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Changing patterns of genetic differentiation in the slender wild oat, Avena barbata. Proc Natl Acad Sci U S A 2022; 119:e2121248119. [PMID: 36161958 DOI: 10.1073/pnas.2121248119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The slender wild oat (Avena barbata) was widely studied in California using allozymes in the 1970s and interpreted as a case of ecotypic adaptation to contrasting moisture environments. However, common garden studies suggested that the moist-associated ("mesic") ecotype had high fitness in both moist and dry habitats, thus predicting an adaptive spread into areas occupied by the dry associated ("xeric") ecotype. To test this prediction, we revisited 100 populations of A. barbata that were screened genetically 40 y ago. As expected, mesic allozyme and morphological markers are much more common than in the 1970s. The less-fit xeric ecotype, while still widespread, has declined markedly in range and frequency. Genotyping by sequencing of modern populations reveals striking genetic uniformity within each of the two ecotypes. In recombinants between the two ecotypes, the mesic allele at a major fitness quantitative trait locus (QTL) shows a high frequency but so do many other genomic regions not identified as fitness QTL. Additional introduced genotypes are diverse and more widespread than in the past, and our results show that these have spread into the former range of the xeric ecotype to an even greater extent than the mesic ecotype has. While these results confirm the prediction of contemporary evolution from common gardens, they also suggest that much of the change has been driven by additional waves of introduced genotypes.
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Perez-Limón S, Li M, Cintora-Martinez GC, Aguilar-Rangel MR, Salazar-Vidal MN, González-Segovia E, Blöcher-Juárez K, Guerrero-Zavala A, Barrales-Gamez B, Carcaño-Macias J, Costich DE, Nieto-Sotelo J, Martinez de la Vega O, Simpson J, Hufford MB, Ross-Ibarra J, Flint-Garcia S, Diaz-Garcia L, Rellán-Álvarez R, Sawers RJH. A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize. G3 (BETHESDA, MD.) 2022; 12:jkab447. [PMID: 35100386 PMCID: PMC8896015 DOI: 10.1093/g3journal/jkab447] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/16/2021] [Indexed: 01/31/2023]
Abstract
Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.
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Affiliation(s)
- Sergio Perez-Limón
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Plant Science, The Pennsylvania State University, State College, PA 16802, USA
| | - Meng Li
- Department of Plant Science, The Pennsylvania State University, State College, PA 16802, USA
| | - G Carolina Cintora-Martinez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - M Rocio Aguilar-Rangel
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - M Nancy Salazar-Vidal
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Evolution and Ecology, UC Davis, CA 95616 USA
| | - Eric González-Segovia
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Karla Blöcher-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Alejandro Guerrero-Zavala
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Benjamin Barrales-Gamez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Jessica Carcaño-Macias
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Denise E Costich
- International Center for Maize and Wheat Improvement (CIMMyT), De México 56237, México
| | - Jorge Nieto-Sotelo
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Octavio Martinez de la Vega
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - June Simpson
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, UC Davis, CA 95616 USA
- Center for Population Biology, and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Sherry Flint-Garcia
- U.S. Department of Agriculture, Agricultural Research Service Plant Genetics Research Unit, Columbia, MO 65211, USA
| | - Luis Diaz-Garcia
- Campo Experimental Pabellón-INIFAP. Carretera Aguascalientes-Zacatecas, Aguascalientes, CP 20660, México
| | - Rubén Rellán-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Ruairidh J H Sawers
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Plant Science, The Pennsylvania State University, State College, PA 16802, USA
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Dong E, Bai Y, Qin L, Liang Q, Liu C, Cai Y. Identification and epistasis analysis of quantitative trait loci for zeaxanthin concentration in maize kernel across different generations and environments. BREEDING SCIENCE 2020; 70:212-220. [PMID: 32523403 PMCID: PMC7272246 DOI: 10.1270/jsbbs.19071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/21/2019] [Indexed: 05/21/2023]
Abstract
Zeaxanthin, a natural fat-soluble pigment, not only increases plant resistance, but also has vital significance for human health. However, quantitative trait loci (QTL) and the epistatic effects of zeaxanthin concentration in maize kernel have not been well studied. To identify QTLs and analyse the epistatic effects of zeaxanthin concentration in maize kernel, two sets of segregating generations derived from the cross between HuangC (a high zeaxanthin concentration inbred line) and Rezi1 (a low zeaxanthin concentration inbred line) were evaluated in three different environments. One major-effect QTL, qZea6a, explains 41.4-71.4% of the phenotypic variation and two QTLs, qZea4a and qZea3a, show LOD > 3 for zeaxanthin concentration detected over two generations and three different environments. Four of the ten QTL pairs show epistatic effects, explaining 7.34-14.3% of the phenotypic variance. Furthermore, additivity was the major allelic action at zeaxanthin concentration QTLs located in F2 and F2:3 populations and plants with homozygous HuangC alleles have a strong genetic ability in enhancing zeaxanthin concentration in maize kernel. These results will contribute to understanding these complex loci better and provide awareness about zeaxanthin concentration to maize breeders and scientists involved in maize research.
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Affiliation(s)
- Erfei Dong
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yang Bai
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Liping Qin
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Qingyuan Liang
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Chaoxian Liu
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yilin Cai
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Corresponding author (e-mail: )
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Hämälä T, Gorton AJ, Moeller DA, Tiffin P. Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia). PLoS Genet 2020; 16:e1008707. [PMID: 32210431 PMCID: PMC7135370 DOI: 10.1371/journal.pgen.1008707] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/06/2020] [Accepted: 03/05/2020] [Indexed: 12/23/2022] Open
Abstract
Pleiotropy, the control of multiple phenotypes by a single locus, is expected to slow the rate of adaptation by increasing the chance that beneficial alleles also have deleterious effects. However, a prediction arising from classical theory of quantitative trait evolution states that pleiotropic alleles may have a selective advantage when phenotypes are distant from their selective optima. We examine the role of pleiotropy in regulating adaptive differentiation among populations of common ragweed (Ambrosia artemisiifolia); a species that has recently expanded its North American range due to human-mediated habitat change. We employ a phenotype-free approach by using connectivity in gene networks as a proxy for pleiotropy. First, we identify loci bearing footprints of local adaptation, and then use genotype-expression mapping and co-expression networks to infer the connectivity of the genes. Our results indicate that the putatively adaptive loci are highly pleiotropic, as they are more likely than expected to affect the expression of other genes, and they reside in central positions within the gene networks. We propose that the conditionally advantageous alleles at these loci avoid the cost of pleiotropy by having large phenotypic effects that are beneficial when populations are far from their selective optima. We further use evolutionary simulations to show that these patterns are in agreement with a model where populations face novel selective pressures, as expected during a range expansion. Overall, our results suggest that highly connected genes may be targets of positive selection during environmental change, even though they likely experience strong purifying selection in stable selective environments.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Amanda J. Gorton
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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Bono LM, Smith LB, Pfennig DW, Burch CL. The emergence of performance trade‐offs during local adaptation: insights from experimental evolution. Mol Ecol 2017; 26:1720-1733. [DOI: 10.1111/mec.13979] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Lisa M. Bono
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Leno B. Smith
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - David W. Pfennig
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Christina L. Burch
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
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Matsubara K, Yamamoto E, Mizobuchi R, Yonemaru JI, Yamamoto T, Kato H, Yano M. Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (Oryza sativa L.). J Hered 2014; 106:113-22. [PMID: 25429024 DOI: 10.1093/jhered/esu065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. Here, we describe reduced fitness of segregants (hybrid breakdown, HB) that emerged in an F2 population derived from a cross between 2 rice (Oryza sativa L.) cultivars, "Tachisugata" (TS) and "Hokuriku 193" (H193), despite both parents and F1s showing normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs for 4 morphological traits associated with the HB and 6 associated with principal component scores calculated from values of the morphological traits in the F2 population. Two-way analysis of variance of the putative QTLs identified 4 QTL pairs showing significant epistasis; among them, a pair on chromosomes 1 and 12 made the greatest contribution to HB. The finding was supported by genetic experiments using F3 progeny. HB emerged only when a plant was homozygous for the TS allele at the QTL on chromosome 1 and homozygous for the H193 allele at the QTL on chromosome 12, indicating that each allele behaves as recessive to the other. Our results support the idea that epistasis is an essential part of hybrid fitness.
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Affiliation(s)
- Kazuki Matsubara
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Eiji Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Ritsuko Mizobuchi
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Jun-ichi Yonemaru
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Toshio Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Hiroshi Kato
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Masahiro Yano
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
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Friedman J. Genetic Determinants and Epistasis for Life History Trait Differences in the Common Monkeyflower,Mimulus guttatus. J Hered 2014; 105:816-27. [DOI: 10.1093/jhered/esu057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bourne EC, Bocedi G, Travis JMJ, Pakeman RJ, Brooker RW, Schiffers K. Between migration load and evolutionary rescue: dispersal, adaptation and the response of spatially structured populations to environmental change. Proc Biol Sci 2014; 281:20132795. [PMID: 24452022 PMCID: PMC3906938 DOI: 10.1098/rspb.2013.2795] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 12/13/2013] [Indexed: 11/12/2022] Open
Abstract
The evolutionary potential of populations is mainly determined by population size and available genetic variance. However, the adaptability of spatially structured populations may also be affected by dispersal: positively by spreading beneficial mutations across sub-populations, but negatively by moving locally adapted alleles between demes. We develop an individual-based, two-patch, allelic model to investigate the balance between these opposing effects on a population's evolutionary response to rapid climate change. Individual fitness is controlled by two polygenic traits coding for local adaptation either to the environment or to climate. Under conditions of selection that favour the evolution of a generalist phenotype (i.e. weak divergent selection between patches) dispersal has an overall positive effect on the persistence of the population. However, when selection favours locally adapted specialists, the beneficial effects of dispersal outweigh the associated increase in maladaptation for a narrow range of parameter space only (intermediate selection strength and low linkage among loci), where the spread of beneficial climate alleles is not strongly hampered by selection against non-specialists. Given that local selection across heterogeneous and fragmented landscapes is common, the complex effect of dispersal that we describe will play an important role in determining the evolutionary dynamics of many species under rapidly changing climate.
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Affiliation(s)
- Elizabeth C. Bourne
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
- Institute of Biological and Environmental Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
- Institute für Biologie—Botanik, Freie Universität Berlin, Altensteinstrasse 6, Berlin 14195, Germany
| | - Greta Bocedi
- Institute of Biological and Environmental Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Justin M. J. Travis
- Institute of Biological and Environmental Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Robin J. Pakeman
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Rob W. Brooker
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Katja Schiffers
- Evolution, Modeling and Analyses of Biodiversity group, Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble Cedex 9, France
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Hartman Y, Uwimana B, Hooftman DAP, Schranz ME, van de Wiel CCM, Smulders MJM, Visser RGF, van Tienderen PH. Genomic and environmental selection patterns in two distinct lettuce crop-wild hybrid crosses. Evol Appl 2013; 6:569-84. [PMID: 23789025 PMCID: PMC3684739 DOI: 10.1111/eva.12043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/20/2012] [Indexed: 11/29/2022] Open
Abstract
Genomic selection patterns and hybrid performance influence the chance that crop (trans)genes can spread to wild relatives. We measured fitness(-related) traits in two different field environments employing two different crop–wild crosses of lettuce. We performed quantitative trait loci (QTL) analyses and estimated the fitness distribution of early- and late-generation hybrids. We detected consistent results across field sites and crosses for a fitness QTL at linkage group 7, where a selective advantage was conferred by the wild allele. Two fitness QTL were detected on linkage group 5 and 6, which were unique to one of the crop–wild crosses. Average hybrid fitness was lower than the fitness of the wild parent, but several hybrid lineages outperformed the wild parent, especially in a novel habitat for the wild type. In early-generation hybrids, this may partly be due to heterosis effects, whereas in late-generation hybrids transgressive segregation played a major role. The study of genomic selection patterns can identify crop genomic regions under negative selection across multiple environments and cultivar–wild crosses that might be applicable in transgene mitigation strategies. At the same time, results were cultivar-specific, so that a case-by-case environmental risk assessment is still necessary, decreasing its general applicability.
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Affiliation(s)
- Yorike Hartman
- Institute for Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam Amsterdam, The Netherlands
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10
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Uwimana B, Smulders MJM, Hooftman DAP, Hartman Y, van Tienderen PH, Jansen J, McHale LK, Michelmore RW, van de Wiel CCM, Visser RGF. Hybridization between crops and wild relatives: the contribution of cultivated lettuce to the vigour of crop-wild hybrids under drought, salinity and nutrient deficiency conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1097-111. [PMID: 22660630 PMCID: PMC3442173 DOI: 10.1007/s00122-012-1897-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 05/11/2012] [Indexed: 05/10/2023]
Abstract
With the development of transgenic crop varieties, crop-wild hybridization has received considerable consideration with regard to the potential of transgenes to be transferred to wild species. Although many studies have shown that crops can hybridize with their wild relatives and that the resulting hybrids may show improved fitness over the wild parents, little is still known on the genetic contribution of the crop parent to the performance of the hybrids. In this study, we investigated the vigour of lettuce hybrids using 98 F(2:3) families from a cross between cultivated lettuce and its wild relative Lactuca serriola under non-stress conditions and under drought, salinity and nutrient deficiency. Using single nucleotide polymorphism markers, we mapped quantitative trait loci associated with plant vigour in the F(2:3) families and determined the allelic contribution of the two parents. Seventeen QTLs (quantitative trait loci) associated with vigour and six QTLs associated with the accumulation of ions (Na(+), Cl(-) and K(+)) were mapped on the nine linkage groups of lettuce. Seven of the vigour QTLs had a positive effect from the crop allele and six had a positive effect from the wild allele across treatments, and four QTLs had a positive effect from the crop allele in one treatment and from the wild allele in another treatment. Based on the allelic effect of the QTLs and their location on the genetic map, we could suggest genomic locations where transgene integration should be avoided when aiming at the mitigation of its persistence once crop-wild hybridization takes place.
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Affiliation(s)
| | | | | | - Yorike Hartman
- IBED, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | | | | | - Leah K. McHale
- Department of Horticulture and Crop Science, Ohio State University, Columbus, USA
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11
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Hartman Y, Hooftman DAP, Uwimana B, van de Wiel CCM, Smulders MJM, Visser RGF, van Tienderen PH. Genomic regions in crop-wild hybrids of lettuce are affected differently in different environments: implications for crop breeding. Evol Appl 2012; 5:629-40. [PMID: 23028403 PMCID: PMC3461145 DOI: 10.1111/j.1752-4571.2012.00240.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 12/21/2011] [Indexed: 11/30/2022] Open
Abstract
Many crops contain domestication genes that are generally considered to lower fitness of crop-wild hybrids in the wild environment. Transgenes placed in close linkage with such genes would be less likely to spread into a wild population. Therefore, for environmental risk assessment of GM crops, it is important to know whether genomic regions with such genes exist, and how they affect fitness. We performed quantitative trait loci (QTL) analyses on fitness(-related) traits in two different field environments employing recombinant inbred lines from a cross between cultivated Lactuca sativa and its wild relative Lactuca serriola. We identified a region on linkage group 5 where the crop allele consistently conferred a selective advantage (increasing fitness to 212% and 214%), whereas on linkage group 7, a region conferred a selective disadvantage (reducing fitness to 26% and 5%), mainly through delaying flowering. The probability for a putative transgene spreading would therefore depend strongly on the insertion location. Comparison of these field results with greenhouse data from a previous study using the same lines showed considerable differences in QTL patterns. This indicates that care should be taken when extrapolating experiments from the greenhouse, and that the impact of domestication genes has to be assessed under field conditions.
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Affiliation(s)
- Yorike Hartman
- Institute for Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam Amsterdam, The Netherlands
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12
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A test of the reproductive economy hypothesis in plants: more offspring per capita come from large (not small) parents in Avena barbata. Evol Ecol 2012. [DOI: 10.1007/s10682-012-9573-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Colautti RI, Lee CR, Mitchell-Olds T. Origin, fate, and architecture of ecologically relevant genetic variation. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:199-204. [PMID: 22341792 PMCID: PMC3413448 DOI: 10.1016/j.pbi.2012.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/11/2012] [Accepted: 01/23/2012] [Indexed: 05/08/2023]
Abstract
Recent advances in molecular genetics combined with field manipulations are yielding new insight into the origin, evolutionary fate, and genetic architecture of phenotypic variation in natural plant populations, with two surprising implications for the evolution of plant genomes. First, genetic loci exhibiting antagonistic pleiotropy across natural environments appear rare relative to loci that are adaptive in one or more environments and neutral elsewhere. These 'conditionally neutral' alleles should sweep to fixation when they arise, yet genome comparisons find little evidence for such selective sweeps. Second, genes under biotic selection tend to be of larger effect than genes under abiotic selection. Recent theory suggests this may be a consequence of high gene flow among populations under selection for local adaptation.
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Affiliation(s)
- Robert I Colautti
- Biology Department, Duke University, Durham, NC 27708, United States.
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14
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Anderson JT, Lee CR, Rushworth CA, Colautti RI, Mitchell-Olds T. Genetic trade-offs and conditional neutrality contribute to local adaptation. Mol Ecol 2012; 22:699-708. [PMID: 22420446 DOI: 10.1111/j.1365-294x.2012.05522.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Divergent natural selection promotes local adaptation and can lead to reproductive isolation of populations in contrasting environments; however, the genetic basis of local adaptation remains largely unresolved in natural populations. Local adaptation might result from antagonistic pleiotropy, where alternate alleles are favoured in distinct habitats, and polymorphism is maintained by selection. Alternatively, under conditional neutrality some alleles may be favoured in one environment but neutral at other locations. Antagonistic pleiotropy maintains genetic variation across the landscape; however, there is a systematic bias against discovery of antagonistic pleiotropy because the fitness benefits of local alleles need to be significant in at least two environments. Here, we develop a generally applicable method to investigate polygenic local adaptation and identify loci that are the targets of selection. This approach evaluates allele frequency changes after selection at loci across the genome to distinguish antagonistic pleiotropy from conditional neutrality and deleterious variation. We investigate local adaptation at the qualitative trait loci (QTL) level in field experiments, in which we expose 177 F(6) recombinant inbred lines and parental lines of Boechera stricta (Brassicaceae) to their parental environments over two seasons. We demonstrate polygenic selection for native alleles in both environments, with 2.8% of the genome exhibiting antagonistic pleiotropy and 8% displaying conditional neutrality. Our study strongly supports antagonistic pleiotropy at one large-effect flowering phenology QTL (nFT): native homozygotes had significantly greater probabilities of flowering than foreign homozygotes in both parental environments. Such large-scale field studies are essential to elucidate the genetic basis of adaptation in natural populations.
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Affiliation(s)
- Jill T Anderson
- Department of Biology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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15
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Interactions among flower-size QTL of Mimulus guttatus are abundant but highly variable in nature. Genetics 2011; 189:1461-71. [PMID: 21926295 DOI: 10.1534/genetics.111.132423] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The frequency and character of interactions among genes influencing complex traits remain unknown. Our ignorance is most acute for segregating variation within natural populations, the epistasis most relevant for quantitative trait evolution. Here, we report a comprehensive survey of interactions among a defined set of flower-size QTL: loci polymorphic within a single natural population of yellow monkeyflower (Mimulus guttatus). We find that epistasis is typical. Observed phenotypes routinely differ from those predicted on the basis of direct allelic affects in the isogenic background, although the direction of deviations is highly variable. Across QTL pairs, there are significantly positive and negative interactions for every trait. Across traits, specific locus pairs routinely exhibit both positive and negative interactions. There was a tendency for negative epistasis to accompany positive direct effects and vice versa for the trait of corolla width, which may be due, at least in part, to the fact that QTL were identified from their direct effects on this trait.
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16
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Grativol C, Hemerly AS, Ferreira PCG. Genetic and epigenetic regulation of stress responses in natural plant populations. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:176-85. [PMID: 21914492 DOI: 10.1016/j.bbagrm.2011.08.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 11/30/2022]
Abstract
Plants have developed intricate mechanisms involving gene regulatory systems to adjust to stresses. Phenotypic variation in plants under stress is classically attributed to DNA sequence variants. More recently, it was found that epigenetic modifications - DNA methylation-, chromatin- and small RNA-based mechanisms - can contribute separately or together to phenotypes by regulating gene expression in response to the stress effect. These epigenetic modifications constitute an additional layer of complexity to heritable phenotypic variation and the evolutionary potential of natural plant populations because they can affect fitness. Natural populations can show differences in performance when they are exposed to changes in environmental conditions, partly because of their genetic variation but also because of their epigenetic variation. The line between these two components is blurred because little is known about the contribution of genotypes and epigenotypes to stress tolerance in natural populations. Recent insights in this field have just begun to shed light on the behavior of genetic and epigenetic variation in natural plant populations under biotic and abiotic stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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Affiliation(s)
- Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil
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Kirk H, Freeland JR. Applications and implications of neutral versus non-neutral markers in molecular ecology. Int J Mol Sci 2011; 12:3966-88. [PMID: 21747718 PMCID: PMC3131602 DOI: 10.3390/ijms12063966] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 11/17/2022] Open
Abstract
The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.
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Affiliation(s)
- Heather Kirk
- Department of Biology, Trent University, Peterborough, Ontario K9J 7B8, Canada; E-Mail:
| | - Joanna R. Freeland
- Department of Biology, Trent University, Peterborough, Ontario K9J 7B8, Canada; E-Mail:
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