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Kottler E. Seed resurrection study unearths evolution of phenotypic plasticity. THE NEW PHYTOLOGIST 2023; 240:1714-1716. [PMID: 37697636 DOI: 10.1111/nph.19240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
This article is a Commentary on Vahsen et al. (2023b), 240: 2121–2136.
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Affiliation(s)
- Ezra Kottler
- University of Colorado Boulder, 1900 Pleasant Street, 334 UCB, Rm N122 Ramaley Bldg, Boulder, CO, 80309, USA
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Christie K, Pierson NR, Holeski LM, Lowry DB. Resurrected seeds from herbarium specimens reveal rapid evolution of drought resistance in a selfing annual. AMERICAN JOURNAL OF BOTANY 2023; 110:e16265. [PMID: 38102863 DOI: 10.1002/ajb2.16265] [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: 06/19/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 12/17/2023]
Abstract
PREMISE Increased aridity and drought associated with climate change are exerting unprecedented selection pressures on plant populations. Whether populations can rapidly adapt, and which life history traits might confer increased fitness under drought, remain outstanding questions. METHODS We utilized a resurrection ecology approach, leveraging dormant seeds from herbarium collections to assess whether populations of Plantago patagonica from the semi-arid Colorado Plateau have rapidly evolved in response to approximately ten years of intense drought in the region. We quantified multiple traits associated with drought escape and drought resistance and assessed the survival of ancestors and descendants under simulated drought. RESULTS Descendant populations displayed a significant shift in resource allocation, in which they invested less in reproductive tissues and relatively more in both above- and below-ground vegetative tissues. Plants with greater leaf biomass survived longer under terminal drought; moreover, even after accounting for the effect of increased leaf biomass, descendant seedlings survived drought longer than their ancestors. CONCLUSIONS Our results document rapid adaptive evolution in response to climate change in a selfing annual and suggest that shifts in tissue allocation strategies may underlie adaptive responses to drought in arid or semi-arid environments. This work also illustrates a novel approach, documenting that under specific circumstances, seeds from herbarium specimens may provide an untapped source of dormant propagules for future resurrection experiments.
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Affiliation(s)
- Kyle Christie
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Natalie R Pierson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Liza M Holeski
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
- Center for Adaptive Western Landscapes, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, 48824, USA
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Yang X, Niu X, Li L, Wang L, Liu C, Liu J, Yuan Q, Pei X. Understanding the molecular mechanism of drought resistance in Shanlan upland rice by transcriptome and phenotype analyses. Int J Biol Macromol 2023; 231:123387. [PMID: 36693603 DOI: 10.1016/j.ijbiomac.2023.123387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Rice (Oryza sativa L.) is an important grain crop worldwide, and drought has become an important factor restricting rice yield. As a unique rice germplasm in Hainan (China), Shanlan upland rice has rich genetic diversity and certain advantage for breeding water-saving and drought-resistance rice. 48 varieties, including 41 Shanlan upland rice, 3 upland rice, and 4 irrigated rice varieties was cultivated in soil pots. The drought resistance was assessed at the seedling stage using the stress coefficients of seven indicators, as the D value calculating from five principal components to rank the varieties. Five cultivars with strong, medium, and low resistance, were selected for transcriptome sequencing. The results of the GSEA analysis showed that free amino acid content increased through the redistribution of energy in Shanlan upland rice to cope with drought stress. In addition, we found that Os03g0623100 was significantly up-regulated under drought stress conditions in varieties with high drought resistance, as compared with low resistance cultivars. The Os03g0623100 was predicted to interact with LEA protein in the STRING database, which may contribute to maintaining the energy metabolisms to under stress conditions. This study provides a view of Shanlan upland rice as a drought-resistant germplasm resource, and a deeper understanding of the molecular mechanism of crop drought resistance.
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Affiliation(s)
- Xinsen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xiaoling Niu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Laiyi Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Liu Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianing Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qianhua Yuan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Johnson SE, Tittes S, Franks SJ. Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought. J Evol Biol 2023; 36:550-562. [PMID: 36721268 DOI: 10.1111/jeb.14152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/22/2022] [Accepted: 12/08/2022] [Indexed: 02/02/2023]
Abstract
While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely nonparallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This nonparallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.
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Affiliation(s)
- Stephen E Johnson
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Steven J Franks
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
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Johnson SE, Hamann E, Franks SJ. Rapid-cycling Brassica rapa evolves even earlier flowering under experimental drought. AMERICAN JOURNAL OF BOTANY 2022; 109:1683-1692. [PMID: 35587234 DOI: 10.1002/ajb2.16002] [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: 12/09/2021] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Changes in climate can impose selection on populations and may lead to rapid evolution. One such climatic stress is drought, which plant populations may respond to with escape (rapid growth and early flowering) or avoidance (slow growth and efficient water-use). However, it is unclear if drought escape would be a viable strategy for populations that already flower early from prior selection. METHODS In an experimental evolution study, we subjected rapid-cycling Brassica rapa (RCBr), which was previously selected for early flowering, to four generations of experimental drought or watered conditions. We then grew ancestral and descendant populations concurrently under drought and watered conditions to assess evolution, plasticity, and adaptation. RESULTS The RCBr populations that evolved under drought had earlier flowering and lower water-use efficiency than the populations that evolved under watered conditions, indicating evolutionary divergence. The drought descendants also had a trend of earlier flowering compared to ancestors, indicating evolution. Evolution of earlier flowering under drought followed the direction of selection and increased fitness and was consistent with studies in natural and experimental populations of this species, suggesting adaptive evolution. CONCLUSIONS We found rapid adaptive evolution of drought escape in RCBr and little evidence for constraints on flowering time evolution, even though RCBr already flowers extremely early. Our results suggest that some populations may harbor sufficient genetic variation for evolution even after strong selection has occurred. Our study also illustrates the utility of combining artificial selection, experimental evolution, and the resurrection approach to study the evolution of functional traits.
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Affiliation(s)
- Stephen E Johnson
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Elena Hamann
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Steven J Franks
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
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Mitchell N, Luu H, Owens GL, Rieseberg LH, Whitney KD. Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus). Evolution 2022; 76:1512-1528. [PMID: 35665925 PMCID: PMC9544064 DOI: 10.1111/evo.14536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 01/22/2023]
Abstract
To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than that of nonhybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to nonhybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and nonhybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus nonrepeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time, while controls did not, although trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus nonhybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.
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Affiliation(s)
- Nora Mitchell
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA,Department of BiologyUniversity of Wisconsin – Eau ClaireEau ClaireWisconsinUSA
| | - Hoang Luu
- Department of Environmental and Plant BiologyOhio UniversityAthensOhioUSA
| | - Gregory L. Owens
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaBritish ColumbiaCanada
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Ćalić I, Groen SC, Choi JY, Joly‐Lopez Z, Hamann E, Natividad MA, Dorph K, Cabral CLU, Torres RO, Vergara GV, Henry A, Purugganan MD, Franks SJ. The influence of genetic architecture on responses to selection under drought in rice. Evol Appl 2022; 15:1670-1690. [PMID: 36330294 PMCID: PMC9624088 DOI: 10.1111/eva.13419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
Accurately predicting responses to selection is a major goal in biology and important for successful crop breeding in changing environments. However, evolutionary responses to selection can be constrained by such factors as genetic and cross‐environment correlations, linkage, and pleiotropy, and our understanding of the extent and impact of such constraints is still developing. Here, we conducted a field experiment to investigate potential constraints to selection for drought resistance in rice (Oryza sativa) using phenotypic selection analysis and quantitative genetics. We found that traits related to drought response were heritable, and some were under selection, including selection for earlier flowering, which could allow drought escape. However, patterns of selection generally were not opposite under wet and dry conditions, and we did not find individual or closely linked genes that influenced multiple traits, indicating a lack of evidence that antagonistic pleiotropy, linkage, or cross‐environment correlations would constrain selection for drought resistance. In most cases, genetic correlations had little influence on responses to selection, with direct and indirect selection largely congruent. The exception to this was seed mass under drought, which was predicted to evolve in the opposite direction of direct selection due to correlations. Because of this indirect effect on selection on seed mass, selection for drought resistance was not accompanied by a decrease in seed mass, and yield increased with fecundity. Furthermore, breeding lines with high fitness and yield under drought also had high fitness and yield under wet conditions, indicating that there was no evidence for a yield penalty on drought resistance. We found multiple genes in which expression influenced both water use efficiency (WUE) and days to first flowering, supporting a genetic basis for the trade‐off between drought escape and avoidance strategies. Together, these results can provide helpful guidance for understanding and managing evolutionary constraints and breeding stress‐resistant crops.
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Affiliation(s)
- Irina Ćalić
- Department of Biological Sciences Fordham University Bronx NY USA
- Institute of Botany University of Cologne Cologne Germany
| | - Simon C. Groen
- Department of Nematology University of California at Riverside Riverside CA USA
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | - Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | - Zoé Joly‐Lopez
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
- Département de Chimie Université du Québec à Montréal Montréal Québec Canada
| | - Elena Hamann
- Department of Biological Sciences Fordham University Bronx NY USA
- Department of Genetics and Odum School of Ecology University of Georgia Athens GA USA
| | | | - Katherine Dorph
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | | | | | - Georgina V. Vergara
- International Rice Research Institute Los Baños Laguna Philippines
- Institute of Crop Science, University of the Philippines Los Baños, 4031 College Laguna Philippines
| | - Amelia Henry
- International Rice Research Institute Los Baños Laguna Philippines
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
- Center for Genomics and Systems Biology NYU Abu Dhabi Research Institute New York University Abu Dhabi, Saadiyat Island Abu Dhabi United Arab Emirates
| | - Steven J. Franks
- Department of Biological Sciences Fordham University Bronx NY USA
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