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Desgroux A, L'Anthoëne V, Roux-Duparque M, Rivière JP, Aubert G, Tayeh N, Moussart A, Mangin P, Vetel P, Piriou C, McGee RJ, Coyne CJ, Burstin J, Baranger A, Manzanares-Dauleux M, Bourion V, Pilet-Nayel ML. Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea. BMC Genomics 2016; 17:124. [PMID: 26897486 PMCID: PMC4761183 DOI: 10.1186/s12864-016-2429-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/02/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. METHODS A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. RESULTS GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. CONCLUSION This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.
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Affiliation(s)
- Aurore Desgroux
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Virginie L'Anthoëne
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- Present Address: Nestlé R&D Center Tours, 101 Avenue Gustave Eiffel, 37097, Tours Cedex 2, France.
| | - Martine Roux-Duparque
- GSP, Domaine Brunehaut, 80200, Estrées-Mons Cedex, France.
- Present Address: Chambre d'Agriculture de l'Aisne, 1 rue René Blondelle, 02007, Laon Cedex, France.
| | - Jean-Philippe Rivière
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Grégoire Aubert
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Nadim Tayeh
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Anne Moussart
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- Terres Inovia, 11 rue de Monceau, CS 60003, 75378, Paris Cedex, France.
| | - Pierre Mangin
- INRA, Domaine Expérimental d'Epoisses, UE0115, 21110, Bretenières Cedex, France.
| | - Pierrick Vetel
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Christophe Piriou
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Rebecca J McGee
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA, 99164-6434, USA.
| | - Clarice J Coyne
- USDA, ARS, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164-6402, USA.
| | - Judith Burstin
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Alain Baranger
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Maria Manzanares-Dauleux
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- AgroCampus Ouest, UMR IGEPP 1349 IGEPP, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Virginie Bourion
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Marie-Laure Pilet-Nayel
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
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Allwright MR, Taylor G. Molecular Breeding for Improved Second Generation Bioenergy Crops. TRENDS IN PLANT SCIENCE 2016; 21:43-54. [PMID: 26541073 DOI: 10.1016/j.tplants.2015.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/18/2015] [Accepted: 10/02/2015] [Indexed: 05/24/2023]
Abstract
There is increasing urgency to develop and deploy sustainable sources of energy to reduce our global dependency on finite, high-carbon fossil fuels. Lignocellulosic feedstocks, used in power and liquid fuel generation, are valuable sources of non-food plant biomass. They are cultivated with minimal inputs on marginal or degraded lands to prevent competition with arable agriculture and offer significant potential for sustainable intensification (the improvement of yield without the necessity for additional inputs) through advanced molecular breeding. This article explores progress made in next generation sequencing, advanced genotyping, association genetics, and genetic modification in second generation bioenergy production. Using poplar as an exemplar where most progress has been made, a suite of target traits is also identified giving insight into possible routes for crop improvement and deployment in the immediate future.
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Affiliation(s)
- Mike R Allwright
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, SO17 1BJ Southampton, UK
| | - Gail Taylor
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, SO17 1BJ Southampton, UK.
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103
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Sehgal D, Singh R, Rajpal VR. Quantitative Trait Loci Mapping in Plants: Concepts and Approaches. MOLECULAR BREEDING FOR SUSTAINABLE CROP IMPROVEMENT 2016. [DOI: 10.1007/978-3-319-27090-6_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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104
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Allwright MR, Payne A, Emiliani G, Milner S, Viger M, Rouse F, Keurentjes JJB, Bérard A, Wildhagen H, Faivre-Rampant P, Polle A, Morgante M, Taylor G. Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.). BIOTECHNOLOGY FOR BIOFUELS 2016; 9:195. [PMID: 27617034 PMCID: PMC5017058 DOI: 10.1186/s13068-016-0603-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/22/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species. RESULTS We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population. CONCLUSIONS The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.
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Affiliation(s)
- Mike Robert Allwright
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Adrienne Payne
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Giovanni Emiliani
- CNR-IVALSA, Sesto Fiorentino, via Madonna del Piano, 10, 50019 Sesto Fiorentino, FI Italy
| | - Suzanne Milner
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Maud Viger
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Franchesca Rouse
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Joost J. B. Keurentjes
- Laboratory of Genetics, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | | | | | | | - Andrea Polle
- Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Michele Morgante
- Dipartimento di Scienze agroalimentari, ambientali e animali, Università di Udine, Via delle Scienze 206, 33100 Udine, Italy
- Istituto di Genomica Applicata (IGA), via J. Linussio 51, 33100 Udine, Italy
| | - Gail Taylor
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
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105
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Kainer D, Lanfear R, Foley WJ, Külheim C. Genomic approaches to selection in outcrossing perennials: focus on essential oil crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2351-65. [PMID: 26239409 DOI: 10.1007/s00122-015-2591-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 07/23/2015] [Indexed: 05/13/2023]
Abstract
The yield of essential oil in commercially harvested perennial species (e.g. 'Oil Mallee' eucalypts, Tea Trees and Hop) is dependent on complex quantitative traits such as foliar oil concentration, biomass and adaptability. These often show large natural variation and some are highly heritable, which has enabled significant gains in oil yield via traditional phenotypic recurrent selection. Analysis of transcript abundance and allelic diversity has revealed that essential oil yield is likely to be controlled by large numbers of quantitative trait loci that range from a few of medium/large effect to many of small effect. Molecular breeding techniques that exploit this information could increase gains per unit time and address complications of traditional breeding such as genetic correlations between key traits and the lower heritability of biomass. Genomic selection (GS) is a technique that uses the information from markers genotyped across the whole genome in order to predict the phenotype of progeny well before they reach maturity, allowing selection at an earlier age. In this review, we investigate the feasibility of genomic selection (GS) for the improvement of essential oil yield. We explore the challenges facing breeders selecting for oil yield, and how GS might deal with them. We then assess the factors that affect the accuracy of genomic estimated breeding values, such as linkage disequilibrium (LD), heritability, relatedness and the genetic architecture of desirable traits. We conclude that GS has the potential to significantly improve the efficiency of selection for essential oil yield.
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Affiliation(s)
- David Kainer
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Robert Lanfear
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - William J Foley
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Carsten Külheim
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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106
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Hoang NV, Furtado A, Botha FC, Simmons BA, Henry RJ. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels. Front Bioeng Biotechnol 2015; 3:182. [PMID: 26636072 PMCID: PMC4646955 DOI: 10.3389/fbioe.2015.00182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels.
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Affiliation(s)
- Nam V. Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Blake A. Simmons
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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De Kort H, Vander Mijnsbrugge K, Vandepitte K, Mergeay J, Ovaskainen O, Honnay O. Evolution, plasticity and evolving plasticity of phenology in the tree species Alnus glutinosa. J Evol Biol 2015; 29:253-64. [DOI: 10.1111/jeb.12777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/13/2015] [Accepted: 10/16/2015] [Indexed: 12/12/2022]
Affiliation(s)
- H. De Kort
- Plant Conservation and Population Biology; Biology Department; University of Leuven; Heverlee Belgium
| | - K. Vander Mijnsbrugge
- Research Institute for Nature and Forest; Geraardsbergen Belgium
- Agency for Nature and Forest; Brussels Belgium
| | - K. Vandepitte
- Plant Conservation and Population Biology; Biology Department; University of Leuven; Heverlee Belgium
| | - J. Mergeay
- Research Institute for Nature and Forest; Geraardsbergen Belgium
| | - O. Ovaskainen
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - O. Honnay
- Plant Conservation and Population Biology; Biology Department; University of Leuven; Heverlee Belgium
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108
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Chen G, Wang X, Hao J, Yan J, Ding J. Genome-Wide Association Implicates Candidate Genes Conferring Resistance to Maize Rough Dwarf Disease in Maize. PLoS One 2015; 10:e0142001. [PMID: 26529245 PMCID: PMC4631334 DOI: 10.1371/journal.pone.0142001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/15/2015] [Indexed: 11/18/2022] Open
Abstract
Maize rough dwarf disease (MRDD) is a destructive viral disease in China, which results in 20-30% of the maize yield losses in affected areas and even as high as 100% in severely infected fields. Understanding the genetic basis of resistance will provide important insights for maize breeding program. In this study, a diverse maize population comprising of 527 inbred lines was evaluated in four environments and a genome-wide association study (GWAS) was undertaken with over 556000 SNP markers. Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions. The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results. Significant correlation (R2 = 0.79) between the MRDD severity and the number of resistance alleles was observed. Consequently, we have broadened the resistant germplasm to MRDD and identified a number of resistance alleles by GWAS. The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.
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Affiliation(s)
- Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoming Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Junjie Hao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junqiang Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
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109
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Remington DL. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins. Evolution 2015; 69:3025-38. [DOI: 10.1111/evo.12775] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 07/06/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
Affiliation(s)
- David L. Remington
- Department of Biology; University of North Carolina at Greensboro; Greensboro North Carolina 27402
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Buchner DA, Nadeau JH. Contrasting genetic architectures in different mouse reference populations used for studying complex traits. Genome Res 2015; 25:775-91. [PMID: 25953951 PMCID: PMC4448675 DOI: 10.1101/gr.187450.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/31/2015] [Indexed: 01/14/2023]
Abstract
Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models.
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Affiliation(s)
- David A Buchner
- Department of Genetics and Genome Sciences, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Joseph H Nadeau
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122, USA
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111
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Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, Fang C, Shen Y, Liu T, Li C, Li Q, Wu M, Wang M, Wu Y, Dong Y, Wan W, Wang X, Ding Z, Gao Y, Xiang H, Zhu B, Lee SH, Wang W, Tian Z. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol 2015; 33:408-14. [PMID: 25643055 DOI: 10.1038/nbt.3096] [Citation(s) in RCA: 631] [Impact Index Per Article: 70.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 11/11/2014] [Indexed: 11/09/2022]
Abstract
Understanding soybean (Glycine max) domestication and improvement at a genetic level is important to inform future efforts to further improve a crop that provides the world's main source of oilseed. We detect 230 selective sweeps and 162 selected copy number variants by analysis of 302 resequenced wild, landrace and improved soybean accessions at >11× depth. A genome-wide association study using these new sequences reveals associations between 10 selected regions and 9 domestication or improvement traits, and identifies 13 previously uncharacterized loci for agronomic traits including oil content, plant height and pubescence form. Combined with previous quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96 correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes. Moreover, we observe that some traits and loci are associated with geographical regions, which shows that soybean populations are structured geographically. This study provides resources for genomics-enabled improvements in soybean breeding.
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Affiliation(s)
- Zhengkui Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yu Jiang
- 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. [2] College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhiheng Gou
- 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Jun Lyu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Weiyu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yanjun Yu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liping Shu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yingjun Zhao
- 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Yanming Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chao Fang
- 1] State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Yanting Shen
- 1] State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Tengfei Liu
- 1] State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Congcong Li
- 1] State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Qing Li
- 1] State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Mian Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- 1] State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Yunshuai Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao Wang
- 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. [2] University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoli Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yuedong Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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112
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Ogura T, Busch W. From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:98-108. [PMID: 25449733 DOI: 10.1016/j.pbi.2014.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 05/20/2023]
Abstract
Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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113
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Montilla-Bascón G, Rispail N, Sánchez-Martín J, Rubiales D, Mur LAJ, Langdon T, Howarth CJ, Prats E. Genome-wide association study for crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) resistance in an oat (Avena sativa) collection of commercial varieties and landraces. FRONTIERS IN PLANT SCIENCE 2015; 6:103. [PMID: 25798140 PMCID: PMC4350391 DOI: 10.3389/fpls.2015.00103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/08/2015] [Indexed: 05/19/2023]
Abstract
Diseases caused by crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) are among the most important constraints for the oat crop. Breeding for resistance is one of the most effective, economical, and environmentally friendly means to control these diseases. The purpose of this work was to identify elite alleles for rust and powdery mildew resistance in oat by association mapping to aid selection of resistant plants. To this aim, 177 oat accessions including white and red oat cultivars and landraces were evaluated for disease resistance and further genotyped with 31 simple sequence repeat and 15,000 Diversity Arrays Technology (DArT) markers to reveal association with disease resistance traits. After data curation, 1712 polymorphic markers were considered for association analysis. Principal component analysis and a Bayesian clustering approach were applied to infer population structure. Five different general and mixed linear models accounting for population structure and/or kinship corrections and two different statistical tests were carried out to reduce false positive. Five markers, two of them highly significant in all models tested were associated with rust resistance. No strong association between any marker and powdery mildew resistance at the seedling stage was identified. However, one DArT sequence, oPt-5014, was strongly associated with powdery mildew resistance in adult plants. Overall, the markers showing the strongest association in this study provide ideal candidates for further studies and future inclusion in strategies of marker-assisted selection.
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Affiliation(s)
- Gracia Montilla-Bascón
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Nicolas Rispail
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Javier Sánchez-Martín
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Diego Rubiales
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Elena Prats
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
- *Correspondence: Elena Prats, Institute for Sustainable Agriculture – Consejo Superior de Investigaciones Científicas, Apartado 4084, E-14080 Córdoba, Spain e-mail:
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114
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Xu B, Tian J, Du Q, Gong C, Pan W, Zhang D. Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa. PLANTA 2014; 240:1269-86. [PMID: 25143249 DOI: 10.1007/s00425-014-2149-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/08/2014] [Indexed: 05/21/2023]
Abstract
In plants, the composition and organization of the cell wall determine cell shape, enable cell expansion, and affect the properties of woody tissues. Cellulose synthase (CesA) genes encode the enzymes involved in the synthesis of cellulose which is the major component of plant primary and secondary cell walls. Here, we isolated a full-length PtoCesA3 cDNA from the stem cambium tissue of Populus tomentosa. Tissue-specific expression profiling showed that PtoCesA3 is highly expressed during primary cell wall formation. Estimation of single nucleotide polymorphism (SNP) diversity and linkage disequilibrium (LD) revealed that PtoCesA3 harbors high SNP diversity (π(T) = 0.00995 and θ(w) = 0.0102) and low LD (r(2) ≥ 0.1, within 1,280 bp). Association analysis in a P. tomentosa association population (460 individuals) showed that seven SNPs (false discovery rate Q < 0.10) and five haplotypes (Q < 0.10) were significantly associated with growth and wood properties, explaining 4.09-7.02% of the phenotypic variance. All significant marker-trait associations were validated in at least one of the three smaller subsets (climatic regions) while five associations were repeated in the linkage population. Variation in RNA transcript abundance among genotypic classes of significant loci was also confirmed in the association or linkage populations. Identification of PtoCesA3 and examining its allelic polymorphisms using association studies open an avenue to understand the mechanism of cellulose synthesis in the primary cell wall and its effects on the properties of woody tissues.
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Affiliation(s)
- Baohua Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
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115
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McKown AD, Guy RD, Quamme L, Klápště J, La Mantia J, Constabel CP, El-Kassaby YA, Hamelin RC, Zifkin M, Azam MS. Association genetics, geography and ecophysiology link stomatal patterning in Populus trichocarpa with carbon gain and disease resistance trade-offs. Mol Ecol 2014; 23:5771-90. [PMID: 25319679 DOI: 10.1111/mec.12969] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/29/2014] [Accepted: 10/12/2014] [Indexed: 01/18/2023]
Abstract
Stomata are essential for diffusive entry of gases to support photosynthesis, but may also expose internal leaf tissues to pathogens. To uncover trade-offs in range-wide adaptation relating to stomata, we investigated the underlying genetics of stomatal traits and linked variability in these traits with geoclimate, ecophysiology, condensed foliar tannins and pathogen susceptibility in black cottonwood (Populus trichocarpa). Upper (adaxial) and lower (abaxial) leaf stomatal traits were measured from 454 accessions collected throughout much of the species range. We calculated broad-sense heritability (H(2) ) of stomatal traits and, using SNP data from a 34K Populus SNP array, performed a genome-wide association studies (GWAS) to uncover genes underlying stomatal trait variation. H(2) values for stomatal traits were moderate (average H(2) = 0.33). GWAS identified genes associated primarily with adaxial stomata, including polarity genes (PHABULOSA), stomatal development genes (BRASSINOSTEROID-INSENSITIVE 2) and disease/wound-response genes (GLUTAMATE-CYSTEINE LIGASE). Stomatal traits correlated with latitude, gas exchange, condensed tannins and leaf rust (Melampsora) infection. Latitudinal trends of greater adaxial stomata numbers and guard cell pore size corresponded with higher stomatal conductance (gs ) and photosynthesis (Amax ), faster shoot elongation, lower foliar tannins and greater Melampsora susceptibility. This suggests an evolutionary trade-off related to differing selection pressures across the species range. In northern environments, more adaxial stomata and larger pore sizes reflect selection for rapid carbon gain and growth. By contrast, southern genotypes have fewer adaxial stomata, smaller pore sizes and higher levels of condensed tannins, possibly linked to greater pressure from natural leaf pathogens, which are less significant in northern ecosystems.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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116
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Crutsinger GM, Rudman SM, Rodriguez-Cabal MA, McKown AD, Sato T, MacDonald AM, Heavyside J, Geraldes A, Hart EM, LeRoy CJ, El-Sabaawi RW. Testing a ‘genes-to-ecosystems’ approach to understanding aquatic-terrestrial linkages. Mol Ecol 2014; 23:5888-903. [DOI: 10.1111/mec.12931] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/04/2014] [Accepted: 09/12/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Gregory M. Crutsinger
- Department of Zoology; University of British Columbia; 4200-6270 University Blvd. Vancouver BC V6T1Z4 Canada
| | - Seth M. Rudman
- Department of Zoology; University of British Columbia; 4200-6270 University Blvd. Vancouver BC V6T1Z4 Canada
| | - Mariano A. Rodriguez-Cabal
- Department of Zoology; University of British Columbia; 4200-6270 University Blvd. Vancouver BC V6T1Z4 Canada
| | - Athena D. McKown
- Department of Forest and Conservation Sciences; University of British Columbia; 2424 Main Mall Vancouver BC V6T 1Z4 Canada
| | - Takuya Sato
- Department of Biology; Graduate school of Science; Kobe University; 1-1 Rokkodai Nada-ku Kobe 657-8501 Japan
| | - Andrew M. MacDonald
- Department of Zoology; University of British Columbia; 4200-6270 University Blvd. Vancouver BC V6T1Z4 Canada
| | - Julian Heavyside
- Department of Zoology; University of British Columbia; 4200-6270 University Blvd. Vancouver BC V6T1Z4 Canada
| | - Armando Geraldes
- Department of Botany; University of British Columbia; 3529-6270 University Blvd. Vancouver BC V6T 1Z4 Canada
| | - Edmund M. Hart
- Department of Zoology; University of British Columbia; 4200-6270 University Blvd. Vancouver BC V6T1Z4 Canada
| | - Carri J. LeRoy
- Environmental Studies Program; The Evergreen State College; 2700 Evergreen Parkway NW Olympia WA 98505 USA
| | - Rana W. El-Sabaawi
- Department of Biology; University of Victoria; Cunningham 202, 3800 Finnerty Rd. Victoria BC V8P 5C2 Canada
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Keefover-Ring K, Ahnlund M, Abreu IN, Jansson S, Moritz T, Albrectsen BR. No evidence of geographical structure of salicinoid chemotypes within Populus tremula. PLoS One 2014; 9:e107189. [PMID: 25299342 PMCID: PMC4191948 DOI: 10.1371/journal.pone.0107189] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/07/2014] [Indexed: 11/18/2022] Open
Abstract
Salicinoids are well-known defense compounds in salicaceous trees and careful screening at the population level is warranted to fully understand their diversity and function. European aspen, Populus tremula, is a foundation species in Eurasia and highly polymorphic in Sweden. We exhaustively surveyed 102 replicated genotypes from the Swedish Aspen collection (SwAsp) for foliar salicinoids using UHPLC-ESI-TOF/MS and identified nine novel compounds, bringing the total to 19 for this species. Salicinoid structure followed a modular architecture of a salicin skeleton with added side groups, alone or in combination. Two main moieties, 2'-cinnamoyl and 2'-acetyl, grouped the SwAsp population into four distinct chemotypes, and the relative allocation of salicinoids was remarkably constant between different environments, implying a highly channeled biosynthesis of these compounds. Slightly more than half of the SwAsp genotypes belonged to the cinnamoyl chemotype. A fraction synthesized the acetyl moiety alone (∼7%) or in combination with cinnamoyl (∼2%), and close to forty percent lacked either of the two characteristic moieties, and thus resemble P. tremuloides in their salicinoid profile. The two most abundant chemotypes were evenly distributed throughout Sweden, unlike geographical patterns reported for SwAsp phenology traits, plant defense genes, and herbivore community associations. Here we present the salicinoid characterization of the SwAsp collection as a resource for future studies of aspen chemical ecology, salicinoid biosynthesis, and genetics.
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Affiliation(s)
- Ken Keefover-Ring
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Maria Ahnlund
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Umeå, Sweden
| | - Ilka Nacif Abreu
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Umeå, Sweden
| | - Stefan Jansson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, Umeå, Sweden
| | - Benedicte Riber Albrectsen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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118
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Dell'Acqua M, Zuccolo A, Tuna M, Gianfranceschi L, Pè ME. Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach. BMC Genomics 2014; 15:801. [PMID: 25236859 PMCID: PMC4177692 DOI: 10.1186/1471-2164-15-801] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/04/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environment depends on how well they adapt to local pedoclimatic conditions. Genomic tools can be used to identify adaptive traits at a DNA level and to further our understanding of evolutionary processes. Here we report the use of genotyping-by-sequencing on local groups of the sequenced monocot model species Brachypodium distachyon. Exploiting population genetics, landscape genomics and genome wide association studies, we evaluate B. distachyon role as a natural probe for identifying genomic loci involved in environmental adaptation. RESULTS Brachypodium distachyon individuals were sampled in nine locations with different ecologies and characterized with 16,697 SNPs. Variations in sequencing depth showed consistent patterns at 8,072 genomic bins, which were significantly enriched in transposable elements. We investigated the structuration and diversity of this collection, and exploited climatic data to identify loci with adaptive significance through i) two different approaches for genome wide association analyses considering climatic variation, ii) an outlier loci approach, and iii) a canonical correlation analysis on differentially sequenced bins. A linkage disequilibrium-corrected Bonferroni method was applied to filter associations. The two association methods jointly identified a set of 15 genes significantly related to environmental adaptation. The outlier loci approach revealed that 5.7% of the loci analysed were under selection. The canonical correlation analysis showed that the distribution of some differentially sequenced regions was associated to environmental variation. CONCLUSIONS We show that the multi-faceted approach used here targeted different components of B. distachyon adaptive variation, and may lead to the discovery of genes related to environmental adaptation in natural populations. Its application to a model species with a fully sequenced genome is a modular strategy that enables the stratification of biological material and thus improves our knowledge of the functional loci determining adaptation in near-crop species. When coupled with population genetics and measures of genomic structuration, methods coming from genome wide association studies may lead to the exploitation of model species as natural probes to identify loci related to environmental adaptation.
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Affiliation(s)
| | | | | | | | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
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119
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Proximal Remote Sensing Buggies and Potential Applications for Field-Based Phenotyping. AGRONOMY-BASEL 2014. [DOI: 10.3390/agronomy4030349] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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120
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McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 203:535-553. [PMID: 24750093 DOI: 10.1111/nph.12815] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/14/2014] [Indexed: 05/02/2023]
Abstract
In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29,355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P<1.7×10(-6)). Markers were found across 19 chromosomes, explained 1-13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jan Hannemann
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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121
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Bonhomme M, André O, Badis Y, Ronfort J, Burgarella C, Chantret N, Prosperi JM, Briskine R, Mudge J, Debéllé F, Navier H, Miteul H, Hajri A, Baranger A, Tiffin P, Dumas B, Pilet-Nayel ML, Young ND, Jacquet C. High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches. THE NEW PHYTOLOGIST 2014; 201:1328-1342. [PMID: 24283472 DOI: 10.1111/nph.12611] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/23/2013] [Indexed: 05/18/2023]
Abstract
• The use of quantitative disease resistance (QDR) is a promising strategy for promoting durable resistance to plant pathogens, but genes involved in QDR are largely unknown. To identify genetic components and accelerate improvement of QDR in legumes to the root pathogen Aphanomyces euteiches, we took advantage of both the recently generated massive genomic data for Medicago truncatula and natural variation of this model legume. • A high-density (≈5.1 million single nucleotide polymorphisms (SNPs)) genome-wide association study (GWAS) was performed with both in vitro and glasshouse phenotyping data collected for 179 lines. • GWAS identified several candidate genes and pinpointed two independent major loci on the top of chromosome 3 that were detected in both phenotyping methods. Candidate SNPs in the most significant locus (σ(A)²= 23%) were in the promoter and coding regions of an F-box protein coding gene. Subsequent qRT-PCR and bioinformatic analyses performed on 20 lines demonstrated that resistance is associated with mutations directly affecting the interaction domain of the F-box protein rather than gene expression. • These results refine the position of previously identified QTL to specific candidate genes, suggest potential molecular mechanisms, and identify new loci explaining QDR against A. euteiches.
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Affiliation(s)
- Maxime Bonhomme
- UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Olivier André
- UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Yacine Badis
- UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | | | | | | | | | - Roman Briskine
- Department of Computer Science and Engineering, University of Minnesota, Saint-Paul, MN, 55455, USA
| | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Frédéric Debéllé
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France
| | - Hélène Navier
- INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France
| | - Henri Miteul
- INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France
| | - Ahmed Hajri
- INRA, UMR 1349 IGEPP, F-35653, Le Rheu Cedex, France
| | | | - Peter Tiffin
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Bernard Dumas
- UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | | | - Nevin D Young
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Christophe Jacquet
- UPS, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
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McKown AD, Guy RD, Klápště J, Geraldes A, Friedmann M, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 201:1263-1276. [PMID: 24491114 DOI: 10.1111/nph.12601] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/09/2013] [Indexed: 05/18/2023]
Abstract
• Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over 2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities. • We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29,354 single nucleotide polymorphisms (SNPs) from 3518 genes, we estimated both broad-sense trait heritability (H(2)) and overall population genetic structure from principal component analysis. • Populus trichocarpa had high phenotypic variation and moderate/high H(2) for many traits. H(2) ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat : moisture indices. Trait H(2) values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component (PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod. • Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Bus A, Körber N, Parkin IAP, Samans B, Snowdon RJ, Li J, Stich B. Species- and genome-wide dissection of the shoot ionome in Brassica napus and its relationship to seedling development. FRONTIERS IN PLANT SCIENCE 2014; 5:485. [PMID: 25324847 PMCID: PMC4179769 DOI: 10.3389/fpls.2014.00485] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/02/2014] [Indexed: 05/22/2023]
Abstract
Knowing the genetic basis of the plant ionome is essential for understanding the control of nutrient transport and accumulation. The aim of this research was to (i) study mineral nutrient concentrations in a large and diverse set of Brassica napus, (ii) describe the relationships between the shoot ionome and seedling development, and (iii) identify genetic regions associated with variation of the shoot ionome. The plant material under study was a germplasm set consisting of 509 inbred lines that was genotyped by a 6K single nucleotide polymorphism (SNP) array and phenotyped by analyzing the concentrations of eleven mineral nutrients in the shoots of 30 days old seedlings. Among mineral concentrations, positive correlations were found, whereas mineral concentrations were mainly negatively correlated with seedling development traits from earlier studies. In a genome-wide association mapping approach, altogether 29 significantly associated loci were identified across seven traits after correcting for multiple testing. The associations included a locus with effects on the concentrations of Cu, Mn, and Zn on chromosome C3, and a genetic region with multiple associations for Na concentration on chromosome A9. This region was situated within an association hotspot close to SOS1, a key gene for Na tolerance in plants.
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Affiliation(s)
- Anja Bus
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Crop Genetics and Biotechnology Unit, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
| | - Niklas Körber
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Crop Genetics and Biotechnology Unit, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
| | - Isobel A. P. Parkin
- Saskatoon Research Centre, Agriculture and Agri-Food CanadaSaskatoon, SK, Canada
| | - Birgit Samans
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Jinquan Li
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Benjamin Stich
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- *Correspondence: Benjamin Stich, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany e-mail:
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Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
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Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
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125
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Viger M, Rodriguez-Acosta M, Rae AM, Morison JIL, Taylor G. Toward improved drought tolerance in bioenergy crops: QTL for carbon isotope composition and stomatal conductance inPopulus. Food Energy Secur 2013. [DOI: 10.1002/fes3.39] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Maud Viger
- Centre for Biological Sciences; Life Sciences Building; University of Southampton; Southampton SO17 1BJ United Kingdom
| | - Maricela Rodriguez-Acosta
- Centre for Biological Sciences; Life Sciences Building; University of Southampton; Southampton SO17 1BJ United Kingdom
| | - Anne M. Rae
- Centre for Biological Sciences; Life Sciences Building; University of Southampton; Southampton SO17 1BJ United Kingdom
| | - James I. L. Morison
- Centre for Forestry and Climate Change; Forest Research; Alice Holt Farnham Surrey United Kingdom
| | - Gail Taylor
- Centre for Biological Sciences; Life Sciences Building; University of Southampton; Southampton SO17 1BJ United Kingdom
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Aprile A, Havlickova L, Panna R, Marè C, Borrelli GM, Marone D, Perrotta C, Rampino P, De Bellis L, Curn V, Mastrangelo AM, Rizza F, Cattivelli L. Different stress responsive strategies to drought and heat in two durum wheat cultivars with contrasting water use efficiency. BMC Genomics 2013; 14:821. [PMID: 24267539 PMCID: PMC4046701 DOI: 10.1186/1471-2164-14-821] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/18/2013] [Indexed: 12/21/2022] Open
Abstract
Background Durum wheat often faces water scarcity and high temperatures, two events that usually occur simultaneously in the fields. Here we report on the stress responsive strategy of two durum wheat cultivars, characterized by different water use efficiency, subjected to drought, heat and a combination of both stresses. Results The cv Ofanto (lower water use efficiency) activated a large set of well-known drought-related genes after drought treatment, while Cappelli (higher water use efficiency) showed the constitutive expression of several genes induced by drought in Ofanto and a modulation of a limited number of genes in response to stress. At molecular level the two cvs differed for the activation of molecular messengers, genes involved in the regulation of chromatin condensation, nuclear speckles and stomatal closure. Noteworthy, the heat response in Cappelli involved also the up-regulation of genes belonging to fatty acid β-oxidation pathway, glyoxylate cycle and senescence, suggesting an early activation of senescence in this cv. A gene of unknown function having the greatest expression difference between the two cultivars was selected and used for expression QTL analysis, the corresponding QTL was mapped on chromosome 6B. Conclusion Ofanto and Cappelli are characterized by two opposite stress-responsive strategies. In Ofanto the combination of drought and heat stress led to an increased number of modulated genes, exceeding the simple cumulative effects of the two single stresses, whereas in Cappelli the same treatment triggered a number of differentially expressed genes lower than those altered in response to heat stress alone. This work provides clear evidences that the genetic system based on Cappelli and Ofanto represents an ideal tool for the genetic dissection of the molecular response to drought and other abiotic stresses. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-821) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Prov,le Lecce Monteroni, I-73100 Lecce, Italy.
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Du Q, Xu B, Pan W, Gong C, Wang Q, Tian J, Li B, Zhang D. Allelic variation in a cellulose synthase gene (PtoCesA4) associated with growth and wood properties in Populus tomentosa. G3 (BETHESDA, MD.) 2013; 3:2069-84. [PMID: 24048648 PMCID: PMC3815066 DOI: 10.1534/g3.113.007724] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/11/2013] [Indexed: 12/12/2022]
Abstract
Lignocellulosic biomass from trees provides a renewable feedstock for biofuels, lumber, pulp, paper, and other uses. Dissecting the mechanism underlying natural variation of the complex traits controlling growth and lignocellulose biosynthesis in trees can enable marker-assisted breeding to improve wood quality and yield. Here, we combined linkage disequilibrium (LD)-based association analysis with traditional linkage analysis to detect the genetic effect of a Populus tomentosa cellulose synthase gene, PtoCesA4. PtoCesA4 is strongly expressed in developing xylem and leaves. Nucleotide diversity and LD in PtoCesA4, sampled from the P. tomentosa natural distribution, revealed that PtoCesA4 harbors high single nucleotide polymorphism (SNP) diversity (πT = 0.0080 and θw = 0.0098) and low LD (r(2) ≥ 0.1, within 1400 bp), demonstrating that the potential of a candidate-gene-based LD approach in understanding the molecular basis underlying quantitative variation in this species. By combining single SNP, multi-SNP, and haplotype-based associations in an association population of 460 individuals with single SNP linkage analysis in a family-based linkage populations (1200 individuals), we identified three strong associations (false discovery rate Q < 0.05) in both populations. These include two nonsynonymous markers (SNP49 associated with α-cellulose content and SNP59 associated with fiber width) and a noncoding marker (SNP18 associated with α-cellulose content). Variation in RNA transcript abundance among genotypic classes of SNP49 was confirmed in these two populations. Therefore, combining different methods allowed us to examine functional PtoCesA4 allelic variation underlying natural variation in complex quantitative traits related to growth and lignocellulosic biosynthesis.
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Affiliation(s)
- Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Baohua Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Wei Pan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Chenrui Gong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Qingshi Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Jiaxing Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Bailian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Department of Forestry, North Carolina State University, Raleigh, North Carolina 27695-8203
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
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Porth I, Klápště J, Skyba O, Friedmann MC, Hannemann J, Ehlting J, El-Kassaby YA, Mansfield SD, Douglas CJ. Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions. THE NEW PHYTOLOGIST 2013; 200:727-742. [PMID: 23889128 DOI: 10.1111/nph.12419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/17/2013] [Indexed: 05/21/2023]
Abstract
High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Wood traits are polygenic in nature, but gene hierarchies can be assessed to identify the most important gene variants controlling specific traits within complex networks defining the overall wood phenotype. We tested a large set of genetic, genomic, and phenotypic information in an integrative approach to predict wood properties in Populus trichocarpa. Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49k Nimblegen (Roche NimbleGen Inc., Madison, WI, USA) array elements and for 28,831 polymorphic single nucleotide polymorphisms (SNPs). Pre-selected transcripts and SNPs with high statistical dependence on phenotypic traits were used in Bayesian network learning procedures with a stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at a much lower logarithm of Bayes factor (logBF) threshold than SNPs and were not accommodated in the networks. Using persistent variables, we constructed cross-validated networks for variability in wood attributes, which contained four to six variables with 94-100% predictive accuracy. Accommodated gene variants revealed the hierarchy in the genetic architecture that underpins substantial phenotypic variability, and represent new tools to support the maximization of response to selection.
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Affiliation(s)
- Ilga Porth
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Oleksandr Skyba
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Michael C Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Jan Hannemann
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5
| | - Juergen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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Eckert AJ, Bower AD, Jermstad KD, Wegrzyn JL, Knaus BJ, Syring JV, Neale DB. Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus). Mol Ecol 2013; 22:5635-50. [PMID: 24134614 DOI: 10.1111/mec.12514] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/26/2022]
Abstract
Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life history strategies as they influence the effective population size (Ne ). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of Ne . An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among plant species. Here, we have estimated the distribution of deleterious fitness effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α) for 11 species of soft pines (subgenus Strobus) using DNA sequence data from 167 orthologous nuclear gene fragments. Most newly arising nonsynonymous mutations were inferred to be so strongly deleterious that they would rarely become fixed. Little evidence for long-term adaptive evolution was detected, as all 11 estimates for α were not significantly different from zero. Nucleotide diversity at synonymous sites, moreover, was strongly correlated with attributes of the DFE across species, thus illustrating a strong consistency with the expectations from the Nearly Neutral Theory of molecular evolution. Application of these patterns to genome-wide expectations for these species, however, was difficult as the loci chosen for the analysis were a biased set of conserved loci, which greatly influenced the estimates of the DFE and α. This implies that genome-wide parameter estimates will need truly genome-wide data, so that many of the existing patterns documented previously for forest trees (e.g. little evidence for signature of selection) may need revision.
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Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 2013; 195:1353-72. [PMID: 24121773 DOI: 10.1534/genetics.113.157198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.
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131
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Plessis A, Ravel C, Bordes J, Balfourier F, Martre P. Association study of wheat grain protein composition reveals that gliadin and glutenin composition are trans-regulated by different chromosome regions. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3627-44. [PMID: 23881399 PMCID: PMC3745720 DOI: 10.1093/jxb/ert188] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wheat grain storage protein (GSP) content and composition are the main determinants of the end-use value of bread wheat (Triticum aestivum L.) grain. The accumulation of glutenins and gliadins, the two main classes of GSP in wheat, is believed to be mainly controlled at the transcriptional level through a network of transcription factors. This regulation network could lead to stable cross-environment allometric scaling relationships between the quantity of GSP classes/subunits and the total quantity of nitrogen per grain. This work conducted a genetic mapping study of GSP content and composition and allometric scaling parameters of grain N allocation using a bread wheat worldwide core collection grown in three environments. The core collection was genotyped with 873 markers for genome-wide association and 167 single nucleotide polymorphism markers in 51 candidate genes for candidate association. The candidate genes included 35 transcription factors (TFs) expressed in grain. This work identified 74 loci associated with 38 variables, of which 19 were candidate genes or were tightly linked with candidate genes. Besides structural GSP genes, several loci putatively trans-regulating GSP accumulation were identified. Seven candidate TFs, including four wheat orthologues of barley TFs that control hordein gene expression, were associated or in strong linkage disequilibrium with markers associated with the composition or quantity of glutenin or gliadin, or allometric grain N allocation parameters, confirming the importance of the transcriptional control of GSP accumulation. Genome-wide association results suggest that the genes regulating glutenin and gliadin compositions are mostly distinct from each other and operate differently.
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Affiliation(s)
- Anne Plessis
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Catherine Ravel
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Jacques Bordes
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - François Balfourier
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - Pierre Martre
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- To whom correspondence should be addressed. E-mail:
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Hussey SG, Mizrachi E, Creux NM, Myburg AA. Navigating the transcriptional roadmap regulating plant secondary cell wall deposition. FRONTIERS IN PLANT SCIENCE 2013; 4:325. [PMID: 24009617 PMCID: PMC3756741 DOI: 10.3389/fpls.2013.00325] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/31/2013] [Indexed: 05/17/2023]
Abstract
The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture, and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW) biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms.
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Affiliation(s)
| | | | | | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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Evaluating adaptive divergence between migratory and nonmigratory ecotypes of a salmonid fish, Oncorhynchus mykiss. G3-GENES GENOMES GENETICS 2013; 3:1273-85. [PMID: 23797103 PMCID: PMC3737167 DOI: 10.1534/g3.113.006817] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. The use of these two approaches in parallel is especially attractive in nonmodel organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a nonmodel fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and nonmigratory ecotypes and to further our understanding about the genetic basis of migration. Restriction site-associated DNA (RAD) tag sequencing was used to identify single-nucleotide polymorphisms (SNPs) in migrant and resident O. mykiss from two systems, one in Alaska and the other in Oregon. A total of 7920 and 6755 SNPs met filtering criteria in the Alaska and Oregon data sets, respectively. Population genetic tests determined that 1423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Previous linkage mapping studies that used RAD DNA tag SNPs were available to determine the position of 1990 markers. Several significant SNPs are located in genome regions that contain quantitative trait loci for migratory-related traits, reinforcing the importance of these regions in the genetic basis of migration/residency. Annotation of genome regions linked to significant SNPs revealed genes involved in processes known to be important in migration (such as osmoregulatory function). This study adds to our growing knowledge on adaptive divergence between migratory and nonmigratory ecotypes of this species; across studies, this complex trait appears to be controlled by many loci of small effect, with some in common, but many loci not shared between populations studied.
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134
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Freeman JS, Potts BM, Downes GM, Pilbeam D, Thavamanikumar S, Vaillancourt RE. Stability of quantitative trait loci for growth and wood properties across multiple pedigrees and environments in Eucalyptus globulus. THE NEW PHYTOLOGIST 2013; 198:1121-1134. [PMID: 23517065 DOI: 10.1111/nph.12237] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/14/2013] [Indexed: 05/05/2023]
Abstract
· Eucalypts are one of the most planted tree genera worldwide, and there is increasing interest in marker-assisted selection for tree improvement. Implementation of marker-assisted selection requires a knowledge of the stability of quantitative trait loci (QTLs). This study aims to investigate the stability of QTLs for wood properties and growth across contrasting sites and multiple pedigrees of Eucalyptus globulus. · Saturated linkage maps were constructed using 663 genotypes from four separate families, grown at three widely separated sites, and were employed to construct a consensus map. This map was used for QTL analysis of growth, wood density and wood chemical traits, including pulp yield. · Ninety-eight QTLs were identified across families and sites: 87 for wood properties and 11 for growth. These QTLs mapped to 38 discrete regions, some of which co-located with candidate genes. Although 16% of QTLs were verified across different families, 24% of wood property QTLs and 38% of growth QTLs exhibited significant genotype-by-environment interaction. · This study provides the most detailed assessment of the effect of environment and pedigree on QTL detection in the genus. Despite markedly different environments and pedigrees, many QTLs were stable, providing promising targets for the application of marker-assisted selection.
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Affiliation(s)
- Jules S Freeman
- School of Plant Science, National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tas., 7001, Australia
- Co-operative Research Centre for Forestry, Private Bag 12, Hobart, Tas., 7001, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore, Qld, 4558, Australia
| | - Brad M Potts
- School of Plant Science, National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tas., 7001, Australia
- Co-operative Research Centre for Forestry, Private Bag 12, Hobart, Tas., 7001, Australia
| | - Geoffrey M Downes
- Co-operative Research Centre for Forestry, Private Bag 12, Hobart, Tas., 7001, Australia
- CSIRO Sustainable Ecosystems, Private Bag 12, Hobart, Tas., 7001, Australia
- Forest Quality Pty. Ltd, PO Box 293, Huonville, Tas., 7109, Australia
| | - David Pilbeam
- Southern Tree Breeding Association Inc., 38 Helen Street, PO Box 1811, Mount Gambier, SA, 5290, Australia
| | - Saravanan Thavamanikumar
- Co-operative Research Centre for Forestry, Private Bag 12, Hobart, Tas., 7001, Australia
- Department of Forest and Ecosystem Science, The University of Melbourne, Water Street, Creswick, Vic., 3363, Australia
- CSIRO Plant Industry, GPO Box 1600, Acton, ACT, 2601, Australia
| | - René E Vaillancourt
- School of Plant Science, National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tas., 7001, Australia
- Co-operative Research Centre for Forestry, Private Bag 12, Hobart, Tas., 7001, Australia
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135
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Yano R, Takebayashi Y, Nambara E, Kamiya Y, Seo M. Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:815-28. [PMID: 23464703 DOI: 10.1111/tpj.12167] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/20/2013] [Accepted: 02/27/2013] [Indexed: 05/20/2023]
Abstract
Seed dormancy is an important adaptive trait that enables germination at the proper time, thereby ensuring plant survival after germination. In Arabidopsis, considerable variation exists in the degree of seed dormancy among wild-type accessions (ecotypes). In this paper, we identify a plant-specific HD2 histone deacetylase gene, HD2B (At5g22650), as a genetic factor associated with seed dormancy. First, genome-wide association mapping of 113 accessions was used to identify single nucleotide polymorphisms that possibly explain natural variation for seed dormancy. Integration of genome-wide association mapping and transcriptome analysis during cold-induced dormancy cycling identified HD2B as the most plausible candidate gene, and quantitative RT-PCR analysis demonstrated that HD2B expression was up-regulated by cold and after-ripening (dry storage of mature seed), treatments that are known to break seed dormancy. Interestingly, quantitative RT-PCR analysis in 106 accessions revealed that the expression of HD2B in imbibed seeds was significantly suppressed in most of the dormant accessions compared with less-dormant accessions, suggesting that suppression of HD2B expression may be important to maintain seed dormancy in dormant accessions. In addition, transgenic seeds of a dormant Cvi-0 accession that carried a 2.5 kb genomic DNA fragment of HD2B cloned from a less-dormant Col-0 accession ((Col)HD2B/Cvi-0) exhibited reduced seed dormancy accompanied by enhanced expression of HD2B when after-ripened or cold-imbibed. Endogenous levels of gibberellin were found to be increased in the imbibed seeds of after-ripened (Col)HD2B/Cvi-0 compared with wild-type Cvi-0. These results suggest that HD2B plays a role in seed dormancy and/or germinability in Arabidopsis thaliana.
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Affiliation(s)
- Ryoichi Yano
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan.
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136
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Tsai CJ. Next-generation sequencing for next-generation breeding, and more. THE NEW PHYTOLOGIST 2013; 198:635-637. [PMID: 23577594 DOI: 10.1111/nph.12245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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137
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The evolution of quantitative traits in complex environments. Heredity (Edinb) 2013; 112:4-12. [PMID: 23612691 DOI: 10.1038/hdy.2013.33] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/12/2013] [Accepted: 03/14/2013] [Indexed: 02/01/2023] Open
Abstract
Species inhabit complex environments and respond to selection imposed by numerous abiotic and biotic conditions that vary in both space and time. Environmental heterogeneity strongly influences trait evolution and patterns of adaptive population differentiation. For example, heterogeneity can favor local adaptation, or can promote the evolution of plastic genotypes that alter their phenotypes based on the conditions they encounter. Different abiotic and biotic agents of selection can act synergistically to either accelerate or constrain trait evolution. The environmental context has profound effects on quantitative genetic parameters. For instance, heritabilities measured in controlled conditions often exceed those measured in the field; thus, laboratory experiments could overestimate the potential for a population to respond to selection. Nevertheless, most studies of the genetic basis of ecologically relevant traits are conducted in simplified laboratory environments, which do not reflect the complexity of nature. Here, we advocate for manipulative field experiments in the native ranges of plant species that differ in mating system, life-history strategy and growth form. Field studies are vital to evaluate the roles of disparate agents of selection, to elucidate the targets of selection and to develop a nuanced perspective on the evolution of quantitative traits. Quantitative genetics field studies will also shed light on the potential for natural populations to adapt to novel climates in highly fragmented landscapes. Drawing from our experience with the ecological model system Boechera (Brassicaceae), we discuss advancements possible through dedicated field studies, highlight future research directions and examine the challenges associated with field studies.
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138
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Longhi S, Hamblin MT, Trainotti L, Peace CP, Velasco R, Costa F. A candidate gene based approach validates Md-PG1 as the main responsible for a QTL impacting fruit texture in apple (Malus x domestica Borkh). BMC PLANT BIOLOGY 2013; 13:37. [PMID: 23496960 PMCID: PMC3599472 DOI: 10.1186/1471-2229-13-37] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 02/22/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Apple is a widely cultivated fruit crop for its quality properties and extended storability. Among the several quality factors, texture is the most important and appreciated, and within the apple variety panorama the cortex texture shows a broad range of variability. Anatomically these variations depend on degradation events occurring in both fruit primary cell wall and middle lamella. This physiological process is regulated by an enzymatic network generally encoded by large gene families, among which polygalacturonase is devoted to the depolymerization of pectin. In apple, Md-PG1, a key gene belonging to the polygalacturonase gene family, was mapped on chromosome 10 and co-localized within the statistical interval of a major hot spot QTL associated to several fruit texture sub-phenotypes. RESULTS In this work, a QTL corresponding to the position of Md-PG1 was validated and new functional alleles associated to the fruit texture properties in 77 apple cultivars were discovered. 38 SNPs genotyped by gene full length resequencing and 2 SSR markers ad hoc targeted in the gene metacontig were employed. Out of this SNP set, eleven were used to define three significant haplotypes statistically associated to several texture components. The impact of Md-PG1 in the fruit cell wall disassembly was further confirmed by the cortex structure electron microscope scanning in two apple varieties characterized by opposite texture performance, such as 'Golden Delicious' and 'Granny Smith'. CONCLUSIONS The results here presented step forward into the genetic dissection of fruit texture in apple. This new set of haplotypes, and microsatellite alleles, can represent a valuable toolbox for a more efficient parental selection as well as the identification of new apple accessions distinguished by superior fruit quality features.
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Affiliation(s)
- Sara Longhi
- Research and Innovation Centre, Foundation Edmund Mach, Via Mach 1, 38010, San Michele all’Adige, TN, Italy
| | - Martha T Hamblin
- Institute for Genomic Diversity, Cornell University, 130 Biotechnology Building, 14853-2703, Ithaca, NY, USA
| | - Livio Trainotti
- Dipartimento di Biologia, Università di Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Cameron P Peace
- Horticulture and Landscape Architecture, Washington State University, PO Box 646414, 99164-6414, Pullman, WA, USA
| | - Riccardo Velasco
- Research and Innovation Centre, Foundation Edmund Mach, Via Mach 1, 38010, San Michele all’Adige, TN, Italy
| | - Fabrizio Costa
- Research and Innovation Centre, Foundation Edmund Mach, Via Mach 1, 38010, San Michele all’Adige, TN, Italy
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139
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Zhang K, Wang J, Zhang L, Rong C, Zhao F, Peng T, Li H, Cheng D, Liu X, Qin H, Zhang A, Tong Y, Wang D. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS One 2013; 8:e57853. [PMID: 23469248 PMCID: PMC3587626 DOI: 10.1371/journal.pone.0057853] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
Grain weight, an essential yield component, is under strong genetic control and markedly influenced by the environment. Here, by genome-wide association analysis with a panel of 94 elite common wheat varieties, 37 loci were found significantly associated with thousand-grain weight (TGW) in one or more environments differing in water and fertiliser levels. Five loci were stably associated with TGW under all 12 environments examined. Their elite alleles had positive effects on TGW. Four, two, three, and two loci were consistently associated with TGW in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), and reduced phosphorus (RP) environments. The elite alleles of the IF-specific loci enhanced TGW under well-resourced conditions, whereas those of the RF-, RN-, or RP-specific loci conferred tolerance to the TGW decrease when irrigation, nitrogen, or phosphorus were reduced. Moreover, the elite alleles of the environment-independent and -specific loci often acted additively to enhance TGW. Four additional loci were found associated with TGW in specific locations, one of which was shown to contribute to the TGW difference between two experimental sites. Further analysis of 14 associated loci revealed that nine affected both grain length and width, whereas the remaining loci influenced either grain length or width, indicating that these loci control grain weight by regulating kernel size. Finally, the elite allele of Xpsp3152 frequently co-segregated with the larger grain haplotype of TaGW2-6A, suggesting probable genetic and functional linkages between Xpsp3152 and GW2 that are important for grain weight control in cereal plants. Our study provides new knowledge on TGW control in elite common wheat lines, which may aid the improvement of wheat grain weight trait in further research.
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Affiliation(s)
- Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Junjun Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Liyi Zhang
- Guizhou Institute of Upland Crops, Guiyang, China
| | - Chaowu Rong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fengwu Zhao
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Tao Peng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Huimin Li
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Dongmei Cheng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiping Tong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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140
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Howe GT, Yu J, Knaus B, Cronn R, Kolpak S, Dolan P, Lorenz WW, Dean JFD. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics 2013; 14:137. [PMID: 23445355 PMCID: PMC3673906 DOI: 10.1186/1471-2164-14-137] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 01/31/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. RESULTS We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. CONCLUSIONS Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.
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Affiliation(s)
- Glenn T Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Jianbin Yu
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, 97331, USA
- Current address, DuPont Pioneer International, Willmar, Minnesota, 56201, USA
| | - Brian Knaus
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, 97331, USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, 97331, USA
| | - Scott Kolpak
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Peter Dolan
- Department of Mathematics, University of Minnesota, Morris, MN, USA
| | - W Walter Lorenz
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
| | - Jeffrey FD Dean
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
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141
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Howe GT, Yu J, Knaus B, Cronn R, Kolpak S, Dolan P, Lorenz WW, Dean JFD. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics 2013. [PMID: 23445355 DOI: 10.1186/1471‐2164‐14‐137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. RESULTS We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. CONCLUSIONS Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.
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Affiliation(s)
- Glenn T Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon 97331, USA.
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142
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Fang C, Li W, Li G, Wang Z, Zhou Z, Ma Y, Shen Y, Li C, Wu Y, Zhu B, Yang W, Tian Z. Cloning of Ln gene through combined approach of map-based cloning and association study in soybean. J Genet Genomics 2013; 40:93-6. [PMID: 23439408 DOI: 10.1016/j.jgg.2013.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 01/15/2013] [Accepted: 01/15/2013] [Indexed: 11/16/2022]
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143
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Pfeifer M, Martis M, Asp T, Mayer KF, Lübberstedt T, Byrne S, Frei U, Studer B. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. PLANT PHYSIOLOGY 2013; 161:571-82. [PMID: 23184232 PMCID: PMC3561004 DOI: 10.1104/pp.112.207282] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/20/2012] [Indexed: 05/18/2023]
Abstract
Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.
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Affiliation(s)
- Matthias Pfeifer
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Mihaela Martis
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Torben Asp
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Klaus F.X. Mayer
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Thomas Lübberstedt
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Stephen Byrne
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Ursula Frei
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
| | - Bruno Studer
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany (M.P., M.M., K.F.X.M.); Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A., S.B.); Department of Agronomy, Iowa State University, Ames, Iowa 50011 (T.L., U.F.); and Institute of Agricultural Sciences, Forage Crop Genetics, Eidgenössisch Technische Hochschule Zurich, 8092 Zurich, Switzerland (B.S.)
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144
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Geraldes A, Difazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N, Porth I, McKown AD, Skyba O, Li E, Fujita M, Klápště J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wasteneys GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QCB, Ehlting J, Douglas CJ, Tuskan GA. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour 2013; 13:306-23. [PMID: 23311503 DOI: 10.1111/1755-0998.12056] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 11/30/2012] [Accepted: 12/03/2012] [Indexed: 02/03/2023]
Abstract
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.
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Affiliation(s)
- A Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
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145
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Negrão S, Almadanim MC, Pires IS, Abreu IA, Maroco J, Courtois B, Gregorio GB, McNally KL, Oliveira MM. New allelic variants found in key rice salt-tolerance genes: an association study. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:87-100. [PMID: 23116435 DOI: 10.1111/pbi.12010] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 05/18/2023]
Abstract
Salt stress is a complex physiological trait affecting plants by limiting growth and productivity. Rice, one of the most important food crops, is rated as salt-sensitive. High-throughput screening methods are required to exploit novel sources of genetic variation in rice and further improve salinity tolerance in breeding programmes. To search for genotypic differences related to salt stress, we genotyped 392 rice accessions by EcoTILLING. We targeted five key salt-related genes involved in mechanisms such as Na(+) /K(+) ratio equilibrium, signalling cascade and stress protection, and we found 40 new allelic variants in coding sequences. By performing association analyses using both general and mixed linear models, we identified 11 significant SNPs related to salinity. We further evaluated the putative consequences of these SNPs at the protein level using bioinformatic tools. Amongst the five nonsynonymous SNPs significantly associated with salt-stress traits, we found a T67K mutation that may cause the destabilization of one transmembrane domain in OsHKT1;5, and a P140A alteration that significantly increases the probability of OsHKT1;5 phosphorylation. The K24E mutation can putatively affect SalT interaction with other proteins thus impacting its function. Our results have uncovered allelic variants affecting salinity tolerance that may be important in breeding.
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Affiliation(s)
- Sónia Negrão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal; iBET, Oeiras, Portugal
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146
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Abstract
Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.).
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Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA.
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147
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Shutu X, Dalong Z, Ye C, Yi Z, Shah T, Ali F, Qing L, Zhigang L, Weidong W, Jiansheng L, Xiaohong Y, Jianbing Y. Dissecting tocopherols content in maize (Zea mays L.), using two segregating populations and high-density single nucleotide polymorphism markers. BMC PLANT BIOLOGY 2012; 12:201. [PMID: 23122295 PMCID: PMC3502391 DOI: 10.1186/1471-2229-12-201] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 10/30/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND Tocopherols, which are vitamin E compounds, play an important role in maintaining human health. Compared with other staple foods, maize grains contain high level of tocopherols. RESULTS Two F(2) populations (K22/CI7 and K22/Dan340, referred to as POP-1 and POP-2, respectively), which share a common parent (K22), were developed and genotyped using a GoldenGate assay containing 1,536 single nucleotide polymorphism (SNP) markers. An integrated genetic linkage map was constructed using 619 SNP markers, spanning a total of 1649.03 cM of the maize genome with an average interval of 2.67 cM. Seventeen quantitative trait loci (QTLs) for all the traits were detected in the first map and 13 in the second. In these two maps, QTLs for different traits were localized to the same genomic regions and some were co-located with candidate genes in the tocopherol biosynthesis pathway. Single QTL was responsible for 3.03% to 52.75% of the phenotypic variation and the QTLs in sum explained 23.4% to 66.52% of the total phenotypic variation. A major QTL (qc5-1/qd5-1) affecting α-tocopherol (αT) was identified on chromosome 5 between the PZA03161.1 and PZA02068.1 in the POP-2. The QTL region was narrowed down from 18.7 Mb to 5.4 Mb by estimating the recombination using high-density markers of the QTL region. This allowed the identification of the candidate gene VTE4 which encodes γ-tocopherol methyltransferase, an enzyme that transforms γ-tocopherol (γT)to αT. CONCLUSIONS These results demonstrate that a few QTLs with major effects and several QTLs with medium to minor effects might contribute to the natural variation of tocopherols in maize grain. The high-density markers will help to fine map and identify the QTLs with major effects even in the preliminary segregating populations. Furthermore, this study provides a simple guide line for the breeders to improve traits that minimize the risk of malnutrition, especially in developing countries.
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Affiliation(s)
- Xu Shutu
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhang Dalong
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Cai Ye
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhou Yi
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Trushar Shah
- Department of Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Farhan Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Cereal Crops Research Institute, Nowshera, Khyber Pukhtoonkhwa, Pakistan
| | - Li Qing
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Li Zhigang
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Wang Weidong
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Li Jiansheng
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Yang Xiaohong
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Yan Jianbing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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148
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Lu FH, Park YJ. An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.). J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2012.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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149
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Li X, Acharya A, Farmer AD, Crow JA, Bharti AK, Kramer RS, Wei Y, Han Y, Gou J, May GD, Monteros MJ, Brummer EC. Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing. BMC Genomics 2012; 13:568. [PMID: 23107476 PMCID: PMC3533575 DOI: 10.1186/1471-2164-13-568] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 10/18/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP) markers for a complex polyploid species. RESULT The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2%) of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO) analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM) analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa) were clearly separated. CONCLUSION We used transcriptome sequencing to discover large numbers of SNPs segregating in elite breeding populations of alfalfa. Little loss of SNP diversity was evident between unimproved and elite alfalfa germplasm. The EST and SNP markers generated from this study are publicly available at the Legume Information System ( http://medsa.comparative-legumes.org/) and can contribute to future alfalfa research and breeding applications.
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Affiliation(s)
- Xuehui Li
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ananta Acharya
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - John A Crow
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Arvind K Bharti
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Robin S Kramer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Yanling Wei
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Yuanhong Han
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Jiqing Gou
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Gregory D May
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Maria J Monteros
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - E Charles Brummer
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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150
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Leinonen PH, Remington DL, Leppälä J, Savolainen O. Genetic basis of local adaptation and flowering time variation in Arabidopsis lyrata. Mol Ecol 2012; 22:709-23. [PMID: 22724431 DOI: 10.1111/j.1365-294x.2012.05678.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding how genetic variation at individual loci contributes to adaptation of populations to different local environments is an important topic in modern evolutionary biology. To date, most evidence has pointed to conditionally neutral quantitative trait loci (QTL) showing fitness effects only in some environments, while there has been less evidence for single-locus fitness trade-offs. At QTL underlying local adaptation, alleles from the local population are expected to show a fitness advantage. Cytoplasmic genomes also can have a role in local adaptation, but the role of cytonuclear interactions in adaptive differentiation has remained largely unknown. We mapped genomic regions underlying adaptive differentiation in multiple fitness components and flowering time in diverged populations of a perennial plant Arabidopsis lyrata. Experimental hybrids for this purpose were grown in natural field conditions of the parental populations in Norway and North Carolina (NC), USA, and in the greenhouse. We found QTL where high fitness and early flowering were associated with local alleles, indicating a role of different selection pressures in phenotypic differentiation. At two QTL regions, a fitness component showing local adaptation between the parental populations also showed signs of putative fitness trade-offs. Beneficial dominance effects of conditionally neutral QTL for different fitness components resulted in hybrid vigour at the Norwegian site in the F(2) hybrids. We also found that cytoplasmic genomes contributed to local adaptation and hybrid vigour by interacting with nuclear QTL, but these interactions did not show evidence for cytonuclear coadaptation (high fitness of local alleles combined with the local cytoplasm).
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