메뉴 건너뛰기




Volumn 9, Issue 11, 2014, Pages

Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOMASS; GENETIC SELECTION; GENETIC TRAIT; GENOMIC SELECTION; GERMPLASM; MORPHOLOGICAL TRAIT; NONHUMAN; PANICUM VIRGATUM; PHENOTYPE; PLANT BREEDING; PLANT GENOME; PREDICTION; ECOTYPE; GENETICS; GROWTH, DEVELOPMENT AND AGING; NEAR INFRARED SPECTROSCOPY; PANICUM; PLOIDY; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84911486846     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0112227     Document Type: Article
Times cited : (54)

References (48)
  • 3
    • 39449097316 scopus 로고    scopus 로고
    • Latitudinal and longitudinal adaptation of switchgrass populations
    • Casler M, Vogel K, Taliaferro C, Ehlke N, Berdahl J, et al. (2007) Latitudinal and longitudinal adaptation of switchgrass populations. Crop Sci 47: 2249-2260.
    • (2007) Crop Sci , vol.47 , pp. 2249-2260
    • Casler, M.1    Vogel, K.2    Taliaferro, C.3    Ehlke, N.4    Berdahl, J.5
  • 4
    • 0347028131 scopus 로고    scopus 로고
    • Latitudinal adaptation of switchgrass populations
    • Casler M, Vogel K, Taliaferro C, Wynia R (2004) Latitudinal adaptation of switchgrass populations. Crop Sci 44: 293-303.
    • (2004) Crop Sci , vol.44 , pp. 293-303
    • Casler, M.1    Vogel, K.2    Taliaferro, C.3    Wynia, R.4
  • 6
    • 0000329526 scopus 로고
    • An analysis of variation between upland and lowland switchgrass, Panicum virgatum L., in central Oklahoma
    • Porter CL Jr (1966) An analysis of variation between upland and lowland switchgrass, Panicum virgatum L., in central Oklahoma. Ecology: 980-992.
    • (1966) Ecology , pp. 980-992
    • Porter, C.L.1
  • 7
    • 80053642386 scopus 로고    scopus 로고
    • Natural hybrids and gene flow between upland and lowland switchgrass
    • Zhang Y, Zalapa J, Jakubowski AR, Price DL, Acharya A, et al. (2011) Natural hybrids and gene flow between upland and lowland switchgrass. Crop Sci 51: 2626-2641.
    • (2011) Crop Sci , vol.51 , pp. 2626-2641
    • Zhang, Y.1    Zalapa, J.2    Jakubowski, A.R.3    Price, D.L.4    Acharya, A.5
  • 8
    • 79960848474 scopus 로고    scopus 로고
    • Postglacial evolution of Panicum virgatum: Centers of diversity and gene pools revealed by SSR markers and cpDNA sequences
    • Zhang Y, Zalapa JE, Jakubowski AR, Price DL, Acharya A, et al. (2011) Postglacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences. Genetica 139: 933-948.
    • (2011) Genetica , vol.139 , pp. 933-948
    • Zhang, Y.1    Zalapa, J.E.2    Jakubowski, A.R.3    Price, D.L.4    Acharya, A.5
  • 9
    • 0036888597 scopus 로고    scopus 로고
    • Incompatibility systems in switchgrass
    • Martinez-Reyna J, Vogel K (2002) Incompatibility systems in switchgrass. Crop Sci 42: 1800-1805.
    • (2002) Crop Sci , vol.42 , pp. 1800-1805
    • Martinez-Reyna, J.1    Vogel, K.2
  • 13
    • 57149098849 scopus 로고    scopus 로고
    • Farm-scale production cost of switchgrass for biomass
    • Perrin R, Vogel K, Schmer M, Mitchell R (2008) Farm-scale production cost of switchgrass for biomass. Bioenerg Res 1: 91-97.
    • (2008) Bioenerg Res , vol.1 , pp. 91-97
    • Perrin, R.1    Vogel, K.2    Schmer, M.3    Mitchell, R.4
  • 14
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • Meuwissen T, Hayes B, Goddard M (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
    • (2001) Genetics , vol.157 , pp. 1819-1829
    • Meuwissen, T.1    Hayes, B.2    Goddard, M.3
  • 15
    • 84876390765 scopus 로고    scopus 로고
    • Whole-genome regression and prediction methods applied to plant and animal breeding
    • de los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MP (2013) Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics 193: 327-345.
    • (2013) Genetics , vol.193 , pp. 327-345
    • De Los Campos, G.1    Hickey, J.M.2    Pong-Wong, R.3    Daetwyler, H.D.4    Calus, M.P.5
  • 16
    • 33745885274 scopus 로고    scopus 로고
    • Strategy for applying genome-wide selection in dairy cattle
    • Schaeffer L (2006) Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet 123: 218-223.
    • (2006) J Anim Breed Genet , vol.123 , pp. 218-223
    • Schaeffer, L.1
  • 17
    • 59349098163 scopus 로고    scopus 로고
    • Invited review: Genomic selection in dairy cattle: Progress and challenges
    • Hayes B, Bowman P, Chamberlain A, Goddard M (2009) Invited review: Genomic selection in dairy cattle: Progress and challenges. J Dairy Sci 92: 433-443.
    • (2009) J Dairy Sci , vol.92 , pp. 433-443
    • Hayes, B.1    Bowman, P.2    Chamberlain, A.3    Goddard, M.4
  • 18
    • 58349092764 scopus 로고    scopus 로고
    • Invited Review: Reliability of genomic predictions for North American Holstein bulls
    • VanRaden P, Van Tassell C, Wiggans G, Sonstegard T, Schnabel R, et al. (2009) Invited Review: Reliability of genomic predictions for North American Holstein bulls. J Dairy Sci 92: 16-24.
    • (2009) J Dairy Sci , vol.92 , pp. 16-24
    • VanRaden, P.1    Van Tassell, C.2    Wiggans, G.3    Sonstegard, T.4    Schnabel, R.5
  • 19
    • 84863591750 scopus 로고    scopus 로고
    • Accuracy and training population design for genomic selection on quantitative traits in elite North American oats
    • Asoro FG, Newell MA, Beavis WD, Scott MP, Jannink JL (2011) Accuracy and training population design for genomic selection on quantitative traits in elite North American oats. Plant Gen 4: 132-144.
    • (2011) Plant Gen , vol.4 , pp. 132-144
    • Asoro, F.G.1    Newell, M.A.2    Beavis, W.D.3    Scott, M.P.4    Jannink, J.L.5
  • 20
    • 84861792509 scopus 로고    scopus 로고
    • Accuracy of genomic selection in European maize elite breeding populations
    • Zhao Y, Gowda M, Liu W, Würschum T, Maurer HP, et al. (2012) Accuracy of genomic selection in European maize elite breeding populations. Theor Appl Genet 124: 769-776.
    • (2012) Theor Appl Genet , vol.124 , pp. 769-776
    • Zhao, Y.1    Gowda, M.2    Liu, W.3    Würschum, T.4    Maurer, H.P.5
  • 21
    • 84856283792 scopus 로고    scopus 로고
    • Riedelsheimer C, Czedik-Eysenberg A, Grieder C, Lisec J, Technow F, et al. Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet 44 217-220 Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet 44: 217-220.
    • Riedelsheimer, C.1    Czedik-Eysenberg, A.2    Grieder, C.3    Lisec, J.4    Technow, F.5
  • 23
    • 78650127985 scopus 로고    scopus 로고
    • Plant breeding with genomic selection: Gain per unit time and cost
    • Heffner EL, Lorenz AJ, Jannink JL, Sorrells ME (2010) Plant breeding with genomic selection: gain per unit time and cost. Crop Sci 50: 1681-1690.
    • (2010) Crop Sci , vol.50 , pp. 1681-1690
    • Heffner, E.L.1    Lorenz, A.J.2    Jannink, J.L.3    Sorrells, M.E.4
  • 24
    • 84857384716 scopus 로고    scopus 로고
    • Genomic selection for growth and wood quality in Eucalyptus: Capturing the missing heritability and accelerating breeding for complex traits in forest trees
    • Resende MD, Resende MF, Sansaloni CP, Petroli CD, Missiaggia AA, et al. (2012) Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytol 194: 116-128.
    • (2012) New Phytol , vol.194 , pp. 116-128
    • Resende, M.D.1    Resende, M.F.2    Sansaloni, C.P.3    Petroli, C.D.4    Missiaggia, A.A.5
  • 25
    • 84859625578 scopus 로고    scopus 로고
    • Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.)
    • Resende MF, Muñoz P, Resende MD, Garrick DJ, Fernando RL, et al. (2012) Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.). Genetics 190: 1503-1510.
    • (2012) Genetics , vol.190 , pp. 1503-1510
    • Resende, M.F.1    Muñoz, P.2    Resende, M.D.3    Garrick, D.J.4    Fernando, R.L.5
  • 26
    • 84855802587 scopus 로고    scopus 로고
    • Accelerating the domestication of trees using genomic selection: Accuracy of prediction models across ages and environments
    • Resende M, Munoz P, Acosta J, Peter G, Davis J, et al. (2012) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytologist 193: 617-624.
    • (2012) New Phytologist , vol.193 , pp. 617-624
    • Resende, M.1    Munoz, P.2    Acosta, J.3    Peter, G.4    Davis, J.5
  • 27
    • 84873505245 scopus 로고    scopus 로고
    • 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, et al. (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 9: e1003215.
    • (2013) PLoS Genet , vol.9 , pp. e1003215
    • Lu, F.1    Lipka, A.E.2    Glaubitz, J.3    Elshire, R.4    Cherney, J.H.5
  • 28
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6: e19379.
    • (2011) Plos One , vol.6 , pp. e19379
    • Elshire, R.J.1    Glaubitz, J.C.2    Sun, Q.3    Poland, J.A.4    Kawamoto, K.5
  • 29
    • 84911500380 scopus 로고    scopus 로고
    • Panicum virgatum v1.1 DOE-JGI. Available
    • Joint Genome Institute (2014) Phytozome 10. Panicum virgatum v1.1 DOE-JGI. Available: http://phytozome.jgi.doe.gov.
    • (2014) Phytozome 10
    • Joint Genome Institute1
  • 31
    • 79953689015 scopus 로고    scopus 로고
    • Quantifying actual and theoretical ethanol yields for switchgrass strains using NIRS analyses
    • Vogel KP, Dien BS, Jung HG, Casler MD, Masterson SD, et al. (2011) Quantifying actual and theoretical ethanol yields for switchgrass strains using NIRS analyses. Bioenerg Res 4: 96-110.
    • (2011) Bioenerg Res , vol.4 , pp. 96-110
    • Vogel, K.P.1    Dien, B.S.2    Jung, H.G.3    Casler, M.D.4    Masterson, S.D.5
  • 33
    • 0003486628 scopus 로고    scopus 로고
    • Release 9.3. SAS Institute. Institute SAS: Sas Inst
    • SAS Institute (2012) The SAS system for Windows. Release 9.3. SAS Institute. Institute SAS: Sas Inst.
    • (2012) The SAS System for Windows
    • SAS Institute1
  • 35
    • 84872179115 scopus 로고    scopus 로고
    • Genetic Analysis of Visually Scored Orange Kernel Color in Maize
    • Chandler K, Lipka AE, Owens BF, Li H, Buckler ES, et al. (2013) Genetic Analysis of Visually Scored Orange Kernel Color in Maize. Crop Sci 53: 189-200.
    • (2013) Crop Sci , vol.53 , pp. 189-200
    • Chandler, K.1    Lipka, A.E.2    Owens, B.F.3    Li, H.4    Buckler, E.S.5
  • 37
    • 84859947989 scopus 로고    scopus 로고
    • The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population
    • Hung HY, Browne C, Guill K, Coles N, Eller M, et al. (2012) The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity (Edinb) 108: 490-499.
    • (2012) Heredity (edinb) , vol.108 , pp. 490-499
    • Hung, H.Y.1    Browne, C.2    Guill, K.3    Coles, N.4    Eller, M.5
  • 38
  • 39
    • 84883250752 scopus 로고    scopus 로고
    • Genome-wide association study and pathway-level analysis of tocochromanol levels in maize grain. G3: Genes, Genomes
    • Lipka AE, Gore MA, Magallanes-Lundback M, Mesberg A, Lin H, et al. (2013) Genome-wide association study and pathway-level analysis of tocochromanol levels in maize grain. G3: Genes, Genomes, Genet 3: 1287-1299.
    • (2013) Genet , vol.3 , pp. 1287-1299
    • Lipka, A.E.1    Gore, M.A.2    Magallanes-Lundback, M.3    Mesberg, A.4    Lin, H.5
  • 40
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase
    • Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629-644.
    • (2006) Am J Hum Genet , vol.78 , pp. 629-644
    • Scheet, P.1    Stephens, M.2
  • 41
    • 0001287271 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani R (1996) Regression shrinkage and selection via the lasso. J Roy Stat Soc B Met: 267-288.
    • (1996) J Roy Stat Soc B Met , pp. 267-288
    • Tibshirani, R.1
  • 42
    • 16244401458 scopus 로고    scopus 로고
    • Regularization and variable selection via the elastic net
    • Zou H, Hastie T (2005) Regularization and variable selection via the elastic net. J Roy Stat Soc B Met 67: 301-320.
    • (2005) J Roy Stat Soc B Met , vol.67 , pp. 301-320
    • Zou, H.1    Hastie, T.2
  • 43
    • 85136354327 scopus 로고    scopus 로고
    • Ridge regression and other kernels for genomic selection with R package rrBLUP
    • Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Gen 4: 250-255.
    • (2011) Plant Gen , vol.4 , pp. 250-255
    • Endelman, J.B.1
  • 44
    • 84894251702 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing. 45. Friedman J, Hastie T, Tibshirani R (2010) Regularization paths for generalized linear models via coordinate descent
    • Team RC (2012) R: A language and environment for statistical computing. 45. Friedman J, Hastie T, Tibshirani R (2010) Regularization paths for generalized linear models via coordinate descent. J Stat Softw 33: 1.
    • (2012) J Stat Softw , vol.33 , pp. 1
    • Team, R.C.1
  • 45
    • 82955176938 scopus 로고    scopus 로고
    • Genomic selection in plant breeding: A comparison of models
    • Heslot N, Yang HP, Sorrells ME, Jannink JL (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52: 146-160.
    • (2012) Crop Sci , vol.52 , pp. 146-160
    • Heslot, N.1    Yang, H.P.2    Sorrells, M.E.3    Jannink, J.L.4
  • 46
    • 84879743015 scopus 로고    scopus 로고
    • Priors in whole-genome regression: The Bayesian alphabet returns
    • Gianola D (2013) Priors in whole-genome regression: the Bayesian alphabet returns. Genetics 194: 573-596.
    • (2013) Genetics , vol.194 , pp. 573-596
    • Gianola, D.1
  • 47
    • 77951987956 scopus 로고    scopus 로고
    • Genomic selection in plant breeding: From theory to practice
    • Jannink J, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9.2 166-177.
    • (2010) Brief Funct Genomics 9.2 , pp. 166-177
    • Jannink, J.1    Lorenz, A.J.2    Iwata, H.3
  • 48
    • 79952661182 scopus 로고    scopus 로고
    • Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model
    • Wolc A, Stricker C, Arango J, Settar P, Fulton JE, et al. (2011) Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model. Genet Sel Evol 43.
    • (2011) Genet Sel Evol , pp. 43
    • Wolc, A.1    Stricker, C.2    Arango, J.3    Settar, P.4    Fulton, J.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.