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Hernández MA, Butler JB, Ammitzboll H, Weller JL, Vaillancourt RE, Potts BM. Genetic control of the operculum and capsule morphology of Eucalyptus globulus. ANNALS OF BOTANY 2022; 130:97-108. [PMID: 35652517 PMCID: PMC9295918 DOI: 10.1093/aob/mcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures. METHODS Samples of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers. KEY RESULTS A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed. CONCLUSIONS Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
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Affiliation(s)
- Mariano A Hernández
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Route 27 - Km 38.3, Bella Vista, Corrientes 3432, Argentina
| | | | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture
| | - René E Vaillancourt
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Brad M Potts
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
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Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw. THE PLANT GENOME 2022; 15:e20174. [PMID: 34806838 DOI: 10.1002/tpg2.20174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
| | | | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56-58, Stockholm, 100 44, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Dep. of Plant Biology, Swedish Univ. of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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Zhu X, Weng Q, Bush D, Zhou C, Zhao H, Wang P, Li F. High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus. FRONTIERS IN PLANT SCIENCE 2022; 13:1099705. [PMID: 37082511 PMCID: PMC10112524 DOI: 10.3389/fpls.2022.1099705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 05/03/2023]
Abstract
Introduction Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms. Method A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis. Results Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4-23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation. Discussion While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.
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Affiliation(s)
- Xianliang Zhu
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qijie Weng
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - David Bush
- Commonwealth Scientific and Industrial Research Organisation (CRISO) Australian Tree Seed Centre, Canberra, ACT, Australia
| | - Changpin Zhou
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Haiwen Zhao
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Ping Wang
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Fagen Li
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- *Correspondence: Fagen Li,
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Ghosh Dasgupta M, Abdul Bari MP, Shanmugavel S, Dharanishanthi V, Muthupandi M, Kumar N, Chauhan SS, Kalaivanan J, Mohan H, Krutovsky KV, Rajasugunasekar D. Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis × E. grandis. Genomics 2021; 113:4276-4292. [PMID: 34785351 DOI: 10.1016/j.ygeno.2021.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 06/20/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022]
Abstract
Globally, Eucalyptus plantations occupy 22 million ha area and is one of the preferred hardwood species due to their short rotation, rapid growth, adaptability and wood properties. In this study, we present results of GWAS in parents and 100 hybrids of Eucalyptus tereticornis × E. grandis using 762 genes presumably involved in wood formation. Comparative analysis between parents predicted 32,202 polymorphic SNPs with high average read depth of 269-562× per individual per nucleotide. Seventeen wood related traits were phenotyped across three diverse environments and GWAS was conducted using 13,610 SNPs. A total of 45 SNP-trait associations were predicted across two locations. Seven large effect markers were identified which explained more than 80% of phenotypic variation for fibre area. This study has provided an array of candidate genes which may govern fibre morphology in this genus and has predicted potential SNPs which can guide future breeding programs in tropical Eucalyptus.
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Affiliation(s)
| | | | | | | | - Muthusamy Muthupandi
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, India
| | - Naveen Kumar
- Institute of Wood Science and Technology, 18(th) Cross Malleshwaram, Bangalore 560 003, India
| | - Shakti Singh Chauhan
- Institute of Wood Science and Technology, 18(th) Cross Malleshwaram, Bangalore 560 003, India
| | | | - Haritha Mohan
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, India
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany; Center for Integrated Breeding Research, George-August University of Göttingen, 37075 Göttingen, Germany; Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia; Laboratory of Population Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843-2138, USA
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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Development, characterization, functional annotation and validation of genomic and genic-SSR markers using de novo next generation sequencing in Melia dubia Cav. 3 Biotech 2021; 11:310. [PMID: 34109095 DOI: 10.1007/s13205-021-02858-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/22/2021] [Indexed: 10/21/2022] Open
Abstract
Melia dubia Cav. (Meliaceae), a fast-growing tropical tree finds use in plywood, pulp and high-value solid wood products. To increase its productivity, we must essentially capture genetic diversity and identify genotypes with superior wood properties. This study aimed to develop novel microsatellite markers from genomic data and validate the markers in M. dubia. Direct Seq-to-SSR approach was adopted and using an in-house Perl script, 426,390 SSR markers identified. For validation, selected 151 markers, of which 50 were genomic markers chosen randomly, and 101 were genic markers identified through BLAST2GO. Amplification was observed in all loci, and 81.4% generated high-quality, reproducible amplicons of the expected size. Out of 50 genomic markers, we used ten highly polymorphic markers to assess genetic diversity among 75 genotypes from three populations. One hundred fourteen alleles were recorded, with a moderate level of diversity and a positive fixation index. Twenty-nine genic markers representing 13 enzymes showing polymorphism for wood stiffness were selected for diversity assessment of 24 genotypes (12 genotypes each with high and low-stress wave velocity). The product size ranged from 87 to 279, covering the majority of the genome. Cluster and structure analysis segregated ~ 80% of the genotypes based on the trait. This is the first report of the development of genic markers from a genomic survey and has proved efficient in differentiating genotypes based on the trait. The markers developed in this study will be useful for genetic mapping, diversity estimation, marker-assisted selection for desired traits and breeding for wood traits in M. dubia. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02858-w.
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Baison J, Zhou L, Forsberg N, Mörling T, Grahn T, Olsson L, Karlsson B, Wu HX, Mellerowicz EJ, Lundqvist SO, García-Gil MR. Genetic control of tracheid properties in Norway spruce wood. Sci Rep 2020; 10:18089. [PMID: 33093525 PMCID: PMC7581746 DOI: 10.1038/s41598-020-72586-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 09/03/2020] [Indexed: 01/20/2023] Open
Abstract
Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.
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Affiliation(s)
- J Baison
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Linghua Zhou
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Nils Forsberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Tommy Mörling
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Thomas Grahn
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
| | - Lars Olsson
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
| | - Bo Karlsson
- Skogforsk, Ekebo 2250, 268 90, Svalov, Sweden
| | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Sven-Olof Lundqvist
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
- IIC, Rosenlundsgatan 48B, 11863, Stockholm, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden.
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Nvsvrot T, Xia W, Xiao Z, Zhan C, Liu M, Yang X, Zhang Y, Wang N. Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar. PHYTOPATHOLOGY 2020; 110:900-906. [PMID: 31958037 DOI: 10.1094/phyto-10-19-0402-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Poplar trees (Populus spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by Melampsora spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (R) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an R gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the R gene could be used as a diagnostic marker for future poplar molecular breeding.
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Affiliation(s)
- Tashbek Nvsvrot
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenxiu Xia
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Logistics Service Group, Wuhan University, Wuhan, 430070, China
| | - Zheng'ang Xiao
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang Zhan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqing Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
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Pancaldi F, Trindade LM. Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:227. [PMID: 32194604 PMCID: PMC7062921 DOI: 10.3389/fpls.2020.00227] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/13/2020] [Indexed: 05/09/2023]
Abstract
The biomass demand to fuel a growing global bio-based economy is expected to tremendously increase over the next decades, and projections indicate that dedicated biomass crops will satisfy a large portion of it. The establishment of dedicated biomass crops raises huge concerns, as they can subtract land that is required for food production, undermining food security. In this context, perennial biomass crops suitable for cultivation on marginal lands (MALs) raise attraction, as they could supply biomass without competing for land with food supply. While these crops withstand marginal conditions well, their biomass yield and quality do not ensure acceptable economic returns to farmers and cost-effective biomass conversion into bio-based products, claiming genetic improvement. However, this is constrained by the lack of genetic resources for most of these crops. Here we first review the advantages of cultivating novel perennial biomass crops on MALs, highlighting management practices to enhance the environmental and economic sustainability of these agro-systems. Subsequently, we discuss the preeminent breeding targets to improve the yield and quality of the biomass obtainable from these crops, as well as the stability of biomass production under MALs conditions. These targets include crop architecture and phenology, efficiency in the use of resources, lignocellulose composition in relation to bio-based applications, and tolerance to abiotic stresses. For each target trait, we outline optimal ideotypes, discuss the available breeding resources in the context of (orphan) biomass crops, and provide meaningful examples of genetic improvement. Finally, we discuss the available tools to breed novel perennial biomass crops. These comprise conventional breeding methods (recurrent selection and hybridization), molecular techniques to dissect the genetics of complex traits, speed up selection, and perform transgenic modification (genetic mapping, QTL and GWAS analysis, marker-assisted selection, genomic selection, transformation protocols), and novel high-throughput phenotyping platforms. Furthermore, novel tools to transfer genetic knowledge from model to orphan crops (i.e., universal markers) are also conceptualized, with the belief that their development will enhance the efficiency of plant breeding in orphan biomass crops, enabling a sustainable use of MALs for biomass provision.
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Affiliation(s)
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Tobias LM, Spokevicius AV, McFarlane HE, Bossinger G. The Cytoskeleton and Its Role in Determining Cellulose Microfibril Angle in Secondary Cell Walls of Woody Tree Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E90. [PMID: 31936868 PMCID: PMC7020502 DOI: 10.3390/plants9010090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022]
Abstract
Recent advances in our understanding of the molecular control of secondary cell wall (SCW) formation have shed light on molecular mechanisms that underpin domestication traits related to wood formation. One such trait is the cellulose microfibril angle (MFA), an important wood quality determinant that varies along tree developmental phases and in response to gravitational stimulus. The cytoskeleton, mainly composed of microtubules and actin filaments, collectively contribute to plant growth and development by participating in several cellular processes, including cellulose deposition. Studies in Arabidopsis have significantly aided our understanding of the roles of microtubules in xylem cell development during which correct SCW deposition and patterning are essential to provide structural support and allow for water transport. In contrast, studies relating to SCW formation in xylary elements performed in woody trees remain elusive. In combination, the data reviewed here suggest that the cytoskeleton plays important roles in determining the exact sites of cellulose deposition, overall SCW patterning and more specifically, the alignment and orientation of cellulose microfibrils. By relating the reviewed evidence to the process of wood formation, we present a model of microtubule participation in determining MFA in woody trees forming reaction wood (RW).
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Affiliation(s)
- Larissa Machado Tobias
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Antanas V. Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Heather E. McFarlane
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
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Baison J, Vidalis A, Zhou L, Chen Z, Li Z, Sillanpää MJ, Bernhardsson C, Scofield D, Forsberg N, Grahn T, Olsson L, Karlsson B, Wu H, Ingvarsson PK, Lundqvist S, Niittylä T, García‐Gil MR. Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:83-100. [PMID: 31166032 PMCID: PMC6852177 DOI: 10.1111/tpj.14429] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/16/2019] [Accepted: 05/20/2019] [Indexed: 05/26/2023]
Abstract
Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
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Affiliation(s)
- John Baison
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Amaryllis Vidalis
- Section of Population Epigenetics and EpigenomicsCentre of Life and Food Sciences WeihenstephanTechnische Universität MünchenLichtenbergstr. 2aMünchen85748Germany
| | - Linghua Zhou
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Zhi‐Qiang Chen
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Zitong Li
- Ecological Genetics Research UnitDepartment of BiosciencesUniversity of HelsinkiP.O. Box 65FI‐00014HelsinkiFinland
| | - Mikko J. Sillanpää
- Department of Mathematical SciencesBiocenter OuluUniversity of OuluPentti Kaiteran katu 1OuluFinland
| | - Carolina Bernhardsson
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
- Department of Ecology and Environmental ScienceUmeå UniversityLinnaeus väg 4-6Umeå907 36Sweden
| | - Douglas Scofield
- Uppsala Multidisciplinary Centre for Advanced Computational ScienceUppsala UniversityLägerhyddsvägen 2Uppsala752 37Sweden
| | - Nils Forsberg
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Thomas Grahn
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
| | - Lars Olsson
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
| | | | - Harry Wu
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Pär K. Ingvarsson
- Department of Ecology and Environmental ScienceUmeå UniversityLinnaeus väg 4-6Umeå907 36Sweden
- Department of Ecology and Genetics: Evolutionary BiologyUppsala UniversityKåbovägen 4Uppsala752 36Sweden
| | - Sven‐Olof Lundqvist
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
- IICRosenlundsgatan 48BSE‐118 63StockholmSweden
| | - Totte Niittylä
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - M Rosario García‐Gil
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
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12
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Non-Destructive Evaluation Techniques and What They Tell Us about Wood Property Variation. FORESTS 2019. [DOI: 10.3390/f10090728] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To maximize utilization of our forest resources, detailed knowledge of wood property variation and the impacts this has on end-product performance is required at multiple scales (within and among trees, regionally). As many wood properties are difficult and time-consuming to measure our knowledge regarding their variation is often inadequate as is our understanding of their responses to genetic and silvicultural manipulation. The emergence of many non-destructive evaluation (NDE) methodologies offers the potential to greatly enhance our understanding of the forest resource; however, it is critical to recognize that any technique has its limitations and it is important to select the appropriate technique for a given application. In this review, we will discuss the following technologies for assessing wood properties both in the field: acoustics, Pilodyn, Resistograph and Rigidimeter and the lab: computer tomography (CT) scanning, DiscBot, near infrared (NIR) spectroscopy, radial sample acoustics and SilviScan. We will discuss these techniques, explore their utilization, and list applications that best suit each methodology. As an end goal, NDE technologies will help researchers worldwide characterize wood properties, develop accurate models for prediction, and utilize field equipment that can validate the predictions. The continued advancement of NDE technologies will also allow researchers to better understand the impact on wood properties on product performance.
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13
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Calleja-Rodriguez A, Li Z, Hallingbäck HR, Sillanpää MJ, Wu HX, Abrahamsson S, García-Gil MR. Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design. J Theor Biol 2019; 462:283-292. [PMID: 30423305 DOI: 10.1016/j.jtbi.2018.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/17/2018] [Accepted: 11/09/2018] [Indexed: 11/28/2022]
Abstract
In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G × E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects.
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Affiliation(s)
- Ainhoa Calleja-Rodriguez
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden; Skogforsk, Box 3, Sävar SE-91821, Sweden
| | - Zitong Li
- Melbourne Integrative Genomics and School of Mathematics and Statistics, the University of Melbourne, Parkville, Victoria 3010, Australia; Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
| | - Henrik R Hallingbäck
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden; Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Science, Uppsala SE-75007, Sweden
| | - Mikko J Sillanpää
- Department of Mathematical Sciences and Biocenter Oulu, University of Oulu, Oulu FI-90014, Finland
| | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden
| | | | - Maria Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden.
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14
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Du Q, Lu W, Quan M, Xiao L, Song F, Li P, Zhou D, Xie J, Wang L, Zhang D. Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects. FRONTIERS IN PLANT SCIENCE 2018; 9:1912. [PMID: 30622554 PMCID: PMC6309013 DOI: 10.3389/fpls.2018.01912] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Wood formation is an excellent model system for quantitative trait analysis due to the strong associations between the transcriptional and metabolic traits that contribute to this complex process. Investigating the genetic architecture and regulatory mechanisms underlying wood formation will enhance our understanding of the quantitative genetics and genomics of complex phenotypic variation. Genome-wide association studies (GWASs) represent an ideal statistical strategy for dissecting the genetic basis of complex quantitative traits. However, elucidating the molecular mechanisms underlying many favorable loci that contribute to wood formation and optimizing GWAS design remain challenging in this omics era. In this review, we summarize the recent progress in GWAS-based functional genomics of wood property traits in major timber species such as Eucalyptus, Populus, and various coniferous species. We discuss several appropriate experimental designs for extensive GWAS in a given undomesticated tree population, such as omics-wide association studies and high-throughput phenotyping technologies. We also explain why more attention should be paid to rare allelic and major structural variation. Finally, we explore the potential use of GWAS for the molecular breeding of trees. Such studies will help provide an integrated understanding of complex quantitative traits and should enable the molecular design of new cultivars.
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Affiliation(s)
- Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Wenjie Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Mingyang Quan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Liang Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Fangyuan Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Peng Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Daling Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Jianbo Xie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Longxin Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, China
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Grattapaglia D, Silva-Junior OB, Resende RT, Cappa EP, Müller BSF, Tan B, Isik F, Ratcliffe B, El-Kassaby YA. Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding. FRONTIERS IN PLANT SCIENCE 2018; 9:1693. [PMID: 30524463 PMCID: PMC6262028 DOI: 10.3389/fpls.2018.01693] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/31/2018] [Indexed: 05/18/2023]
Abstract
Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic dissection approaches such as quantitative trait mapping and association genetics have been fruitless to effectively drive operational marker-assisted selection (MAS) in forest trees, largely because of the complex multifactorial inheritance of most, if not all traits of interest. The convergence of high-throughput genomics and quantitative genetics has established two new paradigms that are changing contemporary tree breeding dogmas. Genomic selection (GS) uses large number of genome-wide markers to predict complex phenotypes. It has the potential to accelerate breeding cycles, increase selection intensity and improve the accuracy of breeding values. Realized genomic relationships matrices, on the other hand, provide innovations in genetic parameters' estimation and breeding approaches by tracking the variation arising from random Mendelian segregation in pedigrees. In light of a recent flow of promising experimental results, here we briefly review the main concepts, analytical tools and remaining challenges that currently underlie the application of genomics data to tree breeding. With easy and cost-effective genotyping, we are now at the brink of extensive adoption of GS in tree breeding. Areas for future GS research include optimizing strategies for updating prediction models, adding validated functional genomics data to improve prediction accuracy, and integrating genomic and multi-environment data for forecasting the performance of genetic material in untested sites or under changing climate scenarios. The buildup of phenotypic and genome-wide data across large-scale breeding populations and advances in computational prediction of discrete genomic features should also provide opportunities to enhance the application of genomics to tree breeding.
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Affiliation(s)
- Dario Grattapaglia
- EMBRAPA Recursos Genéticos e BiotecnologiaBrasília, Brazil
- Programa de Ciências Genômicas e BiotecnologiaUniversidade Católica de Brasília, Brasília, Brazil
- Departamento de Biologia CelularUniversidade de Brasília, Brasília, Brazil
- Department of Forestry and Environmental Resources, North Carolina State UniversityRaleigh, NC, United States
| | - Orzenil B. Silva-Junior
- EMBRAPA Recursos Genéticos e BiotecnologiaBrasília, Brazil
- Programa de Ciências Genômicas e BiotecnologiaUniversidade Católica de Brasília, Brasília, Brazil
| | | | - Eduardo P. Cappa
- Centro de Investigación de Recursos Naturales, Instituto de Recursos BiológicosINTA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y TécnicasBuenos Aires, Argentina
| | - Bárbara S. F. Müller
- EMBRAPA Recursos Genéticos e BiotecnologiaBrasília, Brazil
- Departamento de Biologia CelularUniversidade de Brasília, Brasília, Brazil
| | - Biyue Tan
- Biomaterials DivisionStora Enso AB, Stockholm, Sweden
| | - Fikret Isik
- Department of Forestry and Environmental Resources, North Carolina State UniversityRaleigh, NC, United States
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British ColumbiaVancouver, BC, Canada
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British ColumbiaVancouver, BC, Canada
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Lu N, Mei F, Wang Z, Wang N, Xiao Y, Kong L, Qu G, Ma W, Wang J. Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur. BMC Genet 2018; 19:99. [PMID: 30384853 PMCID: PMC6211571 DOI: 10.1186/s12863-018-0686-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Association study is a powerful means for identifying molecular markers, such as single-nucleotide polymorphisms (SNPs) associated with important traits in forest trees. Catalpa fargesii Bur is a valuable commercial tree in China and identifying SNPs that associate with wood property would make a foundation of the marker-assisted breeding in the future. However, related work has not been reported yet. RESULTS We cloned a 2887 bp long sucrose synthase (SUS) gene from the genome of C. fargesii, which is a key enzyme in sucrose metabolism and also associated to wood formation in trees, coding 806 amino acids that expressed mainly in young branches, xylem, and leaves according to real-time quantitative PCR. Then we identified allelic variations of CfSUS associated with nine wood quality associated traits in Catalpa fargesii Bur. Totally, 135 SNPs were identified through cloning and sequencing the CfSUS locus from a mapping population (including 93 unrelated individuals) and 47 of which were genotyped as common SNPs (minor allele frequency > 5%) in the association population that comprised of 125 unrelated individuals collected from main distribution area. Nucleotide diversity and linkage disequilibrium (LD) analysis showed CfSUS has a relative low SNP diversity (πT = 0.0034) and low LD (r2 dropped below 0.1 within 1600 bp). Using the association analysis, we found 11 common SNPs and 14 haplotypes were significantly associated with the traits (false discovery rate, Q<0.1), explaining 3.21-12.41% of the phenotypic variance. These results provide molecular markers above associated with wood basic density, pore rate, and six other traits of wood, which have potential applications in breeding of Catalpa fargesii Bur. CONCLUSION We first cloned a SUS gene in C. fargesii, then identified several SNPs and haplotypes that associated with wood properties within this gene, suggesting CfSUS participates in the wood formation of C. fargesii. Moreover, molecular markers we identified in this study may be applied into marker-assisted breeding of C. fargesii in the future.
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Affiliation(s)
- Nan Lu
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Fang Mei
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Zhi Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Nan Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Yao Xiao
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Lisheng Kong
- Department of Biology, Centre for Forest Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC Canada
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 People’s Republic of China
| | - Wenjun Ma
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Junhui Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
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17
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Suontama M, Klápště J, Telfer E, Graham N, Stovold T, Low C, McKinley R, Dungey H. Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories. Heredity (Edinb) 2018; 122:370-379. [PMID: 29980794 PMCID: PMC6460750 DOI: 10.1038/s41437-018-0119-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 11/09/2022] Open
Abstract
Genomic selection is expected to enhance the genetic improvement of forest tree species by providing more accurate estimates of breeding values through marker-based relationship matrices compared with pedigree-based methodologies. When adequately robust genomic prediction models are available, an additional increase in genetic gains can be made possible with the shortening of the breeding cycle through elimination of the progeny testing phase and early selection of parental candidates. The potential of genomic selection was investigated in an advanced Eucalyptus nitens breeding population focused on improvement for solid wood production. A high-density SNP chip (EUChip60K) was used to genotype 691 individuals in the breeding population, which represented two seed orchards with different selection histories. Phenotypic records for growth and form traits at age six, and for wood quality traits at age seven were available to build genomic prediction models using GBLUP, which were compared to the traditional pedigree-based alternative using BLUP. GBLUP demonstrated that breeding value accuracy would be improved and substantial increases in genetic gains towards solid wood production would be achieved. Cross-validation within and across two different seed orchards indicated that genomic predictions would likely benefit in terms of higher predictive accuracy from increasing the size of the training data sets through higher relatedness and better utilization of LD.
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Affiliation(s)
- Mari Suontama
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand.
| | - Jaroslav Klápště
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand
| | - Emily Telfer
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand
| | - Natalie Graham
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand
| | - Toby Stovold
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand
| | - Charlie Low
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand
| | - Russell McKinley
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand
| | - Heidi Dungey
- Scion (The New Zealand Forest Research Institute Ltd.), 49 Sala Street, Rotorua, 3046, New Zealand
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Bdeir R, Muchero W, Yordanov Y, Tuskan GA, Busov V, Gailing O. Quantitative trait locus mapping of Populus bark features and stem diameter. BMC PLANT BIOLOGY 2017; 17:224. [PMID: 29179673 PMCID: PMC5704590 DOI: 10.1186/s12870-017-1166-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/10/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Bark plays important roles in photosynthate transport and storage, along with physical and chemical protection. Bark texture varies extensively among species, from smooth to fissured to deeply furrowed, but its genetic control is unknown. This study sought to determine the main genomic regions associated with natural variation in bark features and stem diameter. Quantitative trait loci (QTL) were mapped using an interspecific pseudo-backcross pedigree (Populus trichocarpa x P. deltoides and P. deltoides) for bark texture, bark thickness and diameter collected across three years, two sites and three biological replicates per site. RESULTS QTL specific to bark texture were highly reproducible in shared intervals across sites, years and replicates. Significant positive correlations and co-localization between trait QTL suggest pleiotropic regulators or closely linked genes. A list of candidate genes with related putative function, location close to QTL maxima and with the highest expression level in the phloem, xylem and cambium was identified. CONCLUSION Candidate genes for bark texture included an ortholog of Arabidopsis ANAC104 (PopNAC128), which plays a role in lignified fiber cell and ray development, as well as Pinin and Fasciclin (PopFLA) genes with a role in cell adhesion, cell shape and migration. The results presented in this study provide a basis for future genomic characterization of genes found within the QTL for bark texture, bark thickness and diameter in order to better understand stem and bark development in Populus and other woody perennial plants. The QTL mapping approach identified a list of prime candidate genes for further validation using functional genomics or forward genetics approaches.
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Affiliation(s)
- Roba Bdeir
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Yordan Yordanov
- Departement of Biology, Eastern Illinois University, 600 Lincoln Ave, Charleston, IL 61920 USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Victor Busov
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Oliver Gailing
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
- Present address: Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
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Resende RT, Resende MDV, Silva FF, Azevedo CF, Takahashi EK, Silva-Junior OB, Grattapaglia D. Regional heritability mapping and genome-wide association identify loci for complex growth, wood and disease resistance traits in Eucalyptus. THE NEW PHYTOLOGIST 2017; 213:1287-1300. [PMID: 28079935 DOI: 10.1111/nph.14266] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/08/2016] [Indexed: 05/18/2023]
Abstract
Although genome-wide association studies (GWAS) have provided valuable insights into the decoding of the relationships between sequence variation and complex phenotypes, they have explained little heritability. Regional heritability mapping (RHM) provides heritability estimates for genomic segments containing both common and rare allelic effects that individually contribute too little variance to be detected by GWAS. We carried out GWAS and RHM for seven growth, wood and disease resistance traits in a breeding population of 768 Eucalyptus hybrid trees using EuCHIP60K. Total genomic heritabilities accounted for large proportions (64-89%) of pedigree-based trait heritabilities, providing additional evidence that complex traits in eucalypts are controlled by many sequence variants across the frequency spectrum, each with small contributions to the phenotypic variance. RHM detected 26 quantitative trait loci (QTLs) encompassing 2191 single nucleotide polymorphisms (SNPs), whereas GWAS detected 13 single SNP-trait associations. RHM and GWAS QTLs individually explained 5-15% and 4-6% of the genomic heritability, respectively. RHM was superior to GWAS in capturing larger proportions of genomic heritability. Equated to previously mapped QTLs, our results highlighted genomic regions for further examination towards gene discovery. RHM-QTLs bearing a combination of common and rare variants could be useful enhancements to incorporate prior knowledge of the underlying genetic architecture in genomic prediction models.
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Affiliation(s)
| | - Marcos Deon Vilela Resende
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
- EMBRAPA Forestry Research, Colombo, PR, 83411-000, Brazil
| | - Fabyano Fonseca Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | | | - Orzenil Bonfim Silva-Junior
- EMBRAPA Genetic Resources and Biotechnology - EPqB, 70770-910, Brasilia, DF, Brazil
- Universidade Católica de Brasília - SGAN, 916 modulo B, Brasilia, DF, 70790-160, Brazil
| | - Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology - EPqB, 70770-910, Brasilia, DF, Brazil
- Universidade Católica de Brasília - SGAN, 916 modulo B, Brasilia, DF, 70790-160, Brazil
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Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. Proc Natl Acad Sci U S A 2017; 114:1195-1200. [PMID: 28096391 DOI: 10.1073/pnas.1620119114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.
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Houston K, Burton RA, Sznajder B, Rafalski AJ, Dhugga KS, Mather DE, Taylor J, Steffenson BJ, Waugh R, Fincher GB. A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family. PLoS One 2015; 10:e0130890. [PMID: 26154104 PMCID: PMC4496100 DOI: 10.1371/journal.pone.0130890] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/26/2015] [Indexed: 12/13/2022] Open
Abstract
Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two – rowed and 288 six – rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with CELLULOSE SYNTHASE A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the genes that contribute to cellulose content in cereal culms and to a greater understanding of the interactions between them.
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Affiliation(s)
- Kelly Houston
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
- * E-mail:
| | - Rachel A. Burton
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Beata Sznajder
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Antoni J. Rafalski
- Genetic Discovery Group, DuPont Agricultural Biotechnology, DuPont Pioneer, DuPont Experimental Station, Building E353, Wilmington, DE, 19803, United States of America
| | - Kanwarpal S. Dhugga
- Genetic Discovery Group, DuPont Agricultural Biotechnology, DuPont Pioneer, 7300 NW 62nd Avenue, Johnston, IA, 50131, United States of America
| | - Diane E. Mather
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Jillian Taylor
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, United States of America
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Scotland, Dundee, DD2 5DA, United Kingdom
| | - Geoffrey B. Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
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22
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Allelic Variation in Cinnamyl Alcohol Dehydrogenase (LoCAD) Associated with Wood Properties of Larix olgensis. FORESTS 2015. [DOI: 10.3390/f6051649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sumathi M, Yasodha R. Microsatellite resources of Eucalyptus: current status and future perspectives. BOTANICAL STUDIES 2014; 55:73. [PMID: 28510953 PMCID: PMC5430318 DOI: 10.1186/s40529-014-0073-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/30/2014] [Indexed: 06/07/2023]
Abstract
Eucalyptus is the premier paper pulp, short rotation plantation species grown all over the world. Genetic improvement programs integrating molecular marker tools are in progress in many parts of the globe to increase the productivity. Whole genome sequence and expressed sequence tags (ESTs) of the eucalypts paved way for introduction of molecular genetics and breeding in this genus. Different molecular characterization approaches have been used simultaneously in eucalypts, however, microsatellites or simple sequence repeats (SSRs) with their prolific characteristics could occupy a special niche in Eucalyptus genetic improvement. Further, highly informative SSRs were used for the clonal identity, genetic fidelity and in certification of breeder's rights. Eucalyptus genetic linkage maps generated with microsatellite loci were used successfully to identify quantitative trait loci (QTLs) for various economically important traits. Progressively more numbers of microsatellites are being linked to genes associated with adaptive and functional variations, therefore making their utility broader in genetic applications. Availability of common SSR markers across the species provides an opportunity to validate the expression of QTLs across variable genetic backgrounds and accurately compare the position of QTLs in other species. Recent evidences suggest that the presence of SSRs in micro RNAs of plant species play a role in the quantitative trait expression. Similar studies in eucalypts may provide new insights into the genetic architecture of transcript-level variations and post transcriptional gene regulation. This review on eucalypts microsatellites, highlights the availability and characteristics of genomic and eSSRs and their potential in genetic analysis of natural and breeding populations and also discusses the future prospects in population genetics and marker assisted selection.
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Affiliation(s)
- Murugan Sumathi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, Coimbatore, 641 002 India
| | - Ramasamy Yasodha
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, Coimbatore, 641 002 India
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24
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Cappa EP, El-Kassaby YA, Garcia MN, Acuña C, Borralho NMG, Grattapaglia D, Marcucci Poltri SN. Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus. PLoS One 2013; 8:e81267. [PMID: 24282578 PMCID: PMC3839935 DOI: 10.1371/journal.pone.0081267] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 10/10/2013] [Indexed: 01/01/2023] Open
Abstract
The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus.
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Affiliation(s)
- Eduardo P. Cappa
- Instituto de Recursos Biológicos, Centro de Investigación en Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
- * E-mail:
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Martín N. Garcia
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Cintia Acuña
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Nuno M. G. Borralho
- Private Consultant, Cartaxo, Portugal and Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade Técnica de Lisboa, Lisboa, Portugal
| | - Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology and Genomic Sciences Program, Universidade Católica de Brasília, Brasilia DF, Brazil
| | - Susana N. Marcucci Poltri
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
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25
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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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26
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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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27
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Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, DiFazio SP, Muchero W, Ranjan P, Tuskan GA, Friedmann MC, Ehlting J, Cronk QCB, El-Kassaby YA, Douglas CJ, Mansfield SD. Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. THE NEW PHYTOLOGIST 2013; 200:710-726. [PMID: 23889164 DOI: 10.1111/nph.12422] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/18/2013] [Indexed: 05/02/2023]
Abstract
Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29,233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations. The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3-7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
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Affiliation(s)
- Ilga Porth
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Jaroslav Klapšte
- 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
| | - Jan Hannemann
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5
| | - Athena D McKown
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Robert D Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Priya Ranjan
- 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
| | - Michael C Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Juergen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Carl J Douglas
- Department of Botany, 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
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28
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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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29
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Courtial A, Thomas J, Reymond M, Méchin V, Grima-Pettenati J, Barrière Y. Targeted linkage map densification to improve cell wall related QTL detection and interpretation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1151-65. [PMID: 23358861 DOI: 10.1007/s00122-013-2043-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/09/2013] [Indexed: 05/09/2023]
Abstract
Several QTLs for cell wall degradability and lignin content were previously detected in the F288 × F271 maize RIL progeny, including a set of major QTLs located in bin 6.06. Unexpectedly, allelic sequencing of genes located around the bin 6.06 QTL positions revealed a monomorphous region, suggesting that these QTLs were likely "ghost" QTLs. Refining the positions of all QTLs detected in this population was thus considered, based on a linkage map densification in most important QTL regions, and in several large still unmarked regions. Re-analysis of data with an improved genetic map (173 markers instead of 108) showed that ghost QTLs located in bin 6.06 were then fractionated over two QTL positions located upstream and downstream of the monomorphic region. The area located upstream of bin 6.06 position carried the major QTLs, which explained from 37 to 59 % of the phenotypic variation for per se values and extended on only 6 cM, corresponding to a physical distance of 2.2 Mbp. Among the 92 genes present in the corresponding area of the B73 maize reference genome, nine could putatively be considered as involved in the formation of the secondary cell wall [bHLH, FKBP, laccase, fasciclin, zinc finger C2H2-type and C3HC4-type (two genes), NF-YB, and WRKY]. In addition, based on the currently improved genetic map, eight QTLs were detected in bin 4.09, while only one QTL was highlighted in the initial investigation. Moreover, significant epistatic interaction effects were shown for all traits between these QTLs located in bin 4.09 and the major QTLs located in bin 6.05. Three genes related to secondary cell wall assembly (ZmMYB42, COV1-like, PAL-like) underlay QTL support intervals in this newly identified bin 4.09 region. The current investigations, even if they were based only on one RIL progeny, illustrated the interest of a targeted marker mapping on a genetic map to improve QTL position.
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Affiliation(s)
- Audrey Courtial
- INRA, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
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Porth I, Klápště J, Skyba O, Lai BSK, Geraldes A, Muchero W, Tuskan GA, Douglas CJ, El-Kassaby YA, Mansfield SD. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations. THE NEW PHYTOLOGIST 2013; 197:777-790. [PMID: 23278123 DOI: 10.1111/nph.12014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/18/2012] [Indexed: 05/03/2023]
Abstract
The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations. Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy-Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits. The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified. The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use.
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Affiliation(s)
- Ilga Porth
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Oleksandr Skyba
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ben S K Lai
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Armando Geraldes
- 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
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Du Q, Pan W, Xu B, Li B, Zhang D. Polymorphic simple sequence repeat (SSR) loci within cellulose synthase (PtoCesA) genes are associated with growth and wood properties in Populus tomentosa. THE NEW PHYTOLOGIST 2013; 197:763-776. [PMID: 23278184 DOI: 10.1111/nph.12072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/27/2012] [Indexed: 05/02/2023]
Abstract
Chinese white poplar (Populus tomentosa), an important commercial tree species for timber and pulp production in northern China, has been used to examine the individual genes and allelic diversity responsible for complex traits controlling growth and lignocellulosic biosynthesis. Taking advantage of the low degree of linkage disequilibrium (LD) within P. tomentosa association populations, we examined associations between 15 cellulose synthase (PtoCesA) genes and traits including growth and wood properties. Thirty-six novel simple sequence repeat (SSR) markers within PtoCesA genes were detected by re-sequencing and genotyped in an association population (460 individuals). Single-marker and haplotype-based LD approaches were used to identify significant marker-trait associations. Family-based linkage studies and real-time PCR testing were conducted to validate the functional significance of SSR variation. Fifteen single-marker associations from seven PtoCesA genes and nine haplotype-based associations within six genes were identified in the association population (false discovery rate Q < 0.05). Next, five SSR marker-trait associations (Q < 0.05) from four PtoCesA genes were successfully validated in a linkage mapping population (1200 individuals). The results imply a functional role for these genes in mediating wood properties, demonstrating the potential of combining single-marker and haplotype-based LD approaches to detect functional allelic variation underlying quantitative traits in a low-LD population.
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Affiliation(s)
- Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, 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, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Wei Pan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, 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, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Baohua Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, 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, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Bailian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, 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, No. 35, Qinghua East Road, Beijing, 100083, China
- Department of Forestry, North Carolina State University, Raleigh, NC, 27695-8203, USA
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, 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, No. 35, Qinghua East Road, Beijing, 100083, China
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Kullan ARK, van Dyk MM, Hefer CA, Jones N, Kanzler A, Myburg AA. Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla. BMC Genet 2012; 13:60. [PMID: 22817272 PMCID: PMC3416674 DOI: 10.1186/1471-2156-13-60] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 07/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND F1 hybrid clones of Eucalyptus grandis and E. urophylla are widely grown for pulp and paper production in tropical and subtropical regions. Volume growth and wood quality are priority objectives in Eucalyptus tree improvement. The molecular basis of quantitative variation and trait expression in eucalypt hybrids, however, remains largely unknown. The recent availability of a draft genome sequence (http://www.phytozome.net) and genome-wide genotyping platforms, combined with high levels of genetic variation and high linkage disequilibrium in hybrid crosses, greatly facilitate the detection of quantitative trait loci (QTLs) as well as underlying candidate genes for growth and wood property traits. In this study, we used Diversity Arrays Technology markers to assess the genetic architecture of volume growth (diameter at breast height, DBH) and wood basic density in four-year-old progeny of an interspecific backcross pedigree of E. grandis and E. urophylla. In addition, we used Illumina RNA-Seq expression profiling in the E. urophylla backcross family to identify cis- and trans-acting polymorphisms (eQTLs) affecting transcript abundance of genes underlying QTLs for wood basic density. RESULTS A total of five QTLs for DBH and 12 for wood basic density were identified in the two backcross families. Individual QTLs for DBH and wood basic density explained 3.1 to 12.2% of phenotypic variation. Candidate genes underlying QTLs for wood basic density on linkage groups 8 and 9 were found to share trans-acting eQTLs located on linkage groups 4 and 10, which in turn coincided with QTLs for wood basic density suggesting that these QTLs represent segregating components of an underlying transcriptional network. CONCLUSION This is the first demonstration of the use of next-generation expression profiling to quantify transcript abundance in a segregating tree population and identify candidate genes potentially affecting wood property variation. The QTLs identified in this study provide a resource for identifying candidate genes and developing molecular markers for marker-assisted breeding of volume growth and wood basic density. Our results suggest that integrated analysis of transcript and trait variation in eucalypt hybrids can be used to dissect the molecular basis of quantitative variation in wood property traits.
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Affiliation(s)
- Anand Raj Kumar Kullan
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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Britto D, Pirovani C, Gonzalez E, Silva J, Gesteira A, Cascardo J. Oxidative stress proteins as an indicator of a low quality of eucalyptus clones for the pulp and paper industry. GENETICS AND MOLECULAR RESEARCH 2012; 11:3798-813. [DOI: 10.4238/2012.august.17.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Chavigneau H, Goué N, Delaunay S, Courtial A, Jouanin L, Reymond M, Méchin V, Barrière Y. QTL for floral stem lignin content and degradability in three recombinant inbred line (RIL) progenies of <i>Arabidopsis thaliana</i> and search for candidate genes involved in cell wall biosynthesis and degradability. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojgen.2012.21002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sansaloni C, Petroli C, Pappas G, Da Silva O, Grattapaglia D. How many genes might underlie QTLs for growth and wood quality traits in Eucalyptus? BMC Proc 2011. [PMCID: PMC3240057 DOI: 10.1186/1753-6561-5-s7-p37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Eucalypt pulp yield QTL from Raiz as compared to the literature. BMC Proc 2011. [PMCID: PMC3240069 DOI: 10.1186/1753-6561-5-s7-p48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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García M, Villalba P, Acuña C, Oberschelp J, Harrand L, Surenciski M, Martínez M, Petroli C, Sansaloni C, Faria D, Grattapaglia D, Poltri SM. A genetic linkage map for a Full sib population of Eucalyptus grandisusing SSR, DArT, CG-SSR and EST-SSR markers. BMC Proc 2011. [PMCID: PMC3240045 DOI: 10.1186/1753-6561-5-s7-p26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Li X, Wu HX, Southerton SG. Transcriptome profiling of Pinus radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics. BMC Genomics 2011; 12:480. [PMID: 21962175 PMCID: PMC3224210 DOI: 10.1186/1471-2164-12-480] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 10/01/2011] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The mechanical properties of wood are largely determined by the orientation of cellulose microfibrils in secondary cell walls. Several genes and their allelic variants have previously been found to affect microfibril angle (MFA) and wood stiffness; however, the molecular mechanisms controlling microfibril orientation and mechanical strength are largely uncharacterised. In the present study, cDNA microarrays were used to compare gene expression in developing xylem with contrasting stiffness and MFA in juvenile Pinus radiata trees in order to gain further insights into the molecular mechanisms underlying microfibril orientation and cell wall mechanics. RESULTS Juvenile radiata pine trees with higher stiffness (HS) had lower MFA in the earlywood and latewood of each ring compared to low stiffness (LS) trees. Approximately 3.4 to 14.5% out of 3, 320 xylem unigenes on cDNA microarrays were differentially regulated in juvenile wood with contrasting stiffness and MFA. Greater variation in MFA and stiffness was observed in earlywood compared to latewood, suggesting earlywood contributes most to differences in stiffness; however, 3-4 times more genes were differentially regulated in latewood than in earlywood. A total of 108 xylem unigenes were differentially regulated in juvenile wood with HS and LS in at least two seasons, including 43 unigenes with unknown functions. Many genes involved in cytoskeleton development and secondary wall formation (cellulose and lignin biosynthesis) were preferentially transcribed in wood with HS and low MFA. In contrast, several genes involved in cell division and primary wall synthesis were more abundantly transcribed in LS wood with high MFA. CONCLUSIONS Microarray expression profiles in Pinus radiata juvenile wood with contrasting stiffness has shed more light on the transcriptional control of microfibril orientation and the mechanical properties of wood. The identified candidate genes provide an invaluable resource for further gene function and association genetics studies aimed at deepening our understanding of cell wall biomechanics with a view to improving the mechanical properties of wood.
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Affiliation(s)
- Xinguo Li
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Harry X Wu
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
- Umeå Plant Science Centre, Dept. Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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Freeman JS, Potts BM, Downes GM, Thavamanikumar S, Pilbeam DJ, Hudson CJ, Vaillancourt RE. QTL analysis for growth and wood properties across multiple pedigrees and sites in Eucalyptus globulus. BMC Proc 2011. [PMCID: PMC3239939 DOI: 10.1186/1753-6561-5-s7-o8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Gion JM, Carouché A, Deweer S, Bedon F, Pichavant F, Charpentier JP, Baillères H, Rozenberg P, Carocha V, Ognouabi N, Verhaegen D, Grima-Pettenati J, Vigneron P, Plomion C. Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus. BMC Genomics 2011; 12:301. [PMID: 21651758 PMCID: PMC3130712 DOI: 10.1186/1471-2164-12-301] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 06/08/2011] [Indexed: 11/16/2022] Open
Abstract
Background Eucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly improve growth performance and wood properties (WPs). In this study, an interspecific cross between Eucalyptus urophylla and E. grandis was used to identify major genomic regions (Quantitative Trait Loci, QTL) controlling the variability of WPs. Results Linkage maps were generated for both parent species. A total of 117 QTLs were detected for a series of wood and end-use related traits, including chemical, technological, physical, mechanical and anatomical properties. The QTLs were mainly clustered into five linkage groups. In terms of distribution of QTL effects, our result agrees with the typical L-shape reported in most QTL studies, i.e. most WP QTLs had limited effects and only a few (13) had major effects (phenotypic variance explained > 15%). The co-locations of QTLs for different WPs as well as QTLs and candidate genes are discussed in terms of phenotypic correlations between traits, and of the function of the candidate genes. The major wood property QTL harbours a gene encoding a Cinnamoyl CoA reductase (CCR), a structural enzyme of the monolignol-specific biosynthesis pathway. Conclusions Given the number of traits analysed, this study provides a comprehensive understanding of the genetic architecture of wood properties in this Eucalyptus full-sib pedigree. At the dawn of Eucalyptus genome sequence, it will provide a framework to identify the nature of genes underlying these important quantitative traits.
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Affiliation(s)
- Jean-Marc Gion
- CIRAD, Department of Biological System, Research Unit "Genetic improvement and adaptation of mediterranean and tropical plants" TA A-108/C, Campus International de Baillarguet, 34398 Montpellier Cedex, France.
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Hendry AP, Kinnison MT, Heino M, Day T, Smith TB, Fitt G, Bergstrom CT, Oakeshott J, Jørgensen PS, Zalucki MP, Gilchrist G, Southerton S, Sih A, Strauss S, Denison RF, Carroll SP. Evolutionary principles and their practical application. Evol Appl 2011; 4:159-83. [PMID: 25567966 PMCID: PMC3352551 DOI: 10.1111/j.1752-4571.2010.00165.x] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 09/20/2010] [Indexed: 02/01/2023] Open
Abstract
Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.
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Affiliation(s)
- Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University Montreal, QC, Canada
| | | | - Mikko Heino
- Department of Biology, University of Bergen Bergen, Norway ; International Institute for Applied Systems Analysis Laxenburg, Austria ; Institute of Marine Research Bergen, Norway
| | - Troy Day
- Departments of Mathematics and Statistics and Biology, Queen's University Kingston, ON, Canada
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment, University of California Los Angeles, CA, USA ; Department of Ecology and Evolutionary Biology, University of California Los Angeles, CA, USA
| | - Gary Fitt
- CSIRO Entomology and Cotton Catchment Communities CRC, Long Pocket Laboratories Indooroopilly, Qld, Australia
| | - Carl T Bergstrom
- Department of Biology, University of Washington Seattle, WA, USA
| | - John Oakeshott
- CSIRO Entomology, Black Mountain Canberra, ACT, Australia
| | - Peter S Jørgensen
- Center for Macroecology, Evolution and Climate, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Myron P Zalucki
- School of Biological Sciences, The University of Queensland Brisbane, Qld, Australia
| | - George Gilchrist
- Division of Environmental Biology, National Science Foundation Arlington, VA, USA
| | | | - Andrew Sih
- Department of Environmental Science and Policy, University of California Davis, CA, USA
| | - Sharon Strauss
- Section of Evolution and Ecology, University of California Davis, CA, USA
| | - Robert F Denison
- Ecology Evolution and Behavior, University of Minnesota Saint Paul, MN, USA
| | - Scott P Carroll
- Institute for Contemporary Evolution Davis, CA, USA ; Department of Entomology, University of California Davis, CA, USA
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