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Lin P, Chai J, Wang A, Zhong H, Wang K. High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing. Int J Mol Sci 2024; 25:8840. [PMID: 39201527 PMCID: PMC11354348 DOI: 10.3390/ijms25168840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.
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Affiliation(s)
- Ping Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Jingyu Chai
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Anni Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Huiqi Zhong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Kailiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (P.L.); (J.C.); (A.W.); (H.Z.)
- Zhejiang Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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Shu M, Moran EV. Identifying genetic variation associated with environmental gradients and drought-tolerance phenotypes in ponderosa pine. Ecol Evol 2023; 13:e10620. [PMID: 37841219 PMCID: PMC10576020 DOI: 10.1002/ece3.10620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/05/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023] Open
Abstract
As climate changes, understanding the genetic basis of local adaptation in plants becomes an ever more pressing issue. Combining genotype-environment association (GEA) with genotype-phenotype association (GPA) analysis has an exciting potential to uncover the genetic basis of environmental responses. We use these approaches to identify genetic variants linked to local adaptation to drought in Pinus ponderosa. Over 4 million Single Nucleotide Polymorphisms (SNPs) were identified using 223 individuals from across the Sierra Nevada of California. 927,740 (22.3%) SNPs were retained after filtering for proximity to genes and used in our association analyses. We found 1374 associated with five major climate variables, with the largest number (1151) associated with April 1st snowpack. We also conducted a greenhouse study with various drought-tolerance traits measured in first-year seedlings of a subset of the genotyped trees grown in the greenhouse. 796 SNPs were associated with control-condition trait values, while 1149 were associated with responsiveness of these traits to drought. While no individual SNPs were associated with both the environmental variables and the measured traits, several annotated genes were associated with both, particularly those involved in cell wall formation, biotic and abiotic stress responses, and ubiquitination. However, the functions of many of the associated genes have not yet been determined due to the lack of gene annotation information for conifers. Future studies are needed to assess the developmental roles and ecological significance of these unknown genes.
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Affiliation(s)
- Mengjun Shu
- Life and Environmental SciencesUniversity of CaliforniaMercedCaliforniaUSA
| | - Emily V. Moran
- Life and Environmental SciencesUniversity of CaliforniaMercedCaliforniaUSA
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Ashwath MN, Lavale SA, Santhoshkumar AV, Mohapatra SR, Bhardwaj A, Dash U, Shiran K, Samantara K, Wani SH. Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees. Funct Integr Genomics 2023; 23:297. [PMID: 37700096 DOI: 10.1007/s10142-023-01224-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/26/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.
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Affiliation(s)
- M N Ashwath
- Department of Forest Biology and Tree Improvement, Kerala Agricultural University, Thrissur, Kerala, 680 656, India
| | - Shivaji Ajinath Lavale
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, Kerala, 680 656, India
| | - A V Santhoshkumar
- Department of Forest Biology and Tree Improvement, Kerala Agricultural University, Thrissur, Kerala, 680 656, India
| | - Sourav Ranjan Mohapatra
- Department of Forest Biology and Tree Improvement, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, 751 003, India.
| | - Ankita Bhardwaj
- Department of Silviculture and Agroforestry, Kerala Agricultural University, Thrissur, Kerala, 680 656, India
| | - Umakanta Dash
- Department of Silviculture and Agroforestry, Kerala Agricultural University, Thrissur, Kerala, 680 656, India
| | - K Shiran
- Department of Forest Biology and Tree Improvement, Kerala Agricultural University, Thrissur, Kerala, 680 656, India
| | - Kajal Samantara
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Shabir Hussain Wani
- Mountain Research Center for Field crops, Sher-e-Kashmir University of Agricultural Sciences and Technology Srinagar, Khudwani, Srinagar, Jammu and Kashmir, India.
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Xia H, Hao Z, Shen Y, Tu Z, Yang L, Zong Y, Li H. Genome-wide association study of multiyear dynamic growth traits in hybrid Liriodendron identifies robust genetic loci associated with growth trajectories. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1544-1563. [PMID: 37272730 DOI: 10.1111/tpj.16337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/30/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
The genetic factors underlying growth traits differ over time points or stages. However, most current studies of phenotypes at single time points do not capture all loci or explain the genetic differences underlying growth trajectories. Hybrid Liriodendron exhibits obvious heterosis and is widely cultivated, although its complex genetic mechanism underlying growth traits remains unknown. A genome-wide association study (GWAS) is an effective method for elucidating the genetic architecture by identifying genetic loci underlying complex quantitative traits. In the present study, using a GWAS, we identified robust loci associated with growth trajectories in hybrid Liriodendron populations. We selected 233 hybrid progenies derived from 25 crosses for resequencing, and measured their tree height (H) and diameter at breast height (DBH) for 11 consecutive years; 192 972 high-quality single nucleotide polymorphisms (SNPs) were obtained. The dynamics of the multiyear single-trait GWAS showed that year-specific SNPs predominated, and only five robust SNPs for DBH were identified in at least three different years. Multitrait GWAS analysis with model parameters as latent variables also revealed 62 SNPs for H and 52 for DBH associated with the growth trajectory, displaying different biomass accumulation patterns, among which four SNPs exerted pleiotropic effects. All identified SNPs also exhibited temporal variations in effect sizes and inheritance patterns potentially related to different growth and developmental stages. The haplotypes resulting from these significant SNPs might pyramid favorable loci, benefitting the selection of superior genotypes. The present study provides insights into the genetic architecture of dynamic growth traits and lays a basis for future molecular-assisted breeding.
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Affiliation(s)
- Hui Xia
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziyuan Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yufang Shen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhonghua Tu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Lichun Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yaxian Zong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Huogen Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Eckert AJ, Neale DB. Probing the dark matter of environmental associations yields novel insights into the architecture of adaptation. THE NEW PHYTOLOGIST 2023; 237:1479-1482. [PMID: 36528858 DOI: 10.1111/nph.18639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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Novikova SV, Sharov VV, Oreshkova NV, Simonov EP, Krutovsky KV. Genetic Adaptation of Siberian Larch ( Larix sibirica Ledeb.) to High Altitudes. Int J Mol Sci 2023; 24:ijms24054530. [PMID: 36901960 PMCID: PMC10003562 DOI: 10.3390/ijms24054530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (FST = 0.036) and all 25,143 SNPs (FST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (FST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001).
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Affiliation(s)
- Serafima V. Novikova
- Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Vadim V. Sharov
- Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
- Department of High-Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074 Krasnoyarsk, Russia
- Tauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel
| | - Natalia V. Oreshkova
- Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Evgeniy P. Simonov
- Laboratory of Evolutionary Trophology, A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Konstantin V. Krutovsky
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
- 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 Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, 394087 Voronezh, Russia
- Correspondence: ; Tel.: +49-551-339-3537
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Cappa EP, Chen C, Klutsch JG, Sebastian-Azcona J, Ratcliffe B, Wei X, Da Ros L, Ullah A, Liu Y, Benowicz A, Sadoway S, Mansfield SD, Erbilgin N, Thomas BR, El-Kassaby YA. Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine. BMC Genomics 2022; 23:536. [PMID: 35870886 PMCID: PMC9308220 DOI: 10.1186/s12864-022-08747-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias. Results MT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP. Conclusions The power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08747-7.
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Zhang Y, Li D, Feng X, Wang X, Wang M, Han W, Manzoor MA, Li G, Chen T, Wang H, Cai Y. Whole-genome analysis of CGS, SAHH, SAMS gene families in five Rosaceae species and their expression analysis in Pyrus bretschneideri. PeerJ 2022; 10:e13086. [PMID: 35313526 PMCID: PMC8934043 DOI: 10.7717/peerj.13086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
Cystathionine γ-synthase (CGS), S-adenosyl-L-homocysteine hydrolase (SAHH), and S-adenosy-L-methionine synthetase (SAMS) play an important role in the regulation of plant growth, development, and secondary metabolism. In this study, a total of 6 CGS, 6 SAHH, and 28 SAMS genes were identified from five Rosaceae species (Pyrus bretschneideri, Prunus persica, Prunus mume, Fragaria vesca, and Malus domestica). The evolutionary relationship and microsynteny analysis in five Rosaceae species revealed that duplicated regions were conserved between three gene families (CGS, SAHH, SAMS). Moreover, the chromosomal locations, gene structures, conserved motifs, cis-elements, physicochemical properties, and Ka/Ks analysis were performed by using numerous bioinformatics tools. The expression of different organs showed that the CGS, SAHH and SAMS genes of pear have relatively high expression patterns in flowers and stems, except for PbCGS1. RNA-seq and qRT-PCR combined analysis showed that PbSAMS1 may be involved in the regulation of pear stone cell development. In summary, this study provides the basic information of CGS, SAHH and SAMS genes in five Rosaceae species, further revealing the expression patterns in the pear fruit, which provides the theoretical basis for the regulation of pear stone cells.
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Affiliation(s)
- Yang Zhang
- Anhui Agricultural University, Hefei, China
| | - Decong Li
- Anhui Agricultural University, Hefei, China
| | | | - Xinya Wang
- Anhui Agricultural University, Hefei, China
| | | | | | | | | | | | - Han Wang
- Anhui Agricultural University, Hefei, China
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Lu WX, Zhang BH, Zhang YY, Yang SC. Differentiation of Cold Tolerance in an Artificial Population of a Mangrove Species, Kandelia obovata, Is Associated With Geographic Origins. FRONTIERS IN PLANT SCIENCE 2022; 12:695746. [PMID: 35185942 PMCID: PMC8851163 DOI: 10.3389/fpls.2021.695746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Temperature is one of the climatic factors that shape the geographic distribution of plant populations. Mangroves are temperature-sensitive plants, and their distributions are severely limited by low temperatures. It is unknown, however, to what extent temperature contributes to their population differentiation and evolution. Kandelia obovata (Rhizophoraceae) is a mangrove species with high cold tolerance in the Northern Hemisphere. We investigated the phenotypic responses of an artificial population of K. obovata, with plants transplanted from different source populations, to extremely low temperatures during winter of 2015-2016 in Yueqing County (28°20'N), Zhejiang Province of China. Using two binary traits, "with/without leaves alive on the branches" and "with/without alive buds on the tips of branches," we classified plants in this artificial population into strong, moderate and poor cold resistance groups. We further assessed the genetic diversity, structure and differentiation of these three groups, as well as five natural populations along a latitudinal gradient using ten nuclear and six plastid microsatellite markers. Microsatellite data revealed genetic differentiation among the natural populations along the latitudinal gradient. Molecular data indicated that the cold tolerance of three groups in the artificial population was associated with their geographic origins, and that the most cold-tolerant group came from the northernmost natural population. Our study thus indicates that natural populations of K. obovata may have evolved divergent capacity of cold tolerance.
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Affiliation(s)
- Wen-Xun Lu
- College of the Environment and Ecology, Xiamen University, Xiamen, China
- School of Life Sciences, Peking University, Beijing, China
| | - Bing-Huang Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuan-Ye Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Sheng-Chang Yang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
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Hurel A, de Miguel M, Dutech C, Desprez‐Loustau M, Plomion C, Rodríguez‐Quilón I, Cyrille A, Guzman T, Alía R, González‐Martínez SC, Budde KB. Genetic basis of growth, spring phenology, and susceptibility to biotic stressors in maritime pine. Evol Appl 2021; 14:2750-2772. [PMID: 34950227 PMCID: PMC8674897 DOI: 10.1111/eva.13309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/03/2021] [Indexed: 11/30/2022] Open
Abstract
Forest ecosystems are increasingly challenged by extreme events, for example, drought, storms, pest attacks, and fungal pathogen outbreaks, causing severe ecological and economic losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e., heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, spring phenology, and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), was assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), spring phenology (0.165-0.310), and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021, measured on inoculated, excised branches under controlled conditions), but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4227 genome-wide SNPs revealed several loci significantly associated with each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5, associated with needle discoloration caused by D. sapinea. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.
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Affiliation(s)
- Agathe Hurel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | - Marina de Miguel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- EGFV, INRAEUniversity of BordeauxVillenave‐d'OrnonFrance
| | - Cyril Dutech
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | | | | | | | | | | | | | | | - Katharina B. Budde
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- Büsgen‐InstituteGeorg‐August University GöttingenGöttingenGermany
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12
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Guo X, He C, Cheng F, Zhong Y, Cheng X, Tao X. Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony ( Paeonia rockii) Using Association Mapping. Front Genet 2021; 12:664814. [PMID: 34456963 PMCID: PMC8385368 DOI: 10.3389/fgene.2021.664814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87-110.64%) and a high level of genetic diversity (mean number of alleles, N A = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.
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Affiliation(s)
- Xin Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Peony International Institute, School of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
| | - Chunyan He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Peony International Institute, School of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
| | - Fangyun Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Peony International Institute, School of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
| | - Yuan Zhong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Peony International Institute, School of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.,National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
| | - Xinyun Cheng
- Beijing Guose Peony Technology Co. Ltd., Beijing, China
| | - Xiwen Tao
- Beijing Guose Peony Technology Co. Ltd., Beijing, China
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13
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Genetic Architecture and Genome-Wide Adaptive Signatures Underlying Stem Lenticel Traits in Populus tomentosa. Int J Mol Sci 2021; 22:ijms22179249. [PMID: 34502156 PMCID: PMC8431110 DOI: 10.3390/ijms22179249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/21/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
The stem lenticel is a highly specialized tissue of woody plants that has evolved to balance stem water retention and gas exchange as an adaptation to local environments. In this study, we applied genome-wide association studies and selective sweeping analysis to characterize the genetic architecture and genome-wide adaptive signatures underlying stem lenticel traits among 303 unrelated accessions of P. tomentosa, which has significant phenotypic and genetic variations according to climate region across its natural distribution. In total, we detected 108 significant single-nucleotide polymorphisms, annotated to 88 candidate genes for lenticel, of which 9 causative genes showed significantly different selection signatures among climate regions. Furthermore, PtoNAC083 and PtoMYB46 showed significant association signals and abiotic stress response, so we overexpressed these two genes in Arabidopsis thaliana and found that the number of stem cells in all three overexpression lines was significantly reduced by PtoNAC083 overexpression but slightly increased by PtoMYB46 overexpression, suggesting that both genes are involved in cell division and expansion during lenticel formation. The findings of this study demonstrate the successful application of an integrated strategy for dissecting the genetic basis and landscape genetics of complex adaptive traits, which will facilitate the molecular design of tree ideotypes that may adapt to future climate and environmental changes.
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14
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Meger J, Ulaszewski B, Burczyk J. Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. BMC Genomics 2021; 22:583. [PMID: 34332553 PMCID: PMC8325806 DOI: 10.1186/s12864-021-07907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. RESULTS We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. CONCLUSIONS Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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15
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Cuervo-Alarcon L, Arend M, Müller M, Sperisen C, Finkeldey R, Krutovsky KV. A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.). Sci Rep 2021; 11:2386. [PMID: 33504857 PMCID: PMC7840767 DOI: 10.1038/s41598-021-81594-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Studies of genetic variation underlying traits related to drought tolerance in forest trees are of great importance for understanding their adaptive potential under a climate change scenario. In this study, using a candidate gene approach, associations between SNPs and drought related traits were assessed in saplings of European beech (Fagus sylvatica L.) representing trees growing along steep precipitation gradients. The saplings were subjected to experimentally controlled drought treatments. Response of the saplings was assessed by the evaluation of stem diameter growth (SDG) and the chlorophyll fluorescence parameters FV/FM, PIabs, and PItot. The evaluation showed that saplings from xeric sites were less affected by the drought treatment. Five SNPs (7.14%) in three candidate genes were significantly associated with the evaluated traits; saplings with particular genotypes at these SNPs showed better performance under the drought treatment. The SNPs were located in the cytosolic class I small heat-shock protein, CTR/DRE binding transcription factor, and isocitrate dehydrogenase genes and explained 5.8-13.4% of the phenotypic variance. These findings provide insight into the genetic basis of traits related to drought tolerance in European beech and could support the development of forest conservation management strategies under future climatic conditions.
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Affiliation(s)
- Laura Cuervo-Alarcon
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Matthias Arend
- Physiological Plant Ecology, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Markus Müller
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Christoph Sperisen
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Reiner Finkeldey
- University of Kassel, Mönchebergstrasse 19, 34109, Kassel, Germany
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow, Russia, 119333.
- Laboratory of Foresty Genomics, Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, Russia, 660036.
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.
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16
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De La Torre AR, Wilhite B, Puiu D, St. Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes (Basel) 2021; 12:110. [PMID: 33477542 PMCID: PMC7831106 DOI: 10.3390/genes12010110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species' predictions under climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Benjamin Wilhite
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Daniela Puiu
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - John Bradley St. Clair
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331, USA;
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Steven L. Salzberg
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Brian Allen
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
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17
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Santini F, Kefauver SC, Araus JL, Resco de Dios V, Martín García S, Grivet D, Voltas J. Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery. THE NEW PHYTOLOGIST 2021; 229:245-258. [PMID: 32893885 DOI: 10.1111/nph.16862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Progress in high-throughput phenotyping and genomics provides the potential to understand the genetic basis of plant functional differentiation. We developed a semi-automatic methodology based on unmanned aerial vehicle (UAV) imagery for deriving tree-level phenotypes followed by genome-wide association study (GWAS). An RGB-based point cloud was used for tree crown identification in a common garden of Pinus halepensis in Spain. Crowns were combined with multispectral and thermal orthomosaics to retrieve growth traits, vegetation indices and canopy temperature. Thereafter, GWAS was performed to analyse the association between phenotypes and genomic variation at 235 single nucleotide polymorphisms (SNPs). Growth traits were associated with 12 SNPs involved in cellulose and carbohydrate metabolism. Indices related to transpiration and leaf water content were associated with six SNPs involved in stomata dynamics. Indices related to leaf pigments and leaf area were associated with 11 SNPs involved in signalling and peroxisome metabolism. About 16-20% of trait variance was explained by combinations of several SNPs, indicating polygenic control of morpho-physiological traits. Despite a limited availability of markers and individuals, this study is provides a successful proof-of-concept for the combination of high-throughput UAV-based phenotyping with cost-effective genotyping to disentangle the genetic architecture of phenotypic variation in a widespread conifer.
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Affiliation(s)
- Filippo Santini
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
| | - Shawn Carlisle Kefauver
- AGROTECNIO (Center for Research in Agrotechnology), Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, E-08028, Spain
| | - José Luis Araus
- AGROTECNIO (Center for Research in Agrotechnology), Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, E-08028, Spain
| | - Víctor Resco de Dios
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
- School of Life Science and Engineering, Southwest University of Science and Technology, 59 Qinglong Ave., Mianyang, 621010, China
| | | | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid, E-28040, Spain
| | - Jordi Voltas
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, Lleida, E-25198, Spain
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18
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Chang CYY, Bräutigam K, Hüner NPA, Ensminger I. Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers. THE NEW PHYTOLOGIST 2021; 229:675-691. [PMID: 32869329 DOI: 10.1111/nph.16904] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.
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Affiliation(s)
- Christine Yao-Yun Chang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Experimental Climate Change Research Centre, Western University, London, ON, N6A5B7, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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19
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Yang Y, He R, Zheng J, Hu Z, Wu J, Leng P. Development of EST-SSR markers and association mapping with floral traits in Syringa oblata. BMC PLANT BIOLOGY 2020; 20:436. [PMID: 32957917 PMCID: PMC7507607 DOI: 10.1186/s12870-020-02652-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata. RESULTS In this study, a total of 10,988 SSRs were obtained from 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. Two hundred thirty-four alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait. CONCLUSION The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of floral traits for lilac.
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Affiliation(s)
- Yunyao Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruiqing He
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
| | - Zenghui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
| | - Jing Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China.
| | - Pingsheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
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20
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Liu N, Cheng F. Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. BMC PLANT BIOLOGY 2020; 20:245. [PMID: 32487017 PMCID: PMC7265254 DOI: 10.1186/s12870-020-02449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). RESULTS The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). CONCLUSIONS Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
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Affiliation(s)
- Na Liu
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fangyun Cheng
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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21
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Salimonti A, Carbone F, Romano E, Pellegrino M, Benincasa C, Micali S, Tondelli A, Conforti FL, Perri E, Ienco A, Zelasco S. Association Study of the 5'UTR Intron of the FAD2-2 Gene With Oleic and Linoleic Acid Content in Olea europaea L. FRONTIERS IN PLANT SCIENCE 2020; 11:66. [PMID: 32117401 PMCID: PMC7031445 DOI: 10.3389/fpls.2020.00066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/16/2020] [Indexed: 05/21/2023]
Abstract
Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most ancient and spread tree crop in the Mediterranean basin. An important quality trait for the extra virgin olive oil is the fatty acid composition. In particular, a high content of oleic acid and low of linoleic, linolenic, and palmitic acid is considered very relevant in the health properties of the olive oil. The oleate desaturase enzyme encoding-gene (FAD2-2) is the main responsible for the linoleic acid content in the olive fruit mesocarp and, therefore, in the olive oil revealing to be the most important candidate gene for the linoleic acid biosynthesis. In this study, an in silico and structural analysis of the 5'UTR intron of the FAD2-2 gene was conducted with the aim to explore the natural sequence variability and its role in the gene expression regulation. In order to identify functional allele variants, the 5'UTR intron was isolated and partially sequenced in 97 olive cultivars. The sequence analysis allowed to find a 117-bp insertion including two long duplications never found before in FAD2-2 genes in olive and the existence of many intron-mediated enhancement (IME) elements. The sequence polymorphism analysis led to detect 39 SNPs. The candidate gene association study conducted for oleic and linoleic acids content revealed seven SNPs and one indel significantly associated able to explain a phenotypic variation ranging from 7% to 16% among the years. Our study highlighted new structural variants within the FAD2-2 gene in olive, putatively involved in the regulation mechanisms of gene expression associated with the variation of the content of oleic and linoleic acid.
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Affiliation(s)
- Amelia Salimonti
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Fabrizio Carbone
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Elvira Romano
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | | | - Cinzia Benincasa
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Sabrina Micali
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Roma, Italy
| | - Alessandro Tondelli
- Research Centre for Genomics and Bioinformatics, CREA, Fiorenzuola D’Arda, Italy
| | - Francesca L. Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Enzo Perri
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | | | - Samanta Zelasco
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
- *Correspondence: Samanta Zelasco,
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22
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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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23
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North American Douglas-fir ( P. menziesii) in Europe: establishment and reproduction within new geographic space without consequences for its genetic diversity. Biol Invasions 2019; 21:3249-3267. [PMID: 31929722 PMCID: PMC6936651 DOI: 10.1007/s10530-019-02045-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 06/25/2019] [Indexed: 01/02/2023]
Abstract
Genetic admixture and plasticity along with propagule pressure, large seed dispersal distances and fast adaptation support successful establishment and spread of introduced species outside their native range. Consequently, introductions may display climatic niche shifts in the introduced range. Douglas-fir, a controversial forest and ornamental conifer represented by two ecologically different and hybridising varieties, was transferred multiple times outside the native range in North America. Here, we compare climatic and genetic patterns of 38 native populations from North America with six old Pseudotsuga menziesii populations with natural regeneration in the introduced range in Central Europe. Following variety and geographic origin assessment of introduced populations, genotypic and climatic data were examined for signatures of inter-varietal gene flow, reduced genetic diversity, presence of fine-scale spatial genetic structure (SGS), dispersal patterns, and climate similarities between native and introduced range. In the introduced range, dominating coastal variety originated from a restricted area in the US, whereas the interior variety, with limited presence in the European sites, displayed wider geographic origin. Variety hybrids with contributing coastal, but not the interior parent were identified. Differences in genetic diversity between both ranges, but also among the parent and their respective offspring populations in Europe were not found. Old populations in general lacked any SGS, whereas natural regeneration revealed different patterns of SGS. Distances of propagule dispersal ranged between 2.5 and 92 m. The climate of the studied European introduced range was most similar to the climate of the coastal variety from the western Cascade range from which the majority of the analysed coastal European Douglas-fir, but not the European interior variety, was assigned to originate. The results we present here shed not only light on dynamics of invasive species in the introduced range in general, but also allow for refinement of climatic niche modeling when using lower than species level.
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Habitat preference differentiates the Holocene range dynamics but not barrier effects on two sympatric, congeneric trees (Tristaniopsis, Myrtaceae). Heredity (Edinb) 2019; 123:532-548. [PMID: 31243348 DOI: 10.1038/s41437-019-0243-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
Niche partitioning can lead to differences in the range dynamics of plant species through its impacts on habitat availability, dispersal, or selection for traits that affect colonization and persistence. We investigated whether niche partitioning into upland and riparian habitats differentiates the range dynamics of two closely related and sympatric eastern Australian trees: the mountain water gum (Tristaniopsis collina) and the water gum (T. laurina). Using genomic data from SNP genotyping of 480 samples, we assessed the impact of biogeographic barriers and tested for signals of range expansion. Circuit theory was used to model isolation-by-resistance across three palaeo-environment scenarios: the Last Glacial Maximum, the Holocene Climate Optimum and present-day (1950-2014). Both trees showed similar genetic structure across historically dry barriers, despite evidence of significant environmental niche differentiation and different post-glacial habitat shifts. Tristaniopsis collina exhibits the signature of serial founder effects consistent with recent or rapid range expansion, whilst T. laurina has genetic patterns consistent with long-term persistence in geographically isolated populations despite occupying a broader bioclimatic niche. We found the minor influence of isolation-by-resistance on both species, though other unknown factors appear to shape genetic variation. We postulate that specialized recruitment traits (adapted to flood-disturbance regimes) rather than habitat availability limited post-glacial range expansion in T. laurina. Our findings indicate that niche breadth does not always facilitate range expansion through colonization and migration across barriers, though it can promote long-term persistence in situ.
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The Resistance of Scots Pine (Pinus sylvestris L.) Half-sib Families to Heterobasidion annosum. FORESTS 2019. [DOI: 10.3390/f10030287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study observed the genotypic variation among Scots pine (Pinus sylvestris L.) half-sib families’ susceptibility to Heterobasidion annosum. Scots pine susceptibility was tested in 12 half-sib families by inoculating them with four different H. annosum strains. At two, six, and ten months after the inoculations, the susceptibility indicators (incidence rate, pathogen spread, and mortality rate) were compared and the total phenolic compounds (TPC) in the inoculated and control groups determined using the Folin–Ciocalteu method. Among half-sib families, significant differences were found for seedling mortality (range: 1.3%–21.2%); however, the differences in incidence rate (range: 54%–77%) and pathogen spread (range: 24–53 mm) were not significant. The incidence rate among half-sib families correlated positively and significantly (r = 0.72, p < 0.05) with the mortality rate, while the pathogen spread correlated negatively with mortality, although the correlation was not significant (r = −0.29, p > 0.05). The TPC comparison with susceptibility indicators showed that the half-sib families with lower susceptibility were characterized by the ability to increase TPC after inoculation compared to the control group. This tendency was most apparent in stems and roots six and two months after inoculation, respectively. Correlation analyses revealed that higher TPC in stems six months after inoculation determined a lower incidence rate (r = −0.32, p < 0.05), while higher Change in concentration of total phenolic compounds (TPCΔ) indicated a lower pathogen spread (r = −0.60, p < 0.05). The lowest incidence of the pathogen was determined in half-sib families with the highest TPCΔ in the roots two months after inoculation. The lower susceptibility of Scots pine half-sib families is based on a combination of enhanced constitutive and inducible phenolic defense mechanisms. The data may facilitate the selection of Scots pine half-sib families with low susceptibility for breeding programs and forest management strategies.
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Lin P, Yin H, Yan C, Yao X, Wang K. Association Genetics Identifies Single Nucleotide Polymorphisms Related to Kernel Oil Content and Quality in Camellia oleifera. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:2547-2562. [PMID: 30758959 DOI: 10.1021/acs.jafc.8b03399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Camellia oleifera, as an important nonwood tree species for seed oil in China, has received enormous attention owing to its high unsaturated fatty acid contents benefited to human health. It is necessary to examine allelic diversity of key genes that are associated with oil production in C. oleifera cultivars with a large variation of fatty acid compositions. In this study, we performed the association analysis between four key genes (two CoSAD and two Cofad2) coding fatty acid desaturases and traits including oil content and fatty acid composition. We identified two single nucleotide insertion-deletion (InDel) and 362 single-nucleotide polymorphisms (SNPs) within the four candidate genes by sequencing an association population (216 accessions). Single-marker (or haplotype) and traits association tests were conducted by linkage disequilibrium (LD) approaches to detect significant marker-trait associations. Validation population (279 hybrid individuals from six full-sibs families) studies were performed to validate the function of allelic variations significantly associated. In all, 90 single marker-trait and one haplotype-trait associations were significant in association population, and these loci explained 1.87-17.93% proportion of the corresponding phenotypic variance. Further, six SNP marker-trait associations ( Q < 0.10) from Cofad2-A, CoSAD1, and CoSAD2 were successfully validated in the validation population. The SNP markers identified in this study can potentially be applied for future marker-assisted selection to improve oil content and quality in C. oleifera.
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Affiliation(s)
- Ping Lin
- State Key Laboratory of Tree Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
- Key Laboratory of Forest Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
- Key Laboratory of Forest Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
| | - Chao Yan
- State Key Laboratory of Tree Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
- Key Laboratory of Forest Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
- Experimental Center for Subtropical Forestry , Chinese Academy of Forestry , Fenyi 336600 , China
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
- Key Laboratory of Forest Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
| | - Kailiang Wang
- State Key Laboratory of Tree Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
- Key Laboratory of Forest Genetics and Breeding , Research Institute of Subtropical Forestry, Chinese Academy of Forestry , Hangzhou 311400 , China
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27
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Lea MV, Syring J, Jennings T, Cronn R, Bruederle LP, Neale JR, Tomback DF. Development of nuclear microsatellite loci for Pinus albicaulis Engelm. (Pinaceae), a conifer of conservation concern. PLoS One 2018; 13:e0205423. [PMID: 30335779 PMCID: PMC6193661 DOI: 10.1371/journal.pone.0205423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022] Open
Abstract
Pinus albicaulis (whitebark pine) is a widely-distributed but rapidly declining high elevation western North American tree and a candidate for listing under the U.S. Endangered Species Act. Our objectives were to develop reliable nuclear microsatellite markers that can be used to assess within-population genetic diversity as well as seed and pollen migration dynamics, and to validate markers using two geographically proximal P. albicaulis populations. We identified 1,667 microsatellite-containing sequences from shotgun DNA libraries of P. albicaulis. Primer pairs were designed for 308 unique microsatellite-containing loci, and these were evaluated for PCR amplification success and segregation in a panel of diploid needle tissue. DNA was extracted with an SDS protocol, and primers were screened through gel electrophoresis. Microsatellites were genotyped through fluorescent primer fragment analysis. Ten novel and 13 transferred loci were found to be reproducible in analyses based on 20 foliage samples from each of two locations: Henderson Mountain, Custer Gallatin National Forest, Montana, and Mt. Washburn, Yellowstone National Park, Wyoming (USA). Transferred loci had higher numbers of alleles and expected heterozygosities than novel loci, but also revealed evidence for a higher frequency of null alleles. Eight of the 13 transferred loci deviated significantly from Hardy-Weinberg Equilibrium, and showed large positive FIS values that were likely inflated by null alleles. Mantel’s tests of transferred and novel markers showed no correlation between genetic and geographic distances within or among the two sampled populations. AMOVA suggests that 91% of genetic variability occurs within populations and 9% between the two populations. Studies assessing genetic diversity using these microsatellite loci can help guide future management and restoration activities for P. albicaulis.
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Affiliation(s)
- Marian V. Lea
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - John Syring
- Department of Biology, Linfield College, McMinnville, Oregon, United States of America
| | - Tara Jennings
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, Corvallis, Oregon, United States of America
| | - Richard Cronn
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, Corvallis, Oregon, United States of America
| | - Leo P. Bruederle
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | | | - Diana F. Tomback
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
- * E-mail:
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Mishima K, Hirao T, Tsubomura M, Tamura M, Kurita M, Nose M, Hanaoka S, Takahashi M, Watanabe A. Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don). BMC Genomics 2018; 19:277. [PMID: 29685102 PMCID: PMC5914023 DOI: 10.1186/s12864-018-4581-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/06/2018] [Indexed: 11/30/2022] Open
Abstract
Background Japanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry. Male-sterile marker development in Japanese cedar would facilitate selection of male-sterile plus trees, addressing the widespread social problem of pollinosis and facilitating the identification of heterozygotes, which are useful for breeding. Results This study used next-generation sequencing for single-nucleotide polymorphism discovery in libraries constructed from several organs, including male-sterile and male-fertile strobili. The single-nucleotide polymorphisms obtained were used to construct a high-density linkage map, which enabled identification of a locus on linkage group 9 strongly correlated with male-sterile trait. Expressed sequence tags corresponding to 11 marker loci from 5 isotigs were associated with this locus within 33.4-34.5 cM. These marker loci explained 100% of the phenotypic variation. Several homologs of these sequences are associated with male sterility in rice or Arabidopsis, including a pre-mRNA splicing factor, a DEAD-box protein, a glycosyl hydrolase, and a galactosyltransferase. These proteins are thus candidates for the causal male-sterile gene at the ms-1 locus. After we used a SNaPshot assay to develop markers for marker-assisted selection (MAS), we tested F2 progeny between male-sterile and wild-type plus trees to validate the markers and extrapolated the testing to a larger plus-tree population. We found that two developed from one of the candidates for the causal gene were suitable for MAS. Conclusions More than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar. We developed two SNP markers aimed at MAS that distinguished individuals carrying the male-sterile trait with 100% accuracy, as well as individuals heterozygous at the male-sterile locus, even outside the mapping population. These markers should enable practical MAS for conifer breeding. Electronic supplementary material The online version of this article (10.1186/s12864-018-4581-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tomonori Hirao
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Miho Tamura
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Manabu Kurita
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Mine Nose
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - So Hanaoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Atsushi Watanabe
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan.
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29
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Heer K, Behringer D, Piermattei A, Bässler C, Brandl R, Fady B, Jehl H, Liepelt S, Lorch S, Piotti A, Vendramin G, Weller M, Ziegenhagen B, Büntgen U, Opgenoorth L. Linking dendroecology and association genetics in natural populations: Stress responses archived in tree rings associate with SNP genotypes in silver fir (Abies albaMill.). Mol Ecol 2018; 27:1428-1438. [DOI: 10.1111/mec.14538] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/08/2018] [Indexed: 01/07/2023]
Affiliation(s)
- K. Heer
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - D. Behringer
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
| | - A. Piermattei
- Department of Geography; University of Cambridge; Cambridge UK
- Department of Agricultural, Food and Environmental Sciences; Marche Polytechnic University; Ancona Italy
- Dendro Science; Swiss Federal Research Institute WSL; Birmensdorf Switzerland
| | - C. Bässler
- Bavarian Forest National Park; Grafenau Germany
| | - R. Brandl
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - B. Fady
- INRA; UR Ecologie des Forêts Méditerranéennes; Avignon France
| | - H. Jehl
- Bavarian Forest National Park; Grafenau Germany
| | - S. Liepelt
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
| | - S. Lorch
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - A. Piotti
- National Research Council; Institute of Biosciences and Bioresources; Firenze Italy
| | - G.G. Vendramin
- National Research Council; Institute of Biosciences and Bioresources; Firenze Italy
| | - M. Weller
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - B. Ziegenhagen
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
| | - U. Büntgen
- Department of Geography; University of Cambridge; Cambridge UK
- Dendro Science; Swiss Federal Research Institute WSL; Birmensdorf Switzerland
- CzechGlobe, Global Change Research Institute CAS and Masaryk University; Brno Czech Republic
| | - L. Opgenoorth
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
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30
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Evans MEK, Gugger PF, Lynch AM, Guiterman CH, Fowler JC, Klesse S, Riordan EC. Dendroecology meets genomics in the common garden: new insights into climate adaptation. THE NEW PHYTOLOGIST 2018; 218:401-403. [PMID: 29561071 DOI: 10.1111/nph.15094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- Margaret E K Evans
- Laboratory of Tree-Ring Research, University of Arizona, Tucson, AZ 85721, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
| | - Ann M Lynch
- Laboratory of Tree-Ring Research, University of Arizona, Tucson, AZ 85721, USA
- US Forest Service, Rocky Mountain Research Station, Tucson, AZ 85721, USA
| | | | - Joshua C Fowler
- Laboratory of Tree-Ring Research, University of Arizona, Tucson, AZ 85721, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Stefan Klesse
- Laboratory of Tree-Ring Research, University of Arizona, Tucson, AZ 85721, USA
| | - Erin C Riordan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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Du B, Kreuzwieser J, Dannenmann M, Junker LV, Kleiber A, Hess M, Jansen K, Eiblmeier M, Gessler A, Kohnle U, Ensminger I, Rennenberg H, Wildhagen H. Foliar nitrogen metabolism of adult Douglas-fir trees is affected by soil water availability and varies little among provenances. PLoS One 2018; 13:e0194684. [PMID: 29566035 PMCID: PMC5864041 DOI: 10.1371/journal.pone.0194684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/07/2018] [Indexed: 12/29/2022] Open
Abstract
The coniferous forest tree Douglas-fir (Pseudotsuga menziesii) is native to the pacific North America, and is increasingly planted in temperate regions worldwide. Nitrogen (N) metabolism is of great importance for growth, resistance and resilience of trees. In the present study, foliar N metabolism of adult trees of three coastal and one interior provenance of Douglas-fir grown at two common gardens in southwestern Germany (Wiesloch, W; Schluchsee, S) were characterized in two subsequent years. Both the native North American habitats of the seed sources and the common garden sites in Germany differ in climate conditions. Total and mineral soil N as well as soil water content were higher in S compared to W. We hypothesized that i) provenances differ constitutively in N pool sizes and composition, ii) N pools are affected by environmental conditions, and iii) that effects of environmental factors on N pools differ among interior and coastal provenances. Soil water content strongly affected the concentrations of total N, soluble protein, total amino acids (TAA), arginine and glutamate. Foliar concentrations of total N, soluble protein, structural N and TAA of trees grown at W were much higher than in trees at S. Provenance effects were small but significant for total N and soluble protein content (interior provenance showed lowest concentrations), as well as arginine, asparagine and glutamate. Our data suggest that needle N status of adult Douglas-fir is independent from soil N availability and that low soil water availability induces a re-allocation of N from structural N to metabolic N pools. Small provenance effects on N pools suggest that local adaptation of Douglas-fir is not dominated by N conditions at the native habitats.
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Affiliation(s)
- Baoguo Du
- College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, China
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Jürgen Kreuzwieser
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology (KIT) Campus Alpin, Institute of Meteorology and Climate Research (IMK), Atmospheric Environmental Research (IMK-IFU), Garmisch-Partenkirchen, Germany
| | - Laura Verena Junker
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Anita Kleiber
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Moritz Hess
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
- Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Kirstin Jansen
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Monika Eiblmeier
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Arthur Gessler
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Ulrich Kohnle
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Ingo Ensminger
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- King Saud University, Riyadh, Saudi Arabia
| | - Henning Wildhagen
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
- * E-mail:
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Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/13836_2017_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3-GENES GENOMES GENETICS 2017; 7:3157-3167. [PMID: 28751502 PMCID: PMC5592940 DOI: 10.1534/g3.117.300078] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.
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Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR. Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. BMC Genomics 2017; 18:558. [PMID: 28738815 PMCID: PMC5525293 DOI: 10.1186/s12864-017-3916-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/30/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. RESULTS We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/- 2 h from sunrise and sunset, and +/- 20 days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. CONCLUSIONS Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.
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Affiliation(s)
- Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - Peter C Dolan
- University of Minnesota - Morris, Morris, MN, 56267, USA
| | - Sanjuro Jogdeo
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David B Neale
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - J Bradley St Clair
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
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Mixing It Up: The Role of Hybridization in Forest Management and Conservation under Climate Change. FORESTS 2017. [DOI: 10.3390/f8070237] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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Ganthaler A, Stöggl W, Mayr S, Kranner I, Schüler S, Wischnitzki E, Sehr EM, Fluch S, Trujillo-Moya C. Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust. PLANT MOLECULAR BIOLOGY 2017; 94:229-251. [PMID: 28190131 PMCID: PMC5443855 DOI: 10.1007/s11103-017-0589-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/24/2017] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE Accumulation of phenolic needle metabolites in Norway spruce is regulated by many genes with small and additive effects and is correlated with the susceptibility against fungal attack. Norway spruce accumulates high foliar concentrations of secondary phenolic metabolites, with important functions for pathogen defence responses. However, the molecular genetic basis underlying the quantitative variation of phenolic compounds and their role in enhanced resistance of spruce to infection by needle bladder rust are unknown. To address these questions, a set of 1035 genome-wide single nucleotide polymorphisms (SNPs) was associated to the quantitative variation of four simple phenylpropanoids, eight stilbenes, nine flavonoids, six related arithmetic parameters and the susceptibility to infection by Chrysomyxa rhododendri in an unstructured natural population of Norway spruce. Thirty-one significant genetic associations for the flavonoids gallocatechin, kaempferol 3-glucoside and quercetin 3-glucoside and the stilbenes resveratrol, piceatannol, astringin and isorhapontin were discovered, explaining 22-59% of phenotypic variation, and indicating a regulation of phenolic accumulation by many genes with small and additive effects. The phenolics profile differed between trees with high and low susceptibility to the fungus, underlining the importance of phenolic compounds in the defence mechanisms of Norway spruce to C. rhododendri. Results highlight the utility of association studies in non-model tree species and may enable marker-assisted selection of Norway spruce adapted to severe pathogen attack.
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Affiliation(s)
- Andrea Ganthaler
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria.
- alpS - Centre for Climate Change Adaptation, Grabenweg 68, 6020, Innsbruck, Austria.
| | - Wolfgang Stöggl
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Stefan Mayr
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Ilse Kranner
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Silvio Schüler
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
| | - Elisabeth Wischnitzki
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Eva Maria Sehr
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Silvia Fluch
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Carlos Trujillo-Moya
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
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37
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Finch K, Espinoza E, Jones FA, Cronn R. Source identification of western Oregon Douglas-fir wood cores using mass spectrometry and random forest classification. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1600158. [PMID: 28529831 PMCID: PMC5435404 DOI: 10.3732/apps.1600158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/07/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY We investigated whether wood metabolite profiles from direct analysis in real time (time-of-flight) mass spectrometry (DART-TOFMS) could be used to determine the geographic origin of Douglas-fir wood cores originating from two regions in western Oregon, USA. METHODS Three annual ring mass spectra were obtained from 188 adult Douglas-fir trees, and these were analyzed using random forest models to determine whether samples could be classified to geographic origin, growth year, or growth year and geographic origin. Specific wood molecules that contributed to geographic discrimination were identified. RESULTS Douglas-fir mass spectra could be differentiated into two geographic classes with an accuracy between 70% and 76%. Classification models could not accurately classify sample mass spectra based on growth year. Thirty-two molecules were identified as key for classifying western Oregon Douglas-fir wood cores to geographic origin. DISCUSSION DART-TOFMS is capable of detecting minute but regionally informative differences in wood molecules over a small geographic scale, and these differences made it possible to predict the geographic origin of Douglas-fir wood with moderate accuracy. Studies involving DART-TOFMS, alone and in combination with other technologies, will be relevant for identifying the geographic origin of illegally harvested wood.
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Affiliation(s)
- Kristen Finch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Edgard Espinoza
- National Fish and Wildlife Forensic Laboratory, Ashland, Oregon 97520 USA
| | - F. Andrew Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Richard Cronn
- USDA Forest Service Pacific Northwest Research Station, Corvallis, Oregon 97331 USA
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38
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Di Guardo M, Bink MCAM, Guerra W, Letschka T, Lozano L, Busatto N, Poles L, Tadiello A, Bianco L, Visser RGF, van de Weg E, Costa F. Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1451-1466. [PMID: 28338805 PMCID: PMC5441909 DOI: 10.1093/jxb/erx017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions. Both plant materials were genotyped with a 20K single nucleotide polymorphism (SNP) array and phenotyped with a sophisticated high-resolution texture analyzer. The overall QTL results indicated the fundamental role of chromosome 10 in controlling the mechanical properties, while chromosomes 2 and 14 were more associated with the acoustic response. The latter QTL, moreover, showed a consistent relationship between the QTL-estimated genotypes and the acoustic performance assessed among seedlings. The in silico annotation of these intervals revealed interesting candidate genes potentially involved in fruit texture regulation, as suggested by the gene expression profile. The joint integration of these approaches sheds light on the specific control of fruit texture, enabling important genetic information to assist in the selection of valuable fruit quality apple varieties.
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Affiliation(s)
- Mario Di Guardo
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento, Italy
- Graduate School Experimental Plant Sciences, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Marco C A M Bink
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Walter Guerra
- Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy
| | - Thomas Letschka
- Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy
| | - Lidia Lozano
- Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy
| | - Nicola Busatto
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Lara Poles
- Innovation Fruit Consortium (CIF), via Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Alice Tadiello
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Luca Bianco
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Fabrizio Costa
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
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Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis. Heredity (Edinb) 2016; 118:413-423. [PMID: 27901510 DOI: 10.1038/hdy.2016.115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/30/2016] [Accepted: 10/11/2016] [Indexed: 11/08/2022] Open
Abstract
Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to eliminating some true associations. We developed a new Bayesian approach for identifying the loci underlying an adaptive trait in a multipopulation situation in the presence of possible double confounding due to population stratification and adaptation. With this method we studied the genetic basis of timing of bud set, a surrogate trait for timing of yearly growth cessation that confers local adaptation to the populations of Scots pine (Pinus sylvestris). Population means of timing of bud set were highly correlated with latitude. Most effects at individual loci were small. Interestingly, we found genetic heterogeneity (that is, different sets of loci associated with the trait) between the northern and central European parts of the cline. We also found indications of stronger stabilizing selection toward the northern part of the range. The harsh northern conditions may impose greater selective pressure on timing of growth cessation, and the relative importance of different environmental cues used for tracking the seasons might differ depending on latitude of origin.
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40
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Wu J, Cheng F, Cai C, Zhong Y, Jie X. Association mapping for floral traits in cultivated Paeonia rockii based on SSR markers. Mol Genet Genomics 2016; 292:187-200. [PMID: 27807670 DOI: 10.1007/s00438-016-1266-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/25/2016] [Indexed: 01/29/2023]
Abstract
Tree peony (Paeonia Sect. Moutan) is an economically important ornamental plant, but little is known about the genetic architecture of important ornamental traits. To effectively improve ornamental value, we require a better understanding of genetic architecture in the complex traits of the tree peony. Association mapping is a powerful tool for detection of variation associated with traits. Thus, we examined the genetic diversity and the population structure of 462 unrelated cultivated P. rockii individuals, then performed association mapping to identify simple sequence repeat (SSR) markers associated with 12 floral traits. We observed a moderate level of genetic diversity (PIC = 0.459) and low linkage disequilibrium (LD) between markers, demonstrating that the potential value of an LD approach in elucidating the molecular basis of the quantitative variation in this species. An analysis of population structure revealed three subgroups in the association population. Subsequent single-marker association analysis identified 46 significant associations, involving the 11 traits with 37 SSRs. These loci explained a small proportion of the phenotypic variance, ranging from 2.68 to 23.97% (mean 5.50%). We also validated 15 of the 46 associations in a linkage mapping population of 159 individuals. Finally, five associations were further confirmed in the linkage mapping population, involving the four traits with four SSRs. These results can serve as a foundation for further analyses of the genetic architecture of floral traits, and the SSRs associated in this work have potential applications in marker-assisted breeding in tree peony.
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Affiliation(s)
- Jing Wu
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Fangyun Cheng
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China.
| | - Changfu Cai
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yuan Zhong
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xiao Jie
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
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Wang L, Wang B, Du Q, Chen J, Tian J, Yang X, Zhang D. Allelic variation in PtoPsbW associated with photosynthesis, growth, and wood properties in Populus tomentosa. Mol Genet Genomics 2016; 292:77-91. [PMID: 27722913 DOI: 10.1007/s00438-016-1257-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 10/03/2016] [Indexed: 02/06/2023]
Abstract
Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development. Analysis of nucleotide diversity and LD revealed that PtoPsbW has low single-nucleotide polymorphism (SNP) diversity (π tot = 0.0048 and θ w = 0.0050) and relatively low average value of LD (0.1500), indicating that PtoPsbW is conserved due to its indispensable function. Using single-SNP associations in an association population of 435 individuals, we identified five significant associations at the threshold of P ≤ 0.05, explaining 3.28-15.98 % of the phenotypic variation. Haplotype-based association analyses indicated that 13 haplotypes (P ≤ 0.05) from six blocks were associated with photosynthesis, growth, and wood properties. Our work shows that identifying allelic variation and LD can help to decipher the genetic basis of photosynthesis and could potentially be applied for molecular marker-assisted selection in Populus.
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Affiliation(s)
- Longxin Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 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, Beijing, 100083, China
| | - Bowen Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 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, Beijing, 100083, China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 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, Beijing, 100083, China
| | - Jinhui Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 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, Beijing, 100083, China
| | - Jiaxing Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 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, Beijing, 100083, China
| | - Xiaohui Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 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, Beijing, 100083, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 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, Beijing, 100083, China.
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Hess M, Wildhagen H, Junker LV, Ensminger I. Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat. BMC Genomics 2016; 17:682. [PMID: 27565139 PMCID: PMC5002200 DOI: 10.1186/s12864-016-3022-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 08/16/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two Douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). RESULTS Using linear mixed models we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80 % of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction. CONCLUSIONS The majority of the transcriptome responses in plant leaf tissue is driven by variations in environmental conditions. The small variation between individuals and populations suggests strong conservation of this response within Douglas-fir. Therefore we conclude that plastic transcriptome responses to variations in environmental conditions are only weakly affected by local adaptation in Douglas-fir.
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Affiliation(s)
- Moritz Hess
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Institute for Biology III, Faculty of Biology, Albert Ludwigs University Freiburg, Schänzlestrasse 1, D-79104 Freiburg i. Brsg., Germany
- Present Address: Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Obere Zahlbacher Strasse 69, 55131 Mainz, Germany
| | - Henning Wildhagen
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Present Address: Department of Forest Botany and Tree Physiology, Büsgen-Institute, Georg-August-University Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
| | - Laura Verena Junker
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6 Canada
| | - Ingo Ensminger
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6 Canada
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Hallingbäck HR, Fogelqvist J, Powers SJ, Turrion‐Gomez J, Rossiter R, Amey J, Martin T, Weih M, Gyllenstrand N, Karp A, Lagercrantz U, Hanley SJ, Berlin S, Rönnberg‐Wästljung A. Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology. GLOBAL CHANGE BIOLOGY. BIOENERGY 2016; 8:670-685. [PMID: 27547245 PMCID: PMC4973673 DOI: 10.1111/gcbb.12280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 04/14/2015] [Indexed: 05/06/2023]
Abstract
Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (G × E) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation (Radj2) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).
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Affiliation(s)
- Henrik R. Hallingbäck
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Johan Fogelqvist
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Stephen J. Powers
- Computational and Systems Biology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | | | - Rachel Rossiter
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Joanna Amey
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Tom Martin
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Martin Weih
- Department of Crop Production EcologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Niclas Gyllenstrand
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Angela Karp
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Ulf Lagercrantz
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala University752 36UppsalaSweden
| | - Steven J. Hanley
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Sofia Berlin
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Ann‐Christin Rönnberg‐Wästljung
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
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44
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Daru BH, Berger DK, van Wyk AE. Opportunities for unlocking the potential of genomics for African trees. THE NEW PHYTOLOGIST 2016; 210:772-778. [PMID: 26695092 DOI: 10.1111/nph.13826] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Barnabas H Daru
- Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
- Genomics Research Institute, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
| | - Dave K Berger
- Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
- Genomics Research Institute, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
| | - Abraham E van Wyk
- Department of Plant Science, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa
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45
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Nicolas SD, Péros JP, Lacombe T, Launay A, Le Paslier MC, Bérard A, Mangin B, Valière S, Martins F, Le Cunff L, Laucou V, Bacilieri R, Dereeper A, Chatelet P, This P, Doligez A. Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies. BMC PLANT BIOLOGY 2016; 16:74. [PMID: 27005772 PMCID: PMC4802926 DOI: 10.1186/s12870-016-0754-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND As for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies. RESULTS Starting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance). CONCLUSIONS Our association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment.
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Affiliation(s)
- Stéphane D. Nicolas
- />INRA, UMR AGAP, F-34060 Montpellier, France
- />GQE-Le Moulon, INRA - Univ. Paris-Sud - CNRS - AgroParisTech - Université Paris-Saclay, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | | | | | | | | | | | | | - Sophie Valière
- />INRA, Plateforme Génomique, F-31326 Castanet-Tolosan, France
| | - Frédéric Martins
- />INRA, Plateforme Génomique, F-31326 Castanet-Tolosan, France
- />INSERM, UMR1048, F-31432 Toulouse, France
| | | | | | | | - Alexis Dereeper
- />INRA, UMR AGAP, F-34060 Montpellier, France
- />IRD, UMR IPME, F-34394 Montpellier 5, France
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46
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Prunier J, Verta JP, MacKay JJ. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. THE NEW PHYTOLOGIST 2016; 209:44-62. [PMID: 26206592 DOI: 10.1111/nph.13565] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/14/2015] [Indexed: 05/21/2023]
Abstract
Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.
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Affiliation(s)
- Julien Prunier
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Jukka-Pekka Verta
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany
| | - John J MacKay
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
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47
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Aitken SN, Bemmels JB. Time to get moving: assisted gene flow of forest trees. Evol Appl 2016; 9:271-90. [PMID: 27087852 PMCID: PMC4780373 DOI: 10.1111/eva.12293] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/22/2015] [Indexed: 12/14/2022] Open
Abstract
Geographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a 'local is best' seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of clines. The maintenance of local adaptation despite high gene flow suggests selection for local adaptation to climate is strong. Concerns over maladaptation resulting from climate change have motivated many new genecological and population genomics studies; however, few jurisdictions have implemented assisted gene flow (AGF), the translocation of pre-adapted individuals to facilitate adaptation of planted forests to climate change. Here, we provide evidence that temperate tree species show clines along climatic gradients sufficiently similar for average patterns or climate models to guide AGF in the absence of species-specific knowledge. Composite provenancing of multiple seed sources can be used to increase diversity and buffer against future climate uncertainty. New knowledge will continue to refine and improve AGF as climates warm further.
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Affiliation(s)
- Sally N. Aitken
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Jordan B. Bemmels
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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48
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Prunier J, Tessier G, Bousquet J, MacKay J. From genotypes to phenotypes: expression levels of genes encompassing adaptive SNPs in black spruce. PLANT CELL REPORTS 2015; 34:2111-2125. [PMID: 26260097 DOI: 10.1007/s00299-015-1855-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/30/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
Measuring transcript levels for adaptive genes revealed polymorphisms having cis -effect upon gene expression levels related to phenotype variation in a black spruce natural population. Trees growing in temperate and boreal regions must acclimate to changes in climatic factors such as low winter temperatures to survive to seasonal variations. Common garden studies have shown that genetic variation in quantitative traits helps species to survive and adapt to environmental changes and local conditions. Twenty-four genes carrying SNPs were previously associated with genetic adaptation in black spruce (Picea mariana [Mill.] BSP). The objectives of this study were to investigate the potential role of these genes in regulation of winter acclimation and adaptation by studying their patterns of expression as a function of the physiological stage during the annual growth cycle, tissue type, and their SNP genotypic class. Considerable variability in gene expression was observed between different vegetative tissues or organs, and between physiological stages. The genes were expressed predominantly in tissues that could be linked more directly to winter acclimation and adaptation. The expression levels of several of the genes were significantly related to variation in tree height growth or budset timing and expression level variation related to SNP genotypic classes was observed in four of the genes. An interaction between genotypic classes and physiological stages was also observed for some genes, indicating genotypes with different reaction norms in terms of gene expression.
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Affiliation(s)
- Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada.
| | - Guillaume Tessier
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada
| | - John MacKay
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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49
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Bragg JG, Supple MA, Andrew RL, Borevitz JO. Genomic variation across landscapes: insights and applications. THE NEW PHYTOLOGIST 2015; 207:953-67. [PMID: 25904408 DOI: 10.1111/nph.13410] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 03/09/2015] [Indexed: 05/22/2023]
Abstract
The distribution of genomic variation across landscapes can provide insights into the complex interactions between the environment and the genome that influence the distribution of species, and mediate phenotypic adaptation to local conditions. High throughput sequencing technologies now offer unprecedented power to explore these interactions, allowing powerful inferences about historical processes of colonization, gene flow and divergence, as well as the identification of loci that mediate local adaptation. These 'landscape genomic' approaches have been validated in model species and are now being applied to nonmodel organisms, including foundation species that have substantial effects on ecosystem processes. Here we review the growing field of landscape genomics from a very broad perspective. In particular, we describe the inferential power that is gained by taking a genome-wide view of genetic variation, strategies for study design to best capture adaptive variation, and how to apply this information to practical challenges, such as restoration.
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Affiliation(s)
- Jason G Bragg
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Megan A Supple
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Rose L Andrew
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2350, Australia
| | - Justin O Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, ACT, 0200, Australia
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50
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Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R. A practical guide to environmental association analysis in landscape genomics. Mol Ecol 2015; 24:4348-70. [DOI: 10.1111/mec.13322] [Citation(s) in RCA: 441] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Christian Rellstab
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Andrew J. Eckert
- Department of Biology; Virginia Commonwealth University; Richmond VA 23284 USA
| | - Angela M. Hancock
- Faculty of Molecular Biology; Max F. Perutz Laboratories and University of Vienna; Oskar-Morgenstern-Platz 1 1090 Vienna Austria
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
- ETH Zürich; Institute of Integrative Biology; Universitätstrasse 16 8092 Zürich Switzerland
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