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Wang L, Li J, Lin Y, Dang K, Wan J, Meng S, Qiu X, Wang Q, Mu L, Ding D, Luo H, Tang J. Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis. THE PLANT GENOME 2023; 16:e20293. [PMID: 36478177 DOI: 10.1002/tpg2.20293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/02/2022] [Indexed: 05/10/2023]
Abstract
Important traits related to maize (Zea mays L.) grain yield, such as kernel row number, ear length, kernel number per row, are determined during the development of female inflorescence. There is a significant positive correlation between yield component and the activity of inflorescence meristem (IM). To find the key stage of heterosis in the development of the ear, immature ears (from the IM stage until the end of the floral meristem [FM] stage) of Yudan888 and its parent lines were sampled to assay phenotype and for comparative transcriptomics analysis. The immature ear length of Yudan888 at the IM stage fitted an additive (mid-parental) model, but it showed high parental dominance at the spikelet-pair meristem (SPM) stage. Comparative analysis of transcriptomes suggested significant differences between additive and nonadditive expression patterns for different developmental stages. The number of distinct maternal or paternal genes (DMP) (genes expressed only in one parental line and their hybrid but silenced in another line) was greater than ABF1 (genes expressed in both parental lines but silenced in hybrid) at each stage. Gene Ontology (GO) enrichment suggested that the cell redox homeostasis genes with overdominance expression patterns in hybrids have an important contribution to heterosis. According to our research, an ear length heterosis network was established. The discovery of the inflection point for ear length heterosis allows us for inferring that the transition state of IM to SPM may be the starting point of ear length heterosis. These findings improved the understanding of maize ear length heterosis.
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Affiliation(s)
- Liangfa Wang
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural Univ., Zhengzhou, 450002, China
- The Shennong Laboratory, Zhengzhou, 450002, China
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Identification of miRNAs Mediating Seed Storability of Maize during Germination Stage by High-Throughput Sequencing, Transcriptome and Degradome Sequencing. Int J Mol Sci 2022; 23:ijms232012339. [PMID: 36293196 PMCID: PMC9604548 DOI: 10.3390/ijms232012339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Seed storability is an important trait for improving grain quality and germplasm conservation, but little is known about the regulatory mechanisms and gene networks involved. MicroRNAs (miRNAs) are small non-coding RNAs regulating the translation and accumulation of their target mRNAs by means of sequence complementarity and have recently emerged as critical regulators of seed germination. Here, we used the germinating embryos of two maize inbred lines with significant differences in seed storability to identify the miRNAs and target genes involved. We identified a total of 218 previously known and 448 novel miRNAs by miRNA sequencing and degradome analysis, of which 27 known and 11 newly predicted miRNAs are differentially expressed in two maize inbred lines, as measured by Gene Ontology (GO) enrichment analysis. We then combined transcriptome sequencing and real-time quantitative polymerase chain reaction (RT-PCR) to screen and confirm six pairs of differentially expressed miRNAs associated with seed storability, along with their negative regulatory target genes. The enrichment analysis suggested that the miRNAs/target gene mediation of seed storability occurs via the ethylene activation signaling pathway, hormone synthesis and signal transduction, as well as plant organ morphogenesis. Our results should help elucidate the mechanisms through which miRNAs are involved in seed storability in maize.
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Jin Y, Wang B, Tian L, Zhao L, Guo S, Zhang H, Xu L, Han Z. Identification of miRNAs and their target genes associated with improved maize seed vigor induced by gibberellin. FRONTIERS IN PLANT SCIENCE 2022; 13:1008872. [PMID: 36176685 PMCID: PMC9514094 DOI: 10.3389/fpls.2022.1008872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops and a better understanding of the molecular mechanism associated with maize seed vigor is highly necessary. To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs have been reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6,196 targets were obtained. Function analysis of differentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved maize seed vigor. These findings provide valuable information to understand the involvement of miRNAs with maize seed vigor and these putative genes will be valuable resources for improving the seed vigor in future maize breeding.
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Affiliation(s)
- Yunqian Jin
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou, China / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan, China
| | - Bin Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Lei Tian
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Linxi Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Shulei Guo
- Cereal Institute, Henan Academy of Agricultural Science/Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Hengchao Zhang
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Lengrui Xu
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Zanping Han
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
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Wan J, Wang Q, Zhao J, Zhang X, Guo Z, Hu D, Meng S, Lin Y, Qiu X, Mu L, Ding D, Tang J. Gene expression variation explains maize seed germination heterosis. BMC PLANT BIOLOGY 2022; 22:301. [PMID: 35718761 PMCID: PMC9208091 DOI: 10.1186/s12870-022-03690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Heterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis. RESULTS In this study, there is faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses were conducted. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the differential expression genes between hybrids and either parental line display parental dominance up or higher levels in the reciprocal cross of Zhengdan958, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc. CONCLUSION: Our results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryos and improve the understanding of maize seed germination heterosis.
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Affiliation(s)
- Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Desheng Hu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, China.
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Han Y, Gao Y, Zhou H, Zhai X, Ding Q, Ma L. Mitochondrial genes are involved in the fertility transformation of the thermosensitive male-sterile line YS3038 in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:61. [PMID: 37309316 PMCID: PMC10236089 DOI: 10.1007/s11032-021-01252-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 09/05/2021] [Indexed: 06/14/2023]
Abstract
Heterosis can improve the stress resistance, quality, and yield of crops, and the male sterility of wheat can be utilized to accelerate the breeding process of hybrid. To determine whether mitochondrial genes are involved in the fertility of K-type cytoplasmic male-sterile (CMS) line and the YS-type thermosensitive male-sterile (TMS) line in wheat, we sequenced and assembled the mitochondrial genomes of K519A, 519B, and YS3038 by next-generation sequencing (NGS). The non-synonymous mutations were analyzed, and the first-generation sequencing was conducted to verify the non-synonymous mutation sites. Furthermore, the expression patterns of genes with non-synonymous mutations were analyzed. Finally, the candidate genes were silenced by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) to test the functions of the candidate genes. The results revealed that the mitochondrial genomes of K519A, 519B, and YS3038 were 420,543, 433,560, and 452,567 bp in length, respectively. Besides, 33, 31, and 37 protein-coding genes were identified in K519A, 519B, and YS3038, respectively. There were 14 protein-coding genes and 83 open reading frame (ORF) sequences that differed between K519A and 519B and 10 protein-coding genes and 122 ORF sequences that differed between K519A and YS3038. At the binucleate stage, seven genes (nad6, ORF256, ORF216, ORF138, atp6, nad3, and cox1) were downregulated in K519A compared with 519B, and 10 genes (nad6, atp6, cox3, atp8, nad3, cox1, rps3, ORF216, ORF138, and ORF224) were downregulated in YS3038 compared with K519A. Besides, six genes (nad6, ORF138, cox3, cox1, rps3, and ORF224) were downregulated under fertile conditions relative to sterile conditions in YS3038. Gene silencing analysis showed that the silencing of cox1 significantly reduced the seed setting rate of YS3038, indicating that the cox1 gene may be involved in the fertility transformation of YS3038. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01252-x.
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Affiliation(s)
- Yucui Han
- College of Agronomy, Northwest A&F University, Xianyang, 712100 Yangling, Shaanxi China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004 Hebei China
| | - Yujie Gao
- College of Agronomy, Northwest A&F University, Xianyang, 712100 Yangling, Shaanxi China
| | - Hao Zhou
- College of Agronomy, Northwest A&F University, Xianyang, 712100 Yangling, Shaanxi China
| | - Xiaoguang Zhai
- College of Agronomy, Northwest A&F University, Xianyang, 712100 Yangling, Shaanxi China
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Xianyang, 712100 Yangling, Shaanxi China
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Xianyang, 712100 Yangling, Shaanxi China
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Shu HY, Zhou H, Mu HL, Wu SH, Jiang YL, Yang Z, Hao YY, Zhu J, Bao WL, Cheng SH, Zhu GP, Wang ZW. Integrated Analysis of mRNA and Non-coding RNA Transcriptome in Pepper ( Capsicum chinense) Hybrid at Seedling and Flowering Stages. Front Genet 2021; 12:685788. [PMID: 34490032 PMCID: PMC8417703 DOI: 10.3389/fgene.2021.685788] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/26/2021] [Indexed: 01/22/2023] Open
Abstract
Pepper is an important vegetable in the world. In this work, mRNA and ncRNA transcriptome profiles were applied to understand the heterosis effect on the alteration in the gene expression at the seedling and flowering stages between the hybrid and its parents in Capsicum chinense. Our phenotypic data indicated that the hybrid has dominance in leaf area, plant scope, plant height, and fruit-related traits. Kyoto Encyclopedia of Genes and Genomes analysis showed that nine members of the plant hormone signal transduction pathway were upregulated in the seedling and flowering stages of the hybrid, which was supported by weighted gene coexpression network analysis and that BC332_23046 (auxin response factor 8), BC332_18317 (auxin-responsive protein IAA20), BC332_13398 (ethylene-responsive transcription factor), and BC332_27606 (ethylene-responsive transcription factor WIN1) were candidate hub genes, suggesting the important potential role of the plant hormone signal transduction in pepper heterosis. Furthermore, some transcription factor families, including bHLH, MYB, and HSF were greatly over-dominant. We also identified 2,525 long ncRNAs (lncRNAs), 47 micro RNAs (miRNAs), and 71 circle RNAs (circRNAs) in the hybrid. In particular, downregulation of miR156, miR169, and miR369 in the hybrid suggested their relationship with pepper growth vigor. Moreover, we constructed some lncRNA–miRNA–mRNA regulatory networks that showed a multi-dimension to understand the ncRNA relationship with heterosis. These results will provide guidance for a better understanding of the molecular mechanism involved in pepper heterosis.
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Affiliation(s)
- Huang-Ying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - He Zhou
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Hai-Ling Mu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Shu-Hua Wu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Yi-Li Jiang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Zhuang Yang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Yuan-Yuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Jie Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Wen-Long Bao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Shan-Han Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Guo-Peng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Zhi-Wei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
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Barley Seeds miRNome Stability during Long-Term Storage and Aging. Int J Mol Sci 2021; 22:ijms22094315. [PMID: 33919202 PMCID: PMC8122619 DOI: 10.3390/ijms22094315] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 04/18/2021] [Indexed: 12/18/2022] Open
Abstract
Seed aging is a complex biological process that has been attracting scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that, despite having the same genetic makeup, differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families, i.e., miR159, miR156, miR166, and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along with the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability as detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state.
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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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9
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Chen SY, Su MH, Kremling KA, Lepak NK, Romay MC, Sun Q, Bradbury PJ, Buckler ES, Ku HM. Identification of miRNA-eQTLs in maize mature leaf by GWAS. BMC Genomics 2020; 21:689. [PMID: 33023467 PMCID: PMC7541240 DOI: 10.1186/s12864-020-07073-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022] Open
Abstract
Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.
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Affiliation(s)
- Shu-Yun Chen
- Department of Life Science, National Cheng Kung University, Tainan, 701, Taiwan
| | - Mei-Hsiu Su
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Karl A Kremling
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, 14850, NY, USA
| | - Nicholas K Lepak
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Peter J Bradbury
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Edward S Buckler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, 14850, NY, USA.,United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Hsin-Mei Ku
- Advanced Plant Biotechnology Center, National Chung Hsing University, No 145 Xingda Rd, South Dist, Taichung, 402, Taiwan.
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10
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Sinha P, Singh VK, Saxena RK, Kale SM, Li Y, Garg V, Meifang T, Khan AW, Kim KD, Chitikineni A, Saxena KB, Sameer Kumar CV, Liu X, Xu X, Jackson S, Powell W, Nevo E, Searle IR, Lodha M, Varshney RK. Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1697-1710. [PMID: 31925873 PMCID: PMC7336283 DOI: 10.1111/pbi.13333] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 12/26/2019] [Indexed: 05/20/2023]
Abstract
Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.
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Affiliation(s)
- Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- International Rice Research Institute, South‐Asia HubPatancheruIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- The Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | | | - Vanika Garg
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Kyung Do Kim
- University of GeorgiaAthensUSA
- Myongji UniversityYonginRepublic of Korea
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - K. B. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - C. V. Sameer Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Xun Xu
- BGI‐ShenzhenShenzhenChina
| | | | | | | | | | - Mukesh Lodha
- Centre for Cellular and Molecular Biology (CSIR)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
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11
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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12
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Cavé-Radet A, Giraud D, Lima O, El Amrani A, Aïnouche M, Salmon A. Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae). PLANT MOLECULAR BIOLOGY 2020; 102:55-72. [PMID: 31748889 DOI: 10.1007/s11103-019-00931-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina. The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.
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Affiliation(s)
- Armand Cavé-Radet
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Delphine Giraud
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Oscar Lima
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Malika Aïnouche
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Armel Salmon
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France.
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13
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Li M, Chen T, He JJ, Wu JH, Luo JY, Ye RS, Xie MY, Zhang HJ, Zeng B, Liu J, Xi QY, Jiang QY, Sun JJ, Zhang YL. Plant MIR167e-5p Inhibits Enterocyte Proliferation by Targeting β-Catenin. Cells 2019; 8:cells8111385. [PMID: 31689969 PMCID: PMC6912825 DOI: 10.3390/cells8111385] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/11/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are important negative regulators of genes involved in physiological and pathological processes in plants and animals. It is worth exploring whether plant miRNAs play a cross-kingdom regulatory role in animals. Herein, we found that plant MIR167e-5p regulates the proliferation of enterocytes in vitro. A porcine jejunum epithelial cell line (IPEC-J2) and a human colon carcinoma cell line (Caco-2) were treated with 0, 10, 20, and 40 pmol of synthetic 2′-O-methylated plant MIR167e-5p, followed by a treatment with 20 pmol of MIR167e-5p for 0, 24, 48, and 72 h. The cells were counted, and IPEC-J2 cell viability was determined by the MTT and EdU assays at different time points. The results showed that MIR167e-5p significantly inhibited the proliferation of enterocytes in a dose- and time-dependent manner. Bioinformatics prediction and a luciferase reporter assay indicated that MIR167e-5p targets β-catenin. In IPEC-J2 and Caco-2 cells, MIR167e-5p suppressed proliferation by downregulating β-catenin mRNA and protein levels. MIR167e-5p relieved this inhibition. Similar results were achieved for the β-catenin downstream target gene c-Myc and the proliferation-associated gene PCNA. This research demonstrates that plant MIR167e-5p can inhibit enterocyte proliferation by targeting the β-catenin pathway. More importantly, plant miRNAs may be a new class of bioactive molecules for epigenetic regulation in humans and animals.
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Affiliation(s)
- Meng Li
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jia-Jian He
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jia-Han Wu
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jun-Yi Luo
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Rui-Song Ye
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Mei-Ying Xie
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Hao-Jie Zhang
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Bin Zeng
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jie Liu
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Qian-Yun Xi
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Qing-Yan Jiang
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jia-Jie Sun
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yong-Liang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutritional Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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14
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Zhang L, Zou J, Li S, Wang B, Raboanatahiry N, Li M. Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa. BMC Genomics 2019; 20:649. [PMID: 31412776 PMCID: PMC6694508 DOI: 10.1186/s12864-019-6001-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported. RESULTS Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid. CONCLUSIONS This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shisheng Li
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, 250000, China
| | - Nadia Raboanatahiry
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. .,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China.
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15
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Li M, Chen T, Wang R, Luo JY, He JJ, Ye RS, Xie MY, Xi QY, Jiang QY, Sun JJ, Zhang YL. Plant MIR156 regulates intestinal growth in mammals by targeting the Wnt/β-catenin pathway. Am J Physiol Cell Physiol 2019; 317:C434-C448. [PMID: 31166713 DOI: 10.1152/ajpcell.00030.2019] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are important negative regulators of genes involved in physiological and pathological processes in plants and animals. Recent studies have shown that miRNAs might regulate gene expression among different species in a cross-kingdom manner. However, the specific roles of plant miRNAs in animals remain poorly understood and somewhat. Herein, we found that plant MIR156 regulates proliferation of intestinal cells both in vitro and in vivo. Continuous administration of a high plant miRNA diet or synthetic MIR156 elevated MIR156 levels and inhibited the Wnt/β-catenin signaling pathway in mouse intestine. Bioinformatics predictions and luciferase reporter assays indicated that MIR156 targets Wnt10b. In vitro, MIR156 suppressed proliferation by downregulating the Wnt10b protein and upregulating β-catenin phosphorylation in the porcine jejunum epithelial (IPEC-J2) cell line. Lithium chloride and an MIR156 inhibitor relieved this inhibition. This research is the first to demonstrate that plant MIR156 inhibits intestinal cell proliferation by targeting Wnt10b. More importantly, plant miRNAs may represent a new class of bioactive molecules that act as epigenetic regulators in humans and other animals.
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Affiliation(s)
- Meng Li
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ran Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jun-Yi Luo
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jia-Jian He
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Rui-Song Ye
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Mei-Ying Xie
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qian-Yun Xi
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qing-Yan Jiang
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jia-Jie Sun
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yong-Liang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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16
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Heterotic patterns of primary and secondary metabolites in the oilseed crop Brassica juncea. Heredity (Edinb) 2019; 123:318-336. [PMID: 30911141 DOI: 10.1038/s41437-019-0213-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
Heterosis refers to the superior performance of F1 hybrids over their respective parental inbred lines. Although the genetic and expression basis of heterosis have been previously investigated, the metabolic basis for this phenomenon is poorly understood. In a preliminary morphological study in Brassica juncea, we observed significant heterosis at the 50% flowering stage, wherein both the growth and reproduction of F1 reciprocal hybrids were greater than that of their parents. To identify the possible metabolic causes or consequences of this heterosis, we carried out targeted LC-MS analysis of 48 primary (amino acids and sugars) and secondary metabolites (phytohormones, glucosinolates, flavonoids, and phenolic esters) in five developmental tissues at 50% flowering in hybrids and inbred parents. Principal component analysis (PCA) of metabolites clearly separated inbred lines from their hybrids, particularly in the bud tissues. In general, secondary metabolites displayed more negative heterosis values in comparison to primary metabolites. The tested primary and secondary metabolites displayed both additive and non-additive modes of inheritance in F1 hybrids, wherein the number of metabolites showing an additive mode of inheritance were higher in buds and siliques (52.77-97.14%) compared to leaf tissues (47.37-80%). Partial least regression (PLS) analysis further showed that primary metabolites, in general, displayed higher association with morphological parameters in F1 hybrids. Overall, our results are consistent with a resource-cost model for heterosis in B. juncea, where metabolite allocation in hybrids appears to favor growth, at the expense of secondary metabolism.
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17
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Tian L, Liu H, Ren L, Ku L, Wu L, Li M, Wang S, Zhou J, Song X, Zhang J, Dou D, Liu H, Tang G, Chen Y. MicroRNA 399 as a potential integrator of photo-response, phosphate homeostasis, and sucrose signaling under long day condition. BMC PLANT BIOLOGY 2018; 18:290. [PMID: 30463514 PMCID: PMC6249786 DOI: 10.1186/s12870-018-1460-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/03/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Photoperiod-sensitivity is a critical endogenous regulatory mechanism for plant growth and development under specific environmental conditions, while phosphate and sucrose signaling processes play key roles in cell growth and organ initiation. MicroRNA399 is phosphate-responsive, but, whether it has roles in other metabolic processes remains unknown. RESULTS MicroRNA399 was determined to be sucrose-responsive through a microRNA array assay. High levels of sucrose inhibited the accumulation of microRNA399 family under phosphate starvation conditions in Arabidopsis thaliana. Similarly, exogenous sucrose supplementation also reduced microRNA399 expression in maize at developmental transition stages. RNA sequencing of a near-isogenic line(photoperiod-sensitive) line and its recurrent parent Huangzao4, a photoperiod-insensitive line, was conducted at various developmental stages. Members of microRNA399 family were down-regulated under long-day conditions in the photoperiod-sensitive near-isogenic line that accumulated more sucrose in vivo compared with the control line Huangzao4. CONCLUSION MicroRNA399s may play central roles in the integration of sucrose sensing and photoperiodic responses under long day conditions in maize.
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Affiliation(s)
- Lei Tian
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Haiping Liu
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Ligang Ren
- College of Life Science, Northwest Agriculture and Forestry University, Yangling, 712100 China
| | - Lixia Ku
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Liuji Wu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Mingna Li
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Shunxi Wang
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Jinlong Zhou
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Xiaoheng Song
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Jun Zhang
- Cereal Institute, Henan Academy of Agricultural Science/Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, 450002 China
| | - Dandan Dou
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Huafeng Liu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Yanhui Chen
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002 China
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18
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Ju C, Zhang W, Liu Y, Gao Y, Wang X, Yan J, Yang X, Li J. Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize. BMC PLANT BIOLOGY 2018; 18:171. [PMID: 30111287 PMCID: PMC6094888 DOI: 10.1186/s12870-018-1383-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/01/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Root systems play important roles in crop growth and stress responses. Although genetic mechanism of root traits in maize (Zea mays L.) has been investigated in different mapping populations, root traits have rarely been utilized in breeding programs. Elucidation of the genetic basis of maize root traits and, more importantly, their connection to other agronomic trait(s), such as grain yield, may facilitate root trait manipulation and maize germplasm improvement. In this study, we analyzed genome-wide genetic loci for maize seedling root traits at three time-points after seed germination to identify chromosomal regions responsible for both seedling root traits and other agronomic traits in a recombinant inbred line (RIL) population (Zong3 × Yu87-1). RESULTS Eight seedling root traits were examined at 4, 9, and 14 days after seed germination, and thirty-six putative quantitative trait loci (QTLs), accounting for 9.0-23.2% of the phenotypic variation in root traits, were detected. Co-localization of root trait QTLs was observed at, but not between, the three time-points. We identified strong or moderate correlations between root traits controlled by each co-localized QTL region. Furthermore, we identified an overlap in the QTL locations of seedling root traits examined here and six other traits reported previously in the same RIL population, including grain yield-related traits, plant height-related traits, and traits in relation to stress responses. Maize chromosomal bins 1.02-1.03, 1.07, 2.06-2.07, 5.05, 7.02-7.03, 9.04, and 10.06 were identified QTL hotspots for three or four more traits in addition to seedling root traits. CONCLUSIONS Our identification of co-localization of root trait QTLs at, but not between, each of the three time-points suggests that maize seedling root traits are regulated by different sets of pleiotropic-effect QTLs at different developmental stages. Furthermore, the identification of QTL hotspots suggests the genetic association of seedling root traits with several other traits and reveals maize chromosomal regions valuable for marker-assisted selection to improve root systems and other agronomic traits simultaneously.
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Affiliation(s)
- Chuanli Ju
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Wei Zhang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ya Liu
- Maize Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097 China
| | - Yufeng Gao
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaofan Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jiansheng Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
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19
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Proteomic analysis reveals that auxin homeostasis influences the eighth internode length heterosis in maize (Zea mays). Sci Rep 2018; 8:7159. [PMID: 29739966 PMCID: PMC5940786 DOI: 10.1038/s41598-018-23874-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 03/20/2018] [Indexed: 11/09/2022] Open
Abstract
Ear height is an important maize morphological trait that influences plant lodging resistance in the field, and is based on the number and length of internodes under the ear. To explore the effect of internodes on ear height, the internodes under the ear were analysed in four commercial hybrids (Jinsai6850, Zhengdan958, Xundan20, and Yuyu22) from different heterotic groups in China. The eighth internode, which is the third aboveground extended internode, exhibited high-parent or over high-parent heterosis and contributed considerably to ear height. Thus, the proteome of the eighth internode was examined. Sixty-six protein spots with >1.5-fold differences in accumulation (P < 0.05) among the four hybrids were identified by mass spectrometry and data analyses. Most of the differentially accumulated proteins exhibited additive accumulation patterns, but with epistatic effects on heterosis performance. Proteins involved in phenylpropanoid and benzoxazinoid metabolic pathways were observed to influence indole-3-acetic acid biosynthesis and polar auxin transport during internode development. Moreover, indole-3-acetic acid content was positively correlated with the eighth internode length, but negatively correlated with the extent of the heterosis of the eighth internode length.
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20
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Ma X, Zhang X, Zhao K, Li F, Li K, Ning L, He J, Xin Z, Yin D. Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Seed Expansion in Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2018; 9:349. [PMID: 29662498 PMCID: PMC5890158 DOI: 10.3389/fpls.2018.00349] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 05/22/2023]
Abstract
Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering (DAF) in two peanut eighth-generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1,082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.
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Affiliation(s)
| | | | | | | | | | | | | | - Zeyu Xin
- *Correspondence: Dongmei Yin, Zeyu Xin,
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21
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Wang H, Zhang X, Yang H, Liu X, Li H, Yuan L, Li W, Fu Z, Tang J, Kang D. Identification of heterotic loci associated with grain yield and its components using two CSSL test populations in maize. Sci Rep 2016; 6:38205. [PMID: 27917917 PMCID: PMC5137037 DOI: 10.1038/srep38205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 11/07/2016] [Indexed: 11/17/2022] Open
Abstract
Heterosis has widely been used to increase grain yield and quality. In this study, the genetic basis of heterosis on grain yield and its main components in maize were examined over 2 years in two locations in two test populations constructed from a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058). Of the 169 heterotic loci (HL) associated with grain yield and its five components identified in CSSL × Zheng58 and CSSL × Xun9058 test populations, only 25 HL were detected in both populations. The comparison of quantitative trait loci (QTLs) detected in the CSSL population with HL detected in the two test populations revealed that only 15.46% and 17.35% of the HL in the given populations respectively, shared the same chromosomal regions as that of the corresponding QTLs and showed dominant effects as well as pleiotropism with additive and dominant effects. In addition, most of the HL (74.23% and 74.49%) had overdominant effects. These results suggest that overdominance is the main contributor to the effects of heterosis on grain yield and its components in maize, and different HL are associated with heterosis for different traits in different hybrids.
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Affiliation(s)
- Hongqiu Wang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangge Zhang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huili Yang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoyang Liu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huimin Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liang Yuan
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiyuan Fu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, China
| | - Dingming Kang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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22
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Wu FY, Tang CY, Guo YM, Yang MK, Yang RW, Lu GH, Yang YH. Comparison of miRNAs and Their Targets in Seed Development between Two Maize Inbred Lines by High-Throughput Sequencing and Degradome Analysis. PLoS One 2016; 11:e0159810. [PMID: 27463682 PMCID: PMC4962988 DOI: 10.1371/journal.pone.0159810] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/10/2016] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in plant growth, development, and response to environment. For identifying and comparing miRNAs and their targets in seed development between two maize inbred lines (i.e. PH6WC and PH4CV), two sRNAs and two degradome libraries were constructed. Through high-throughput sequencing and miRNA identification, 55 conserved and 24 novel unique miRNA sequences were identified in two sRNA libraries; moreover, through degradome sequencing and analysis, 137 target transcripts corresponding to 38 unique miRNA sequences were identified in two degradome libraries. Subsequently, 16 significantly differentially expressed miRNA sequences were verified by qRT-PCR, in which 9 verified sequences obviously target 30 transcripts mainly involved with regulation in flowering and development in embryo. Therefore, the results suggested that some miRNAs (e.g. miR156, miR171, miR396 and miR444) related reproductive development might differentially express in seed development between the PH6WC and PH4CV maize inbred lines in this present study.
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Affiliation(s)
- Feng-Yao Wu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Cheng-Yi Tang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yu-Min Guo
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Min-Kai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Rong-Wu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Gui-Hua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yong-Hua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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23
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Li D, Liu Z, Gao L, Wang L, Gao M, Jiao Z, Qiao H, Yang J, Chen M, Yao L, Liu R, Kan Y. Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L. PLoS One 2016; 11:e0153168. [PMID: 27082634 PMCID: PMC4833412 DOI: 10.1371/journal.pone.0153168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/24/2016] [Indexed: 11/23/2022] Open
Abstract
The development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels, and miRNAs play important roles during this process. Although a number of miRNAs have been identified in maize seed, the ones involved in the early development of grains and in different lines of maize have not been well studied. Here, we profiled four small RNA libraries, each constructed from groups of immature grains of Zea mays inbred line Chang 7–2 collected 4–6, 7–9, 12–14, and 18–23 days after pollination (DAP). A total of 40 known (containing 111 unique miRNAs) and 162 novel (containing 196 unique miRNA candidates) miRNA families were identified. For conserved and novel miRNAs with over 100 total reads, 44% had higher accumulation before the 9th DAP, especially miR166 family members. 42% of miRNAs had highest accumulation during 12–14 DAP (which is the transition stage from embryogenesis to nutrient storage). Only 14% of miRNAs had higher expression 18–23 DAP. Prediction of potential targets of all miRNAs showed that 165 miRNA families had 377 target genes. For miR164 and miR166, we showed that the transcriptional levels of their target genes were significantly decreased when co-expressed with their cognate miRNA precursors in vivo. Further analysis shows miR159, miR164, miR166, miR171, miR390, miR399, and miR529 families have putative roles in the embryogenesis of maize grain development by participating in transcriptional regulation and morphogenesis, while miR167 and miR528 families participate in metabolism process and stress response during nutrient storage. Our study is the first to present an integrated dynamic expression pattern of miRNAs during maize kernel formation and maturation.
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Affiliation(s)
- Dandan Li
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zongcai Liu
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lei Gao
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Lifang Wang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Meijuan Gao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zhujin Jiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Huili Qiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Jianwei Yang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Min Chen
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- * E-mail: (RYL); (YCK)
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
- * E-mail: (RYL); (YCK)
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24
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Li Y, Wang C, Liu X, Song J, Li H, Sui Z, Zhang M, Fang S, Chu J, Xin M, Xie C, Zhang Y, Sun Q, Ni Z. Up-regulating the abscisic acid inactivation gene ZmABA8ox1b contributes to seed germination heterosis by promoting cell expansion. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2889-900. [PMID: 27034328 PMCID: PMC4861030 DOI: 10.1093/jxb/erw131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Heterosis has been widely used in agriculture, but the underlying molecular principles are still largely unknown. During seed germination, we observed that maize (Zea mays) hybrid B73/Mo17 was less sensitive than its parental inbred lines to exogenous abscisic acid (ABA), and endogenous ABA content in hybrid embryos decreased more rapidly than in the parental inbred lines. ZmABA8ox1b, an ABA inactivation gene, was consistently more highly up-regulated in hybrid B73/Mo17 than in its parental inbred lines at early stages of seed germination. Moreover, ectopic expression of ZmABA8ox1b obviously promoted seed germination in Arabidopsis Remarkably, microscopic observation revealed that cell expansion played a major role in the ABA-mediated maize seed germination heterosis, which could be attributed to the altered expression of cell wall-related genes.
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Affiliation(s)
- Yangyang Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Cheng Wang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Jian Song
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Hongjian Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Ming Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Shuang Fang
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Yirong Zhang
- National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China National Plant Gene Research Center (Beijing), Beijing 100193, China
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25
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Hardigan MA, Crisovan E, Hamilton JP, Kim J, Laimbeer P, Leisner CP, Manrique-Carpintero NC, Newton L, Pham GM, Vaillancourt B, Yang X, Zeng Z, Douches DS, Jiang J, Veilleux RE, Buell CR. Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum. THE PLANT CELL 2016; 28:388-405. [PMID: 26772996 PMCID: PMC4790865 DOI: 10.1105/tpc.15.00538] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 12/29/2015] [Accepted: 01/14/2016] [Indexed: 05/02/2023]
Abstract
Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways.
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Affiliation(s)
- Michael A Hardigan
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Emily Crisovan
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jeongwoon Kim
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Parker Laimbeer
- Department of Horticulture, Virginia Tech, Blacksburg, Virginia 24061
| | - Courtney P Leisner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | | | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gina M Pham
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Xueming Yang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | | | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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26
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Wang J, Jian H, Wang T, Wei L, Li J, Li C, Liu L. Identification of microRNAs Actively Involved in Fatty Acid Biosynthesis in Developing Brassica napus Seeds Using High-Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1570. [PMID: 27822220 PMCID: PMC5075540 DOI: 10.3389/fpls.2016.01570] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/05/2016] [Indexed: 05/21/2023]
Abstract
Seed development has a critical role during the spermatophyte life cycle. In Brassica napus, a major oil crop, fatty acids are synthesized and stored in specific tissues during embryogenesis, and understanding the molecular mechanism underlying fatty acid biosynthesis during seed development is an important research goal. In this study, we constructed three small RNA libraries from early seeds at 14, 21, and 28 days after flowering (DAF) and used high-throughput sequencing to examine microRNA (miRNA) expression. A total of 85 known miRNAs from 30 families and 1160 novel miRNAs were identified, of which 24, including 5 known and 19 novel miRNAs, were found to be involved in fatty acid biosynthesis.bna-miR156b, bna-miR156c, bna-miR156g, novel_mir_1706, novel_mir_1407, novel_mir_173, and novel_mir_104 were significantly down-regulated at 21 DAF and 28 DAF, whereas bna-miR159, novel_mir_1081, novel_mir_19 and novel_mir_555 were significantly up-regulated. In addition, we found that some miRNAs regulate functional genes that are directly involved in fatty acid biosynthesis and that other miRNAs regulate the process of fatty acid biosynthesis by acting on a large number of transcription factors. The miRNAs and their corresponding predicted targets were partially validated by quantitative RT-PCR. Our data suggest that diverse and complex miRNAs are involved in the seed development process and that miRNAs play important roles in fatty acid biosynthesis during seed development.
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Affiliation(s)
- Jia Wang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Nanchong Academy of Agricultural SciencesNanchong, China
| | - Hongju Jian
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Tengyue Wang
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Lijuan Wei
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Chao Li
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Guizhou Province Institute of Oil CropsGuiyang, China
- *Correspondence: Chao Li
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Liezhao Liu
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27
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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28
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Jin X, Fu Z, Lv P, Peng Q, Ding D, Li W, Tang J. Identification and Characterization of microRNAs during Maize Grain Filling. PLoS One 2015; 10:e0125800. [PMID: 25951054 PMCID: PMC4423906 DOI: 10.1371/journal.pone.0125800] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 03/26/2015] [Indexed: 12/23/2022] Open
Abstract
The grain filling rate is closely associated with final grain yield of maize during the period of maize grain filling. To identify the key microRNAs (miRNAs) and miRNA-dependent gene regulation networks of grain filling in maize, a deep-sequencing technique was used to research the dynamic expression patternsof miRNAs at four distinct developmental grain filling stages in Zhengdan 958, which is an elite hybrid and cultivated widely in China. The sequencing result showed that the expression amount of almost all miRNAs was changing with the development of the grain filling and formed in seven groups. After normalization, 77 conserved miRNAs and 74 novel miRNAs were co-detected in these four samples. Eighty-one out of 162 targets of the conserved miRNAs belonged to transcriptional regulation (81, 50%), followed by oxidoreductase activity (18, 11%), signal transduction (16, 10%) and development (15, 9%). The result showed that miRNA 156, 393, 396 and 397, with their respective targets, might play key roles in the grain filling rate by regulating maize growth, development and environment stress response. The result also offered novel insights into the dynamic change of miRNAs during the developing process of maize kernels and assistedin the understanding of how miRNAs are functioning about the grain filling rate.
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Affiliation(s)
- Xining Jin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Panqing Lv
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qian Peng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Li
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- * E-mail:
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Investigating the molecular genetic basis of heterosis for internode expansion in maize by microRNA transcriptomic deep sequencing. Funct Integr Genomics 2014; 15:261-70. [PMID: 25394807 DOI: 10.1007/s10142-014-0411-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 01/17/2023]
Abstract
Heterosis has been used widely in the breeding of maize and other crops and plays an important role in increasing yield, improving quality, and enhancing stress resistance, but its molecular mechanism is far from clear. To determine whether microRNA (miRNA)-dependent gene regulation is responsible for heterosis of elongating internodes below the ear and ear height in maize, a deep-sequencing strategy was applied to the elite hybrid Xundan20, which is currently cultivated widely in China, and its two parents. RNA was extracted from the eighth internode because it shows clear internode length heterosis. A total of 99 conserved maize miRNAs were detected in both the hybrid and parental lines. Most of these miRNAs were expressed nonadditively in the hybrid compared with its parental lines. These results indicated that miRNAs might participate in heterosis during internode expansion in maize and exert an influence on ear and plant height via the repression of their target genes. In total, eight novel miRNAs belonging to four miRNA families were predicted in the expanding internode. Global repression of miRNAs in the hybrid, which might result in enhanced gene expression, might be one reason why the hybrid shows longer internodes and taller seedlings compared with its parental lines.
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30
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Zhang L, Peng Y, Wei X, Dai Y, Yuan D, Lu Y, Pan Y, Zhu Z. Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5989-6002. [PMID: 25129133 PMCID: PMC4203131 DOI: 10.1093/jxb/eru337] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yonggang Peng
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yan Dai
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Dawei Yuan
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yufei Lu
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yangyang Pan
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
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Kong X, Zhang M, Xu X, Li X, Li C, Ding Z. System analysis of microRNAs in the development and aluminium stress responses of the maize root system. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1108-21. [PMID: 24985700 DOI: 10.1111/pbi.12218] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes through mRNA cleavage or translational inhibition. miRNA is known to play an important role in the root development and environmental responses in both the Arabidopsis and rice. However, little information is available to form a complete view of miRNAs in the development of the maize root system and Al stress responses in maize. Four sRNA libraries were generated and sequenced from the early developmental stage of primary roots (PRY), the later developmental stage of maize primary roots (PRO), seminal roots (SR) and crown roots (CR). Through integrative analysis, we identified 278 miRNAs (246 conserved and 32 novel ones) and found that the expression patterns of miRNAs differed dramatically in different maize roots. The potential targets of the identified conserved and novel miRNAs were also predicted. In addition, our data showed that CR is more resistant to Al stress compared with PR and SR, and the differentially expressed miRNAs are likely to play significant roles in different roots in response to environmental stress such as Al stress. Here, we demonstrate that the expression patterns of miRNAs are highly diversified in different maize roots. The differentially expressed miRNAs are correlated with both the development and environmental responses in the maize root. This study not only improves our knowledge about the roles of miRNAs in maize root development but also reveals the potential role of miRNAs in the environmental responses of different maize roots.
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Affiliation(s)
- Xiangpei Kong
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, China
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Fu D, Xiao M, Hayward A, Jiang G, Zhu L, Zhou Q, Li J, Zhang M. What is crop heterosis: new insights into an old topic. J Appl Genet 2014; 56:1-13. [PMID: 25027629 DOI: 10.1007/s13353-014-0231-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/28/2014] [Accepted: 07/01/2014] [Indexed: 01/09/2023]
Abstract
Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically diverse individuals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the 'omics' of heterosis and the role of non-coding regions, particularly in relation to energy-use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive 'omics' networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.
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Affiliation(s)
- Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China,
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Han J, Xie H, Sun Q, Wang J, Lu M, Wang W, Guo E, Pan J. Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica). Gene 2014; 546:367-77. [PMID: 24862217 DOI: 10.1016/j.gene.2014.05.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 02/06/2023]
Abstract
MiRNAs are a novel group of non-coding small RNAs that negatively regulate gene expression. Many miRNAs have been identified and investigated extensively in plant species with sequenced genomes. However, few miRNAs have been identified in foxtail millet (Setaria italica), which is an ancient cereal crop of great importance for dry land agriculture. In this study, 271 foxtail millet miRNAs belonging to 44 families were identified using a bioinformatics approach. Twenty-three pairs of sense/antisense miRNAs belonging to 13 families, and 18 miRNA clusters containing members of 8 families were discovered in foxtail millet. We identified 432 potential targets for 38 miRNA families, most of which were predicted to be involved in plant development, signal transduction, metabolic pathways, disease resistance, and environmental stress responses. Gene ontology (GO) analysis revealed that 101, 56, and 23 target genes were involved in molecular functions, biological processes, and cellular components, respectively. We investigated the expression patterns of 43 selected miRNAs using qRT-PCR analysis. All of the miRNAs were expressed ubiquitously with many exhibiting different expression levels in different tissues. We validated five predicted targets of four miRNAs using the RNA ligase mediated rapid amplification of cDNA end (5'-RLM-RACE) method.
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Affiliation(s)
- Jun Han
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
| | - Hao Xie
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Qingpeng Sun
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jun Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi 046011, China
| | - Min Lu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Weixiang Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi 046011, China
| | - Jinbao Pan
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
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Liu YX, Wang M, Wang XJ. Endogenous small RNA clusters in plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:64-71. [PMID: 24769055 PMCID: PMC4411336 DOI: 10.1016/j.gpb.2014.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/09/2014] [Accepted: 04/15/2014] [Indexed: 11/25/2022]
Abstract
In plants, small RNAs (sRNAs) usually refer to non-coding RNAs (ncRNAs) with lengths of 20–24 nucleotides. sRNAs are involved in the regulation of many essential processes related to plant development and environmental responses. sRNAs in plants are mainly grouped into microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the latter can be further classified into trans-acting siRNAs (ta-siRNAs), repeat-associated siRNAs (ra-siRNAs), natural anti-sense siRNAs (nat-siRNAs), etc. Many sRNAs exhibit a clustered distribution pattern in the genome. Here, we summarize the features and functions of cluster-distributed sRNAs, aimed to not only provide a thorough picture of sRNA clusters (SRCs) in plants, but also shed light on the identification of new classes of functional sRNAs.
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Affiliation(s)
- Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Liu H, Qin C, Chen Z, Zuo T, Yang X, Zhou H, Xu M, Cao S, Shen Y, Lin H, He X, Zhang Y, Li L, Ding H, Lübberstedt T, Zhang Z, Pan G. Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing. BMC Genomics 2014; 15:25. [PMID: 24422852 PMCID: PMC3901417 DOI: 10.1186/1471-2164-15-25] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages. RESULTS We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed. CONCLUSIONS This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
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Meng F, Liu H, Wang K, Liu L, Wang S, Zhao Y, Yin J, Li Y. Development-associated microRNAs in grains of wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2013; 13:140. [PMID: 24060047 PMCID: PMC4015866 DOI: 10.1186/1471-2229-13-140] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/20/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes by mRNA degradation or translational repression. Numerous plant miRNAs have been identified. Evidence is increasing for their crucial roles during plant development. In the globally important crop of wheat (Triticum aestivum L.), the process by which grains are formed determines yield and end-use quality. However, little is known about miRNA-mediated developmental regulation of grain production. Here, we applied high-throughput sRNA sequencing and genome-wide mining to identify miRNAs potentially involved in the developmental regulation of wheat grains. RESULTS Four sRNA libraries were generated and sequenced from developing grains sampled at 5, 15, 25, and 30 days after pollination (DAP). Through integrative analysis, we identified 605 miRNAs (representing 540 families) and found that 86 are possibly involved in the control of grain-filling. Additionally, 268 novel miRNAs (182 families) were identified, with 18 of them also potentially related to that maturation process. Our target predictions indicated that the 104 grain filling-associated miRNAs might target a set of wheat genes involved in various biological processes, including the metabolism of carbohydrates and proteins, transcription, cellular transport, cell organization and biogenesis, stress responses, signal transduction, and phytohormone signaling. Together, these results demonstrate that the developmental steps by which wheat grains are filled is correlated with miRNA-mediated gene regulatory networks. CONCLUSIONS We identified 605 conserved and 268 novel miRNAs from wheat grains. Of these, 104 are potentially involved in the regulation of grain-filling. Our dataset provides a useful resource for investigating miRNA-mediated regulatory mechanisms in cereal grains, and our results suggest that miRNAs contribute to this regulation during a crucial phase in determining grain yield and flour quality.
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Affiliation(s)
- Fanrong Meng
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Liu
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Ketao Wang
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Lulu Liu
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Shaohui Wang
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanhong Zhao
- College of Agriculture, Ludong University, Yantai 264025, China
| | - Jun Yin
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Yongchun Li
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
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Zhao Y, Xu Z, Mo Q, Zou C, Li W, Xu Y, Xie C. Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize. ANNALS OF BOTANY 2013; 112:633-42. [PMID: 23788746 PMCID: PMC3718221 DOI: 10.1093/aob/mct133] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS MicroRNAs (miRNAs) play an important role in the responses and adaptation of plants to many stresses including low nitrogen (LN). Characterizing relevant miRNAs will improve our understanding of nitrogen (N) use efficiency and LN tolerance and thus contribute to sustainable maize production. The objective of this study was to identify novel and known miRNAs and their targets involved in the response and adaptation of maize (Zea mays) to LN stress. METHODS MiRNAs and their targets were identified by combined analysis of deep sequencing of small RNA and degradome libraries. The identity of target genes was confirmed by gene-specific RNA ligase-mediated rapid amplification of 5' cDNA ends (RLM-RACE) and by quantitative expression analysis. KEY RESULTS Over 150 million raw reads of small RNA and degradome sequence data were generated. A total of 46 unique mature miRNA sequences belonging to 23 maize miRNA families were sequenced. Eighty-five potentially new miRNAs were identified, with corresponding miRNA* also identified for 65 of them. Twenty-five new miRNAs showed >2-fold relative change in response to LN. In addition to known miR169 species, two novel putative miR169 species were identified. Deep sequencing of miRNAs and the degradome, and RLM-RACE and quantitative polymerase chain reaction (PCR) analyses of their targets showed that miRC10- and miRC68-mediated target cleavage may play a major role among miR169 families in the adaptation to LN by maize seedlings. CONCLUSIONS Small RNA and degradome sequencing combined with quantitative reverse transcription-PCR and RLM-RACE verification enabled the efficient identification of miRNAs and their target genes. The generated data sets and the two novel miR169 species that were identified will contribute to our understanding of the physiological basis of adaptation to LN stress in maize plants.
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Affiliation(s)
- Yongping Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Zhenhua Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Qiaocheng Mo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
- Anhui Agricultural University, Hefei, Anhui Province, 230036, China
| | - Cheng Zou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Wenxue Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- For correspondence. E-mail or
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
- For correspondence. E-mail or
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He G, He H, Deng XW. Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis. J Genet Genomics 2013; 40:205-10. [DOI: 10.1016/j.jgg.2013.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/28/2013] [Accepted: 03/28/2013] [Indexed: 01/09/2023]
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Reciprocal cross differences in Drosophila melanogaster longevity: an evidence for non-genomic effects in heterosis phenomenon? Biogerontology 2013; 14:153-63. [PMID: 23529279 DOI: 10.1007/s10522-013-9419-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/21/2013] [Indexed: 12/20/2022]
Abstract
Reciprocal cross effects (i.e., differences between reciprocal hybrids that are developed by reversing the strains from which the dam and the sire are taken) are commonly used as a measure of sex-linkage or maternal effects. However, the papers reporting parental effects on life span of experimental animals are scarce. In order to investigate the potential of parent-of-origin effects for the longevity of hybrids, we determined the life spans of the inbred lines of Drosophila melanogaster [Oregon-R (OR), Canton-S (CS) and Uman (Um)] that differ significantly in longevity, as well as the life span of the progeny from the reciprocal crosses among them. The hybridization caused the increase in both flies' mean and maximum life span mainly shifting the survival curves upward proportionally at all ages. This resulted in the reduction in the Gompertz intercept (frailty) whereas the Gompertz slope (the rate of aging) was predominantly unchanged. Better-parent heterosis was observed in hybrids between OR and Um inbred lines and the extent of heterosis was more pronounced in hybrids between CS and Um inbred lines if long-lived parent was used as the female parent, and short-lived parent was used as the male parent in the crossing scheme. Such discrepancy in life span between reciprocal crosses may indicate that non-chromosomal factors are significantly contributing to a heterotic response. Our data are in line with the previous reports suggesting the involvement of non-genomic factors, particularly epigenetic events attributed to hybridization, in the manifestation of heterosis.
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Baranwal VK, Mikkilineni V, Zehr UB, Tyagi AK, Kapoor S. Heterosis: emerging ideas about hybrid vigour. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6309-14. [PMID: 23095992 DOI: 10.1093/jxb/ers291] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Perceived by Charles Darwin in many vegetable plants and rediscovered by George H Shull and Edward M East in maize, heterosis or hybrid vigour is one of the most widely utilized phenomena, not only in agriculture but also in animal breeding. Although, numerous studies have been carried out to understand its genetic and/or molecular basis in the past 100 years, our knowledge of the underlying molecular processes that results in hybrid vigour can best be defined as superficial. Even after century long deliberations, there is no consensus on the relative/individual contribution of the genetic/epigenetic factors in the manifestation of heterosis. However, with the recent advancements in functional genomics, transcriptomics, proteomics, and metabolomics-related technologies, the riddle of heterosis is being reinvestigated by adopting systems-level approaches to understand the underlying molecular mechanisms. A number of intriguing hypotheses are converging towards the idea of a cumulative positive effect of the differential expression of a variety of genes, on one or several yield-affecting metabolic pathways or overall energy-use efficiency, as the underlying mechanism for the manifestation of heterosis. Presented here is a brief account of clues gathered from various investigative approaches targeted towards better scientific understanding of this process.
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Affiliation(s)
- Vinay Kumar Baranwal
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, New Delhi-110021, India
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Kaeppler S. Heterosis: Many Genes, Many Mechanisms—End the Search for an Undiscovered Unifying Theory. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/682824] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Heterosis is the increase in vigor that is observed in progenies of matings of diverse individuals from different species, isolated populations, or selected strains within species or populations. Heterosis has been of immense economic value in agriculture and has important implications regarding the fitness and fecundity of individuals in natural populations. Genetic models based on complementation of deleterious alleles, especially in the context of linkage and epistasis, are consistent with many observed manifestations of heterosis. The search for the genes and alleles that underlie heterosis, as well as for broader allele-independent, genomewide mechanisms, has encompassed many species and systems. Common themes across these studies indicate that sequence diversity is necessary but not sufficient to produce heterotic phenotypes, and that the molecular pathways that produce heterosis involve chromatin modification, transcriptional control, translation and protein processing, and interactions between and within developmental and biochemical pathways. Taken together, there are many and diverse molecular mechanisms that translate DNA into phenotype, and it is the combination of all these mechanisms across many genes that produce heterosis in complex traits.
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Affiliation(s)
- Shawn Kaeppler
- Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
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