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RADseq approaches and applications for forest tree genetics

RADseq approaches and applications for forest tree genetics As tree species vary extensively in genome size, complexity, and resource development, reduced representation methods have been increasingly employed for the generation of population genomic data. By allowing rapid marker discovery and genotyping for thousands of genomic regions in many individuals without requiring genomic resources, restriction site-associated DNA sequencing (RADseq) methods have dramatically improved our ability to bring population genomic perspectives to non-model trees. The rapid recent increase in studies of trees utilizing RADseq suggests that it is likely to become among the most common approaches for generating genome-wide data for a variety of applications. Here we provide a practical review of RADseq and its application to research areas of tree genetics. We briefly review RADseq laboratory methods and consider analytical approaches for assembly, variant calling, and bioinformatic processing. To guide considerations for study design, we use in silico analyses of eight available tree genomes to illustrate how expected marker number and density vary across laboratory approaches and genome sizes, and to consider the ability of RADseq designs to query coding regions. We review the empirical use of RADseq for different research objectives, considering its strengths and limitations. Many studies have used RADseq data to perform genome scans for selection, although limited marker density and linkage disequilibrium will often compromise its utility for such analyses. Regardless of this limitation, RADseq offers a powerful and inexpensive technique for generating genome-wide SNP data that can greatly contribute to research spanning phylogenetic and population genetic inference, linkage mapping, and quantitative genetic parameter estimation for tree genetics. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Tree Genetics & Genomes Springer Journals

RADseq approaches and applications for forest tree genetics

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Publisher
Springer Journals
Copyright
Copyright © 2018 by Springer-Verlag GmbH Germany, part of Springer Nature
Subject
Life Sciences; Forestry; Plant Genetics and Genomics; Plant Breeding/Biotechnology; Tree Biology; Biotechnology
ISSN
1614-2942
eISSN
1614-2950
DOI
10.1007/s11295-018-1251-3
Publisher site
See Article on Publisher Site

Abstract

As tree species vary extensively in genome size, complexity, and resource development, reduced representation methods have been increasingly employed for the generation of population genomic data. By allowing rapid marker discovery and genotyping for thousands of genomic regions in many individuals without requiring genomic resources, restriction site-associated DNA sequencing (RADseq) methods have dramatically improved our ability to bring population genomic perspectives to non-model trees. The rapid recent increase in studies of trees utilizing RADseq suggests that it is likely to become among the most common approaches for generating genome-wide data for a variety of applications. Here we provide a practical review of RADseq and its application to research areas of tree genetics. We briefly review RADseq laboratory methods and consider analytical approaches for assembly, variant calling, and bioinformatic processing. To guide considerations for study design, we use in silico analyses of eight available tree genomes to illustrate how expected marker number and density vary across laboratory approaches and genome sizes, and to consider the ability of RADseq designs to query coding regions. We review the empirical use of RADseq for different research objectives, considering its strengths and limitations. Many studies have used RADseq data to perform genome scans for selection, although limited marker density and linkage disequilibrium will often compromise its utility for such analyses. Regardless of this limitation, RADseq offers a powerful and inexpensive technique for generating genome-wide SNP data that can greatly contribute to research spanning phylogenetic and population genetic inference, linkage mapping, and quantitative genetic parameter estimation for tree genetics.

Journal

Tree Genetics & Genomes – Springer Journals

Published: May 21, 2018

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  • The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)
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  • Landscape genomic insights into the historic migration of mountain hemlock in response to Holocene climate change
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  • Seed dispersal at alpine treeline: an assessment of seed movement within the alpine treeline ecotone
    Johnson, JS; Gaddis, KD; Cairns, DM; Krutovsky, KV
  • Targeted capture in evolutionary and ecological genomics
    Jones, MR; Good, JM
  • Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq
    Karam, MJ; Lefévre, F; Dagher-Kharrat, MB; Pinosio, S; Vendramin, G
  • High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra
    Konar, A; Choudhury, O; Bullis, R; Fiedler, L; Kruser, JM; Stephens, MT; Gailing, O; Schlarbaum, S; Coggeshall, MV; Staton, ME; Carlson, JE; Emrich, S; Romero-Severson, J
  • ANGSD: analysis of next generation sequencing data
    Korneliussen, TS; Albrechtsen, A; Nielsen, R
  • Genomic selection for fruit quality traits in apple (Malus x domestica Borkh.)
    Kumar, S; Chagné, D; Bink, MCAM; Volz, RK; Whitworth, C; Carlisle, C
  • RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic eels
    Laporte, M; Pavey, SA; Rougeux, C; Pierron, F; Lauzent, M; Budzinski, H; Labadie, P; Geneste, E; Couture, P; Baudrimont, M; Bernatchez, L
  • Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)
    Larson, WA; Seeb, LW; Everett, MV; Waples, RK; Templin, WD; Seeb, JE
  • The utility of single nucleotide polymorphism (SNP) data in phylogenetics
    Leaché, AD; Oaks, JR
  • SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches
    Lepais, O; Weir, JT
  • Fast and accurate short read alignment with burrows-wheeler transform
    Li, H; Durbin, R
  • The sequence alignment/map format and SAMtools
    Li, H; Handsaker, B; Wysoker, A; Fennell, T; Ruan, J; Homer, N; Marth, G; Abecasis, G; Durbin, R
  • Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA
    Lind, BM; Friedline, CJ; Wegrzyn, JL; Maloney, PE; Vogler, DR; Neale, DB; Eckert, AJ
  • Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species
    Lindtke, D; Gompert, Z; Lexer, C; Buerkle, CA
  • Epigenetic regulation of transposable elements in plants
    Lisch, D
  • How important are transposons for plant evolution?
    Lisch, D
  • Phylogeny of Morella rubra and its relatives (Myricaceae) and genetic resources of Chinese bayberry using RAD sequencing
    Liu, L; Jin, X; Chen, N; Li, X; Li, P; Fu, C
  • Estimating phylogenetic trees from genome-scale data
    Liu, L; Xi, Z; Wu, S; Davis, CC; Edwards, SV
  • Construction of a SNP-based genetic linkage map for kiwifruit using next-generation restriction-site-associated DNA sequencing (RADseq)
    Liu, CY; Li, DW; Zhou, JH; Zhang, Q; Tian, H; Yao, XH
  • Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation
    Lowry, DB; Hoban, S; Kelley, JL; Lotterhos, KE; Reed, LK; Antolin, MF; Storfer, A
  • Responsible RAD: striving for best practices in population genomic studies of adaptation
    Lowry, DB; Hoban, S; Kelley, JL; Lotterhos, KE; Reed, LK; Antolin, MF; Storfer, A
  • Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol
    Lu, F; Lipka, AE; Glaubitz, J; Elshire, R; Cherney, JH; Casler, MD; Buckler, ES; Costich, DE
  • Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.)
    Lu, M; Krutovsky, KV; Nelson, CD; Koralewski, TE; Byram, TD; Loopstra, CA
  • Highly variable reproductive isolation among pairs of Catostomus species
    Mandeville, EG; Parchman, TL; McDonald, DB; Buerkle, CA
  • The first high-density sequence characterized SNP-based linkage map of olive (Olea europaea L. subsp. europaea) developed using genotyping by sequencing
    Marchese, A
  • Next-generation sequencing platforms
    Mardis, ER
  • Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case study in Carex sect. Racemosae
    Massatti, R; Reznicek, AA; Knowles, LL
  • Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
    Mastretta-Yanes, A; Arrigo, N; Alvarez, N; Jorgensen, T; Piñero, D; Emerson, B
  • Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations
    McGee, MD; Neches, RY; Seehausen, O
  • The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    McKenna, A; Hanna, M; Banks, E; Sivachenko, A; Cibulskis, K; Kernytsky, A; Garimella, K; Altshuler, D; Gabriel, S; Daly, M; DePristo, MA
  • RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on breaking RAD by Lowry et al. (2016)
    McKinney, GJ; Larson, WA; Seeb, LW; Seeb, JE
  • Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa
    McKown, AD; Guy, RD; Klápště, J; Geraldes, A; Friedmann, M; Cronk, QC; El-Kassaby, YA; Mansfield, SD; Douglas, CJ
  • A genetic legacy of introgression confounds phylogeny and biogeography in oaks
    McVay, JD; Hipp, AL; Manos, PS
  • Adaptation in plant genomes: bigger is different
    Mei, W; Stetter, MG; Gates, DJ; Stitzer, MC; Ross-Ibarra, J
  • GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data
    Melo, AT; Bartaula, R; Hale, I
  • Genomic selection: a paradigm shift in animal breeding
    Meuwissen, T; Hayes, B; Goddard, M
  • Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
    Miller, MR; Dunham, JP; Amores, A; Cresko, WA; Johnson, EA
  • ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments
    Mora-Márquez, F; García-Olivares, V; Emerson, B; López de Heredia, U
  • Geographic variation in forest trees: genetic basis and application of knowledge in silviculture
    Morgenstern, EK
  • Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)
    Mori, K; Shirasawa, K; Nogata, H; Hirata, C; Tashiro, K; Habu, T; Kim, S; Himeno, S; Kuhara, S; Ikegami, H
  • Multiplexed-shotgun-genotyping data resolve phylogeny within a very recently derived insular lineage
    Mort, ME; Crawford, DJ; Kelly, JK; Santos-Guerra, A; Sequeira, MM; Moura, M; Caujapé-Castells, J
  • De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies
    Mousavi, M; Tong, C; Liu, F; Tao, S; Wu, J; Li, H; Shi, J
  • The genome of Eucalyptus grandis
    Myburg, AA; Grattapaglia, D; Tuskan, GA; Hellsten, U; Hayes, RD; Grimwood, J; Jenkins, J; Lindquist, E; Tice, H; Bauer, D; Goodstein, DM; Dubchak, I; Poliakov, A; Mizrachi, E; Kullan, ARK; Hussey, SG; Pinard, D; van der Merwe, K; Singh, P; van Jaarsveld, I; Silva-Junior, OB; Togawa, RC; Pappas, MR; Faria, DA; Sansaloni, CP; Petroli, CD; Yang, X; Ranjan, P; Tschaplinski, TJ; Ye, CY; Li, T; Sterck, L; Vanneste, K; Murat, F; Soler, M; Clemente, HS; Saidi, N; Cassan-Wang, H; Dunand, C; Hefer, CA; Bornberg-Bauer, E; Kersting, AR; Vining, K; Amarasinghe, V; Ranik, M; Naithani, S; Elser, J; Boyd, AE; Liston, A; Spatafora, JW; Dharmwardhana, P; Raja, R; Sullivan, C; Romanel, E; Alves-Ferreira, M; Külheim, C; Foley, W; Carocha, V; Paiva, J; Kudrna, D; Brommonschenkel, SH; Pasquali, G; Byrne, M; Rigault, P; Tibbits, J; Spokevicius, A; Jones, RC; Steane, DA; Vaillancourt, RE; Potts, BM; Joubert, F; Barry, K; Pappas, GJ; Strauss, SH; Jaiswal, P; Grima-Pettenati, J; Salse, J; van de Peer, Y; Rokhsar, DS; Schmutz, J
  • Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
    Nadeau, NJ; Ruiz, M; Salazar, P; Counterman, B; Medina, JA; Ortiz-Zuazaga, H; Morrison, A; McMillan, WO; Jiggins, CD; Papa, R
  • Phylogenetic relationships of Aurantioideae (Rutaceae) based on RAD-Seq
    Nagano, Y; Mimura, T; Kotoda, N; Matsumoto, R; Nagano, AJ; Honjo, MN; Kudoh, H; Yamamoto, M
  • Genotyping-by-sequencing in ecological and conservation genomics
    Narum, SR; Buerkle, CA; Davey, JW; Miller, MR; Hohenlohe, PA
  • Population, quantitative and comparative genomics of adaptation in forest trees
    Neale, DB; Ingvarsson, PK
  • Forest tree genomics: growing resources and applications
    Neale, DB; Kremer, A
  • Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
    Neale, DB; Wegrzyn, JL; Stevens, KA; Zimin, AV; Puiu, D; Crepeau, MW; Cardeno, C; Koriabine, M; Holtz-Morris, AE; Liechty, JD; Martínez-García, PJ; Vasquez-Gross, HA; Lin, BY; Zieve, JJ; Dougherty, WM; Fuentes-Soriano, S; Wu, LS; Gilbert, D; Marçais, G; Roberts, M; Holt, C; Yandell, M; Davis, JM; Smith, KE; Dean, JFD; Lorenz, W; Whetten, RW; Sederoff, R; Wheeler, N; McGuire, PE; Main, D; Loopstra, CA; Mockaitis, K; deJong, PJ; Yorke, JA; Salzberg, SL; Langley, CH
  • The Douglas-fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae
    Neale, DB; McGuire, PE; Wheeler, NC; Stevens, KA; Crepeau, MW; Cardeno, C; Zimin, AV; Puiu, D; Pertea, GM; Sezen, UU
  • Hybrid speciation and independent evolution in lineages of alpine butterflies
    Nice, CC; Gompert, Z; Fordyce, JA; Forister, ML; Lucas, LK; Buerkle, CA
  • Genotype and SNP calling from next-generation sequencing data
    Nielsen, R; Paul, JS; Albrechtsen, A; Song, YS
  • SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
    Nielsen, R; Korneliussen, T; Albrechtsen, A; Li, Y; Wang, J
  • The Norway spruce genome sequence and conifer genome evolution
    Nystedt, B; Street, NR; Wetterbom, A; Zuccolo, A; Lin, Y; Scofield, DG; Vezzi, F; Delhomme, N; Giacomello, S; Alexeyenko, A
  • Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories
    O’Loughlin, SM; Magesa, S; Mbogo, C; Mosha, F; Midega, J; Lomas, S; Burt, A
  • Genotyping by sequencing reveals the interspecific C. maxima/C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits
    Oueslati, A; Slhi-Hannachi, A; Luro, F; Vignes, H; Mournet, P; Ollitrault, P
  • Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing
    Pais, AL; Whetten, RW; Xiang, QYJ
  • Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers
    Pan, J; Wang, B; Pei, ZY; Zhao, W; Gao, J; Mao, JF; Wang, XR
  • Genome-wide association genetics of an adaptive trait in lodgepole pine
    Parchman, TL; Gompert, Z; Mudge, J; Schilkey, FD; Benkman, CW; Buerkle, C
  • Lost in parameter space: a road map for stacks
    Paris, JR; Stevens, JR; Catchen, JM
  • Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot
    Paun, O; Turner, B; Trucchi, E; Munzinger, J; Chase, MW; Samuel, R
  • Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners
    Pavy, N; Gagnon, F; Rigault, P; Blais, S; Deschênes, A; Boyle, B; Pelgas, B; Deslauriers, M; Clément, S; Lavigne, P; Lamothe, M; Cooke, JEK; Jaramillo-Correa, JP; Beaulieu, J; Isabel, N; Mackay, J; Bousquet, J
  • Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species
    Peterson, BK; Weber, JN; Kay, EH; Fisher, HS; Hoekstra, HE
  • Some evolutionary consequences of being a tree
    Petit, RJ; Hampe, A
  • A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny
    Pham, KK; Hipp, AL; Manos, PS; Cronn, RC
  • First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill
    Pinosio, S; González-Martínez, S; Bagnoli, F; Cattonaro, F; Grivet, D; Marroni, F; Lorenzo, Z; Pausas, J; Verdú, M; Vendramin, G
  • High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)
    Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, JM; Grivet, D; de Miguel, M; de María, N; Cervera, MT; Bagnoli, F; Isik, F; Vendramin, GG; González-Martínez, SC
  • Genotyping-by-sequencing for plant breeding and genetics
    Poland, JA; Rife, TW
  • Population genetic inference from genomic sequence variation
    Pool, JE; Hellmann, I; Jensen, JD; Nielsen, R
  • Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)
    Pootakham, W; Jomchai, N; Ruang-areerate, P; Shearman, JR; Sonthirod, C; Sangsrakru, D; Tragoonrung, S; Tangphatsornruang, S
  • Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)
    Pootakham, W; Ruang-Areerate, P; Jomchai, N; Sonthirod, C; Sangsrakru, D; Yoocha, T; Theerawattanasuk, K; Nirapathpongporn, K; Romruensukharom, P; Tragoonrung, S
  • Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms
    Porth, I; Klapšte, J; Skyba, O; Hannemann, J; McKown, AD; Guy, RD; DiFazio, SP; Muchero, W; Ranjan, P; Tuskan, GA
  • The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation
    Pritchard, JK; Pickrell, JK; Coop, G
  • dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
    Puritz, JB; Hollenbeck, CM; Gold, JR
  • Demystifying the RAD fad
    Puritz, JB; Matz, MV; Toonen, RJ; Weber, JN; Bolnick, DI; Bird, CE
  • Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations
    Pyhäjärvi, T; Garcia-Gil, MR; Knürr, T; Mikkonen, M; Wachowiak, W; Savolainen, O
  • Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris
    Pyhäjärvi, T; Kujala, ST; Savolainen, O
  • Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.)
    Quesada, T; Gopal, V; Cumbie, WP; Eckert, AJ; Wegrzyn, JL; Neale, DB; Goldfarb, B; Huber, DA; Casella, G; Davis, JM
  • A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods
    Ratcliffe, B; El-Dien, OG; Klápště, J; Porth, I; Chen, C; Jaquish, B; El-Kassaby, Y
  • Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees
    Resende, MDV; Resende, MFR; Sansaloni, CP; Petroli, CD; Missiaggia, AA; Aguiar, AM; Abad, JM; Takahashi, EK; Rosado, AM; Faria, DA
  • Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments
    Resende, MFR; Muñoz, P; Acosta, JJ; Peter, G; Davis, JM; Grattapaglia, D; Resende, MDV; Kirst, M
  • Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.)
    Resende, MFR; Muñoz, P; Resende, MDV; Garrick, DJ; Fernando, RL; Davis, JM; Jokela, EJ; Martin, TA; Peter, GF; Kirst, M
  • A marker-based method for inferences about quantitative inheritance in natural populations
    Ritland, K
  • Marker-inferred relatedness as a tool for detecting heritability in nature
    Ritland, K
  • Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
    Robinson, MR; Santure, AW; DeCauwer, I; Sheldon, BC; Slate, J
  • Sampling strategies for frequency spectrum-based population genomic inference
    Robinson, JD; Coffman, AJ; Hickerson, MJ; Gutenkunst, RN
  • Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection
    Rodríguez-Ezpeleta, N; Bradbury, IR; Mendibil, I; Álvarez, P; Cotano, U; Irigoien, X
  • Genome divergence during evolutionary diversification as revealed in replicate lake–stream stickleback population pairs
    Roesti, M; Hendry, AP; Salzburger, W; Berner, D
  • Inferring phylogenies from RAD sequence data
    Rubin, BE; Ree, RH; Moreau, CS
  • A role for migration-linked genes and genomic islands in divergence of a songbird
    Ruegg, K; Anderson, EC; Boone, J; Pouls, J; Smith, TB
  • High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species
    Sakaguchi, S; Sugino, T; Yoshihiko, T; Ito, M; Crisp, MD; Bowman, DMJS; Nagano, AJ; Honjo, MN; Yasugi, M; Kudoh, H
  • Gene flow and local adaptation in trees
    Savolainen, O; Pyhäjärvi, T; Knürr, T
  • Ecological genomics of local adaptation
    Savolainen, O; Lascoux, M; Merilä, J
  • A RAD-based linkage map of kiwifruit (Actinidia chinensis Pl.) as a tool to improve the genome assembly and to scan the genomic region of the gender determinant for the marker-assisted breeding
    Scaglione, D; Fornasiero, A; Pinto, C; Cattonaro, F; Spadotto, A; Infante, R; Meneses, C; Messina, R; Lain, O; Cipriani, G
  • Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus
    Shafer, ABA; Gattepaille, LM; Stewart, REA; Wolf, JBW
  • Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
    Shafer, A; Peart, CR; Tusso, S; Maayan, I; Brelsford, A; Wheat, CW; Wolf, JB
  • Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis
    Silva-Junior, OB; Grattapaglia, D
  • A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species
    Silva-Junior, OB; Faria, DA; Grattapaglia, D
  • Estimating individual admixture proportions from next generation sequencing data
    Skotte, L; Korneliussen, TS; Albrechtsen, A
  • Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa
    Slavov, GT; DiFazio, SP; Martin, J; Schackwitz, W; Muchero, W; Rodgers-Melnick, E; Lipphardt, MF; Pennacchio, CP; Hellsten, U; Pennacchio, LA
  • Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis
    Slavov, GT; Nipper, R; Robson, P; Farrar, K; Allison, GG; Bosch, M; Clifton-Brown, JC; Donnison, IS; Jensen, E
  • Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate
    Sork, V; Aitken, S; Dyer, R; Eckert, A; Legendre, P; Neale, D
  • First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae)
    Sork, VL; Fitz-Gibbon, ST; Puiu, D; Crepeau, M; Gugger, PF; Sherman, R; Stevens, K; Langley, CH; Pellegrini, M; Salzberg, SL
  • AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data
    Sovic, MG; Fries, AC; Gibbs, HL
  • RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    Stamatakis, A
  • The loci of evolution: how predictable is genetic evolution?
    Stern, DL; Orgogozo, V
  • Sequence of the sugar pine megagenome
    Stevens, KA; Wegrzyn, JL; Zimin, A; Puiu, D; Crepeau, M; Cardeno, C; Paul, R; Gonzalez-Ibeas, D; Koriabine, M; Holtz-Morris, AE; Martínez-García, PJ; Sezen, UU; Marçais, G; Jermstad, K; McGuire, PE; Loopstra, CA; Davis, JM; Eckert, A; de Jong, P; Yorke, JA; Salzberg, SL; Neale, DB; Langley, CH
  • Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species
    Stölting, KN; Nipper, R; Lindtke, D; Caseys, C; Waeber, S; Castiglione, S; Lexer, C
  • Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae)
    Sun, Y; Surget-Groba, Y; Gao, S
  • The use of marker-based relationship information to estimate the heritability of body weight in a natural population: a cautionary tale
    Thomas, SC; Coltman, DW; Pemberton, JM
  • Advances and limits of using population genetics to understand local adaptation
    Tiffin, P; Ross-Ibarra, J
  • Construction of high-density linkage maps of Populus deltoides × P. simonii using restriction-site associated DNA sequencing
    Tong, C; Li, H; Wang, Y; Li, X; Ou, J; Wang, D; Xu, H; Ma, C; Lang, X; Liu, G
  • Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
    Torkamaneh, D; Laroche, J; Bastien, M; Abed, A; Belzile, F
  • The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    Tuskan, GA; DiFazio, S; Jansson, S; Bohlmann, J; Grigoriev, I; Hellsten, U; Putnam, N; Ralph, S; Rombauts, S; Salamov, A; Schein, J; Sterck, L; Aerts, A; Bhalerao, RR; Bhalerao, RP; Blaudez, D; Boerjan, W; Brun, A; Brunner, A; Busov, V; Campbell, M; Carlson, J; Chalot, M; Chapman, J; Chen, GL; Cooper, D; Coutinho, PM; Couturier, J; Covert, S; Cronk, Q; Cunningham, R; Davis, J; Degroeve, S; Dejardin, A; dePamphilis, C; Detter, J; Dirks, B; Dubchak, I; Duplessis, S; Ehlting, J; Ellis, B; Gendler, K; Goodstein, D; Gribskov, M; Grimwood, J; Groover, A; Gunter, L; Hamberger, B; Heinze, B; Helariutta, Y; Henrissat, B; Holligan, D; Holt, R; Huang, W; Islam-Faridi, N; Jones, S; Jones-Rhoades, M; Jorgensen, R; Joshi, C; Kangasjarvi, J; Karlsson, J; Kelleher, C; Kirkpatrick, R; Kirst, M; Kohler, A; Kalluri, U; Larimer, F; Leebens-Mack, J; Leple, JC; Locascio, P; Lou, Y; Lucas, S; Martin, F; Montanini, B; Napoli, C; Nelson, DR; Nelson, C; Nieminen, K; Nilsson, O; Pereda, V; Peter, G; Philippe, R; Pilate, G; Poliakov, A; Razumovskaya, J; Richardson, P; Rinaldi, C; Ritland, K; Rouze, P; Ryaboy, D; Schmutz, J; Schrader, J; Segerman, B; Shin, H; Siddiqui, A; Sterky, F; Terry, A; Tsai, CJ; Uberbacher, E; Unneberg, P; Vahala, J; Wall, K; Wessler, S; Yang, G; Yin, T; Douglas, C; Marra, M; Sandberg, G; van de Peer, Y; Rokhsar, D
  • The genome of the domesticated apple (Malus domestica Borkh.)
    Velasco, R; Zharkikh, A; Affourtit, J; Dhingra, A; Cestaro, A; Kalyanaraman, A; Fontana, P; Bhatnagar, SK; Troggio, M; Pruss, D; Salvi, S; Pindo, M; Baldi, P; Castelletti, S; Cavaiuolo, M; Coppola, G; Costa, F; Cova, V; Dal Ri, A; Goremykin, V; Komjanc, M; Longhi, S; Magnago, P; Malacarne, G; Malnoy, M; Micheletti, D; Moretto, M; Perazzolli, M; Si-Ammour, A; Vezzulli, S; Zini, E; Eldredge, G; Fitzgerald, LM; Gutin, N; Lanchbury, J; Macalma, T; Mitchell, JT; Reid, J; Wardell, B; Kodira, C; Chen, Z; Desany, B; Niazi, F; Palmer, M; Koepke, T; Jiwan, D; Schaeffer, S; Krishnan, V; Wu, C; Chu, VT; King, ST; Vick, J; Tao, Q; Mraz, A; Stormo, A; Stormo, K; Bogden, R; Ederle, D; Stella, A; Vecchietti, A; Kater, MM; Masiero, S; Lasserre, P; Lespinasse, Y; Allan, AC; Bus, V; Chagné, D; Crowhurst, RN; Gleave, AP; Lavezzo, E; Fawcett, JA; Proost, S; Rouzé, P; Sterck, L; Toppo, S; Lazzari, B; Hellens, RP; Durel, CE; Gutin, A; Bumgarner, RE; Gardiner, SE; Skolnick, M; Egholm, M; van de Peer, Y; Salamini, F; Viola, R
  • The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
    Verde, I; Abbott, AG; Scalabrin, S; Jung, S; Shu, S; Marroni, F; Zhebentyayeva, T; Dettori, MT; Grimwood, J; Cattonaro, F
  • Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
    Verdu, CF; Guichoux, E; Quevauvillers, S; Thier, O; Laizet, Y; Delcamp, A; Gévaudant, F; Monty, A; Porté, AJ; Lejeune, P
  • Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation
    Vieira, FG; Fumagalli, M; Albrechtsen, A; Nielsen, R
  • Heritability in the genomics era—concepts and misconceptions
    Visscher, PM; Hill, WG; Wray, NR
  • Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
    Wagner, CE; Keller, I; Wittwer, S; Selz, OM; Mwaiko, S; Greuter, L; Sivasundar, A; Seehausen, O
  • Pedigrees or markers: which are better in estimating relatedness and inbreeding coefficient?
    Wang, J
  • Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers
    Wang, N; Thomson, M; Bodles, WJ; Crawford, RM; Hunt, HV; Featherstone, AW; Pellicer, J; Buggs, RJ
  • Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species
    Wang, J; Street, NR; Scofield, DG; Ingvarsson, PK
  • Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation
    Wegrzyn, JL; Liechty, JD; Stevens, KA; Wu, LS; Loopstra, CA; Vasquez-Gross, HA; Dougherty, WM; Lin, BY; Zieve, JJ; Martínez-García, PJ
  • Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)
    Yeaman, S; Hodgins, KA; Suren, H; Nurkowski, KA; Rieseberg, LH; Holliday, JA; Aitken, SN
  • Convergent local adaptation to climate in distantly related conifers
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