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Baker RL, Brock GL, Newsome EL, Zhao M. Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11605. [PMID: 39184197 PMCID: PMC11342231 DOI: 10.1002/aps3.11605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 08/27/2024]
Abstract
Premise Most traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships. Methods We apply network modeling, a common gene co-expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus Brassica. Results We identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure-function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids. Discussion Phenotypic network analysis may provide important insights into the effects of selection on non-target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.
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Affiliation(s)
- Robert L. Baker
- Inventory and Monitoring DivisionNational Park ServiceFort Collins80525ColoradoUSA
| | | | - Eastyn L. Newsome
- Department of Botany and Plant PathologyPurdue UniversityWest Lafayette47907IndianaUSA
| | - Meixia Zhao
- Department of Microbiology and Cell ScienceUniversity of FloridaGainesville32611FloridaUSA
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2
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Marks RA, Delgado P, Makonya GM, Cooper K, VanBuren R, Farrant JM. Higher order polyploids exhibit enhanced desiccation tolerance in the grass Microchloa caffra. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3612-3623. [PMID: 38511472 PMCID: PMC11156804 DOI: 10.1093/jxb/erae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
Desiccation tolerance evolved recurrently across diverse plant lineages to enable survival in water-limited conditions. Many resurrection plants are polyploid, and several groups have hypothesized that polyploidy contributed to the evolution of desiccation tolerance. However, due to the vast phylogenetic distance between resurrection plant lineages, the rarity of desiccation tolerance, and the prevalence of polyploidy in plants, this hypothesis has been difficult to test. Here, we surveyed natural variation in morphological, reproductive, and desiccation tolerance traits across several cytotypes of a single species to test for links between polyploidy and increased resilience. We sampled multiple natural populations of the resurrection grass Microchloa caffra across an environmental gradient ranging from mesic to xeric in South Africa. We describe two distinct ecotypes of M. caffra that occupy different extremes of the environmental gradient and exhibit consistent differences in ploidy, morphological, reproductive, and desiccation tolerance traits in both field and common growth conditions. Interestingly, plants with more polyploid genomes exhibited consistently higher recovery from desiccation, were less reproductive, and were larger than plants with smaller genomes and lower ploidy. These data indicate that selective pressures in increasingly xeric sites may play a role in maintaining and increasing desiccation tolerance and are mediated by changes in ploidy.
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Affiliation(s)
- Rose A Marks
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
| | - Paula Delgado
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
| | - Givemore Munashe Makonya
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
- Washington State University, Irrigated Agriculture Research and Extension Centre, Prosser, WA 99350, USA
| | - Keren Cooper
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
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3
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Huang DQ, Ma XG, Sun H. Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae). FRONTIERS IN PLANT SCIENCE 2024; 14:1268546. [PMID: 38239226 PMCID: PMC10794568 DOI: 10.3389/fpls.2023.1268546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Polyploidization is a process that typically leads to instantaneous reproductive isolation and has, therefore, been considered as one of the major evolutionary forces in the species-rich Hengduan Mountains (HM), yet this topic remains poorly studied in the region. Allium sikkimense and its relatives (about eight species) compose a natural diploid-polyploid complex with the highest diversity in the HM and adjacent areas. A combination of nuclear ribosomal DNA (nrDNA), plastome, transcriptome, and ploidy identification through chromosome counting and flow cytometry is employed to reconstruct the phylogenetic relationships in this complex and to investigate the frequency and the evolutionary significance of polyploidy in the complex. The plastome failed to resolve the phylogenetic relationships of the different species in the A. sikkimense complex, and the phylogenetic tree based on nrDNA also has limited resolution. However, our study reveals a well-resolved phylogenetic framework for species in the A. sikkimense complex using more than 1,000 orthologous genes from the transcriptome data. Previously recognized morphospecies A. sikkimense are non-monophyletic and comprise at least two independently evolved lineages (i.e., cryptic species), each forming a clade with different diploid species in this complex. The embedded pattern of octoploid A. jichouense and tetraploid A. sp. nov. within different polyploid samples of A. sikkimense supports a possible scenario of budding speciation (via niche divergence). Furthermore, our results reveal that co-occurring species in the A. sikkimense complex usually have different ploidy levels, suggesting that polyploidy is an important process for reproductive isolation of sympatric Allium species. Phylogenetic network analyses suggested that the phylogenetic relationships of the A. sikkimense complex, allowing for reticulation events, always fit the dataset better than a simple bifurcating tree. In addition, the included or exserted filaments, which have long been used to delimit species, are highly unreliable taxonomically due to their extensive parallel and convergent evolution.
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Affiliation(s)
- De-Qing Huang
- College of Pharmacy, Guilin Medical University, Guilin, China
| | - Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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4
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Scarrow M, Chen N, Namaganda A, Sun G. N 6-Methyladenosine and physiological response divergence confer autotetraploid enhanced salt tolerance compared to its diploid Hordeum bulbosum. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:2013-2021. [PMID: 36573150 PMCID: PMC9789291 DOI: 10.1007/s12298-022-01260-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Polyploid species have played an essential role in plant evolution, exemplified by adaptive advantages to abiotic stress. N 6-Methyladenosine (m6A) is suggested to play an important role in stress response. However, whether genome doubling affects m6A to increase autopolyploids stress tolerance is still unclear. This study aims to compare physiological (maintaining osmoregulatory homeostasis) and m6A changes between autotetraploid and diploid wild barley (Hordeum bulbosum) in response to salt (NaCl) stress. Results showed that autotetraploids physiologically had enhanced stress tolerance based on the measured parameters of relative water content, water loss, proline, H2O2, and chlorophyll. Diploid H. bulbosum experienced an excessive abundance of proline following salt stress where tetraploids had beneficial proline accumulation and thus enhanced osmoregulation. The significantly higher level of proline and H2O2 in diploid than in autotetraploid implies that diploids suffered higher osmotic stress than autotetraploid. Autotetraploid produced enough proline to protect stress, but not so much to cause toxicity. m6A in total RNA showed no significant difference between ploidies in controls, but was significantly higher in autotetraploids than in diploids during stress and recovery. These results suggest that increased m6A might be one of molecular mechanisms that increases salt tolerance in autotetraploid H. bulbosum compared to diploids, which enhances the adaptation of autopolyploids. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01260-x.
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Affiliation(s)
| | - Ning Chen
- Biology Department, Saint Mary’s University, Halifax, NS Canada
| | | | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, NS Canada
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Li S, Moller CA, Mitchell NG, Martin DG, Sacks EJ, Saikia S, Labonte NR, Baldwin BS, Morrison JI, Ferguson JN, Leakey ADB, Ainsworth EA. The leaf economics spectrum of triploid and tetraploid C 4 grass Miscanthus x giganteus. PLANT, CELL & ENVIRONMENT 2022; 45:3462-3475. [PMID: 36098093 PMCID: PMC9825850 DOI: 10.1111/pce.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
The leaf economics spectrum (LES) describes multivariate correlations in leaf structural, physiological and chemical traits, originally based on diverse C3 species grown under natural ecosystems. However, the specific contribution of C4 species to the global LES is studied less widely. C4 species have a CO2 concentrating mechanism which drives high rates of photosynthesis and improves resource use efficiency, thus potentially pushing them towards the edge of the LES. Here, we measured foliage morphology, structure, photosynthesis, and nutrient content for hundreds of genotypes of the C4 grass Miscanthus× giganteus grown in two common gardens over two seasons. We show substantial trait variations across M.× giganteus genotypes and robust genotypic trait relationships. Compared to the global LES, M.× giganteus genotypes had higher photosynthetic rates, lower stomatal conductance, and less nitrogen content, indicating greater water and photosynthetic nitrogen use efficiency in the C4 species. Additionally, tetraploid genotypes produced thicker leaves with greater leaf mass per area and lower leaf density than triploid genotypes. By expanding the LES relationships across C3 species to include C4 crops, these findings highlight that M.× giganteus occupies the boundary of the global LES and suggest the potential for ploidy to alter LES traits.
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Affiliation(s)
- Shuai Li
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Institute for Sustainability, Energy, and EnvironmentUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Christopher A. Moller
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Global Change and Photosynthesis Research Unit, USDA ARSUrbanaIllinoisUSA
| | - Noah G. Mitchell
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Global Change and Photosynthesis Research Unit, USDA ARSUrbanaIllinoisUSA
| | - Duncan G. Martin
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Erik J. Sacks
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Sampurna Saikia
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Nicholas R. Labonte
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Brian S. Baldwin
- Department of Plant and Soil SciencesMississippi State UniversityStarkvilleMississippiUSA
| | - Jesse I. Morrison
- Department of Plant and Soil SciencesMississippi State UniversityStarkvilleMississippiUSA
| | - John N. Ferguson
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Andrew D. B. Leakey
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Elizabeth A. Ainsworth
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Global Change and Photosynthesis Research Unit, USDA ARSUrbanaIllinoisUSA
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [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: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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Shah S, Rastogi S, Vashisth D, Rout PK, Lal RK, Lavania UC, Shasany AK. Altered Developmental and Metabolic Gene Expression in Basil Interspecific Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:1873. [PMID: 35890507 PMCID: PMC9321874 DOI: 10.3390/plants11141873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
To understand the altered developmental changes and associated gene expression in inter-genomic combinations, a study was planned in two diverse yet closely related species of Ocimum, targeting their hybrid F1 and amphidiploids. The existing developmental variations between F1 and amphidiploids was analyzed through phenotypical and anatomical assessments. The absence of 8330 transcripts of F1 in amphidiploids and the exclusive presence of two transcripts related to WNK lysine-deficient protein kinase and geranylgeranyl transferase type-2 subunit beta 1-like proteins in amphidiploids provided a set of genes to compare the suppressed and activated functions between F1 and amphidiploids. The estimation of eugenol and methyleugenol, flavonoid, lignin and chlorophyll content was correlated with the average FPKM and differential gene expression values and further validated through qRT-PCR. Differentially expressed genes of stomatal patterning and development explained the higher density of stomata in F1 and the larger size of stomata in amphidiploids. Gene expression study of several transcription factors putatively involved in the growth and developmental processes of plants clearly amalgamates the transcriptome data linking the phenotypic differences in F1 and amphidiploids. This investigation describes the influence of interspecific hybridization on genes and transcription factors leading to developmental changes and alleviation of intergenomic instability in amphidiploids.
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Affiliation(s)
- Saumya Shah
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
| | - Shubhra Rastogi
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
| | - Divya Vashisth
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
| | - Prashant Kumar Rout
- Department of Phytochemistry, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India;
| | - Raj Kishori Lal
- Department of Genetics and Plant Breeding, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (R.K.L.); (U.C.L.)
| | - Umesh Chandra Lavania
- Department of Genetics and Plant Breeding, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (R.K.L.); (U.C.L.)
- Department of Botany, University of Lucknow, Lucknow 226007, India
| | - Ajit Kumar Shasany
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
- ICAR-National Institute for Plant Biotechnology (NIPB), Pusa Campus, New Delhi 110012, India
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Vimala Y, Lavania UC, Singh M, Lavania S, Srivastava S, Basu S. Realization of Lodging Tolerance in the Aromatic Grass, Cymbopogon khasianus Through Ploidy Intervention. FRONTIERS IN PLANT SCIENCE 2022; 13:908659. [PMID: 35615136 PMCID: PMC9125236 DOI: 10.3389/fpls.2022.908659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Artificial polyploidy that brings about increase in cell size confers changes in histo-morphology leading to altered phenotype, causing changes in physiological attributes and enhanced concentration of secondary metabolites. The altered phenotype is generally a manifestation of tissue hardiness reflected as robust plant type. Based on a case study undertaken on an industrially important grass, Cymbopogon khasianus (2n = 60) valued for its citral rich essential oil, here we report that the artificial polyploidy not only brings about enhancement in concentration of essential oil but also facilitates lodging tolerance. The latter is contributed by ploidy mediated changes that occur to the cells and tissues in various plant organs by way of increased wall thickening, tissue enhancement and epidermal depositions that enable robust features. An exhaustive illustrated account covering various micro-/macro-morphological, skeletal and histochemical features constituting growth and development vis-a-vis ploidy mediated changes is presented highlighting the novelties realized on account of induced polyploidy.
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Affiliation(s)
- Yerramilli Vimala
- Department of Botany, Chaudhary Charan Singh (CCS) University, Meerut, India
| | | | - Madhavi Singh
- Department of Botany, University of Lucknow, Lucknow, India
| | - Seshu Lavania
- Department of Botany, University of Lucknow, Lucknow, India
| | - Sarita Srivastava
- Department of Botany, Chowdhary Mahadev Prasad (CMP) College (Constituent College of Central University of Allahabad), Prayagraj, India
| | - Surochita Basu
- Department of Botany, Tripura University (A Central University), Agartala, India
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Robinson ML, Schilmiller AL, Wetzel WC. A domestic plant differs from its wild relative along multiple axes of within-plant trait variability and diversity. Ecol Evol 2022; 12:e8545. [PMID: 35127045 PMCID: PMC8794722 DOI: 10.1002/ece3.8545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/28/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022] Open
Abstract
For 10,000 years humans have altered plant traits through domestication and ongoing crop improvement, shaping plant form and function in agroecosystems. To date, studies have focused on how these processes shape whole-plant or average traits; however, plants also have characteristic levels of trait variability among their repeated parts, which can be heritable and mediate critical ecological interactions. Here, we examine an underappreciated scale of trait variation-among leaves, within plants-that may have changed through the process of domestication and improvement. Variability at this scale may itself be a target of selection, or be shaped as a by-product of the domestication process. We explore how levels of among-leaf trait variability differ between cultivars and wild relatives of alfalfa (Medicago sativa), a key forage crop with a 7,000-year domestication history. We grew individual plants from 30 wild populations and 30 cultivars, and quantified variability in a broad suite of physical, nutritive, and chemical leaf traits, including measures of chemical dissimilarity (beta diversity) among leaves within each plant. We find that trait variability has changed over the course of domestication, with effects often larger than changes in trait means. Domestic alfalfa had elevated among-leaf variability in SLA, trichomes, and C:N; increased diversity in defensive compounds; and reduced variability in phytochemical composition. We also elucidate fundamental relationships between trait means and variability, and between overall production of secondary metabolites and patterns of chemical diversity. We conclude that within-plant variability is an overlooked dimension of trait diversity in a globally critical agricultural crop. Trait variability is actually higher in cultivated plants compared to wild progenitors for multiple nutritive, physical, and chemical traits, highlighting a scale of variation that may mitigate loss of trait diversity at other scales in alfalfa agroecosystems, and in other crops with similar histories of domestication and improvement.
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Affiliation(s)
- Moria L. Robinson
- Department of EntomologyMichigan State UniversityEast LansingMichiganUSA
- Kellogg Biological StationMichigan State UniversityEast LansingMichiganUSA
- Ecology, Evolution, and Behavior ProgramMichigan State UniversityEast LansingMichiganUSA
| | | | - William C. Wetzel
- Department of EntomologyMichigan State UniversityEast LansingMichiganUSA
- Kellogg Biological StationMichigan State UniversityEast LansingMichiganUSA
- Ecology, Evolution, and Behavior ProgramMichigan State UniversityEast LansingMichiganUSA
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
- AgBioResearchMichigan State UniversityEast LansingMichiganUSA
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Zhang K, Mason AS, Farooq MA, Islam F, Quezada-Martinez D, Hu D, Yang S, Zou J, Zhou W. Challenges and prospects for a potential allohexaploid Brassica crop. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2711-2726. [PMID: 34089067 DOI: 10.1007/s00122-021-03845-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/23/2021] [Indexed: 05/28/2023]
Abstract
The production of a new allohexaploid Brassica crop (2n = AABBCC) is increasingly attracting international interest: a new allohexaploid crop could benefit from several major advantages over the existing Brassica diploid and allotetraploid species, combining genetic diversity and traits from all six crop species with additional allelic heterosis from the extra genome. Although early attempts to produce allohexaploids showed mixed results, recent technological and conceptual advances have provided promising leads to follow. However, there are still major challenges which exist before this new crop type can be realized: (1) incorporation of sufficient genetic diversity to form a basis for breeding and improvement of this potential crop species; (2) restoration of regular meiosis, as most allohexaploids are genetically unstable after formation; and (3) improvement of agronomic traits to the level of "elite" breeding material in the diploid and allotetraploid crop species. In this review, we outline these major prospects and challenges and propose possible plans to produce a stable, diverse and agronomically viable allohexaploid Brassica crop.
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Affiliation(s)
- Kangni Zhang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Muhammad A Farooq
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Daniela Quezada-Martinez
- Plant Breeding Department, Justus Liebig University, 35392, Giessen, Germany
- Plant Breeding Department, The University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Su Yang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
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Ploidy differentiation and floral scent divergence in Buddleja macrostachya (Scrophulariaceae) complex. BIOCHEM SYST ECOL 2021. [DOI: 10.1016/j.bse.2021.104271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Pegg TJ, Gladish DK, Baker RL. Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11437. [PMID: 34268017 PMCID: PMC8272585 DOI: 10.1002/aps3.11437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/19/2021] [Indexed: 05/22/2023]
Abstract
PREMISE Fluorescence microscopy is an effective tool for viewing plant internal anatomy. However, using fluorescent antibodies or labels hinders throughput. We present a minimal protocol that takes advantage of inherent autofluorescence and aldehyde-induced fluorescence in plant cellular and subcellular structures to markedly increase throughput in cellular and ultrastructural visualization. METHODS AND RESULTS Twelve species distributed across the plant phylogeny were each subjected to five fixative treatments: 1% paraformaldehyde and 2% glutaraldehyde, 2% paraformaldehyde, 2% glutaraldehyde, formalin-acid-alcohol (FAA), and 70% ethanol. Samples were prepared by embedding and mechanically sectioning or via whole mount. A confocal laser scanning system was used to collect micrographs. We evaluated and compared fixative influence on sample structural preservation and tissue autofluorescence. CONCLUSIONS Formaldehyde fixation of Viridiplantae taxa samples generates useful structural data while requiring no additional histological staining or clearing. In addition, a fluorescence-capable microscope is the only specialized equipment required for image acquisition. The minimal protocol developed in this experiment enables high-throughput sample processing by eliminating the need for multi-day preparations.
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Affiliation(s)
- Timothy J. Pegg
- Department of BiologyMiami UniversityOxfordOhio45056USA
- Graduate Program in BotanyMiami UniversityOxfordOhio45056USA
| | - Daniel K. Gladish
- Department of BiologyMiami UniversityOxfordOhio45056USA
- Graduate Program in BotanyMiami UniversityOxfordOhio45056USA
| | - Robert L. Baker
- Department of BiologyMiami UniversityOxfordOhio45056USA
- Graduate Program in BotanyMiami UniversityOxfordOhio45056USA
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13
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Scarrow M, Wang Y, Sun G. Molecular regulatory mechanisms underlying the adaptability of polyploid plants. Biol Rev Camb Philos Soc 2020; 96:394-407. [PMID: 33098261 DOI: 10.1111/brv.12661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
Polyploidization influences the genetic composition and gene expression of an organism. This multi-level genetic change allows the formation of new regulatory pathways leading to increased adaptability. Although both forms of polyploidization provide advantages, autopolyploids were long thought to have little impact on plant divergence compared to allopolyploids due to their formation through genome duplication only, rather than in combination with hybridization. Recent advances have begun to clarify the molecular regulatory mechanisms such as microRNAs, alternative splicing, RNA-binding proteins, histone modifications, chromatin remodelling, DNA methylation, and N6 -methyladenosine (m6A) RNA methylation underlying the evolutionary success of polyploids. Such research is expanding our understanding of the evolutionary adaptability of polyploids and the regulatory pathways that allow adaptive plasticity in a variety of plant species. Herein we review the roles of individual molecular regulatory mechanisms and their potential synergistic pathways underlying plant evolution and adaptation. Notably, increasing interest in m6A methylation has provided a new component in potential mechanistic coordination that is still predominantly unexplored. Future research should attempt to identify and functionally characterize the evolutionary impact of both individual and synergistic pathways in polyploid plant species.
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Affiliation(s)
- Margaret Scarrow
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041000, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
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14
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Newsome EL, Brock GL, Lutz J, Baker RL. Variation within laminae: Semi-automated methods for quantifying leaf venation using phenoVein. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11346. [PMID: 32477842 PMCID: PMC7249269 DOI: 10.1002/aps3.11346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/18/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Physiological processes may vary within leaf laminae; however, the accompanying heterogeneity in leaf venation is rarely investigated because its quantification can be time consuming. Here we introduce accelerated protocols using existing software to increase sample throughput and ask whether laminae venation varies among three crop types and four subspecies of Brassica rapa. METHODS FAA (formaldehyde, glacial acetic acid, and ethanol)-fixed samples were stored in ethanol. Without performing any additional clearing or staining, we tested two methods of image acquisition at three locations along the proximal-distal axis of the laminae and estimated the patterns of venation using the program phenoVein. We developed and made available an R script to handle the phenoVein output and then analyzed our data using linear mixed-effects models. RESULTS Beyond fixation and storage, staining and clearing are not necessary to estimate leaf venation using phenoVein if the images are acquired using a stereomicroscope. All estimates of venation required some manual adjustment. We found a significant effect of location within the laminae for all aspects of venation. DISCUSSION By removing the clearing and staining steps and utilizing the semi-automated program phenoVein, we quickly and cheaply acquired leaf venation data. Venation may be an important target for crop breeding efforts, particularly if intralaminar variation correlates with variation in physiological processes, which remains an open question.
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Affiliation(s)
- Eastyn L. Newsome
- Department of BiologyMiami University700 E High StreetOxfordOhio45056USA
| | - Grace L. Brock
- Department of BiologyMiami University700 E High StreetOxfordOhio45056USA
| | - Jared Lutz
- Department of BiologyMiami University700 E High StreetOxfordOhio45056USA
| | - Robert L. Baker
- Department of BiologyMiami University700 E High StreetOxfordOhio45056USA
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15
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Tamayo‐Ordóñez MC, Ayil‐Gutiérrez BA, Tamayo‐Ordóñez YJ, Rodríguez‐Zapata LC, Monforte‐González M, De la Cruz‐Arguijo EA, García‐Castillo MJ, Sánchez‐Teyer LF. Review and in silico analysis of fermentation, bioenergy, fiber, and biopolymer genes of biotechnological interest in
Agave
L. for genetic improvement and biocatalysis. Biotechnol Prog 2018; 34:1314-1334. [DOI: 10.1002/btpr.2689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/04/2018] [Accepted: 06/26/2018] [Indexed: 12/17/2022]
Affiliation(s)
- M. C. Tamayo‐Ordóñez
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP. 97200, Mérida Yucatán Mexico
| | - B. A. Ayil‐Gutiérrez
- CONACYT‐ Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro, s/n, Esq. Elías Piña Reynosa 88710 Mexico
| | - Y. J. Tamayo‐Ordóñez
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP. 97200, Mérida Yucatán Mexico
| | - L. C. Rodríguez‐Zapata
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP. 97200, Mérida Yucatán Mexico
| | - M. Monforte‐González
- Unidad de Bioquímica Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP. 97200, Mérida Yucatán Mexico
| | - E. A. De la Cruz‐Arguijo
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro, s/n, Esq. Elías Piña Reynosa 88710 Mexico
| | - M. J. García‐Castillo
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP. 97200, Mérida Yucatán Mexico
| | - L. F. Sánchez‐Teyer
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP. 97200, Mérida Yucatán Mexico
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Baker RL, Leong WF, Welch S, Weinig C. Mapping and Predicting Non-Linear Brassica rapa Growth Phenotypes Based on Bayesian and Frequentist Complex Trait Estimation. G3 (BETHESDA, MD.) 2018; 8:1247-1258. [PMID: 29467188 PMCID: PMC5873914 DOI: 10.1534/g3.117.300350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/08/2018] [Indexed: 12/23/2022]
Abstract
Predicting phenotypes based on genotypes and understanding the effects of complex multi-locus traits on plant performance requires a description of the underlying developmental processes, growth trajectories, and their genomic architecture. Using data from Brassica rapa genotypes grown in multiple density settings and seasons, we applied a hierarchical Bayesian Function-Valued Trait (FVT) approach to fit logistic growth curves to leaf phenotypic data (length and width) and characterize leaf development. We found evidence of genetic variation in phenotypic plasticity of rate and duration of leaf growth to growing season. In contrast, the magnitude of the plastic response for maximum leaf size was relatively small, suggesting that growth dynamics vs. final leaf sizes have distinct patterns of environmental sensitivity. Consistent with patterns of phenotypic plasticity, several QTL-by-year interactions were significant for parameters describing leaf growth rates and durations but not leaf size. In comparison to frequentist approaches for estimating leaf FVT, Bayesian trait estimation resulted in more mapped QTL that tended to have greater average LOD scores and to explain a greater proportion of trait variance. We then constructed QTL-based predictive models for leaf growth rate and final size using data from one treatment (uncrowded plants in one growing season). Models successfully predicted non-linear developmental phenotypes for genotypes not used in model construction and, due to a lack of QTL-by-treatment interactions, predicted phenotypes across sites differing in plant density.
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Affiliation(s)
- R L Baker
- Department of Biology, Miami University, Oxford, OH 45056,
| | - W F Leong
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - S Welch
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - C Weinig
- Department of Molecular Biology and
- Department of Botany, University of Wyoming, Laramie, WY 82071
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Males J. Geography, environment and organismal traits in the diversification of a major tropical herbaceous angiosperm radiation. AOB PLANTS 2018; 10:ply008. [PMID: 29479409 PMCID: PMC5814923 DOI: 10.1093/aobpla/ply008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
The generation of plant diversity involves complex interactions between geography, environment and organismal traits. Many macroevolutionary processes and emergent patterns have been identified in different plant groups through the study of spatial data, but rarely in the context of a large radiation of tropical herbaceous angiosperms. A powerful system for testing interrelated biogeographical hypotheses is provided by the terrestrial bromeliads, a Neotropical group of extensive ecological diversity and importance. In this investigation, distributional data for 564 species of terrestrial bromeliads were used to estimate variation in the position and width of species-level hydrological habitat occupancy and test six core hypotheses linking geography, environment and organismal traits. Taxonomic groups and functional types differed in hydrological habitat occupancy, modulated by convergent and divergent trait evolution, and with contrasting interactions with precipitation abundance and seasonality. Plant traits in the Bromeliaceae are intimately associated with bioclimatic differentiation, which is in turn strongly associated with variation in geographical range size and species richness. These results emphasize the ecological relevance of structural-functional innovation in a major plant radiation.
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Affiliation(s)
- Jamie Males
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
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Haritha G, Malathi S, Divya B, Swamy BPM, Mangrauthia SK, Sarla N. Oryza nivara Sharma et Shastry. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-71997-9_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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