterization of tetraploid E. urophylla was performed. Chromosome duplication brought about slower growing trees with thicker leaves, larger cells, higher net photosynthetic rates, and a higher content of certain secondary metabolites. Additionally, the molecular mechanisms for the variation in the tetraploid's characteristics were studied. The qRT-PCR results showed that genes mediating the tetraploid characteristics showed the same change trend as those of the characteristics, which verified that tetraploid trait variation was mainly caused by gene expression changes. Furthermore, although the tetraploid had no growth advantage compared with the diploid, it can provide important germplasm resources for future breeding, especially for the creation of triploids.
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Affiliation(s)
- Zhao Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | | | - Bingfa Qiu
- Guangxi Dongmen Forest Farm, Chongzuo, China
| | - Zhongcai Ma
- Guangxi Dongmen Forest Farm, Chongzuo, China
| | - Te Lu
- Science and Technology Section, Chifeng Research Institute of Forestry Science, Chifeng, China
| | - Xiangyang Kang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Jun Yang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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Wu W, Liao T, Du K, Wei H, Kang X. Transcriptome comparison of different ploidy reveals the mechanism of photosynthetic efficiency superiority of triploid poplar. Genomics 2021; 113:2211-2220. [PMID: 34022341 DOI: 10.1016/j.ygeno.2021.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/11/2021] [Accepted: 05/17/2021] [Indexed: 11/29/2022]
Abstract
Triploid poplars have obvious growth advantages, especially in leaf development and photosynthetic characteristics, but the molecular mechanism has not been revealed yet. In order to better understand the regulation mechanisms of leaf and chlorophyll development in the triploid poplars, we combined the leaf phenotypic data with the transcriptomic data of the 5th, 10th, and 25th leaves from triploid and diploid poplars, using weighted gene co-expression network analysis (WGCNA), and revealed that PpnGRF5-1 had a strong correlation with leaf development and net photosynthetic rate (Pn). PpnGRF5-1 overexpression transgenic plants showed that the leaf area, Pn, and chlorophyll concentration were significantly increased. Transcriptomic data analysis of the third leaf from PpnGRF5-1 overexpression transgenic plants showed that PpnGRF5-1 could up-regulate the expression levels of chlorophyll synthesis genes and down-regulate the transcription of chlorophyll degradation enzymes. Overall, our studies have greatly expanded our understanding of the molecular mechanisms regulating triploid growth dominance.
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Affiliation(s)
- Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China
| | - Ting Liao
- Beijing Academy of Forestry and Pomology Sciences, Beijing 100093, PR China
| | - Kang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China; National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China; Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, United States
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China; National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China; Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China.
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Biological pathway expression complementation contributes to biomass heterosis in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2023278118. [PMID: 33846256 DOI: 10.1073/pnas.2023278118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The mechanisms underlying heterosis have long remained a matter of debate, despite its agricultural importance. How changes in transcriptional networks during plant development are relevant to the continuous manifestation of growth vigor in hybrids is intriguing and unexplored. Here, we present an integrated high-resolution analysis of the daily dynamic growth phenotypes and transcriptome atlases of young Arabidopsis seedlings (parental ecotypes [Col-0 and Per-1] and their F1 hybrid). Weighted gene coexpression network analysis uncovered divergent expression patterns between parents of the network hub genes, in which genes related to the cell cycle were more highly expressed in one parent (Col-0), whereas those involved in photosynthesis were more highly expressed in the other parent (Per-1). Notably, the hybrid exhibited spatiotemporal high-parent-dominant expression complementation of network hub genes in the two pathways during seedling growth. This suggests that the integrated capacities of cell division and photosynthesis contribute to hybrid growth vigor, which could be enhanced by temporal advances in the progression of leaf development in the hybrid relative to its parents. Altogether, this study provides evidence of expression complementation between fundamental biological pathways in hybrids and highlights the contribution of expression dominance in heterosis.
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Dai Y, Sun X, Wang C, Li F, Zhang S, Zhang H, Li G, Yuan L, Chen G, Sun R, Zhang S. Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization. BMC Genomics 2021; 22:236. [PMID: 33823810 PMCID: PMC8022416 DOI: 10.1186/s12864-021-07510-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/05/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization. RESULTS There was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting 'XBJ' to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting 'JWW'; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, including MTHFR2, CPRD49, AAP8, endoglucanase 10, BXLs, GATLs, and WRKYs. Additionally, five genes related to flower development, BBX32 (binds to the FT promoter), SUS1 (increases FT expression), TSF (the closest homologue of FT), PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions. CONCLUSION The present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.
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Affiliation(s)
- Yun Dai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Xiao Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenggang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lingyun Yuan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Guohu Chen
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Meena RK, Reddy KS, Gautam R, Maddela S, Reddy AR, Gudipalli P. Improved photosynthetic characteristics correlated with enhanced biomass in a heterotic F 1 hybrid of maize (Zea mays L.). PHOTOSYNTHESIS RESEARCH 2021; 147:253-267. [PMID: 33555518 DOI: 10.1007/s11120-021-00822-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/15/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a phenomenon wherein F1 hybrid often displays phenotypic superiority and surpasses its parents in terms of growth and agronomic traits. Investigations on the physiological and biochemical properties of the heterotic F1 hybrid are important to uncover the mechanisms underlying heterosis in plants. In the present study, the photosynthetic capacity of a heterotic F1 hybrid of Zea mays L. (DHM 117) that exhibited a higher growth rate and increased biomass was compared with its parental inbreds at vegetative and reproductive stages in the field during 2017 and 2018. The net photosynthetic rate (Pn), stomatal conductance (gs), transpiration rate (E) as well as foliar carbohydrates were higher in F1 hybrid than parental inbreds at vegetative and reproductive stages. An increase in total chlorophyll content along with better chlorophyll a fluorescence characteristics including effective quantum yield of photosystem II (ΔF/Fm'), maximum quantum yield of PSII (Fv/Fm), photochemical quenching (qp) and decreased non-photochemical quenching (NPQ) was observed in F1 hybrid than the parental inbreds. Further, the expression of potential genes related to C4 photosynthesis was considerably upregulated in F1 hybrid than the parental inbreds during vegetative and reproductive stages. Moreover, the F1 hybrid exhibited distinct heterosis in yield with 63% and 62% increase relative to parental inbreds during 2017 and 2018. We conclude that improved photosynthetic efficiency associated with increased foliar carbohydrates could have contributed to higher growth rate, biomass and yield in the F1 hybrid.
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Affiliation(s)
- Rajesh Kumar Meena
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Kanubothula Sitarami Reddy
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Ranjana Gautam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Surender Maddela
- Institute of Biotechnology, Prof. Jayashankar Telangana State Agricultural University, Hyderabad, 500 030, Telangana, India
| | - Attipalli Ramachandra Reddy
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India
| | - Padmaja Gudipalli
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, Telangana, India.
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Hou G, Dong Y, Zhu F, Zhao Q, Li T, Dou D, Ma X, Wu L, Ku L, Chen Y. MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis. BMC PLANT BIOLOGY 2020; 20:541. [PMID: 33256592 PMCID: PMC7708177 DOI: 10.1186/s12870-020-02751-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/22/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Zhengdan 958 (Zheng 58 × Chang 7-2), a commercial hybrid that is produced in a large area in China, is the result of the successful use of the heterotic pattern of Reid × Tang-SPT. The jointing stage of maize is the key period from vegetative to reproductive growth, which determines development at later stages and heterosis to a certain degree. MicroRNAs (miRNAs) play vital roles in the regulation of plant development, but how they function in the sixth leaf at the six-leaf (V6) stage to influence jointing stage heterosis is still unclear. RESULT Our objective was to study miRNAs in four hybrid combinations developed in accordance with the Reid × Tang-SPT pattern, Zhengdan 958, Anyu 5 (Ye 478 × Chang 7-2), Ye 478 × Huangzaosi, Zheng 58 × Huangzaosi, and their parental inbred lines to explore the mechanism related to heterosis. A total of 234 miRNAs were identified in the sixth leaf at the V6 stage, and 85 miRNAs were differentially expressed between the hybrid combinations and their parental inbred lines. Most of the differentially expressed miRNAs were non-additively expressed, which indicates that miRNAs may participate in heterosis at the jointing stage. miR164, miR1432 and miR528 families were repressed in the four hybrid combinations, and some miRNAs, such as miR156, miR399, and miR395 families, exhibited different expression trends in different hybrid combinations, which may result in varying effects on the heterosis regulatory mechanism. CONCLUSIONS The potential targets of the identified miRNAs are related to photosynthesis, the response to plant hormones, and nutrient use. Different hybrid combinations employ different mature miRNAs of the same miRNA family and exhibit different expression trends that may result in enhanced or repressed gene expression to regulate heterosis. Taken together, our results reveal a miRNA-mediated network that plays a key role in jointing stage heterosis via posttranscriptional regulation.
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Affiliation(s)
- Gege Hou
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Yahui Dong
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Fangfang Zhu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Qiannan Zhao
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Tianyi Li
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Dandan Dou
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Xingli Ma
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Liancheng Wu
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Lixia Ku
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China
| | - Yanhui Chen
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzi Lake University District, Zhengdong New District, Zhengzhou, 450046, Henan, People's Republic of China.
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Du K, Liao T, Ren Y, Geng X, Kang X. Molecular Mechanism of Vegetative Growth Advantage in Allotriploid Populus. Int J Mol Sci 2020; 21:ijms21020441. [PMID: 32284503 PMCID: PMC7014019 DOI: 10.3390/ijms21020441] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/30/2019] [Accepted: 01/07/2020] [Indexed: 12/15/2022] Open
Abstract
Allotriploid poplar has a prominent vegetative growth advantage that impacts dramatically on lumber yield. The growth regulation is complex which involves abundant genes, metabolic and signaling pathways, while the information about the functional control process is very little. We used high-throughput sequencing and physiological index measurement to obtain a global overview of differences between allotriploid and diploid Populus. The genes related to plant growth advantage show a higher expression compared to diploid, and most of them are revolved around hormones, photosynthesis and product accumulation. Thus, allotriploid Populus showed more efficient photosynthesis, carbon fixation, sucrose and starch synthesis, and metabolism as well as augmented biosynthesis of auxin, cytokinin, and gibberellin. These data enable the connection of metabolic processes, signaling pathways, and specific gene activity, which will underpin the development of network models to elucidate the process of triploid Populus advantage growth.
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Affiliation(s)
- Kang Du
- Beijing Advanced Innovation Center for Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China; (K.D.); (Y.R.); (X.G.)
| | - Ting Liao
- Beijing Academy of Forestry and Pomology Sciences No. 12 A Rui Wang Fen, Fragrance Hills Haidian District, Beijing 100093, China
| | - Yongyu Ren
- Beijing Advanced Innovation Center for Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China; (K.D.); (Y.R.); (X.G.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China
| | - Xining Geng
- Beijing Advanced Innovation Center for Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China; (K.D.); (Y.R.); (X.G.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China; (K.D.); (Y.R.); (X.G.)
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China
- Correspondence: ; Tel.: +86-10-6233-6168
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Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
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Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
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Gallusci P, Dai Z, Génard M, Gauffretau A, Leblanc-Fournier N, Richard-Molard C, Vile D, Brunel-Muguet S. Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues. TRENDS IN PLANT SCIENCE 2017; 22:610-623. [PMID: 28587758 DOI: 10.1016/j.tplants.2017.04.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/12/2017] [Accepted: 04/28/2017] [Indexed: 05/21/2023]
Abstract
Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits.
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Affiliation(s)
- Philippe Gallusci
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Univ. Bordeaux, 33140 Villenave d'Ornon, France.
| | | | - Arnaud Gauffretau
- UMR Agronomie, AgroParisTech, INRA, 78850, Thiverval-Grignon, France
| | | | - Céline Richard-Molard
- UMR ECOSYS, INRA AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Denis Vile
- LEPSE, INRA-SupAgro, 34060, Montpellier, France
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Gao S, Yan Q, Chen L, Song Y, Li J, Fu C, Dong M. Effects of ploidy level and haplotype on variation of photosynthetic traits: Novel evidence from two Fragaria species. PLoS One 2017; 12:e0179899. [PMID: 28644876 PMCID: PMC5482484 DOI: 10.1371/journal.pone.0179899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/06/2017] [Indexed: 12/26/2022] Open
Abstract
To reveal the effects of ploidy level and haplotype on photosynthetic traits, we chose 175 genotypes of wild strawberries belonging to two haplotypes at two types of ploidy levels (diploidy and tetraploidy) and measured photosynthetic traits. Our results revealed that ploidy significantly affected the characteristics of light-response curves, CO2-response curves, and leaf gas exchange parameters, except intercellular CO2 concentration (Ci). Tetraploid species had a lower light saturation point (LSP) and CO2 saturation point (CSP), higher light compensation point (LCP), dark respiration (Rd), and CO2 compensation point (CCP) than diploid species. Furthermore, tetraploid species have lower photosynthetic capacity than diploid species, including net photosynthetic rate (Pn), stomatal conductivity (Gs), and transpiration rate (Tr). In addition, haplotype had a significant effect on LSP, CSP, Tr, and Ci as well as a significant interactive effect between ploidy and haplotype on the maximal photosynethic rate of the light-response curve and Rd. Most of the variance existed within haplotypes among individuals. These results suggest that polyploidization was the main driver for the evolution of photosynthesis with increasing ploidy level (i.e. from diploidy to tetraploidy in Fragaria species), while the origin of a chromosome could also affect the photosynthetic traits and the polyploidization effect on photosynthetic traits.
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Affiliation(s)
- Song Gao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, China
- Research Institute of Zhejiang University-Taizhou, Taizhou, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Qiaodi Yan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Yaobin Song
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, and College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming Dong
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, and College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Arango J, Beltrán J, Nuñez J, Chavarriaga P. Evidence of Epigenetic Mechanisms Affecting Carotenoids. Subcell Biochem 2017; 79:295-307. [PMID: 27485227 DOI: 10.1007/978-3-319-39126-7_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Epigenetic mechanisms are able to regulate plant development by generating non-Mendelian allelic interactions. An example of these are the responses to environmenal stimuli that result in phenotypic variability and transgression amongst important crop traits. The need to predict phenotypes from genotypes to understand the molecular basis of the genotype-by-environment interaction is a research priority. Today, with the recent discoveries in the field of epigenetics, this challenge goes beyond analyzing how DNA sequences change. Here we review examples of epigenetic regulation of genes involved in carotenoid synthesis and degradation, cases in which histone- and/or DNA-methylation, and RNA silencing at the posttranscriptional level affect carotenoids in plants.
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Affiliation(s)
- Jacobo Arango
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.
| | - Jesús Beltrán
- Agronomy and Horticulture Department, University of Nebraska-Lincoln, Beadle Center 1901 Vine Street, Lincoln, NE, 68588-0660, USA
| | - Jonathan Nuñez
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Paul Chavarriaga
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
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