1
|
Applications of Molecular Markers for Developing Abiotic-Stress-Resilient Oilseed Crops. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010088. [PMID: 36676037 PMCID: PMC9867252 DOI: 10.3390/life13010088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Globally, abiotic stresses, such as temperature (heat or cold), water (drought and flooding), and salinity, cause significant losses in crop production and have adverse effects on plant growth and development. A variety of DNA-based molecular markers, such as SSRs, RFLPs, AFLPs, SNPs, etc., have been used to screen germplasms for stress tolerance and the QTL mapping of stress-related genes. Such molecular-marker-assisted selection strategies can quicken the development of tolerant/resistant cultivars to withstand abiotic stresses. Oilseeds such as rapeseed, mustard, peanuts, soybeans, sunflower, safflower, sesame, flaxseed, and castor are the most important source of edible oil worldwide. Although oilseed crops are known for their capacity to withstand abiotic challenges, there is a significant difference between actual and potential yields due to the adaptation and tolerance to severe abiotic pressures. This review summarizes the applications of molecular markers to date to achieve abiotic stress tolerance in major oilseed crops. The molecular markers that have been reported for genetic diversity studies and the mapping and tagging of genes/QTLs for drought, heavy metal stress, salinity, flooding, cold and heat stress, and their application in the MAS are presented.
Collapse
|
2
|
Genetic structure of Rhinoceros Rock Iguanas, Cyclura cornuta, in the Dominican Republic, with insights into the impact of captive facilities and the taxonomic status of Cyclura on Mona Island. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01290-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
3
|
Wills DM, Fang Z, York AM, Holland JB, Doebley JF. Defining the Role of the MADS-Box Gene, Zea Agamous-like1, a Target of Selection During Maize Domestication. J Hered 2019; 109:333-338. [PMID: 28992108 DOI: 10.1093/jhered/esx073] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/02/2017] [Indexed: 11/12/2022] Open
Abstract
Genomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time. To determine the trait(s) controlled by zagl1 that was (were) the target(s) of selection during maize domestication, we created a set of recombinant chromosome isogenic lines that differ for the maize versus teosinte alleles of zagl1 and which carry cross-overs between zagl1 and its neighbor genes. These lines were grown in a randomized trial and scored for flowering time and domestication related traits. The results indicated that the maize versus teosinte alleles of zagl1 affect flowering time as expected, as well as multiple traits related to ear size with the maize allele conferring larger ears with more kernels. Our results suggest that zagl1 may have been under selection during domestication to increase the size of the maize ear.
Collapse
Affiliation(s)
- David M Wills
- Laboratory of Genetics, The University of Wisconsin-Madison, Madison, WI.,USDA-ARS Plant Genetics Research Unit, Columbia, MO
| | - Zhou Fang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC.,Bayer Corporation, Morrisville, NC
| | - Alessandra M York
- Laboratory of Genetics, The University of Wisconsin-Madison, Madison, WI
| | - James B Holland
- USDA-ARS Plant Science Research Unit, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC
| | - John F Doebley
- Laboratory of Genetics, The University of Wisconsin-Madison, Madison, WI
| |
Collapse
|
4
|
Genotyping and Sequencing Technologies in Population Genetics and Genomics. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2017_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
5
|
Chen Y, Peng Z, Wu C, Ma Z, Ding G, Cao G, Ruan S, Lin S. Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers. PLoS One 2017; 12:e0175571. [PMID: 28406956 PMCID: PMC5391013 DOI: 10.1371/journal.pone.0175571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/28/2017] [Indexed: 11/19/2022] Open
Abstract
Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption.
Collapse
Affiliation(s)
- Yu Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- State Forestry Administration Engineering Research Center of Chinese Fir, Fuzhou, Fujian, China
| | - Zhuqing Peng
- Department of Nature, Fujian Museum, Fuzhou, Fujian, China
| | - Chao Wu
- State Forestry Administration Engineering Research Center of Chinese Fir, Fuzhou, Fujian, China
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhihui Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Guochang Ding
- State Forestry Administration Engineering Research Center of Chinese Fir, Fuzhou, Fujian, China
| | - Guangqiu Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- State Forestry Administration Engineering Research Center of Chinese Fir, Fuzhou, Fujian, China
| | - Shaoning Ruan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- State Forestry Administration Engineering Research Center of Chinese Fir, Fuzhou, Fujian, China
- * E-mail: (SR); (SL)
| | - Sizu Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- State Forestry Administration Engineering Research Center of Chinese Fir, Fuzhou, Fujian, China
- * E-mail: (SR); (SL)
| |
Collapse
|
6
|
Chhatre VE, Rajora OP. Genetic divergence and signatures of natural selection in marginal populations of a keystone, long-lived conifer, Eastern White Pine (Pinus strobus) from Northern Ontario. PLoS One 2014; 9:e97291. [PMID: 24859159 PMCID: PMC4032246 DOI: 10.1371/journal.pone.0097291] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 04/17/2014] [Indexed: 11/19/2022] Open
Abstract
Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (Ne) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and Ne than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and Ne between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.
Collapse
Affiliation(s)
- Vikram E. Chhatre
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Om P. Rajora
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| |
Collapse
|
7
|
Andrew RL, Rieseberg LH. DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES. Evolution 2013; 67:2468-82. [DOI: 10.1111/evo.12106] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/20/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany, University of British Columbia, 3529-6270 University Blvd; Vancouver; British Columbia; V6T 1Z4; Canada
| | | |
Collapse
|
8
|
Hopkins R, Levin DA, Rausher MD. Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii. Evolution 2011; 66:469-85. [PMID: 22276542 DOI: 10.1111/j.1558-5646.2011.01452.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Character displacement, which arises when species diverge in sympatry to decrease competition for resources or reproductive interference, has been observed in a wide variety of plants and animals. A classic example of reproductive character displacement, presumed to be caused by reinforcing selection, is flower-color variation in the native Texas wildflower Phlox drummondii. Here, we use population genetic analyses to investigate molecular signatures of selection on flower-color variation in this species. First, we quantify patterns of neutral genetic variation across the range of P. drummondii to demonstrate that restricted gene flow and genetic drift cannot explain the pattern of flower-color divergence in this species. There is evidence of extensive gene flow across populations with different flower colors, suggesting selection caused flower-color divergence. Second, analysis of sequence variation in the genes underlying this divergence reveals a signature of a selective sweep in one of the two genes, further indicating selection is responsible for divergence in sympatry. The lack of a signature of selection at the second locus does not necessarily indicate a lack of selection on this locus but instead brings attention to the uncertainty in depending on molecular signatures to identify selection.
Collapse
Affiliation(s)
- Robin Hopkins
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.
| | | | | |
Collapse
|
9
|
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: 95] [Impact Index Per Article: 7.3] [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.
Collapse
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
| | | | | |
Collapse
|
10
|
Shi MM, Michalski SG, Chen XY, Durka W. Isolation by elevation: genetic structure at neutral and putatively non-neutral loci in a dominant tree of subtropical forests, Castanopsis eyrei. PLoS One 2011; 6:e21302. [PMID: 21701584 PMCID: PMC3118804 DOI: 10.1371/journal.pone.0021302] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/24/2011] [Indexed: 11/18/2022] Open
Abstract
Background The distribution of genetic diversity among plant populations growing along elevational gradients can be affected by neutral as well as selective processes. Molecular markers used to study these patterns usually target neutral processes only, but may also be affected by selection. In this study, the effects of elevation and successional stage on genetic diversity of a dominant tree species were investigated controlling for neutrality of the microsatellite loci used. Methodology/Principal Findings Diversity and differentiation among 24 populations of Castanopsis eyrei from different elevations (251–920 m) and successional stages were analysed by eight microsatellite loci. We found that one of the loci (Ccu97H18) strongly deviated from a neutral model of differentiation among populations due to either divergent selection or hitchhiking with an unknown selected locus. The analysis showed that C. eyrei populations had a high level of genetic diversity within populations (AR = 7.6, HE = 0.82). Genetic variation increased with elevation for both the putatively selected locus Ccu97H18 and the neutral loci. At locus Ccu97H18 one allele was dominant at low elevations, which was replaced at higher elevations by an increasing number of other alleles. The level of genetic differentiation at neutral loci was similar to that of other Fagaceae species (FST = 0.032, = 0.15). Population differentiation followed a model of isolation by distance but additionally, strongly significant isolation by elevation was found, both for neutral loci and the putatively selected locus. Conclusions/Significance The results indicate higher gene flow among similar elevational levels than across different elevational levels and suggest a selective influence of elevation on the distribution of genetic diversity in C. eyrei. The study underlines the importance to check the selective neutrality of marker loci in analyses of population structure.
Collapse
Affiliation(s)
- Miao-Miao Shi
- Helmholtz Centre for Environmental Research - UFZ, Department of Community Ecology (BZF), Halle, Germany.
| | | | | | | |
Collapse
|
11
|
Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, Li Y, Bergelson J, Borevitz JO, Nordborg M, Vitek O, Salt DE. A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet 2010; 6:e1001193. [PMID: 21085628 PMCID: PMC2978683 DOI: 10.1371/journal.pgen.1001193] [Citation(s) in RCA: 267] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 10/01/2010] [Indexed: 01/26/2023] Open
Abstract
The genetic model plant Arabidopsis thaliana, like many plant species, experiences a range of edaphic conditions across its natural habitat. Such heterogeneity may drive local adaptation, though the molecular genetic basis remains elusive. Here, we describe a study in which we used genome-wide association mapping, genetic complementation, and gene expression studies to identify cis-regulatory expression level polymorphisms at the AtHKT1;1 locus, encoding a known sodium (Na(+)) transporter, as being a major factor controlling natural variation in leaf Na(+) accumulation capacity across the global A. thaliana population. A weak allele of AtHKT1;1 that drives elevated leaf Na(+) in this population has been previously linked to elevated salinity tolerance. Inspection of the geographical distribution of this allele revealed its significant enrichment in populations associated with the coast and saline soils in Europe. The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments.
Collapse
Affiliation(s)
- Ivan Baxter
- United States Department of Agriculture–Agricultural Research Service, Plant Genetics Research Unit, Donald Danforth Plant Sciences Center, St. Louis, Missouri, United States of America
| | - Jessica N. Brazelton
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Danni Yu
- Department of Statistics, Purdue University, West Lafayette, Indiana, United States of America
| | - Yu S. Huang
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Brett Lahner
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Elena Yakubova
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Yan Li
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Justin O. Borevitz
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Olga Vitek
- Department of Statistics, Purdue University, West Lafayette, Indiana, United States of America
| | - David E. Salt
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| |
Collapse
|
12
|
Schluter D, Marchinko KB, Barrett RDH, Rogers SM. Natural selection and the genetics of adaptation in threespine stickleback. Philos Trans R Soc Lond B Biol Sci 2010; 365:2479-86. [PMID: 20643737 DOI: 10.1098/rstb.2010.0036] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Growing knowledge of the molecular basis of adaptation in wild populations is expanding the study of natural selection. We summarize ongoing efforts to infer three aspects of natural selection--mechanism, form and history--from the genetics of adaptive evolution in threespine stickleback that colonized freshwater after the last ice age. We tested a mechanism of selection for reduced bony armour in freshwater by tracking genotype and allele frequency changes at an underlying major locus (Ectodysplasin) in transplanted stickleback populations. We inferred disruptive selection on genotypes at the same locus in a population polymorphic for bony armour. Finally, we compared the distribution of phenotypic effect sizes of genes underlying changes in body shape with that predicted by models of adaptive peak shifts following colonization of freshwater. Studies of the effects of selection on genes complement efforts to identify the molecular basis of adaptive differences, and improve our understanding of phenotypic evolution.
Collapse
Affiliation(s)
- Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada.
| | | | | | | |
Collapse
|
13
|
Edelist C, Raffoux X, Falque M, Dillmann C, Sicard D, Rieseberg LH, Karrenberg S. Differential expression of candidate salt-tolerance genes in the halophyte Helianthus paradoxus and its glycophyte progenitors H. annuus and H. petiolaris (Asteraceae). AMERICAN JOURNAL OF BOTANY 2009; 96:1830-1838. [PMID: 21622304 DOI: 10.3732/ajb.0900067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Adaptation to different habitats is considered to be a major force in the generation of organismal diversity. Understanding the genetic mechanisms that produce such adaptations will provide insights into long-standing questions in evolutionary biology and, at the same time, improve predictions of plant responses to changing environmental conditions. Here we used semiquantitative RT-PCR to study the expression of eight candidate salt-tolerance genes in leaves of the highly salt-tolerant diploid hybrid species Helianthus paradoxus and its salt-sensitive progenitor species H. annuus and H. petiolaris. Samples were collected after germination and growth under four different treatments: nonsaline (control), near-natural saline, saline with increased K(+), and saline with decreased Mg(2+) and Ca(2+). Three individuals from three populations per species were used. The hybrid species H. paradoxus constitutively under- or overexpressed genes related to potassium and calcium transport (homologues of KT1, KT2, ECA1), suggesting that these genes may contribute to the adaptation of H. paradoxus to salinity. In two other genes, variation between populations within species exceeded species level variation. Furthermore, homologues of the potassium transporter HAK8 and of a transcriptional regulator were generally overexpressed in saline treatments, suggesting that these genes are involved in sustained growth under saline conditions in Helianthus.
Collapse
Affiliation(s)
- Cécile Edelist
- University Paris-Sud, UMR 0320 / UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | | | | | | | | | | | | |
Collapse
|
14
|
HEGARTY MATTHEWJ, BARKER GARYL, BRENNAN ADRIANC, EDWARDS KEITHJ, ABBOTT RICHARDJ, HISCOCK SIMONJ. Extreme changes to gene expression associated with homoploid hybrid speciation. Mol Ecol 2009; 18:877-89. [DOI: 10.1111/j.1365-294x.2008.04054.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
15
|
Hitchhiking both ways: effect of two interfering selective sweeps on linked neutral variation. Genetics 2008; 180:301-16. [PMID: 18716333 DOI: 10.1534/genetics.108.089706] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The neutral polymorphism pattern in the vicinity of a selective sweep can be altered by both stochastic and deterministic factors. Here, we focus on the impact of another selective sweep in the region of influence of a first one. We study the signature left on neutral polymorphism by positive selection at two closely linked loci, when both beneficial mutations reach fixation. We show that, depending on the timing of selective sweeps and on their selection coefficients, the two hitchhiking effects can interfere with each other, leading to less reduction in heterozygosity than a single selective sweep of the same magnitude and more importantly to an excess of intermediate-frequency variants relative to neutrality under some parameter values. This pattern can be sustained and potentially alter the detection of positive selection, including by provoking spurious detection of balancing selection. In situations where positive selection is suspected a priori at several closely linked loci, the polymorphism pattern in the region may also be informative about their selective histories.
Collapse
|
16
|
St-Cyr J, Derome N, Bernatchez L. The transcriptomics of life-history trade-offs in whitefish species pairs (Coregonussp.). Mol Ecol 2008; 17:1850-70. [PMID: 18312278 DOI: 10.1111/j.1365-294x.2008.03696.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J St-Cyr
- Québec Océan, Département de Biologie, Pavillon Charles-Eugène Marchand, Université Laval, Québec, Québec, Canada G1V 0A6
| | | | | |
Collapse
|
17
|
Karrenberg S, Widmer A. Ecologically relevant genetic variation from a non-Arabidopsis perspective. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:156-162. [PMID: 18329951 DOI: 10.1016/j.pbi.2008.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 01/18/2008] [Accepted: 01/21/2008] [Indexed: 05/26/2023]
Abstract
Ecologically relevant genetic variation occurs in genes harbouring alleles that are adaptive in some environments but not in others. Analysis of this type of genetic variation in model organisms has made substantial progress, and is now being expanded to other species in order to better cover the diversity of plant life. Recent advances in connecting ecological and molecular studies in non-model species have been made with regard to edaphic and climatic adaptation, plant reproduction, life-history parameters and biotic interactions. New research avenues that increase biological complexity and ecological relevance by integrating ecological experiments with population genetic and functional genomic approaches provide new insights into the genetic basis of ecologically relevant variation.
Collapse
Affiliation(s)
- Sophie Karrenberg
- ETH Zurich, Institute of Integrative Biology, Plant Ecological Genetics, Universitaetstr. 16, 8092 Zurich, Switzerland
| | | |
Collapse
|
18
|
Gross BL, Turner KG, Rieseberg LH. Selective sweeps in the homoploid hybrid species Helianthus deserticola: evolution in concert across populations and across origins. Mol Ecol 2008; 16:5246-58. [PMID: 18092993 DOI: 10.1111/j.1365-294x.2007.03574.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The evolution of different populations within a species in response to selective pressures can potentially happen in three different ways. It can occur in parallel, where similar changes occur independently in each population in response to selection; in concert, where the spread of an adaptive mutation across a species' range results in a single allele fixing in each population; or populations can diverge in response to local selective pressures. We explored these possibilities in populations of the homoploid hybrid species Helianthus deserticola relative to its parental species Helianthus annuus and Helianthus petiolaris using an analysis of variation in 96 expressed sequence tag-based microsatellites. A total of nine loci showed evidence consistent with recent selection at either the species or population level, although two of these genes were discarded because the apparent sweep did not occur relative to the parent from which the locus was derived. Between one and five loci showed a putative sweep across the entire species range with the same microsatellite allele fixed in each population. This pattern is consistent with evolution in concert despite geographical isolation and potential independent origins of the populations. Only one population of H. deserticola showed candidate sweeps that were unique compared to the rest of the species, and this population has also potentially experienced recent admixture with the parental species.
Collapse
Affiliation(s)
- Briana L Gross
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
| | | | | |
Collapse
|
19
|
Sapir Y, Moody ML, Brouillette LC, Donovan LA, Rieseberg LH. Patterns of genetic diversity and candidate genes for ecological divergence in a homoploid hybrid sunflower, Helianthus anomalus. Mol Ecol 2007; 16:5017-29. [PMID: 17944850 DOI: 10.1111/j.1365-294x.2007.03557.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Natural hybridization accompanied by a shift in niche preference by hybrid genotypes can lead to hybrid speciation. Natural selection may cause the fixation of advantageous alleles in the ecologically diverged hybrids, and the loci experiencing selection should exhibit a reduction in allelic diversity relative to neutral loci. Here, we analyzed patterns of genetic diversity at 59 microsatellite loci associated with expressed sequence tags (ESTs) in a homoploid hybrid sunflower species, Helianthus anomalus. We used two indices, ln RV and ln RH, to compare variation and heterozygosity (respectively) at each locus between the hybrid species and its two parental species, H. annuus and H. petiolaris. Mean values of ln RV and ln RH were significantly lower than zero, which implies that H. anomalus experienced a population bottleneck during its recent evolutionary history. After correcting for the apparent bottleneck, we found six loci with a significant reduction in variation or with heterozygosity in the hybrid species, compared to one or both of the parental species. These loci should be viewed as a ranked list of candidate loci, pending further sequencing and functional analyses. Sequence data were generated for two of the candidate loci, but population genetics tests failed to detect deviations from neutral evolution at either locus. Nonetheless, a greater than eight-fold excess of nonsynonymous substitutions was found near a putative N-myristoylation motif at the second locus (HT998), and likelihood-based models indicated that the protein has been under selection in H. anomalus in the past and, perhaps, in one or both parental species. Finally, our data suggest that selective sweeps may have united populations of H. anomalus isolated by a mountain range, indicating that even low gene-flow species may be held together by the spread of advantageous alleles.
Collapse
Affiliation(s)
- Yuval Sapir
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | | | | | | | | |
Collapse
|
20
|
Kane NC, Rieseberg LH. Genetics and evolution of weedy Helianthus annuus populations: adaptation of an agricultural weed. Mol Ecol 2007; 17:384-94. [PMID: 17725567 DOI: 10.1111/j.1365-294x.2007.03467.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Agricultural weeds are a major cost to economies throughout the world, and have evolved from numerous plant species in many different plant families. Despite their ubiquity, we do not yet know how easily or often weeds evolve from their wild ancestors or the kinds of genes underlying their evolution. Here we report on the evolution of weedy populations of the common sunflower Helianthus annuus. We analysed 106 microsatellites in 48 individuals from each of six wild and four weed populations of the species. The statistical tests lnRV and lnRH were used to test for significant reductions in genetic variability at each locus in weedy populations compared to nearby wild populations. Between 1% and 6% of genes were significant outliers with reduced variation in weedy populations, implying that a small but not insignificant fraction of the genome may be under selection and involved in adaptation of weedy sunflowers. However, there did not appear to be a substantial reduction in variation across the genome, suggesting that effective population sizes have remained very large during the recent evolution of these weedy populations. Additional analyses showed that weedy populations are more closely related to nearby wild populations than to each other, implying that weediness likely evolved multiple times within the species, although a single origin followed by gene flow with local populations cannot be ruled out. Together, our results point to the relative ease with which weedy forms of this species can evolve and persist despite the potentially high levels of geneflow with nearby wild populations.
Collapse
Affiliation(s)
- Nolan C Kane
- Department of Biology, Jordan Hall, 1001 E. Third Street, Indiana University, Bloomington, Indiana 47405, USA.
| | | |
Collapse
|