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Halder T, Stroeher E, Liu H, Chen Y, Yan G, Siddique KHM. Protein biomarkers for root length and root dry mass on chromosomes 4A and 7A in wheat. J Proteomics 2024; 291:105044. [PMID: 37931703 DOI: 10.1016/j.jprot.2023.105044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023]
Abstract
Improving the wheat (Triticum aestivum L.) root system is important for enhancing grain yield and climate resilience. Total root length (RL) and root dry mass (RM) significantly contribute to water and nutrient acquisition directly impacting grain yield and stress tolerance. This study used label-free quantitative proteomics to identify proteins associated with RL and RM in wheat near-isogenic lines (NILs). NIL pair 6 had 113 and NIL pair 9 had 30 differentially abundant proteins (DAPs). Three of identified DAPs located within the targeted genomic regions (GRs) of NIL pairs 6 (qDT.4A.1) and 9 (QHtscc.ksu-7A), showed consistent gene expressions at the protein and mRNA transcription (qRT-PCR) levels for asparagine synthetase (TraesCS4A02G109900), signal recognition particle 19 kDa protein (TraesCS7A02G333600) and 3,4-dihydroxy-2-butanone 4-phosphate synthase (TraesCS7A02G415600). This study discovered, for the first time, the involvement of these proteins as candidate biomarkers for increased RL and RM in wheat. However, further functional validation is required to ascertain their practical applicability in wheat root breeding. SIGNIFICANCE OF THE STUDY: Climate change has impacted global demand for wheat (Triticum aestivum L.). Root traits such as total root length (RL) and root dry mass (RM) are crucial for water and nutrient uptake and tolerance to abiotic stresses such as drought, salinity, and nutrient imbalance in wheat. Improving RL and RM could significantly enhance wheat grain yield and climate resilience. However, breeding for these traits has been limited by lack of appropriate root phenotyping methods, advanced genotypes, and the complex nature of the wheat genome. In this study, we used a semi-hydroponic root phenotyping system to collect accurate root data, near-isogenic lines (NILs; isolines with similar genetic backgrounds but contrasting target genomic regions (GRs)) and label-free quantitative proteomics to explore the molecular mechanisms underlying high RL and RM in wheat. We identified differentially abundant proteins (DAPs) and their molecular pathways in NIL pairs 6 (GR: qDT.4A.1) and 9 (GR: QHtscc.ksu-7A), providing a foundation for further molecular investigations. Furthermore, we identified three DAPs within the target GRs of the NIL pairs with differential expression at the transcript level, as confirmed by qRT-PCR analysis which could serve as candidate protein biomarkers for RL and RM improvement.
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Affiliation(s)
- Tanushree Halder
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh.
| | - Elke Stroeher
- Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - Yinglong Chen
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kadambot H M Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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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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Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules 2023; 13:1110. [PMID: 37509146 PMCID: PMC10377273 DOI: 10.3390/biom13071110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Sunflower is a hybrid crop that is considered moderately drought-tolerant and adapted to new cropping systems required for the agro-ecological transition. Here, we studied the impact of hybridity status (hybrids vs. inbred lines) on the responses to drought at the molecular and eco-physiological level exploiting publicly available datasets. Eco-physiological traits and leaf proteomes were measured in eight inbred lines and their sixteen hybrids grown in the high-throughput phenotyping platform Phenotoul-Heliaphen. Hybrids and parental lines showed different growth strategies: hybrids grew faster in the absence of water constraint and arrested their growth more abruptly than inbred lines when subjected to water deficit. We identified 471 differentially accumulated proteins, of which 256 were regulated by drought. The amplitude of up- and downregulations was greater in hybrids than in inbred lines. Our results show that hybrids respond more strongly to water deficit at the molecular and eco-physiological levels. Because of presence/absence polymorphism, hybrids potentially contain more genes than their parental inbred lines. We propose that detrimental homozygous mutations and the lower number of genes in inbred lines lead to a constitutive defense mechanism that may explain the lower growth of inbred lines under well-watered conditions and their lower reactivity to water deficit.
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Affiliation(s)
- Harold Duruflé
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
- INRAE, ONF, BioForA, 45075 Orleans, France
| | - Thierry Balliau
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Nicolas Blanchet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Adeline Chaubet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Alexandra Duhnen
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Nicolas Pouilly
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Mélisande Blein-Nicolas
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Brigitte Mangin
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Maury
- INRAE, INP-ENSAT Toulouse, UMR AGIR, Université de Toulouse, 31000 Toulouse, France
| | | | - Michel Zivy
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
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Petrova A, Sibgatullina G, Gorshkova T, Kozlova L. Dynamics of cell wall polysaccharides during the elongation growth of rye primary roots. PLANTA 2022; 255:108. [PMID: 35449484 DOI: 10.1007/s00425-022-03887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
In cells of growing rye roots, xyloglucans and homogalacturonans demonstrate developmental stage specificity, while different xylans have tissue specificity. Mannans, arabinans and galactans are also detected within the protoplast. Mannans form films on sections of fresh material. The primary cell walls of plants represent supramolecular exocellular structures that are mainly composed of polysaccharides. Cell wall properties and architecture differ between species and across tissues within a species. We revised the distribution of cell wall polysaccharides and their dynamics during elongation growth and histogenesis in rye roots using nonfixed material and the spectrum of antibodies. Rye is a member of the Poaceae family and thus has so-called type II primary cell walls, which are supposed to be low in pectins and xyloglucans and instead have arabinoxylans and mixed-linkage glucans. However, rye cell walls at the earliest stages of cell development were enriched with the epitopes of xyloglucans and homogalacturonans. Mixed-linkage glucan, which is often considered an elongation growth-specific polysaccharide in plants with type II cell walls, did not display such dynamics in rye roots. The cessation of elongation growth and even the emergence of root hairs were not accompanied by the disappearance of mixed-linkage glucans from cell walls. The diversity of xylan motifs recognized by different antibodies was minimal in the meristem zone of rye roots, but this diversity increased and showed tissue specificity during root growth. Antibodies specific for xyloglucans, galactans, arabinans and mannans bound the cell content. When rye root cells were cut, the epitopes of xyloglucans, galactans and arabinans remained within the cell content, while mannans developed net-like or film-like structures on the surface of sections.
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Affiliation(s)
- Anna Petrova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky str., 2/31, 420111, Kazan, Russia
| | - Gusel Sibgatullina
- The Laboratory of Biophysics of Synaptic Processes, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky str., 2/31, 420111, Kazan, Russia
| | - Tatyana Gorshkova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky str., 2/31, 420111, Kazan, Russia
| | - Liudmila Kozlova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky str., 2/31, 420111, Kazan, Russia.
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5
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Birdseye D, de Boer LA, Bai H, Zhou P, Shen Z, Schmelz EA, Springer NM, Briggs SP. Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins. Proc Natl Acad Sci U S A 2021; 118:e2109332118. [PMID: 34782463 PMCID: PMC8617506 DOI: 10.1073/pnas.2109332118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
The use of hybrids is widespread in agriculture, yet the molecular basis for hybrid vigor (heterosis) remains obscure. To identify molecular components that may contribute to trait heterosis, we analyzed paired proteomic and transcriptomic data from seedling leaf and mature leaf blade tissues of maize hybrids and their inbred parents. Nuclear- and plastid-encoded subunits of complexes required for protein synthesis in the chloroplast and for the light reactions of photosynthesis were expressed above midparent and high-parent levels, respectively. Consistent with previous reports in Arabidopsis, ethylene biosynthetic enzymes were expressed below midparent levels in the hybrids, suggesting a conserved mechanism for heterosis between monocots and dicots. The ethylene biosynthesis mutant, acs2/acs6, largely phenocopied the hybrid proteome, indicating that a reduction in ethylene biosynthesis may mediate the differences between inbreds and their hybrids. To rank the relevance of expression differences to trait heterosis, we compared seedling leaf protein levels to the adult plant height of 15 hybrids. Hybrid/midparent expression ratios were most positively correlated with hybrid/midparent plant height ratios for the chloroplast ribosomal proteins. Our results show that increased expression of chloroplast ribosomal proteins in hybrid seedling leaves is mediated by reduced expression of ethylene biosynthetic enzymes and that the degree of their overexpression in seedlings can quantitatively predict adult trait heterosis.
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Affiliation(s)
- Devon Birdseye
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Laura A de Boer
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Hua Bai
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Zhouxin Shen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Eric A Schmelz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Steven P Briggs
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093;
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6
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Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
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Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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Li Z, Zhu A, Song Q, Chen HY, Harmon FG, Chen ZJ. Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis. THE PLANT CELL 2020; 32:3706-3722. [PMID: 33004616 PMCID: PMC7721322 DOI: 10.1105/tpc.20.00320] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 05/04/2023]
Abstract
Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.
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Affiliation(s)
- Zhi Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andan Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Helen Y Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Frank G Harmon
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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Xiao R, Yuan Y, Zhu F, He S, Ge Q, Wang X, Taha R, Chen K. Transcriptomics and proteomics-based analysis of heterosis on main economic traits of silkworm, Bombyx mori. J Proteomics 2020; 229:103941. [PMID: 32805450 DOI: 10.1016/j.jprot.2020.103941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/11/2020] [Accepted: 08/09/2020] [Indexed: 11/15/2022]
Abstract
The application of silkworm hybrids have promoted the innovation and development of agricultural technology, but the mechanism of heterosis in silkworm has not been explained clearly. In this study, the heterosis of silkworm in the aspects of body weight, silk gland and cocoon weight was investigated by means of silkworm hybridization and multi-omics approaches, including transcriptome and proteome. The results showed that heterosis of silkworm body weight, silk gland and cocoon weight was overdominant, but only part of genes and proteins were overdominant, and most of genes and proteins were non-additive. Combined analysis obtained six up-regulated genes and four down-regulated genes that were consistent both in transcriptome and proteome. Gene functional enrichment analysis indicated that most up-regulated genes and proteins were mostly related to metabolism, which led to accelerated metabolism and protein synthesis and contributing to improved heterosis. The up-regulation of 6-phosphate glucose dehydrogenase (G6PDH), phosphatidylethanolamine-binding protein (PEBP) and sHSP20.4, which are involved in metabolism, might be related to silk gland heterosis. SIGNIFICANCE: A combination of transcriptomic and proteomic analysis was used to understand the molecular mechanism of silkworm heterosis. We found that the phenotypic traits of silkworm are overdominant, while the analysis of transcriptome and proteome showed that only part of genes and proteins were overdominant, and most of genes and proteins were non-additive. Some of the genes had unique expression in F1, which was speculated that genes under heterozygous condition may result in rearrangement and cause metabolic changes in the hybrids. Those both up-regulated in transcriptomic and proteomic analysis were found to be involved in various metabolic processes, so as to accelerate metabolism and protein synthesis, thus exhibiting heterosis.
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Affiliation(s)
- Rui Xiao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yi Yuan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Feifei Zhu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Suqun He
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qi Ge
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xueqi Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Rehab Taha
- Plant Protection Research Institute, Agricultural Research Center, Egypt
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China.
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Rockenbach MF, Corrêa CCG, Heringer AS, Freitas ILJ, Santa-Catarina C, do Amaral-Júnior AT, Silveira V. Differentially abundant proteins associated with heterosis in the primary roots of popcorn. PLoS One 2018; 13:e0197114. [PMID: 29758068 PMCID: PMC5951555 DOI: 10.1371/journal.pone.0197114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/26/2018] [Indexed: 12/21/2022] Open
Abstract
Although heterosis has significantly contributed to increases in worldwide crop production, the molecular mechanisms regulating this phenomenon are still unknown. In the present study, we used a comparative proteomic approach to explore hybrid vigor via the proteome of both the popcorn L54 ♀ and P8 ♂ genotypes and the resultant UENF/UEM01 hybrid cross. To analyze the differentially abundant proteins involved in heterosis, we used the primary roots of these genotypes to analyze growth parameters and extract proteins. The results of the growth parameter analysis showed that the mid- and best-parent heterosis were positive for root length and root dry matter but negative for root fresh matter, seedling fresh matter, and protein content. The comparative proteomic analysis identified 1343 proteins in the primary roots of hybrid UENF/UEM01 and its parental lines; 220 proteins were differentially regulated in terms of protein abundance. The mass spectrometry proteomic data are available via ProteomeXchange with identifier “PXD009436”. A total of 62 regulated proteins were classified as nonadditive, of which 53.2% were classified as high parent abundance (+), 17.8% as above-high parent abundance (+ +), 16.1% as below-low parent abundance (− −), and 12.9% as low parent abundance (-). A total of 22 biological processes were associated with nonadditive proteins; processes involving translation, ribosome biogenesis, and energy-related metabolism represented 45.2% of the nonadditive proteins. Our results suggest that heterosis in the popcorn hybrid UENF/UEM01 at an early stage of plant development is associated with an up-regulation of proteins related to synthesis and energy metabolism.
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Affiliation(s)
- Mathias F. Rockenbach
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Caio C. G. Corrêa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Angelo S. Heringer
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Ismael L. J. Freitas
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), UENF, Campos dos Goytacazes, RJ, Brazil
| | | | - Antônio T. do Amaral-Júnior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), UENF, Campos dos Goytacazes, RJ, Brazil
- * E-mail: (VS); (ATAJ)
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil
- * E-mail: (VS); (ATAJ)
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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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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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15
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Han P, Lu X, Mi F, Dong J, Xue C, Li J, Han B, Zhang X. Proteomic analysis of heterosis in the leaves of sorghum-sudangrass hybrids. Acta Biochim Biophys Sin (Shanghai) 2016; 48:161-73. [PMID: 26792642 DOI: 10.1093/abbs/gmv126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/08/2015] [Indexed: 01/15/2023] Open
Abstract
Sorghum-sudangrass hybrids are widely used for forage and silage in the animal husbandry industry due to their hardiness. The heterozygous first generation of sorghum-sudangrass hybrids displays performance superior to their homozygous, parental inbred lines. In order to study the molecular details underlying its heterosis, the leaves of sorghum-sudangrass hybrids and their parents were compared using mass spectrometry-based proteomics. Results showed that among the 996 proteins that were identified, 32 proteins showed 'additive accumulation expression patterns', indicating that the protein abundance in sorghum-sudangrass hybrids showed no significant difference from the average of their parents. Additionally, 74 proteins showed 'nonadditive accumulation expression patterns' (the proteins abundance in the hybrids showed significant difference from the average of their parents). Both additive and nonadditive proteins were mainly involved in photosynthesis and carbohydrate metabolism. More upregulated additive and nonadditive proteins were in the hybrids than in their parents, suggesting that additive and nonadditive proteins are essential to the vigor of sorghum-sudangrass hybrids. The nonadditive proteins were enriched in photosynthesis, carbohydrate metabolism, and protein oligomerization, but the additive proteins were not enriched in any pathway, which indicated that the nonadditive proteins could be greater contributors to heterosis than additive proteins. Furthermore, the highly activated photosynthetic pathway in nonadditive proteins implies that photosynthesis in hybrids is heightened to assimilate more organic matter, resulting in an increased yield. Our results provide a proof-of-concept that reveals the molecular components of heterosis in sorghum-sudangrass hybrid leaves and serves as an important step for future genetic manipulation of specific proteins to improve the performance of hybrids.
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Affiliation(s)
- Pingan Han
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Xiaoping Lu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Fugui Mi
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Jing Dong
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Chunlei Xue
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Jianke Li
- Chinese Academy of Agricultural Science, Institute of Apicultural Research, Beijing 100093, China
| | - Bin Han
- Chinese Academy of Agricultural Science, Institute of Apicultural Research, Beijing 100093, China
| | - Xiaoyu Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
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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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Dan Z, Hu J, Zhou W, Yao G, Zhu R, Huang W, Zhu Y. Hierarchical additive effects on heterosis in rice (Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2015; 6:738. [PMID: 26442051 PMCID: PMC4566041 DOI: 10.3389/fpls.2015.00738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/31/2015] [Indexed: 05/21/2023]
Abstract
Exploitation of heterosis in crops has contributed greatly to improvement in global food and energy production. In spite of the pervasive importance of heterosis, a complete understanding of its mechanisms has remained elusive. In this study, a small test-crossed rice population was constructed to investigate the formation mechanism of heterosis for 13 traits. The results of the relative mid-parent heterosis and modes of inheritance of all investigated traits demonstrated that additive effects were the foundation of heterosis for complex traits in a hierarchical structure, and multiplicative interactions among the component traits were the framework of heterosis in complex traits. Furthermore, new balances between unit traits and related component traits provided hybrids with the opportunity to achieve an optimal degree of heterosis for complex traits. This study dissected heterosis of both reproductive and vegetative traits from the perspective of hierarchical structure for the first time. Additive multiplicative interactions of component traits were proven to be the origin of heterosis in complex traits. Meanwhile, more attention should be paid to component traits, rather than complex traits, in the process of revealing the mechanism of heterosis.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Wei Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Guoxin Yao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
- *Correspondence: Wenchao Huang and Yingguo Zhu, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Bayi Road, Wuhan 430072, China, ;
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
- *Correspondence: Wenchao Huang and Yingguo Zhu, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Bayi Road, Wuhan 430072, 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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Affiliation(s)
- Jesús Jorrín-Novo
- Agricultural and Plant Proteomics, Biochemistry and Molecular Biology, University of Córdoba, Cordoba, Spain.
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