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Razzaque S, Juenger TE. Seed traits and recruitment interact with habitats to generate patterns of local adaptation in a perennial grass. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3111-3124. [PMID: 38381563 DOI: 10.1093/jxb/erae063] [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: 06/16/2023] [Accepted: 02/20/2024] [Indexed: 02/23/2024]
Abstract
A fundamental challenge in the field of ecology involves understanding the adaptive traits and life history stages regulating the population dynamics of species across diverse habitats. Seed traits and early seedling vigor are thought to be key functional traits in plants, with important consequences for recruitment, establishment, and population persistence. However, little is known about how diverse seed traits interact with seed and microsite availability to impact plant populations. Here, we performed a factorial experiment involving seed addition and surface soil disturbance to explore the combined effects of seed and site availability using genotypes characterized by varying seed mass and dormancy traits. Additionally, we included hybrids that exhibited recombined seed trait relationships compared with natural genotypes, allowing us to assess the impact of specific seed traits on establishment across different sites. We detected a significant three-way interaction between seed addition, site conditions, and soil surface disturbance, influencing both seedling establishment and adult recruitment in Panicum hallii, a perennial grass found in coastal mesic (lowland) and inland xeric (upland) habitats. This establishment/recruitment pattern suggests that mesic and xeric establishment at foreign sites is constrained by the interplay of seed and site limitations. Notably, soil surface disturbance facilitated establishment and recruitment of the xeric genotype while limiting the mesic genotype across all sites. Our results highlight the importance of seed size and dormancy as key factors impacting seedling establishment and adult recruitment, suggesting a potential interactive relationship between these traits.
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Affiliation(s)
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
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2
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Bhaskara GB, Haque T, Bonnette JE, Napier JD, Bauer D, Schmutz J, Juenger TE. Evolutionary Analyses of Gene Expression Divergence in Panicum hallii: Exploring Constitutive and Plastic Responses Using Reciprocal Transplants. Mol Biol Evol 2023; 40:msad210. [PMID: 37738160 PMCID: PMC10556983 DOI: 10.1093/molbev/msad210] [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: 05/23/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST-QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.
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Affiliation(s)
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jason E Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diane Bauer
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Razzaque S, Heckman RW, Juenger TE. Seed size variation impacts local adaptation and life-history strategies in a perennial grass. Proc Biol Sci 2023; 290:20222460. [PMID: 37132240 PMCID: PMC10154936 DOI: 10.1098/rspb.2022.2460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/03/2023] [Indexed: 05/04/2023] Open
Abstract
Seed mass is an ecologically important trait that often differs considerably among ecotypes. Yet, because few studies examine the impacts of seed mass on adult life-history traits, its role in local adaptation is unclear. In this study, using accessions of Panicum hallii that spanned the two major ecotypes, we examined whether covariation between seed mass, seedling and reproductive traits impacts ecotypic divergence and local adaptation. The perennial grass P. hallii has two distinct ecotypes-a large-seeded upland ecotype adapted to xeric environments and a small-seeded lowland ecotype adapted to mesic environments. In the greenhouse, seed mass varied greatly across P. hallii genotypes in a manner consistent with ecotypic divergence. Seed mass covaried significantly with several seedling and reproductive traits. At field sites representing the habitats of the two ecotypes, seed mass had different impacts on seedling and adult recruitment: selection favoured large seeds in upland habitat and small seeds in lowland habitat, which was consistent with local adaptation. By demonstrating the central role of seed mass in ecotypic differences in P. hallii and its importance to seedling and adult recruitment under field conditions, these studies show that early life-history traits can promote local adaptation and potentially explain ecotype formation.
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Affiliation(s)
- Samsad Razzaque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Robert W. Heckman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
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Razzaque S, Juenger TE. The ecology and quantitative genetics of seed and seedling traits in upland and lowland ecotypes of a perennial grass. Evol Lett 2022; 6:460-473. [PMID: 36579162 PMCID: PMC9783394 DOI: 10.1002/evl3.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/23/2022] Open
Abstract
Plants have evolved diverse reproductive allocation strategies and seed traits to aid in dispersal, persistence in the seed bank, and establishment. In particular, seed size, dormancy, and early seedling vigor are thought to be key functional traits with important recruitment and fitness consequences across abiotic stress gradients. Selection for favored seed-trait combinations, or against maladaptive combinations, is likely an important driver shaping recruitment strategies. Here, we test for seed-trait plasticity and patterns of recruitment using two genotypes representative of contrasting upland and lowland ecotypes of Panicum hallii with field experiments in native versus foreign habitats. Furthermore, we test whether seed traits have been under directional selection in P. hallii using the v-test based on trait variance in a genetic cross. Finally, we evaluate the genetic architecture of ecotypic divergence for these traits with quantitative trait locus (QTL) mapping. Field experiments reveal little plasticity but support a hypothesis of adaptation divergence among ecotypes based on recruitment. Patterns of segregation within recombinant hybrids provides strong support for directional selection driving ecotypic divergence in seed traits. Genetic mapping revealed a polygenic architecture with evidence of genetic correlation between seed mass, dormancy, and seedling vigor. Our results suggest that the evolution of these traits may involve constraints that affect the direction of adaptive divergence. For example, seed size and germination percentage shared two colocalized QTL with antagonistic additive effects. This supports the hypothesis of a functional genetic relationship between these traits, resulting in either large seed/strong dormancy or small seed/weak dormancy trait combinations. Overall, our study provides insights into the factors facilitating and potentially constraining ecotypic differentiation in seed traits.
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Affiliation(s)
- Samsad Razzaque
- Department of Integrative BiologyUniversity of Texas at AustinAustinTexas78712,Current Address: Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCalifornia92037
| | - Thomas E. Juenger
- Department of Integrative BiologyUniversity of Texas at AustinAustinTexas78712
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Palacio-Mejía JD, Grabowski PP, Ortiz EM, Silva-Arias GA, Haque T, Des Marais DL, Bonnette J, Lowry DB, Juenger TE. Geographic patterns of genomic diversity and structure in the C 4 grass Panicum hallii across its natural distribution. AOB PLANTS 2021; 13:plab002. [PMID: 33708370 PMCID: PMC7937184 DOI: 10.1093/aobpla/plab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 06/01/2023]
Abstract
Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C4 grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.
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Affiliation(s)
| | - Paul P Grabowski
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Edgardo M Ortiz
- Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Freising, Germany
| | - Gustavo Adolfo Silva-Arias
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David L Des Marais
- Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Khasanova A, Lovell JT, Bonnette J, Weng X, Jenkins J, Yoshinaga Y, Schmutz J, Juenger TE. The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass. FRONTIERS IN PLANT SCIENCE 2019; 10:366. [PMID: 31019518 PMCID: PMC6458277 DOI: 10.3389/fpls.2019.00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/08/2019] [Indexed: 05/16/2023]
Abstract
Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - John T. Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
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Lovell JT, Jenkins J, Lowry DB, Mamidi S, Sreedasyam A, Weng X, Barry K, Bonnette J, Campitelli B, Daum C, Gordon SP, Gould BA, Khasanova A, Lipzen A, MacQueen A, Palacio-Mejía JD, Plott C, Shakirov EV, Shu S, Yoshinaga Y, Zane M, Kudrna D, Talag JD, Rokhsar D, Grimwood J, Schmutz J, Juenger TE. The genomic landscape of molecular responses to natural drought stress in Panicum hallii. Nat Commun 2018; 9:5213. [PMID: 30523281 PMCID: PMC6283873 DOI: 10.1038/s41467-018-07669-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/16/2018] [Indexed: 11/21/2022] Open
Abstract
Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.
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Affiliation(s)
- John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, 35806, AL, USA.
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA.
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, 48824, MI, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA
| | - Brandon Campitelli
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Sean P Gordon
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA
- Zymergen Inc, Emeryville, 94608, CA, USA
| | - Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, 48824, MI, USA
| | - Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Alice MacQueen
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA
| | | | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
| | - Shengqiang Shu
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Yuko Yoshinaga
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Matt Zane
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Dave Kudrna
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85719, AZ, USA
| | - Jason D Talag
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85719, AZ, USA
| | - Daniel Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, CA, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, 35806, AL, USA.
- Department of Energy, Joint Genome Institute, Walnut Creek, 94598, CA, USA.
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, 78712, TX, USA.
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Gould BA, Palacio-Mejia JD, Jenkins J, Mamidi S, Barry K, Schmutz J, Juenger TE, Lowry DB. Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae). BMC Genomics 2018; 19:792. [PMID: 30384830 PMCID: PMC6211516 DOI: 10.1186/s12864-018-5179-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/17/2018] [Indexed: 11/13/2022] Open
Abstract
Background Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptation contribute to the formation of ecotypically differentiated groups of plants is just beginning to be understood through population genomic studies. We used whole genome sequencing combined with association study of climate to discover the drivers of differentiation in the perennial C4 grass Panicum hallii. Results Sequencing of 89 natural accessions of P.hallii revealed complex population structure across the species range. Major population genomic separation was found between subspecies P.hallii var. hallii and var. filipes as well as between at least four major unrecognized subgroups within var. hallii. At least 139 genomic SNPs were significantly associated with temperature or precipitation across the range and these SNPs were enriched for non-synonymous substitutions. SNPs associated with temperature and aridity were more often found in or near genes than expected by chance and enriched for putative involvement in dormancy processes, seed maturation, response to hyperosmosis and salinity, abscisic acid metabolism, hormone metabolism, and drought recovery. Conclusions Both geography and climate adaptation contribute significantly to patterns of genome-wide variation in P.hallii. Population subgroups within P.hallii may represent early stages in the formation of ecotypes. Climate associated loci identified here represent promising targets for future research in this and other perennial grasses. Electronic supplementary material The online version of this article (10.1186/s12864-018-5179-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Billie A Gould
- Myriad Women's Health, South San Francisco, CA, 94080, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.,Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA. .,Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
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10
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Milano ER, Payne CE, Wolfrum E, Lovell J, Jenkins J, Schmutz J, Juenger TE. Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:25. [PMID: 29434668 PMCID: PMC5797396 DOI: 10.1186/s13068-018-1033-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 01/27/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Biofuels derived from lignocellulosic plant material are an important component of current renewable energy strategies. Improvement efforts in biofuel feedstock crops have been primarily focused on increasing biomass yield with less consideration for tissue quality or composition. Four primary components found in the plant cell wall contribute to the overall quality of plant tissue and conversion characteristics, cellulose and hemicellulose polysaccharides are the primary targets for fuel conversion, while lignin and ash provide structure and defense. We explore the genetic architecture of tissue characteristics using a quantitative trait loci (QTL) mapping approach in Panicum hallii, a model lignocellulosic grass system. Diversity in the mapping population was generated by crossing xeric and mesic varietals, comparative to northern upland and southern lowland ecotypes in switchgrass. We use near-infrared spectroscopy with a primary analytical method to create a P. hallii specific calibration model to quickly quantify cell wall components. RESULTS Ash, lignin, glucan, and xylan comprise 68% of total dry biomass in P. hallii: comparable to other feedstocks. We identified 14 QTL and one epistatic interaction across these four cell wall traits and found almost half of the QTL to localize to a single linkage group. CONCLUSIONS Panicum hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (P. virgatum). We used high throughput phenotyping to map genomic regions that impact natural variation in leaf tissue composition. Understanding the genetic architecture of tissue traits in a tractable model grass system will lead to a better understanding of cell wall structure as well as provide genomic resources for bioenergy crop breeding programs.
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Affiliation(s)
- Elizabeth R. Milano
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712 USA
| | - Courtney E. Payne
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Ed Wolfrum
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - John Lovell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712 USA
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712 USA
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Grant JN, Burris JN, Stewart CN, Lenaghan SC. Improved tissue culture conditions for the emerging C 4 model Panicum hallii. BMC Biotechnol 2017; 17:39. [PMID: 28449656 PMCID: PMC5408410 DOI: 10.1186/s12896-017-0359-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Panicum hallii Vasey (Hall's panicgrass) is a compact, perennial C4 grass in the family Poaceae, which has potential to enable bioenergy research for switchgrass (Panicum virgatum L.). Unlike P. hallii, switchgrass has a large genome, allopolyploidy, self-incompatibility, a long life cycle, and large stature-all suboptimal traits for rapid genetics research. Herein we improved tissue culture methodologies for two inbred P. hallii populations: FIL2 and HAL2, to enable further development of P. hallii as a model C4 plant. RESULTS The optimal seed-derived callus induction medium was determined to be Murashige and Skoog (MS) medium supplemented with 40 mg L-1 L-cysteine, 300 mg L-1 L-proline, 3% sucrose, 1 g L-1 casein hydrolysate, 3 mg L-1 2,4-dichlorophenoxyacetic acid (2,4-D), and 45 μg L-1 6-benzylaminopurine (BAP), which resulted in callus induction of 51 ± 29% for FIL2 and 81 ± 19% for HAL2. The optimal inflorescence-derived callus induction was observed on MP medium (MS medium supplemented with 2 g L-1 L-proline, 3% maltose, 5 mg L-1 2,4-D, and 500 μg L-1 BAP), resulting in callus induction of 100 ± 0.0% for FIL2 and 84 ± 2.4% for HAL2. Shoot regeneration rates of 11.5 ± 0.8 shoots/gram for FIL2 and 11.3 ± 0.6 shoots/gram for HAL2 were achieved using seed-induced callus, whereas shoot regeneration rates of 26.2 ± 2.6 shoots/gram for FIL2 and 29.3 ± 3.6 shoots/gram for HAL2 were achieved from inflorescence-induced callus. Further, cell suspension cultures of P. hallii were established from seed-derived callus, providing faster generation of callus tissue compared with culture using solidified media (1.41-fold increase for FIL2 and 3.00-fold increase for HAL2). CONCLUSIONS Aside from abbreviated tissue culture times from callus induction to plant regeneration for HAL2, we noted no apparent differences between FIL2 and HAL2 populations in tissue culture performance. For both populations, the cell suspension cultures outperformed tissue cultures on solidified media. Using the methods developed in this work, P. hallii callus was induced from seeds immediately after harvest in a shorter time and with higher frequencies than switchgrass. For clonal propagation, P. hallii callus was established from R1 inflorescences, similar to switchgrass, which further strengthens the potential of this plant as a C4 model for genetic studies. The rapid cycling (seed-to-seed time) and ease of culture, further demonstrate the potential utility of P. hallii as a C4 model plant.
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Affiliation(s)
- Joshua N Grant
- Department of Plant Science, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996, USA
| | - Jason N Burris
- Department of Plant Science, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Department of Plant Science, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996, USA.
| | - Scott C Lenaghan
- Department of Food Science, University of Tennessee, 2600 River Drive, Knoxville, TN, 37996, USA.
- Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, 1512 Middle Drive, Knoxville, TN, 37996, USA.
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Lovell JT, Schwartz S, Lowry DB, Shakirov EV, Bonnette JE, Weng X, Wang M, Johnson J, Sreedasyam A, Plott C, Jenkins J, Schmutz J, Juenger TE. Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass. Genome Res 2016; 26:510-8. [PMID: 26953271 PMCID: PMC4817774 DOI: 10.1101/gr.198135.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/26/2016] [Indexed: 01/18/2023]
Abstract
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass,Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with transeffects.Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% oft rans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and transregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
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Affiliation(s)
- John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Scott Schwartz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - David B Lowry
- Department of Plant Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 42008, Republic of Tatarstan, Russia
| | - Jason E Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Christopher Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
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Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. THE NEW PHYTOLOGIST 2015; 205:402-14. [PMID: 25252269 PMCID: PMC4265272 DOI: 10.1111/nph.13027] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/31/2014] [Indexed: 05/08/2023]
Abstract
The process of plant speciation often involves the evolution of divergent ecotypes in response to differences in soil water availability between habitats. While the same set of traits is frequently associated with xeric/mesic ecotype divergence, it is unknown whether those traits evolve independently or if they evolve in tandem as a result of genetic colocalization either by pleiotropy or genetic linkage. The self-fertilizing C4 grass species Panicum hallii includes two major ecotypes found in xeric (var. hallii) or mesic (var. filipes) habitats. We constructed the first linkage map for P. hallii by genotyping a reduced representation genomic library of an F2 population derived from an intercross of var. hallii and filipes. We then evaluated the genetic architecture of divergence between these ecotypes through quantitative trait locus (QTL) mapping. Overall, we mapped QTLs for nine morphological traits that are involved in the divergence between the ecotypes. QTLs for five key ecotype-differentiating traits all colocalized to the same region of linkage group five. Leaf physiological traits were less divergent between ecotypes, but we still mapped five physiological QTLs. We also discovered a two-locus Dobzhansky-Muller hybrid incompatibility. Our study suggests that ecotype-differentiating traits may evolve in tandem as a result of genetic colocalization.
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Affiliation(s)
- David B Lowry
- Department of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA; Division of Science and Environmental Policy, California State University, Monterey Bay, 100 Campus Center, Seaside, CA, 93955, USA
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Henry RJ, Nevo E. Exploring natural selection to guide breeding for agriculture. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:655-62. [PMID: 24975385 DOI: 10.1111/pbi.12215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 04/13/2014] [Accepted: 05/15/2014] [Indexed: 05/02/2023]
Abstract
Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate-resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.
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Affiliation(s)
- Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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