PUBLICATIONS

2019

  • de Almeida Filho, J.E., Guimarães, J.F.R., Fonsceca, E.S.F., Vilela de Resende, M.D., Muñoz, P., Kirst, M., de Resende Júnior, M.F.R. (2019) Genomic prediction of additive and non-additive effects using genetic markers and pedigrees. G3 9:2739-2748.

  • de Bem Oliveira, I., Resende, M.F.R.Jr., Ferrão, L.F.V., Amadeu, R.R., Endelman, J.B., Kirst, M., Coelho, A.S.G., Munoz, P.R. (2019) Genomic prediction of autotetraploids: influence of relationship matrices, allele dosage, and continuous genotyping calls in phenotype prediction. G3 9:1189-1198.

  • Acosta, J.J., Fahrenkrog, A.M., Neves, L.G., Resende, M.F.R., Dervinis, C., Davis, J.M., Holliday, J.A., Kirst, M. (2019) Exome resequencing reveals evolutionary history, genomic diversity, and targets of selection in the conifers Pinus taeda and Pinus elliottii. Genome Biol Evol. 11:508-520.

2018

  • Müller, B.S.F., J.E. de Almeida Filho, B.M. de Lima, C.C. Garcia, A. Missiaggia, A.M. Aguiar, E. Takahashi, M. Kirst, S.A. Gezan, O.B. Silva-Junior, L.G. Neves and D. Grattapaglia. (2018) Independent and Joint-GWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations. New Phytologist [Epub ahead of print]

  • Inostroza, L., M. Bhakta, H. Acuña, C. Vásquez, J. Ibáñez, J. Tapia, M. Wenbin, M. Kirst, M. Resende Jr. and P. Munoz. (2018) Understanding the complexity of cold tolerance in white clover using temperature gradient locations and a GWAS approach. The Plant Genome 11: NNN.

  • Ferrão, L.F.V., J. Benevenuto, I.D.B. Oliveira, C. Cellon, J. Olmstead, M. Kirst, M.F.R. Resende Jr. and P. Munoz. (2018) Insights into the genetic basis of blueberry fruit-related traits using diploid and polyploid models in a GWAS context. Frontiers in Ecology and Evolution 6:107.

  • de Moraes, B.F.X., R.F. dos Santos, B.M. de Lima, A.M. Aguiar, A.A. Missiaggia, D. da Costa Dias, G.D.P.S. Rezende, F.M.A. Goncalves, J.J. Acosta, M. Kirst, M.F.R. Resende Jr. and P.R. Munoz. (2018) Genomics selection prediction models comparing sequence capture and SNP array genotyping methods. Molecular Breeding 38:115.

  • Mukrimin, M., A. Kovalchuk, L.G. Neves, E.H.A. Jaber, M. Haapanen, M. Kirst and F.O. Asiegbu. (2018) Genome-wide exon-capture approach identifies genetic variants of Norway spruce genes associated with susceptibility to Heterobasidion parviporum infection. Frontiers in Plant Sciences 9:793.

  • Hodel, R.G., L.M. Chandler, A.M. Fahrenkrog, M. Kirst, M.A. Gitzendanner, D.E. Soltis and P.S. Soltis. (2018) Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella. Current Opinion in Plant Biology 42:81-89.

2017

  • Fahrenkrog, A.M., L.G. Neves, M.F.R. Resende Jr., C. Dervinis, R. Davenport, W.B. Barbazuk and M. Kirst. (2017) Population genomics of the eastern cottonwood (Populus deltoides). Ecololgy and Evolution 7:9426-9440.

  • Conde, D., A. Moreno-Cortes, C. Dervinis, J.M. Ramos-Sánchez, M. Kirst, M. Perales, P. Gonzalez-Melendi and I. Allona. (2017) Overexpression of DEMETER, a DNA methylase, promotes early apical bud maturation in poplar. Plant Cell and Environment. 40:2806-2819.

  • Conde, D., A.L. Le Gac, M. Perales, C. Dervinis, M. Kirst, S. Maury, P. Gonzales-Melendi and I. Allona. (2017) Chilling-responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break. Plant Cell Environment 40:2236-2249.

  • Muller, B.S.F., L.G. Neves, J.E. de Almeida Filho, M.F.R. Resende Jr., P.R. Munoz, P.E.T. dos Santos, E.P. Filho, M. Kirst and D. Grattapaglia. (2017) Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. BMC Genomics 18:524.

  • Tieman, D., G. Zhu, M.F. Resende Jr., T. Lin, C. Nguyen, D. Bies, J.L. Rambla, K.S. Beltran, M. Taylor, B. Zhang, H. Ikeda, Z. Liu, J. Fisher, I. Zemach, A. Monforte, D. Zamir, A. Granell, M. Kirst, S. Huang and H. Klee. (2017) A chemical genetic roadmap to improved tomato flavor. Science 355:391-394.

 

2016

  • Fahrenkrog, A.M., L.G. Neves, M.F. Resende Jr., A. I. Vazquez, G. de Los Campos, C. Dervinis, R. Sykes, M. Davis, R. Davenport, W.B. Barbazuk and M. Kirst. (2017) Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides. New Phytologist 213:799-811.

  • Vazquez, A.I., Y. Veturi, M. Behring, S. Shrestha, M. Kirst, M.F. Resende Jr. and G. de los Campos. (2016) Increased proportion of variance explained and prediction accuracy of survival of breast cancer patients with use of whole-genome multiomic profiles. Genetics 203:1425-38

  • de Almeida Filhog, J.E., J.F. Guimarães, F.F.E. Silva, M.D. de Resende, P. Muñozg, M. Kirstg and M.F. Resendeg Jr. (2016) The contribution of dominance to phenotype prediction in a pine breeding and simulated population. Heredity 117:33-41.

  • Ramos, S.L., G. Dequigiovanni, A.M. Sebbenn, M.T. Lopes, P.Y. Kageyama, J.L. de Macêdo, M. Kirst and E.A. Veasey. (2016) Spatial genetic structure, genetic diversity and pollen dispersal in a harvested population of Astrocaryum aculeatum in the Brazilian Amazon. BMC Genetics 17:63.

  • Ribeiro, C.L., C.M. Silva, D.R. Drost, E. Novaes, C.R. Novaes, C. Dervinis and M. Kirst. (2016) Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus. BMC Plant Biology 16:66.

  • Goncalves, E.C., A.C. Wilkie, M. Kirst and B. Rathinasabapathi. (2016) Metabolic regulation of  triacylglycerol accumulation in the green algae: identification of potential targets for engineering to improve oil yield. Plant Biotechnol Journal 14:1649-60.

 

2015

  • Drost, D.R., S. Puranik, E. Novaes, C.R. Novaes, C. Dervinis, O. Gailing and M. Kirst. (2015) Genetical genomics of Populus leaf shape variation. BMC Plant Biology 15:166.

  • Muñoz, P.R., M.F. Resende Jr., S.A. Gezan, M.D. Resende, G. de Los Campos, M. Kirst, D. Huber and G.F. Peter. (2015) Unraveling additive from nonadditive effects using genomic relationship matrices. Genetics 198:1759-1768.

  • Westbrook, J.W., A.R. Walker, L.G. Neves, P. Munoz, M.F. Resende Jr., D.B. Neale, J.L. Wegrzyn, D.A. Huber, M. Kirst, J.M. Davis and G.F. Peter. (2015) Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis  across environments, ages, and populations. New Phytologist 205:627-641.

  • Westbrook, J.W., V.E. Chhatre, L.S. Wu, S. Chamala, L.G. Neves, P. Muñoz, P.J. Martínez-García, D.B. Neale, M. Kirst, K. Mockaitis, C.D. Nelson, G.F. Peter, J.M. Davis and C.S. Echt. (2015) A consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype-phenotype discovery populations of Pinus taeda. G3 5:1685-1694.

 

2014

  • Munoz, P.R., M.F.Jr. Resende, D.A. Huber, T. Quesada, M.D.V. Resende, D.B. Neale, J.L. Wegrzyn, M. Kirst and G.F. Peter. (2014) Genomic relationship matrix for correcting pedigree errors in breeding populations: impact on genetic parameters and genomic selection accuracy. Crop Sciences 54:1115-1123.

  • Nevesg, L.G., J.M. Davis, W.B. Barbazuk and M. Kirst. (2014) A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping. Genes, Genomes, Genetics 10:29-37.

  • Quesada, T., M.F. Resende Jr., P. Muñoz, J.L. Wegrzyn, D.B. Neale, M. Kirst, G.F. Peter, S.A. Gezan, C.D. Nelson and J.M. Davis. (2014) Mapping fusiform rust resistance genes within a complex mating design of loblolly pine. Forests 5:347-362.

  • White, T., J. Davis, S. Gezan, J. Hulcr, E. Jokela, M. Kirst, T.A. Martin, G. Peter, G. Powell and J. Smith. (2014) Breeding for value in a changing world: past achievements and future prospects. New Forests 45:301-309.

  • Zhang, J., E. Novaes, M. Kirst and G.F. Peter. (2014) Comparison of pyrolysis mass spectrometry and near infrared spectroscopy for genetic analysis of lignocellulose chemical composition in Populus. Forests 5:466-481.

 

2013

  • Albert V.A., J.J. Acosta, N.S. Altman, J.S. Ammiraju, S. Arikit, M.J. Axtell, S. Ayyampalayam, W.B. Barbazuk, R.A. Bruenn, J.M. Burnette IIIrd, V. Burtet-Sarramegna, L. Carretero-Paulet, S. Chamala, A.S. Chanderbali, T.H. Chang, F. Chen, J.Q. Chen, V. Chiang, A. de Kochko, E. De Paoli, C.W. dePamphilis, J.P. Der, R. Determann, J.C. Estill, N.P. Farrell, B. Fogliani, C. Guo, J. Harholt, A. Harkess, L.R. Herrera-Estrella, E. Ibarra-Laclette, Y. Jiao, C. Job, D. Job, S. Kim, M. Kirst, H. Kong, T. Lan, J. Leebens-Mack, G. Li, L. Li, J. Liu, K. Liu, E. Lyons, H. Ma, W. Mei, B.C. Meyers, J.D. Palmer, J. Park, S.P. Pissis, V. Poncet, X. Qi, L. Rajjou, P. Ralph, S. Rounsley, D. Sankoff, S.C. Schuster, R. Sederoff, S. Shahid, D.E. Soltis, P.S. Soltis, Y.H. Sun, J. Talag, H. Tang, L. Tomsho, P. Ulvskov, M. Villegente, E. Wafula, S. Wanke, S.R. Wessler, R.A. Wing, J.Y. Xue, T.F. Yeh, X. Yu, J. Zhai, X. Zhang and C. Zheng. (2013) The Amborella genome and the evolution of flowering plants. Science 342: 1467-1472.

  • Maron, L.G., C.T. Guimarães, M. Kirst, P.S. Albert, J.A. Birchler, P.J. Bradbury, E.S. Buckler, A.E. Coluccio, T.V. Danilova, D. Kudrna, J.V. Magalhaes, M.A. Piñeros, M.C. Schatz, R.A. Wing and L.V. Kochian. (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy-number. Proceedings of the National Academy of Sciences of the USA 110:5241-5246.

  • Neves, L.G., J.M. Davis, W.B. Barbazuk and M. Kirst. (2013) Whole-exome targeted sequencing of the uncharacterized pine genome. Plant Journal 75:146-156.

  • Westbrook, J.W., M.F. Jr. Resende, P. Munoz, A.R. Walker, J.L. Wegrzyn, C.D. Nelson, D.B. Neale, M. Kirst, D.A. Huber, S.A. Gezan, G.F. Peter and J.M. Davis. (2013) Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential. New Phytologist 199:89-100.

 

2012

  • Resende, M.F.Jr., P. Muñoz, M.D. Resende, D.J. Garrick, R.L. Fernando, J.M. Davis, E.J. Jokela, T.A. Martin, G.F. Peter and M. Kirst. (2012) Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.). Genetics 190:1503-1510.

  • Harfouche, A., R. Meilan, M. Kirst, M. Morgante, W. Boerjan, M. Sabatti and S. Mugnozza. (2012) Accelerating the domestication of forest trees in a changing world. Trends in Plant Sciences 17:64-72.

  • Resende, M.F.R., P. Muñoz, J.J. Acosta, G.F. Peter, J.M. Davis, D. Grattapaglia, M.D.V. Resende and M. Kirst. (2012) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytologist 193:617-624.

2011

  • Villar, E., C. Klopp, C. Noirot, E. Novaes, M. Kirst, C. Plomion and J.M. Gion. (2011) RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus. BMC Genomics 12:538.

  • Prosdocimi, F., D. Bittencourt, F.R. da Silva, M. Kirst, P.C. Motta and E.L. Rech. (2011) Spinning gland transcriptomics from two main clades of spiders (order: Araneae) – insights on their molecular, anatomical and behavioral evolution. PLoS One 6:e21634.

  • Neves, L.G., E. Mc Mamani, A.C. Alfenas, M. Kirst and D. Grattapaglia. (2011) A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. BMC Genomics 12:189.

  • Grattapaglia, D., O.B. Silva-Junior, M. Kirst, B.M. de Lima, D.A. Faria, G.J. Pappas Jr. (2011) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biology 11:65.

  • Lourenço, V.M., A.M. Pires and M. Kirst. (2011) Robust linear regression methods in association studies. Bioinformatics 27:815-21.

 

2010

  • Novaes, E., M. Kirst, V. Chiang, H. Winter-Sederoff and R. Sederoff. (2010) Lignin and biomass: a negative correlation for wood formation and lignin content in trees. Plant Physiology 154:555-561.

  • Mattiello, L., M. Kirst, F.R. da Silva, R.A. Jorge and M. Menossi. (2010) Transcriptional profile of maize roots under acid soil growth. BMC Plant Biology 10:196.

  • Visscher, A.M., A.L. Paul, M. Kirst, C.L. Guy, A.C. Schuerger and R.J. Ferl. (2010) Growth performance and root transcriptome remodeling of Arabidopsis in response to Mars-like levels of magnesium sulfate. PLoS One 5:e12348.

  • Drost, D.R., C.I. Benedict, A. Berg, E. Novaes, C.R. Novaes, Q. Yu, C. Dervinis, J.M. Maia, J. Yap, B. Miles and M. Kirst. (2010) Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proceeding of the National Academy of Sciences of the USA 107:8492-8497.

  • Krill, A.M., M. Kirst, L.V. Kochian, E.S. Buckler and O.A. Hoekenga. (2010) Association and linkage analysis of aluminum tolerance genes in maize. PLoS One 5:e9958.

2009

  • Brunings, A.M., L.E. Datnoff, J.F. Ma, N. Mitani, Y. Nagamura, B. Rathinasabapathi and M. Kirst. (2009) Differential gene expression of rice in response to silicon and rice blast fungus Magnaporthe oryzae. Annals of Applied Biology 155: 161-170.

  • Visscher, A.M., A-L. Paul, M. Kirst, A.K. Alling, S. Silverstone, G. Nechitailo, M. Nelson, W.F. Dempster, M. Van Thillo, J.P. Allen and R.J. Ferl. (2009) Effects of a spaceflight environment on heritable changes in wheat gene expression. Astrobiology 9:359-367.

  • Drost, D.R., E. Novaes, C. Boaventura-Novaes, C.I. Benedict, R.S. Brown, T. Yin, G.A. Tuskan and M. Kirst. (2009) A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species localizes a large fraction of the unassembled Populus trichocarpa genome sequence. Plant Journal 58: 1054-1067.

  • Grattapaglia, D., C. Plomion, M. Kirst and R.R. Sederoff. (2009) Genomics of growth traits in forest trees. Current Opinion in Plant Biology 12:148-156.

  • Novaes, E., L.F. Osorio, D.R. Drost, B.L. Miles, C. Boaventura-Novaes, C.I. Benedict, C. Dervinis, Q. Yup, R. Sykes, M. Davis, T.A. Martin, G.F. Peter and M. Kirst. (2009) Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels. New Phytologist 182:878-890.

 

2008

  • Quesada, T., Z. Li, C. Dervinis, Y. Li, P.N. Bocock, G.A. Tuskan, G. Casella, J.M. Davis and M. Kirst. (2008) Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytologist 180:408-420.

  • Novaes, E., D.R. Drost, W.G. Farmerie, G.J. Pappas Jr., D. Grattapaglia, R.R. Sederoff and M. Kirst. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9:312-325.

  • Grattapaglia, D. and M. Kirst. (2008) Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytologist 179:911-929.

  • Maron, L.G., M. Kirst, C. Mao, M. Menossi and L.V. Kochian. (2008) Transcriptional profiling of Al toxicity and tolerance responses in maize roots. New Phytologist 179: 116-128.

  • Ma, C.-X., Q. Yu, A. Berg, D. Drost, E. Novaes, G. Fu, J.S. Yap, A. Tang, M. Kirst, Y. Cui and R. Wu. (2008) A pleiotropic model for mapping phenotypic plasticity of a count trait. Genetics 179: 627-636.

 

2007

  • Gore, M., P. Bradbury, R. Hogers, M. Kirst, E. Verstege, J. van Oeveren, J. Peleman, E. Buckler and M. van Eijk. (2007) Evaluation of target preparation methods for single feature polymorphism detection in large complex plant genomes. Crop Science 47: S135-S148.

2006

  • Kirst, M., R. Caldo, P. Casati, G. Tanimoto, V. Walbot, R.P. Wise and E.S. Buckler. (2006) Genetic diversity contribution to errors in short-oligonucleotide microarray analysis. Plant Biotechnology Journal 4: 489-498.

  • Tuskan, G.A., S.P. DiFazio, U. Hellsten, S. Jansson, S. Rombauts, N. Putnam, L. Sterck, J. Bohlmann, J. Schein, R.R. Bhalerao, R.P. Bhalerao, D. Blaudez, W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G. Chen, D. Cooper, P.M. Coutinho, J. Couturier, S.F. Covert, R. Cunningham, J. Davis, S. Degroeve, C. dePamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, I. Grigoriev, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, N. Islam-Faridi, M. Jones-Rhoades, R. Jorgensen, C. Joshi, J. Kangasjärvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J.C. Leplé, A. Déjardin, G. Pilate, P. Locascio, S. Lucas, F. Martin, B. Montanini, C. Napoli, D.R. Nelson, C.D. Nelson, K.M. Nieminen, O. Nilsson, G. Peter, R. Philippe, A. Poliakov, S. Ralph, P. Richardson, C. Rinaldi, K. Ritland, P. Rouzé, D. Ryaboy, A. Salamov, J. Schrader, B. Segerman, F. Sterky, C. Souza, C. Tsai, P. Unneberg, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, G. Sandberg, Y. van de Peer and D. Rokhsar (2006) The genome of western black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313:1596-1604.

  • Tieman, D.M., M. Zeigler, E.A. Schmelz, M.G. Taylor, P. Bliss, M. Kirst and H.J. Klee. (2006) Identification of loci affecting flavour volatile emissions in tomato fruits. Journal of Experimental Botany 57:887-896.

 

2005

  • Kirst, M., C.J. Basten, A. Myburg, Z.-B. Zeng and R. Sederoff. (2005) Genetic architecture of transcript level variation in differentiating xylem of Eucalyptus hybrids. Genetics 169:2295-2303.

  • Kirst, M., C.M. Cordeiro, G.D.S.P. Rezende and D. Grattapaglia. (2005) Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. Journal of Heredity 96:161-166.

 

2004

  • Egertsdotter, U., L.M. van Zyl, J. MacKay, G. Peter, M. Kirst, C. Clark, R. Whetten and R. Sederoff. (2004) Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes. Plant Biology 6:654-663.

  • Kirst, M., A. Myburg, M.E. Kirst, J. Scott and R. Sederoff. (2004) Quantitative analysis of transcript variation on microarrays reveals coordinated downregulation of lignin gene transcripts associated with two quantitative trait loci for growth in a Eucalyptus hybrid backcross. Plant Physiology 135:2368-2378.

 

2003

  • Kirst, M., A.F. Johnson, C. Baucom, E. Ulrich, K. Hubbard, R. Staggs, C. Paule, E. Retzel, R. Whetten and R. Sederoff. (2003) Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the U.S.A 100:7383-7388.

  • Brondani, R.P.V., F.A. Gaiotto, A.A. Missiaggia, M. Kirst, R. Gribel and D. Grattapaglia (2003) Microsatellite markers for Ceiba pentandra (Bombacaceae), an endangered tree species of the Amazon forest. Molecular Ecology Notes 3:177-179.