Genotyping-by-sequencing GBS offers several advantages over array-based genotyping, including low development costs, reduced ascertainment bias, and the potential to estimate relative dosage. I am particularly interested in using GBS to genotype polyploid crop species and wide hybrids.
Genetic improvement of sorghum as a bioenergy crop Sorghum is also of interest as a bioenergy crop in its own right. A seed-planted bioenergy crop enjoys several advantages over a vegetatively-propagated crop, including reduced plantings costs, quicker establishment, and accelerated scaling-up of desired genotypes. Of particular interest are seed-planted intergeneric hybrids that use sorghum as the female parent and related polyploids in the Saccharinae as pollen donors.
Genetic architecture of complex traits in sorghum Sorghums diploid, sequenced genome and phylogenetic proximity to Saccharum and Miscanthus, both complex polyploids, make it a logical model for studying the genetic control of quantitative traits in the Saccharinae clade of grasses. Traits relevant to bioenergy feedstock development are of particular interest: flowering phenology, carbon allocation, perenniality, and plant architecture.
The maize ear The evolution of maize from its wild progenitor teosinte was originally discredited because the maize ear looks so different from the female inflorescence of teosinte. I’m following up on some work initiated during my postdoc to assess the contribution of specific gene families to the awesome phenotypic diversity observed in maize ears.
Assistant Professor, Department of Crop Sciences, University of Illinois (2010-present)
Hayes CM, Burow GB, Brown PJ, Thurber C, Xin Z, Burke JJ. Natural variation in synthesis and catabolism genes influences dhurrin content in sorghum (Sorghum bicolor L. Moench). The Plant Genome, in press.
Chuck GS, Brown PJ, Meeley R, Hake S. Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordial initiation. Proc Natl Acad Sci USA, in press.
Barrios Perez I, Brown PJ (2014) The role of ROS signaling in cross-tolerance: from model to crop. Front Plant Sci 5: 754
Higgins RH, Thurber CS, Assaranurak I, Brown PJ (2014) Multi-parental mapping of height and flowering QTL in partially-isogenic sorghum populations. Genes, Genomes, Genetics 4:1681-1687: 1593-1602
Gardner KM, Brown PJ, Cooke TF, Cann S, Costa F, Bustamante CD, Velasco R, Troggio M, Myles S. (2014) Fast and cost-effective genetic mapping in apple using next-generation sequencing. Genes, Genomes, Genetics 4:1681-1687
Chen SF, Danao MG, Singh V, Brown PJ (2014) Determining sucrose and glucose levels in dual-purpose sorghum stalks by Fourier transform near infrared (FT-NIR) spectroscopy. J Sci Food Agric 94(12): 2569-2576.
Chang S, Thurber CS, Brown PJ, Hartman GL, Lambert KN, Domier LL (2014) Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS ONE 9(6): e99427.
Thurber CS, Ma JM, Higgins RH, Brown PJ (2013) Retrospective genomic analysis of sorghum adaptation to temperate zone grain production. Genome Biology 14(6): R68.
Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci USA 110: 453-458.
Dweikat I, Weil C, Moose S, Kochian L, Mosier N, Ileleji K, Brown PJ, Peer W, Murphy A, Taheripour F, McCann M, Carpita N (2012) Envisioning the transition to a next-generation biofuels industry in the US Midwest. Biofuels, Bioproducts & Biorefining 6: 376-386
Poland J, Brown PJ, Sorrells M, Jannink J-L. (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7: e32253.
Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, Holland JB, Flint-Garcia S, McMullen MD, Buckler ES, Rocheford TR. (2011) Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genetics 7: e1002383.
Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F, Aradhya MK, Prins B, Reynolds A, Chia J-M, Ware D, Bustamante C, Buckler ES. (2011) Genetic structure and domestication history of the grape. Proc Natl Acad Sci USA 108: 3530-3535.
Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford T, McMullen MD, Holland JB, Buckler ES. (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162.
Brown PJ, Myles SM, Kresovich S. (2010) Genetic support for phenotype-based racial classification in sorghum. Crop Science, 51: 224-230
Buckler ES, Holland JB, Bradbury P, Acharya C, Brown PJ, Brown C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman M, Harjes C, Guill K, Kroon D, Larsson S, Lepak N, Li H, Mitchell SE, Pressoir G, Peiffer J, Oropeza Rosas M, Rocheford T, Romay C, Romero S, Salvo S, Villeda HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen M. (2009) The genetic architecture of maize flowering time. Science 325: 714-718.
Pressoir G*, Brown PJ*, Zhu W, Mitchell SE, Upadyalula N, Rocheford T, Buckler ES, Kresovich S (2009) Natural variation in maize architecture is mediated by allelic variation at the PINOID ortholog barren inflorescence2.Plant J. 58: 618-628. * contributed equally
Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES. (2009) Association mapping: critical considerations shift from genotyping to experimental design (Review). Plant Cell 21: 2194-2202.
McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya CB, Bottoms C, Brown PJ, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Rosas MO, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland J, Buckler ES (2009) Genetic properties of the maize nested association mapping population. Science 325:737-740.
Brown PJ, Franks C, Rooney WL, Kresovich S (2008) Efficient mapping of plant height QTL in a sorghum association population with introgressed dwarfing genes. Genetics 180: 629-637.
Zelitch I, Schultes NP, Peterson RB, Brown PJ, Brutnell TP (2008) High glycolate oxidase activity is required for survival of maize in normal air. Plant Physiol 149: 195-204.
Casa AM, Pressoir G, Brown PJ, Mitchell SE, Rooney WL, Tuinstra M, Franks C, Kresovich S (2008) Community resources and strategies for association mapping in sorghum. Crop Sci 48:30-40.
Feltus FA, Hart GE, Schertz KF, Casa AM, Kresovich S, Klein PE, Brown PJ, Paterson AH (2006) Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations. Theor Appl Genet 112:1295-305.
Brown PJ, Klein PE, Bortiri E, Acharya CB, Rooney WL, Kresovich S (2006) Inheritance of inflorescence architecture in sorghum. Theor Appl Genet 113:931-42.