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Baldauf JA, Hochholdinger F. Molecular dissection of heterosis in cereal roots and their rhizosphere. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:173. [PMID: 37474870 PMCID: PMC10359381 DOI: 10.1007/s00122-023-04419-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
Heterosis is already manifested early in root development. Consistent with the dominance model of heterosis, gene expression complementation is a general mechanism that contributes to phenotypic heterosis in maize hybrids. Highly heterozygous F1-hybrids outperform their parental inbred lines, a phenomenon known as heterosis. Utilization of heterosis is of paramount agricultural importance and has been widely applied to increase yield in many crop cultivars. Plant roots display heterosis for many traits and are an important target for further crop improvement. To explain the molecular basis of heterosis, several genetic hypotheses have been proposed. In recent years, high-throughput gene expression profiling techniques have been applied to investigate hybrid vigor. Consistent with the classical genetic dominance model, gene expression complementation has been demonstrated to be a general mechanism to contribute to phenotypic heterosis in diverse maize hybrids. Functional classification of these genes supported the notion that gene expression complementation can dynamically promote hybrid vigor under fluctuating environmental conditions. Hybrids tend to respond differently to available nutrients in the soil. It was hypothesized that hybrid vigor is promoted through a higher nutrient use efficiency which is linked to an improved root system performance of hybrids in comparison to their inbred parents. Recently, the interaction between soil microbes and their plant host was added as further dimension to disentangle heterosis in the belowground part of plants. Soil microbes influenced the performance of maize hybrids as illustrated in comparisons of sterile soil and soil inhabited by beneficial microorganisms.
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Affiliation(s)
- Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany.
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Luo JH, Wang M, Jia GF, He Y. Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2933-2946. [PMID: 33606877 PMCID: PMC8023220 DOI: 10.1093/jxb/erab074] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/12/2021] [Indexed: 05/14/2023]
Abstract
Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.
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Affiliation(s)
- Jin-Hong Luo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Min Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Gui-Fang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
- Correspondence:
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Zhang X, Ma C, Wang X, Wu M, Shao J, Huang L, Yuan L, Fu Z, Li W, Zhang X, Guo Z, Tang J. Global transcriptional profiling between inbred parents and hybrids provides comprehensive insights into ear-length heterosis of maize (Zea mays). BMC PLANT BIOLOGY 2021; 21:118. [PMID: 33637040 PMCID: PMC7908659 DOI: 10.1186/s12870-021-02890-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Maize (Zea mays) ear length, which is an important yield component, exhibits strong heterosis. Understanding the potential molecular mechanisms of ear-length heterosis is critical for efficient yield-related breeding. RESULTS Here, a joint netted pattern, including six parent-hybrid triplets, was designed on the basis of two maize lines harboring long (T121 line) and short (T126 line) ears. Global transcriptional profiling of young ears (containing meristem) was performed. Multiple comparative analyses revealed that 874 differentially expressed genes are mainly responsible for the ear-length variation between T121 and T126 lines. Among them, four key genes, Zm00001d049958, Zm00001d027359, Zm00001d048502 and Zm00001d052138, were identified as being related to meristem development, which corroborated their roles in the superior additive genetic effects on ear length in T121 line. Non-additive expression patterns were used to identify candidate genes related to ear-length heterosis. A non-additively expressed gene (Zm00001d050649) was associated with the timing of meristematic phase transition and was determined to be the homolog of tomato SELF PRUNING, which assists SINGLE FLOWER TRUSS in driving yield-related heterosis, indicating that Zm00001d050649 is a potential contributor to drive heterotic effect on ear length. CONCLUSION Our results suggest that inbred parents provide genetic and heterotic effects on the ear lengths of their corresponding F1 hybrids through two independent pathways. These findings provide comprehensive insights into the transcriptional regulation of ear length and improve the understanding of ear-length heterosis in maize.
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Affiliation(s)
- Xiangge Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Chenchen Ma
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Xiaoqing Wang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Mingbo Wu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Jingkuan Shao
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Li Huang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Liang Yuan
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Weihua Li
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450018, China.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 433200, China.
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Wang D, Mu Y, Hu X, Ma B, Wang Z, Zhu L, Xu J, Huang C, Pan Y. Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively. BMC PLANT BIOLOGY 2021; 21:34. [PMID: 33422018 PMCID: PMC7796551 DOI: 10.1186/s12870-020-02806-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/20/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids. RESULTS Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. CONCLUSIONS Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.
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Affiliation(s)
- Daoping Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yongying Mu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Xiaojiao Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, People's Republic of China
| | - Bo Ma
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, People's Republic of China
| | - Zhibo Wang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, People's Republic of China
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Jiang Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Changling Huang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, People's Republic of China.
| | - Yinghong Pan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, People's Republic of China.
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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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Baldauf JA, Vedder L, Schoof H, Hochholdinger F. Robust non-syntenic gene expression patterns in diverse maize hybrids during root development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:865-876. [PMID: 31638701 DOI: 10.1093/jxb/erz452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Distantly related maize (Zea mays L.) inbred lines exhibit an exceptional degree of structural genomic diversity, which is probably unique among plants. This study systematically investigated the developmental and genotype-dependent regulation of the primary root transcriptomes of a genetically diverse panel of maize F1-hybrids and their parental inbred lines. While we observed substantial transcriptomic changes during primary root development, we demonstrated that hybrid-associated gene expression patterns, including differential, non-additive, and allele-specific transcriptome profiles, are particularly robust to these developmental fluctuations. For instance, differentially expressed genes with preferential expression in hybrids were highly conserved during development in comparison to their parental counterparts. Similarly, in hybrids a major proportion of non-additively expressed genes with expression levels between the parental values were particularly conserved during development. Importantly, in these expression patterns non-syntenic genes that evolved after the separation of the maize and sorghum lineages were systemically enriched. Furthermore, non-syntenic genes were substantially linked to the conservation of all surveyed gene expression patterns during primary root development. Among all F1-hybrids, between ~40% of the non-syntenic genes with unexpected allelic expression ratios and ~60% of the non-syntenic differentially and non-additively expressed genes were conserved and therefore robust to developmental changes. Hence, the enrichment of non-syntenic genes during primary root development might be involved in the developmental adaptation of maize roots and thus the superior performance of hybrids.
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Affiliation(s)
- Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Lucia Vedder
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
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7
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MEENA RK, PULLAIAHGARI D, GUDIPALLI P. Proteomic analysis of heterotic seed germination in maize using F1 hybrid DHM 117 and its parental inbreds. Turk J Biol 2018; 42:345-363. [PMID: 30814898 PMCID: PMC6392162 DOI: 10.3906/biy-1803-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
A number of differentially expressed proteins (DEPs) were identified in comparative two-dimensional gel electrophoresis analysis of dry and 24-h water-imbibed seeds of maize F1 hybrid DHM 117 (BML 6 × BML 7) and its parental inbreds. Of the DEPs, 53.4% (86/161) in dry seeds and 58% (127/219) in water-imbibed seeds exhibited a nonadditive pattern in the F1 hybrid as compared to parental inbreds. A total of 30 DEPs were categorized into different biological processes, most of which were related to metabolism and energy (34%), followed by storage proteins (27%), stress response (23%), transcription and translation (7%), cell cycle (3%), and hormone biosynthesis (3%). The transcript accumulation pattern of 8 selected genes corresponding to DEPs was examined using qRTPCR. Interestingly, LEA protein Rab28 showed higher accumulation in dry seeds at both protein and transcript levels, whereas indole3-acetaldehyde oxidase showed lower accumulation in water-imbibed seeds of the F1 hybrid than the female parent at the protein level. Thus, the DEPs particularly involved in metabolic and energy processes, as well as hormone biosynthesis in the F 1 hybrid, might be responsible for heterotic seed germination in the F1 hybrid. The DEPs identified in this study provide a scope for improving the seed germination trait of agricultural crops.
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Affiliation(s)
- Rajesh Kumar MEENA
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
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Gachibowli, Hyderabad, Telangana
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India
| | - Durgeshwar PULLAIAHGARI
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
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Gachibowli, Hyderabad, Telangana
,
India
| | - Padmaja GUDIPALLI
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
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Gachibowli, Hyderabad, Telangana
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India
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8
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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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Hochholdinger F, Marcon C, Baldauf JA, Yu P, Frey FP. Proteomics of Maize Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:143. [PMID: 29556242 PMCID: PMC5844967 DOI: 10.3389/fpls.2018.00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/25/2018] [Indexed: 05/19/2023]
Abstract
Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.
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10
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Hu X, Wang H, Li K, Wu Y, Liu Z, Huang C. Genome-wide proteomic profiling reveals the role of dominance protein expression in heterosis in immature maize ears. Sci Rep 2017; 7:16130. [PMID: 29170427 PMCID: PMC5700959 DOI: 10.1038/s41598-017-15985-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/06/2017] [Indexed: 01/02/2023] Open
Abstract
Heterosis refers to the phenomenon in which hybrid progeny show superior performance relative to their parents. Early maize ear development shows strong heterosis in ear architecture traits and greatly affects grain yield. To explore the underlying molecular mechanisms, genome-wide proteomics of immature ears of maize hybrid ZD909 and its parents were analyzed using tandem mass tag (TMT) technology. A total of 9,713 proteins were identified in all three genotypes. Among them, 3,752 (38.6%) proteins were differentially expressed between ZD909 and its parents. Multiple modes of protein action were discovered in the hybrid, while dominance expression patterns accounted for 63.6% of the total differentially expressed proteins (DEPs). Protein pathway enrichment analysis revealed that high parent dominance proteins mainly participated in carbon metabolism and nitrogen assimilation processes. Our results suggested that the dominant expression of favorable alleles related to C/N metabolism in the hybrid may be essential for ZD909 ear growth and heterosis formation. Integrated analysis of proteomic and quantitative trait locus (QTL) data further support our DEP identification and provide useful information for the discovery of genes associated with ear development. Our study provides comprehensive insight into the molecular mechanisms underlying heterosis in immature maize ears from a proteomic perspective.
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Affiliation(s)
- Xiaojiao Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Hongwu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Kun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Yujin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Zhifang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China.
| | - Changling Huang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China.
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Ning F, Wu X, Zhang H, Wu Z, Niu L, Yang H, Wang W. Accumulation Profiles of Embryonic Salt-Soluble Proteins in Maize Hybrids and Parental Lines Indicate Matroclinous Inheritance: A Proteomic Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:1824. [PMID: 29118775 PMCID: PMC5661082 DOI: 10.3389/fpls.2017.01824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/10/2017] [Indexed: 05/29/2023]
Abstract
Maize is one of the most widely cultivated crops. It accumulates a large quantity of seed storage proteins, which are important for seed development and germination, and contribute to the nutritional quality of seeds. Based on solubility, the storage proteins are divided into albumins (water-soluble), globulins (salt-soluble), prolamins (alcohol-soluble), and glutelins (acid- or alkali-soluble). Maize hybrids are cultivated due to the superior performance of F1 hybrids than that of their parents, a phenomenon known as heterosis. However, the accumulation patterns of seed storage proteins in maize embryos between the hybrids and their parental inbred lines have not been compared. In the present study, two elite inbred lines of China, Zheng 58 and Chang 7-2, and their reciprocal hybrids (Zheng 58 × Chang 7-2 and Chang 7-2 × Zheng 58) were used to explore parental influences on the accumulation patterns of seed storage proteins in maize embryos. For this purpose, we focused on seed salt-soluble proteins (SSPs) in our experiments. The SSPs were selectively extracted from maize mature embryos after extensive removal of water-soluble albumin and separated using two-dimensional gel electrophoresis (2-DE), followed by mass spectrometry analysis. Our results indicated that the 2-DE SSP profiles of hybrids closely resembled those of their maternal parent rather than the paternal parent. In other words, 2-DE SSP profiles of Zheng 58 × Chang 7-2 were more similar those of Zheng 58 whereas such profiles of Chang 7-2 × Zheng 58 were more similar to those of Chang 7-2 although the 2-DE profiles of all four maize types were quite similar. In total, 12 relatively abundant SSPs spots representing five kinds of proteins were identified, of which nine protein spots displayed non-additive accumulation in at least one hybrid. This study provided additional data on dominance and partial dominance effects on maize hybrids embryos. Besides, earlier studies on accumulation profiles of globulin-1 (also known as vicilin), which is one of the most abundant globulins in maize embryos, also support the above results. This study would be helpful in revealing the mechanisms underlying SSPs accumulation patterns in the hybrids.
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The disadvantages of being a hybrid during drought: A combined analysis of plant morphology, physiology and leaf proteome in maize. PLoS One 2017; 12:e0176121. [PMID: 28419152 PMCID: PMC5395237 DOI: 10.1371/journal.pone.0176121] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/05/2017] [Indexed: 12/02/2022] Open
Abstract
A comparative analysis of various parameters that characterize plant morphology, growth, water status, photosynthesis, cell damage, and antioxidative and osmoprotective systems together with an iTRAQ analysis of the leaf proteome was performed in two inbred lines of maize (Zea mays L.) differing in drought susceptibility and their reciprocal F1 hybrids. The aim of this study was to dissect the parent-hybrid relationships to better understand the mechanisms of the heterotic effect and its potential association with the stress response. The results clearly showed that the four examined genotypes have completely different strategies for coping with limited water availability and that the inherent properties of the F1 hybrids, i.e. positive heterosis in morphological parameters (or, more generally, a larger plant body) becomes a distinct disadvantage when the water supply is limited. However, although a greater loss of photosynthetic efficiency was an inherent disadvantage, the precise causes and consequences of the original predisposition towards faster growth and biomass accumulation differed even between reciprocal hybrids. Both maternal and paternal parents could be imitated by their progeny in some aspects of the drought response (e.g., the absence of general protein down-regulation, changes in the levels of some carbon fixation or other photosynthetic proteins). Nevertheless, other features (e.g., dehydrin or light-harvesting protein contents, reduced chloroplast proteosynthesis) were quite unique to a particular hybrid. Our study also confirmed that the strategy for leaving stomata open even when the water supply is limited (coupled to a smaller body size and some other physiological properties), observed in one of our inbred lines, is associated with drought-resistance not only during mild drought (as we showed previously) but also during more severe drought conditions.
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Dahal D, Newton KJ, Mooney BP. Quantitative Proteomics of Zea mays Hybrids Exhibiting Different Levels of Heterosis. J Proteome Res 2016; 15:2445-54. [DOI: 10.1021/acs.jproteome.5b01120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Diwakar Dahal
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Kathleen J. Newton
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Brian P. Mooney
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
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Ma J, Li J, Cao Y, Wang L, Wang F, Wang H, Li H. Comparative Study on the Transcriptome of Maize Mature Embryos from Two China Elite Hybrids Zhengdan958 and Anyu5. PLoS One 2016; 11:e0158028. [PMID: 27332982 PMCID: PMC4917089 DOI: 10.1371/journal.pone.0158028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 06/08/2016] [Indexed: 11/30/2022] Open
Abstract
Zhengdan958 and Anyu5 are two elite maize hybrids of China, which manifest similar paternal lines (Chang7-2) but different maternal lines (Zheng58 and Ye478). Zhengdan958 has a 10–15% yield advantage over Anyu5. In this study, we applied digital gene expression technology to analyze transcriptomes of mature embryos from the two hybrids and their parents, aimed to investigate molecular mechanism of heterosis and genetic effects of maternal lines. Results showed that 71.66% and 49.70% of differentially expressed genes exhibited non-additive expression in Zhengdan958 and Anyu5, respectively. The number of non-additive genes involved in abiotic and biotic stress responses in Zhengdan958 was higher than that in Anyu5, which was in agreement with their phenotypic performance. Furthermore, common over-dominance and under-dominance genes (137 and 162, respectively) between the two hybrids focused on plant development and abiotic stress response. Zhengdan958 contained 97 maternal expression-level dominance (maternal-ELD) genes, and the number was higher than that of Anyu5 (45). Common up-regulated maternal-ELD genes were significantly enriched in meristem and shoot development while common down-regulated maternal-ELD genes were involved in pyruvate metabolic process, negative regulation of catalytic activity and response to stress. Therefore, non-additive genes mainly contribute to heterosis in Zhengdan958, including many genes for plant development, abiotic and biotic stress responses. Maternal effects may play important roles in maize heterosis.
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Affiliation(s)
- Juan Ma
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Jingjing Li
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yanyong Cao
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Lifeng Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Fei Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Hao Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Huiyong Li
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- * E-mail:
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Proteomic patterns associated with heterosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:908-15. [PMID: 26721744 DOI: 10.1016/j.bbapap.2015.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/29/2015] [Accepted: 12/18/2015] [Indexed: 12/14/2022]
Abstract
Heterosis is characterized by higher seed yields, plant biomass or other traits in heterozygotes or hybrids compared with their genetically divergent parents, which are often homozygous. Despite extensive investigation of heterosis and its wide application in crops such as maize, rice, wheat and sorghum, its molecular basis is still enigmatic. In the past century, some pioneers have proposed multigene models referring to the complementation of allelic and gene expression variation, which is likely to be an important contributor to heterosis. In addition, there are potential interactions of epigenetic variation involved in heterosis via novel mechanisms. At the level of gene expression, many recent studies have revealed that the heterosis phenomenon can be deciphered not only at the transcriptional level but also at the proteomic level. This review presents an update on the information supporting the involvement of proteomic patterns in heterosis and a possible future direction of the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Proteomic Analysis of Silk Viability in Maize Inbred Lines and Their Corresponding Hybrids. PLoS One 2015; 10:e0144050. [PMID: 26630375 PMCID: PMC4668103 DOI: 10.1371/journal.pone.0144050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 11/12/2015] [Indexed: 12/25/2022] Open
Abstract
A long period of silk viability is critical for a good seed setting rate in maize (Zea mays L.), especially for inbred lines and hybrids with a long interval between anthesis and silking. To explore the molecular mechanism of silk viability and its heterosis, three inbred lines with different silk viability characteristics (Xun928, Lx9801, and Zong3) and their two hybrids (Xun928×Zong3 and Lx9801×Zong3) were analyzed at different developmental stages by a proteomic method. The differentially accumulated proteins were identified by mass spectrometry and classified into metabolism, protein biosynthesis and folding, signal transduction and hormone homeostasis, stress and defense responses, and cellular processes. Proteins involved in nutrient (methionine) and energy (ATP) supply, which support the pollen tube growth in the silk, were important for silk viability and its heterosis. The additive and dominant effects at a single locus, as well as complex epistatic interactions at two or more loci in metabolic pathways, were the primary contributors for mid-parent heterosis of silk viability. Additionally, the proteins involved in the metabolism of anthocyanins, which indirectly negatively regulate local hormone accumulation, were also important for the mid-parent heterosis of silk viability. These results also might imply the developmental dependence of heterosis, because many of the differentially accumulated proteins made distinct contributions to the heterosis of silk viability at specific developmental stages.
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Di G, Luo X, Huang M, Chen J, Kong X, Miao X, Ke C. Proteomic profiling of eggs from a hybrid abalone and its parental lines: Haliotis discus hannai Ino and Haliotis gigantea. Anim Genet 2015; 46:646-54. [PMID: 26447358 DOI: 10.1111/age.12330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2015] [Indexed: 11/29/2022]
Abstract
Proteomic analysis was performed on the eggs of hybrid abalone and their corresponding parental lines. A total of 915 ± 19 stained protein spots were detected from Haliotis discus hannai♀ × H. discus hannai♂ (DD), 935 ± 16 from H. gigantea♀ × H. gigantea♂ (GG) and 923 ± 13 from H. gigantea♀ × H. discus hannai♂ (GD). The spots from DD and GD were clustered together. The distance between DD and GG was maximal by hierarchical cluster analysis. A total of 112 protein gel spots were identified; of these, 59 were abalone proteins. The proteins were involved in major biological processes including energy metabolism, proliferation, apoptosis, signal transduction, immunity, lipid metabolism, electron carrier proteins, protein biosynthesis and decomposition, and cytoskeletal structure. Three of 20 differential expression protein spots involved in energy metabolism exhibited as upregulated in GD, 13 spots exhibited additivity, and four spots exhibited as downregulated in the offspring. Eleven protein spots were expressed at the highest level in DD. The proteins involved in stress responses included superoxide dismutase, peroxiredoxin 6, thioredoxin peroxidase and glutathione-S-transferase. Two of seven differential expression protein spots involved in response to stress exhibited as upregulated in GD, three exhibited additivity, and two exhibited as downregulated. These results might suggest that proteomic approaches are suitable for the analysis of hybrids and the functional prediction of abalone hybridization.
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Affiliation(s)
- Guilan Di
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China.,State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Miaoqin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jun Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xianghui Kong
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xiulian Miao
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Proteomic analysis of muscle between hybrid abalone and parental lines Haliotis gigantea Reeve and Haliotis discus hannai Ino. Heredity (Edinb) 2015; 114:564-74. [PMID: 25669609 DOI: 10.1038/hdy.2014.124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 02/06/2023] Open
Abstract
To understand the potential molecular mechanism of heterosis, protein expression patterns were compared from hybrids of Haliotis gigantea (G) and Haliotis discus hannai (D) using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight analyses. Expression differences were observed in muscle samples from the four groups with 673±21.0 stained spots for H. discus hannai ♀ × H. discus hannai ♂ (DD), 692±25.6 for H. gigantea ♀ × H. gigantea ♂ (GG), 679±16.2 for H. discus hannai ♀ × H. gigantea ♂ (DG) (F1 hybrid) and 700±19 for H. gigantea ♀ × H. discus hannai ♂ (GD) (F1 hybrid). Different 2-DE image muscle protein spots had a mirrored relationship between purebreds and the F1 hybrid, suggesting that all stained spots in F1 hybrid muscle were on 2-DEs from parents. DD and DG clustered together first, and then clustered with GD, whereas the distance of DD and GG was maximal according to hierarchical cluster analysis. We identified 136 differentially expressed protein spots involved in major biological processes, including energy metabolism and stress response. Most energy metabolism proteins were additive, and stress-induced proteins displayed additivity or over-dominance. In these 136 identified protein spots, hybrid offspring with additivity or over-dominance accounted for 68.38%. Data show that a proteomic approach can provide functional prediction of abalone interspecific hybridization.
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Petersen R, Djozgic H, Rieger B, Rapp S, Schmidt ER. Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis. BMC PLANT BIOLOGY 2015; 15:34. [PMID: 25648715 PMCID: PMC4352258 DOI: 10.1186/s12870-014-0356-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/27/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Primary roots (radicles) represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals. Few studies have analyzed primary roots at a molecular level, and were mostly limited to Arabidopsis. Here we study the primary root transcriptomes of standard type, heterozygous columnar and homozygous columnar apple (Malus x domestica) by RNA-Seq and quantitative real-time PCR. The columnar growth habit is characterized by a stunted main axis and the development of short fruit spurs instead of long lateral branches. This compact growth possesses economic potential because it allows high density planting and mechanical harvesting of the trees. Its molecular basis has been identified as a nested Gypsy-44 retrotransposon insertion; however the link between the insertion and the phenotype as well as the timing of the phenotype emergence are as yet unclear. We extend the transcriptomic studies of columnar tissues to the radicles, which are the earliest developmental stage and investigate whether homozygous columnar seedlings are viable. RESULTS Radicles mainly express genes associated with primary metabolism, growth and development. About 200 genes show differential regulation in a comparison of heterozygous columnar radicles with non-columnar radicles, whereas the comparison of homozygous columnar radicles with non-columnar radicles yields about 300 differentially regulated genes. Genes involved in cellulose and phenylpropanoid biosynthesis, cell wall modification, transcription and translation, ethylene and jasmonate biosynthesis are upregulated in columnar radicles. Genes in the vicinity of the columnar-specific Gypsy-44 insertion experience an especially strong differential regulation: the direct downstream neighbor, dmr6-like, is downregulated in heterozygous columnar radicles, but strongly upregulated in columnar shoot apical meristems. CONCLUSIONS The transcriptomic profile of primary roots reflects their pivotal role in growth and development. Homozygous columnar embryos are viable and form normal radicles under natural conditions, and selection towards heterozygous plants most likely occurs due to breeders' preferences. Cell wall and phytohormone biosynthesis and metabolism experience differential regulation in columnar radicles. Presumably the first step of the differential regulation most likely happens within the region of the retrotransposon insertion and its tissue-specificity suggests involvement of one (or several) tissue-specific regulator(s).
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Affiliation(s)
- Romina Petersen
- Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany.
| | - Haris Djozgic
- Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany.
| | - Benjamin Rieger
- Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany.
| | - Steffen Rapp
- Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany.
| | - Erwin Robert Schmidt
- Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany.
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20
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Guo B, Chen Y, Li C, Wang T, Wang R, Wang B, Hu S, Du X, Xing H, Song X, Yao Y, Sun Q, Ni Z. Maize (Zea mays L.) seedling leaf nuclear proteome and differentially expressed proteins between a hybrid and its parental lines. Proteomics 2014; 14:1071-87. [PMID: 24677780 DOI: 10.1002/pmic.201300147] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 01/10/2014] [Accepted: 01/24/2014] [Indexed: 12/27/2022]
Abstract
To better understand the underlying molecular basis of leaf development in maize, a reference map of nuclear proteins in basal region of seedling leaf was established using a combination of 2DE and MALDI-TOF-MS. In total, 441 reproducible protein spots in nuclear proteome of maize leaf basal region were detected with silver staining in a pH range of 3-10, among which 203 spots corresponding to 163 different proteins were identified. As expected, proteins implicated in RNA and protein-associated functions were overrepresented in nuclear proteome. Remarkably, a high percentage (10%) of proteins was identified to be involved in cell division and growth. In addition, comparative nuclear proteomic analysis in leaf basal region of highly heterotic hybrid Mo17/B73 and its parental lines was also performed and 52 of 445 (11.69%) detected protein spots were differentially expressed between the hybrid and its parental lines, among which 16 protein spots displayed nonadditively expressed pattern. These results indicated that hybridization between two parental lines can cause changes in the expression of a variety of nuclear proteins, which may be responsible for the observed leaf size heterosis.
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Affiliation(s)
- Baojian Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Chuan Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Tianya Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Rui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Bo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Sha Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Xiaofen Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Xiao Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE); Beijing Key Laboratory of Crop Genetic Improvement; China Agricultural University; Beijing China
- National Plant Gene Research Centre (Beijing); Beijing China
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Wang Z, Xue Z, Wang T. Differential Analysis of Proteomes and Metabolomes Reveals Additively Balanced Networking for Metabolism in Maize Heterosis. J Proteome Res 2014; 13:3987-4001. [DOI: 10.1021/pr500337j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zizhang Wang
- Key Laboratory of Plant Molecular
Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhen Xue
- Key Laboratory of Plant Molecular
Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tai Wang
- Key Laboratory of Plant Molecular
Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Mohayeji M, Capriotti AL, Cavaliere C, Piovesana S, Samperi R, Stampachiacchiere S, Toorchi M, Lagana A. Heterosis profile of sunflower leaves: A label free proteomics approach. J Proteomics 2014; 99:101-10. [DOI: 10.1016/j.jprot.2014.01.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 12/24/2022]
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23
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Marcon C, Lamkemeyer T, Malik WA, Ungrue D, Piepho HP, Hochholdinger F. Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC–MS. J Proteomics 2013; 93:295-302. [DOI: 10.1016/j.jprot.2013.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/28/2013] [Accepted: 04/11/2013] [Indexed: 01/10/2023]
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Comparative proteomic analysis of embryos between a maize hybrid and its parental lines during early stages of seed germination. PLoS One 2013; 8:e65867. [PMID: 23776561 PMCID: PMC3679168 DOI: 10.1371/journal.pone.0065867] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022] Open
Abstract
In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. It was observed that maize hybrid Zong3/87-1 exhibited an earlier onset or heterosis in radicle emergence. To get insights into the underlying mechanism of heterosis in radicle emergence, differential proteomic analysis between hybrid and its parental lines was performed. In total, the number of differentially expressed protein spots between hybrid and its parental lines in dry and 24 h imbibed seed embryos were 134 and 191, respectively, among which 47.01% (63/134) and 34.55% (66/191) protein spots displayed nonadditively expressed pattern. Remarkably, 54.55% of nonadditively accumulated proteins in 24 h imbibed seed embryos displayed above or equal to the level of the higher parent patterns. Moreover, 155 differentially expressed protein spots were identified, which were grouped into eight functional classes, including transcription & translation, energy & metabolism, signal transduction, disease & defense, storage protein, transposable element, cell growth & division and unclassified proteins. In addition, one of the upregulated proteins in F1 hybrids was ZmACT2, a homolog of Arabidopsis thaliana ACT7 (AtACT7). Expressing ZmACT2 driven by the AtACT7 promoter partially complemented the low germination phenotype in the Atact7 mutant. These results indicated that hybridization between two parental lines can cause changes in the expression of a variety of proteins, and it is concluded that the altered pattern of gene expression at translational level in the hybrid may be responsible for the observed heterosis.
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Komatsu S, Yanagawa Y. Cell wall proteomics of crops. FRONTIERS IN PLANT SCIENCE 2013; 4:17. [PMID: 23403621 PMCID: PMC3566523 DOI: 10.3389/fpls.2013.00017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/23/2013] [Indexed: 05/23/2023]
Abstract
Cell wall proteins play key roles in cell structure and metabolism, cell enlargement, signal transduction, responses to environmental stress, and many other physiological events. Agricultural crops are often used for investigating stress tolerance because cultivars with differing degrees of tolerance are available. Abiotic and biotic stress factors markedly influence the geographical distribution and yields of many crop species. Crop cell wall proteomics is of particular importance for improving crop productivity, particularly under unfavorable environmental conditions. To better understand the mechanisms underlying stress response in crops, cell wall proteomic analyses are being increasingly utilized. In this review, the methods of purification and purity assays of cell wall protein fractions from crops are described, and the results of protein identification using gel-based and gel-free proteomic techniques are presented. Furthermore, protein composition of the cell walls of rice, wheat, maize, and soybean are compared, and the role of cell wall proteins in crops under flooding and drought stress is discussed. This review will be useful for clarifying the role of the cell wall of crops in response to environmental stresses.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Yuki Yanagawa
- Plant Science Center, RIKEN Yokohama InstituteYokohama, Japan
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Pechanova O, Takáč T, Šamaj J, Pechan T. Maize proteomics: An insight into the biology of an important cereal crop. Proteomics 2013. [DOI: 10.1002/pmic.201200275] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Olga Pechanova
- Mississippi State Chemical Laboratory; Mississippi State University; Mississippi State; MS; USA
| | - Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science; Palacký University; Olomouc; Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science; Palacký University; Olomouc; Czech Republic
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station,; Mississippi State University; Mississippi State; MS; USA
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27
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Di G, You W, Yu J, Wang D, Ke C. Genetic changes in muscle protein following hybridization between Haliotis diversicolor
reeve Japan and Taiwan populations revealed using a proteomic approach. Proteomics 2013; 13:845-59. [DOI: 10.1002/pmic.201200351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/28/2012] [Accepted: 11/14/2012] [Indexed: 12/23/2022]
Affiliation(s)
- Guilan Di
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Jinjin Yu
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Dexiang Wang
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
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28
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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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29
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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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30
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Paschold A, Jia Y, Marcon C, Lund S, Larson NB, Yeh CT, Ossowski S, Lanz C, Nettleton D, Schnable PS, Hochholdinger F. Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genome Res 2012; 22:2445-54. [PMID: 23086286 PMCID: PMC3514674 DOI: 10.1101/gr.138461.112] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ∼10% of expressed genes exhibited nonadditive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis, 1124 genes that were expressed in the hybrids were expressed in only one of the two parents. For 65 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome.
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Affiliation(s)
- Anja Paschold
- Institute of Crop Science and Resource Conservation, Division of Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
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31
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Ding D, Wang Y, Han M, Fu Z, Li W, Liu Z, Hu Y, Tang J. MicroRNA transcriptomic analysis of heterosis during maize seed germination. PLoS One 2012; 7:e39578. [PMID: 22761829 PMCID: PMC3384671 DOI: 10.1371/journal.pone.0039578] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 05/23/2012] [Indexed: 12/13/2022] Open
Abstract
Heterosis has been utilized widely in the breeding of maize and other crops, and plays an important role in increasing yield, improving quality and enhancing stresses resistance, but the molecular mechanism responsible for heterosis is far from clear. To illustrate whether miRNA-dependent gene regulation is responsible for heterosis during maize germination, a deep-sequencing technique was applied to germinating embryos of a maize hybrid, Yuyu22, which is cultivated widely in China and its parental inbred lines, Yu87-1 and Zong3. The target genes of several miRNAs showing significant expression in the hybrid and parental lines were predicted and tested using real-time PCR. A total of 107 conserved maize miRNAs were co-detected in the hybrid and parental lines. Most of these miRNAs were expressed non-additively in the hybrid compared to its parental lines. These results indicated that miRNAs might participate in heterosis during maize germination and exert an influence via the decay of their target genes. Novel miRNAs were predicted follow a rigorous criterion and only the miRNAs detected in all three samples were treated as a novel maize miRNA. In total, 34 miRNAs belonged to 20 miRNA families were predicted in germinating maize seeds. Global repression of miRNAs in the hybrid, which might result in enhanced gene expression, might be one reason why the hybrid showed higher embryo germination vigor compared to its parental lines.
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Affiliation(s)
- Dong Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yinju Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Mingshui Han
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhiyuan Fu
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Weihua Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zonghua Liu
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yanmin Hu
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jihua Tang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- * E-mail:
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32
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Yan H, Li K, Ding H, Liao C, Li X, Yuan L, Li C. Root morphological and proteomic responses to growth restriction in maize plants supplied with sufficient N. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1067-75. [PMID: 21353328 DOI: 10.1016/j.jplph.2010.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 05/16/2023]
Abstract
The primary objective of this study was to better understand how root morphological alteration stimulates N uptake in maize plants after root growth restriction, by investigating the changes in length and number of lateral roots, (15)NO(3)(-) influx, the expression level of the low-affinity Nitrate transporter ZmNrt1.1, and proteomic composition of primary roots. Maize seedlings were hydroponically cultured with three different types of root systems: an intact root system, embryonic roots only, or primary roots only. In spite of sufficient N supply, root growth restriction stimulated compensatory growth of remaining roots, as indicated by the increased lateral root number and root density. On the other hand, there was no significant difference in (15)NO(3)(-) influx between control and primary root plants; neither in ZmNrt1.1 expression levels in primary roots of different treatments. Our data suggested that increased N uptake by maize seedlings experiencing root growth restriction is attributed to root morphological adaptation, rather than explained by the variation in N uptake activity. Eight proteins were differentially accumulated in embryonic and primary root plants compared to control plants. These differentially accumulated proteins were closely related to signal transduction and increased root growth.
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Affiliation(s)
- Huifeng Yan
- The Key Laboratory of Plant Nutrition, Department of Plant Nutrition, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
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33
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Goff SA. A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding. THE NEW PHYTOLOGIST 2011; 189:923-937. [PMID: 21166808 DOI: 10.1111/j.1469-8137.2010.03574.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Hybrids between genetically diverse varieties display enhanced growth, and increased total biomass, stress resistance and grain yield. Gene expression and metabolic studies in maize, rice and other species suggest that protein metabolism plays a role in the growth differences between hybrids and inbreds. Single trait heterosis can be explained by the existing theories of dominance, overdominance and epistasis. General multigenic heterosis is observed in a wide variety of different species and is likely to share a common underlying biological mechanism. This review presents a model to explain differences in growth and yield caused by general multigenic heterosis. The model describes multigenic heterosis in terms of energy-use efficiency and faster cell cycle progression where hybrids have more efficient growth than inbreds because of differences in protein metabolism. The proposed model is consistent with the observed variation of gene expression in different pairs of inbred lines and hybrid offspring as well as growth differences in polyploids and aneuploids. It also suggests an approach to enhance yield gains in both hybrid and inbred crops via the creation of an appropriate computational analysis pipeline coupled to an efficient molecular breeding program.
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Affiliation(s)
- Stephen A Goff
- iPlant Collaborative, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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34
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Fu Z, Jin X, Ding D, Li Y, Fu Z, Tang J. Proteomic analysis of heterosis during maize seed germination. Proteomics 2011; 11:1462-72. [DOI: 10.1002/pmic.201000481] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 12/21/2010] [Accepted: 01/18/2011] [Indexed: 12/29/2022]
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35
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Marcon C, Schützenmeister A, Schütz W, Madlung J, Piepho HP, Hochholdinger F. Nonadditive protein accumulation patterns in Maize (Zea mays L.) hybrids during embryo development. J Proteome Res 2010; 9:6511-22. [PMID: 20973536 DOI: 10.1021/pr100718d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Heterosis describes the superior performance of heterozygous F(1)-hybrid plants compared to their homozygous parental inbred lines. In the present study, heterosis was detected for length, weight, and the time point of seminal root primordia initiation in maize (Zea mays L.) embryos of the reciprocal F(1)-hybrids UH005xUH250 and UH250xUH005. A two-dimensional gel electrophoresis (2-DE) proteome survey of the most abundant proteins of the reciprocal hybrids and their parental inbred lines 25 and 35 days after pollination revealed that 141 of 597 detected proteins (24%) exhibited nonadditive accumulation in at least one hybrid. Approximately 44% of all nonadditively accumulated proteins displayed an expression pattern that was not distinguishable from the low parent value. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analyses and subsequent functional classification of the 141 proteins revealed that development, protein metabolism, redox-regulation, glycolysis, and amino acid metabolism were the most prominent functional classes among nonadditively accumulated proteins. In 35-day-old embryos of the hybrid UH250xUH005, a significant up-regulation of enzymes related to glucose metabolism which often exceeded the best parent values was observed. A comparison of nonadditive protein accumulation between rice and maize embryo data sets revealed a significant overlap of nonadditively accumulated proteins suggesting conserved organ- or tissue-specific regulatory mechanisms in monocots related to heterosis.
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Affiliation(s)
- Caroline Marcon
- Department of General Genetics, University of Tuebingen, ZMBP, Center for Plant Molecular Biology, 72076 Tuebingen, Germany
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36
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Zhang X, Liu F, Wang W, Li S, Wang C, Zhang X, Wang Y, Wang K. Primary analysis of QTG contribution to heterosis in upland cotton. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-4020-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Liu Y, von Behrens I, Muthreich N, Schütz W, Nordheim A, Hochholdinger F. Regulation of the pericycle proteome in maize (Zea mays L.) primary roots by RUM1 which is required for lateral root initiation. Eur J Cell Biol 2010; 89:236-41. [DOI: 10.1016/j.ejcb.2009.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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38
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Muthreich N, Schützenmeister A, Schütz W, Madlung J, Krug K, Nordheim A, Piepho HP, Hochholdinger F. Regulation of the maize (Zea mays L.) embryo proteome by RTCS which controls seminal root initiation. Eur J Cell Biol 2010; 89:242-9. [DOI: 10.1016/j.ejcb.2009.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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39
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Saleem M, Lamkemeyer T, Schützenmeister A, Madlung J, Sakai H, Piepho HP, Nordheim A, Hochholdinger F. Specification of cortical parenchyma and stele of maize primary roots by asymmetric levels of auxin, cytokinin, and cytokinin-regulated proteins. PLANT PHYSIOLOGY 2010; 152:4-18. [PMID: 19933382 PMCID: PMC2799342 DOI: 10.1104/pp.109.150425] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 11/18/2009] [Indexed: 05/19/2023]
Abstract
In transverse orientation, maize (Zea mays) roots are composed of a central stele that is embedded in multiple layers of cortical parenchyma. The stele functions in the transport of water, nutrients, and photosynthates, while the cortical parenchyma fulfills metabolic functions that are not very well characterized. To better understand the molecular functions of these root tissues, protein- and phytohormone-profiling experiments were conducted. Two-dimensional gel electrophoresis combined with electrospray ionization tandem mass spectrometry identified 59 proteins that were preferentially accumulated in the cortical parenchyma and 11 stele-specific proteins. Hormone profiling revealed preferential accumulation of indole acetic acid and its conjugate indole acetic acid-aspartate in the stele and predominant localization of the cytokinin cis-zeatin, its precursor cis-zeatin riboside, and its conjugate cis-zeatin O-glucoside in the cortical parenchyma. A root-specific beta-glucosidase that functions in the hydrolysis of cis-zeatin O-glucoside was preferentially accumulated in the cortical parenchyma. Similarly, four enzymes involved in ammonium assimilation that are regulated by cytokinin were preferentially accumulated in the cortical parenchyma. The antagonistic distribution of auxin and cytokinin in the stele and cortical parenchyma, together with the cortical parenchyma-specific accumulation of cytokinin-regulated proteins, suggest a molecular framework that specifies the function of these root tissues that also play a role in the formation of lateral roots from pericycle and endodermis cells.
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40
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Römisch-Margl L, Spielbauer G, Schützenmeister A, Schwab W, Piepho HP, Genschel U, Gierl A. Heterotic patterns of sugar and amino acid components in developing maize kernels. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:369-381. [PMID: 19898829 DOI: 10.1007/s00122-009-1190-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 10/14/2009] [Indexed: 05/28/2023]
Abstract
Heterosis is the superior performance of hybrids over their inbred parents. Despite its importance, little is known about the genetic and molecular basis of this phenomenon. Heterosis has been extensively exploited in plant breeding, particularly in maize (Zea mays, L.), and is well documented in the B73 and Mo17 maize inbred lines and their F1 hybrids. In this study, we determined the dry matter, the levels of starch and protein components and a total of 24 low-molecular weight metabolites including sugars, sugar-phosphates, and free amino acids, in developing maize kernels between 8 and 30 days post-pollination (DPP) of the hybrid B73 x Mo17 and its parental lines. The tissue specificity of amino acid and protein content was investigated between 16 and 30 DPP. Key observations include: (1) most of the significant differences in the investigated tissue types occurred between Mo17 and the other two genotypes; (2) heterosis of dry matter and metabolite content was detectable from the early phase of kernel development onwards; (3) the majority of metabolites exhibited an additive pattern. Nearly 10% of the metabolites exhibited nonadditive effects such as overdominance, underdominance, and high-parent and low-parent dominance; (4) The metabolite composition was remarkably dependent on kernel age, and this large developmental effect could possibly mask genotypic differences; (5) the metabolite profiles and the heterotic patterns are specific for endosperm and embryo. Our findings illustrate the power of metabolomics to characterize heterotic maize lines and suggest that the metabolite composition is a potential marker in the context of heterosis research.
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Affiliation(s)
- Lilla Römisch-Margl
- Lehrstuhl für Genetik, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Ramann-Str 8, 85354 Freising, Germany.
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41
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Fiévet JB, Dillmann C, de Vienne D. Systemic properties of metabolic networks lead to an epistasis-based model for heterosis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:463-73. [PMID: 19916003 PMCID: PMC2793392 DOI: 10.1007/s00122-009-1203-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 10/22/2009] [Indexed: 05/10/2023]
Abstract
The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype-phenotype relationship. From the generalization of Kacser and Burns' biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genetic variability by varying in silico enzyme concentrations. Then we "crossed" virtual parents to get 1,000 hybrids, and showed that best-parent heterosis was frequently observed. The decomposition of the flux value into genetic effects, with the help of a novel multilocus epistasis index, revealed that antagonistic additive-by-additive epistasis effects play the major role in this framework of the genotype-phenotype relationship. This result is consistent with various observations in quantitative and evolutionary genetics, and provides a model unifying the genetic effects underlying heterosis.
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Affiliation(s)
- Julie B. Fiévet
- AgroParisTech, UMR 0320/UMR 8120 Génétique Végétale, 91190 Gif-sur-Yvette, France
| | - Christine Dillmann
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, 91190 Gif-sur-Yvette, France
| | - Dominique de Vienne
- UMR de Génétique Végétale, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Ferme du Moulon, 91190 Gif-sur-Yvette, France
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42
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Paschold A, Marcon C, Hoecker N, Hochholdinger F. Molecular dissection of heterosis manifestation during early maize root development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:383-8. [PMID: 19526205 DOI: 10.1007/s00122-009-1082-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 05/21/2009] [Indexed: 05/22/2023]
Abstract
Heterosis is of paramount agronomic importance and has been successfully exploited in maize hybrid breeding for decades. Nevertheless, the molecular basis of heterosis remains elusive. Heterosis is not only observed in adult traits like yield or plant height, but is already detected during embryo and seedling development. Hence, the maize (Zea mays L.) primary root which is the first organ that emerges after germination is a suitable model to study heterosis manifestation. Various seedling root traits including primary root length and lateral root density display heterosis. Microarray studies suggest organ specific patterns of nonadditive gene expression in maize hybrids. Moreover, such experiments support the notion that global expression trends in maize primary roots are conserved between different hybrids. Furthermore, nonadditive expression patterns of specific genes such as a SUPEROXIDE DISMUTASE 2 might contribute to the early manifestation of heterosis. Proteome profiling experiments of maize hybrid primary roots revealed nonadditive accumulation patterns that were distinct from the corresponding RNA profiles underscoring the importance of posttranscriptional processes such as protein modifications that might be related to heterosis. Finally, analysis of selected metabolites imply that a subtle regulation of particular biochemical pathways such as the phenylpropanoid pathway in hybrids might contribute to the manifestation of heterosis in maize primary roots. In the future, recently developed molecular tools will facilitate the analysis of the molecular principles underlying heterosis in maize roots.
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Affiliation(s)
- Anja Paschold
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), University of Tuebingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
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43
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Saleem M, Lamkemeyer T, Schützenmeister A, Fladerer C, Piepho HP, Nordheim A, Hochholdinger F. Tissue Specific Control of the Maize (Zea mays L.) Embryo, Cortical Parenchyma, and Stele Proteomes by RUM1 Which Regulates Seminal and Lateral Root Initiation. J Proteome Res 2009; 8:2285-97. [DOI: 10.1021/pr8009287] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Muhammad Saleem
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Tobias Lamkemeyer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - André Schützenmeister
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Claudia Fladerer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Hans-Peter Piepho
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Alfred Nordheim
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Frank Hochholdinger
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
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Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I. Plant proteomics update (2007–2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009; 72:285-314. [DOI: 10.1016/j.jprot.2009.01.026] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Hochholdinger F, Tuberosa R. Genetic and genomic dissection of maize root development and architecture. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:172-7. [PMID: 19157956 DOI: 10.1016/j.pbi.2008.12.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 11/26/2008] [Accepted: 12/06/2008] [Indexed: 05/21/2023]
Abstract
The complex architecture and plasticity of the maize root system is controlled by a plethora of genes. Mutant analyses have identified genes regulating shoot-borne root initiation (RTCS) and root hair elongation (RTH1 and RTH3). Quantitative trait locus (QTL) studies have highlighted the importance of seminal roots, lateral roots, and root hairs in phosphorus acquisition. Additionally, QTLs that influence root features were shown to affect yield under different water regimes and under flooding conditions. Finally, proteome and transcriptome analyses provided insights into maize root development and identified candidate genes associated with cell specification, and lateral root initiation in pericycle cells. The targeted application of forward-genetics and reverse-genetics approaches will accelerate the unraveling of the functional basis of root development and architecture.
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Affiliation(s)
- Frank Hochholdinger
- University of Tuebingen, Center for Plant Molecular Biology (ZMBP), Department of General Genetics, Auf der Morgenstelle 28, 72076 Tuebingen, Germany.
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