{"id":499,"date":"2026-03-05T16:01:23","date_gmt":"2026-03-05T23:01:23","guid":{"rendered":"https:\/\/labs.agsci.colostate.edu\/leach\/?post_type=research&#038;p=499"},"modified":"2026-03-05T16:02:21","modified_gmt":"2026-03-05T23:02:21","slug":"biomass","status":"publish","type":"research","link":"https:\/\/labs.agsci.colostate.edu\/leach\/research\/biomass\/","title":{"rendered":"Biomass"},"content":{"rendered":"\n<!-- block -->\n<div class=\"custom-block-wrapper media-object-block stacked lite top-spacing-default bottom-spacing-default\">\n\n    <!-- component -->\n    <div class=\"media-object left\">\n\n        <!-- image container -->\n        <div class=\"object-container left half\" style=\"background-image:url(https:\/\/labs.agsci.colostate.edu\/leach\/wp-content\/uploads\/sites\/23\/2026\/03\/paultricepaddy-e1578613638744.jpg);\">\n\n            \n\n        <\/div>\n        <!-- END image container -->\n\n        <!-- text -->\n        <p class=\"object-text half\">\n\n            Summary<br \/>\r\nOne aspect of research in the Leach Lab has focused on biomass and bioenergy and how plants can be optimized for food, forage, and energy.<br \/>\r\nThis page serves to compile and synthesize various components of this research in one place.<br \/>\r\n<br \/>\r\nGenerally our objectives are:<br \/>\r\n<br \/>\r\nTo identify and characterize plant genes influencing total biomass<br \/>\r\nTo develop more efficient ways to measure key plant traits in field conditions (the phenotypes)<br \/>\r\nTo characterize the relationships between plant composition and forage\/bioenergy traits<br \/>\r\nTo better visualize genetic information on different plant species, varieties and more<br \/>\r\nTo translate what we learn in model crops such as rice, to dedicated crops such as switchgrass<br \/>\r\n<br \/>\r\nBigger, Better Plants<br \/>\r\nBy screening a rice recombinant inbred line population (RIL) between two varieties that express different biomass and bioenergy phenotypes, we aim to discover genes for example, that make the \u201cbig\u201d plants \u201cbig\u201d.  Additionally, by screening a separate population of mutant rice lines, we have identified a mutation that leads to additional grain and biomass production in a specific rice variety.\n        <\/p>\n        <!-- END text -->\n\n    <\/div>\n    <!-- END component -->\n\n<\/div>\n<!-- END block -->\n\n\n<!-- block -->\n<div class=\"custom-block-wrappper text-block stylized lite top-spacing-default bottom-spacing-default\">\n\n    <p><strong>High Throughput Phenotyping<\/strong><br \/>\nWith the advent of next generation sequencing, genetic information is plentiful and inexpensive.\u00a0However linking genetic information to phenotypes \u2013 how plant genes are expressed in an environment \u2013 remains a challenge and depends on our ability to accurately measure many important phenotypes on large numbers of plants.\u00a0 To this end, we are developing a tractor based, GPS positioned array of sensors to measure many plants in a field at once.<\/p>\n<p>Paul Tanger, a graduate student in the Leach Lab, after training as a\u00a0<a href=\"http:\/\/sustainability.colostate.edu\/SLF\" target=\"_new\">Sustainability Leadership Fellow<\/a>, was inspired to produce a video highlighting the high throughput phenotyping system we developed.\u00a0 IRRI has plans to expand the use of this system to many other studies and measurement of useful traits.<\/p>\n\n<\/div>\n<!-- END block -->\n\n\n<!-- block -->\n<div class=\"custom-block-wrapper video-block stacked dark top-spacing-default bottom-spacing-default\">\n\n    <!-- component -->\n    <div class=\"video\">\n\n        <!-- image container -->\n        <div class=\"object-container responsive-embed widescreen\">\n\n            <iframe loading=\"lazy\" title=\"A Complete Harvest: the Future of Rice as BioEnergy\" width=\"640\" height=\"360\" src=\"https:\/\/www.youtube.com\/embed\/05XlkiTrQH8?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n        <\/div>\n        <!-- END image container -->\n\n    <\/div>\n    <!-- END component -->\n\n    <!-- text -->\n    <div class=\"text-content\">\n\n        \n    <\/div>\n    <!-- END text -->\n\n<\/div>\n<!-- END block -->\n\n\n<!-- block -->\n<div class=\"custom-block-wrappper text-block stacked lite top-spacing-default bottom-spacing-default\">\n\n    <p><strong>Lignin Levers<\/strong><br \/>\nThis project aims to determine the role of two important genes in lignin biosynthesis. Lignin is a critical lever in downstream bioenergy processes through its abundance in the complex matrix of plant cell walls. If the amount of lignin can be optimized, enzymatic digestion of cellulose or thermochemical conversion of lignin can be made more sustainable. We propose to use rice as our model plant, then translate our findings to its close relative, switchgrass, a strong perennial, drought tolerant bioenergy feedstock. This research was recently funded by the\u00a0<a href=\"http:\/\/www.c2b2web.org\/\" target=\"_new\">Colorado Center for Biorefining and Biofuels<\/a>\u00a0and begins January 2014.<\/p>\n<p><strong>Visualizing Genomes<\/strong><br \/>\nComparative genomics approaches are uniquely powerful for the identification of functional elements of genomes that have been conserved over longer evolutionary timescales.\u00a0 We have used comparative genomic approaches to reveal important patterns of conservation in whole genome plant alignments.\u00a0 We have assembled a genome browser to visualize and compare this information:<br \/>\n<a href=\"http:\/\/genome.genetics.rutgers.edu\/\">http:\/\/genome.genetics.rutgers.edu\/<\/a><\/p>\n<p><strong>Translation to Other Crops<\/strong><br \/>\nWe have developed populations of switchgrass, a potential bioenergy crop, to link the genetics between switchgrass and other model crop species such as rice.\u00a0 We are investigating gene expression differences between these populations as a means to identify key genes responsible for biomass and other important traits.<\/p>\n<p><strong>Project Leads and Collaborators<\/strong><br \/>\nPrincipal Investigators:<\/p>\n<ul>\n<li>Jan E. Leach<\/li>\n<li><a href=\"http:\/\/www.biology.colostate.edu\/people\/dbush\/\" target=\"_new\">Daniel R. Bush<\/a>, CSU<\/li>\n<li><a href=\"http:\/\/kernlab.rutgers.edu\/\" target=\"_new\">Andrew D. Kern<\/a>, Rutgers<\/li>\n<li><a href=\"http:\/\/www.irri.org\/about-us\/our-people\/experts\/hei-leung\" target=\"_new\">Hei Leung<\/a>, IRRI<\/li>\n<li><a href=\"http:\/\/www.mckaylab.colostate.edu\/\" target=\"_new\">John K. McKay<\/a>, CSU<\/li>\n<li><a href=\"http:\/\/www.hort.vt.edu\/bzhao\/index.html\" target=\"_new\">Bingyu Zhao<\/a>, Virginia Tech<\/li>\n<\/ul>\n<p>Collaborators:<\/p>\n<ul>\n<li>Courtney Jahn, CSU<\/li>\n<li>Steve Klassen, IRRI<\/li>\n<li>Jillian Lang, CSU<\/li>\n<li>Ken McNally, IRRI<\/li>\n<li>Julius Mojica, CSU<\/li>\n<li>Paul Tanger, CSU<\/li>\n<li>Brad Tonnessen, CSU<\/li>\n<\/ul>\n<p><strong>Funding<\/strong><br \/>\nFunding for the projects described here is generously provided by these institutions and grants:<\/p>\n<ul>\n<li class=\"index\">U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, grant DE-FG02-08ER64629 and U.S. Department of Agriculture, National Institutes of Food and Agriculture, USDA-NIFA award 2008-35504-0485 to Leach, Bush, Kern, Leung, McKay and Zhao<\/li>\n<li class=\"index\">U.S. Agency for International Development, IRRI-USAID Linkage grant DRPC2011-42 to Leach and Leung<\/li>\n<li class=\"index\">CSU\u00a0<a href=\"http:\/\/energy.colostate.edu\/\" target=\"_new\">Clean Energy Supercluster<\/a>\u00a0seed grant to Tanger, Jahn, Leach<\/li>\n<li class=\"index\">Colorado Center for Biorefining and Biofuels (<a href=\"http:\/\/www.c2b2web.org\/\" target=\"_new\">C2B2<\/a>) seed grant to Lang, Tanger, Tonnessen, Leach<\/li>\n<li class=\"index\">U.S. National Science Foundation\u00a0<a href=\"http:\/\/www.igert.org\/\" target=\"_new\">IGERT<\/a>\u00a0fellowship to Tanger<\/li>\n<\/ul>\n<p><strong>Publications<\/strong><\/p>\n<ul>\n<li>Tanger, P., Vega-S\u00e1nchez, M.E., Fleming, M., Tran, K., Singh, S., Abrahamson, J.B., Jahn, C.E., Santoro, N., Naredo, E.B., Baraoidan, M., Danku, J.M.C., Salt, D.E., McNally, K.L., Leung, H., Ronald, P.C., Bush, D.R., McKay, J.K., Leach, J.E. 2015. Cell wall composition of rice straw varies among environments, varieties, and tissue types: impacts on bioenergy potential.\u00a0<em>BioEnergy Research<\/em>.\u00a0<a href=\"http:\/\/link.springer.com\/article\/10.1007\/s12155-014-9573-y\" target=\"_new\">DOI: 10.1007\/s12155-014-9573-y<\/a>.<\/li>\n<li>Tanger, P., Field, J. L., Jahn, C. E., DeFoort, M. W., and Leach, J. E. (2013). Biomass for thermochemical conversion: targets and challenges.\u00a0<a href=\"http:\/\/www.frontiersin.org\/Journal\/10.3389\/fpls.2013.00218\/abstract\" target=\"_new\">Front. Plant Sci. 4:, 218<\/a><\/li>\n<li>Yang Z, Z Shen, H Tetreault, L Johnson, B Friebe, T Frazier, LK Huang, B Xu, C Burklew, X-Q\u00a0 Zhang, B Zhao, 2013. Production of autopolyploid lowland switchgrass lines through in vitro chromosome doubling.\u00a0<a href=\"http:\/\/link.springer.com\/article\/10.1007%2Fs12155-013-9364-x#page-1\" target=\"_new\">Bioenergy Research<\/a><\/li>\n<li>Sathitsuksanoh N, B Xu, B Zhao, YH Zhang, 2013. Overcoming biomass recalcitrance by combining genetically modified switchgrass and cellulose solvent-based lignocellulose pretreatment.\u00a0<a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0073523\" target=\"_new\">PLoS ONE 8(9): e73523<\/a><\/li>\n<li>Bandillo N, Raghavan C, Muyco PA, Sevilla MA, Lobina IT, Dilla-Ermita CJ, Tung CW, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redo\u00f1a E, Leung H. 2013. Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding Rice\u00a0\u00a0<a href=\"http:\/\/link.springer.com\/article\/10.1186%2F1939-8433-6-11#page-1\" target=\"_new\">doi: 10.1186\/1939-8433-6-11<\/a><\/li>\n<li>Xu B, N Sathitsuksanoh, Y Tang, MK Udvardi, JY Zhang, Z Shen, M Balota, K Harich, PY-H Zhang, B Zhao, 2012. Overexpression of\u00a0<em>AtLOV1<\/em>\u00a0in switchgrass alters plant architecture, lignin content, and flowering time.\u00a0<a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0047399\" target=\"_new\">PLoS One, 7(12): e47399<\/a><\/li>\n<li>Hupalo D, AD Kern. Conservation and functional element discovery in 20 angiosperm plant genomes. 2013. Mol Biol Evol Mar 11\u00a0<a href=\"http:\/\/mbe.oxfordjournals.org\/content\/30\/7\/1729.long\" target=\"_new\">doi:pii:g3.113.005637v1<\/a><\/li>\n<li>Jahn, C. E., Mckay, J. K., Mauleon, R., Stephens, J., McNally, K. L., Bush, D. R., Leung, H., and Leach, J. E. (2011). Genetic Variation in Biomass Traits among 20 Diverse Rice Varieties.\u00a0<a href=\"http:\/\/www.plantphysiol.org\/content\/early\/2010\/11\/09\/pp.110.165654\" target=\"_new\">Plant Physiology 155, 157\u2013168<\/a><\/li>\n<\/ul>\n<p><strong>Publicity<\/strong><\/p>\n<ul>\n<li>\u201c<a href=\"http:\/\/agrilinks.org\/blog\/rice-pathology-research-food-security-gains-interview-jan-leach\" target=\"_new\">From rice pathology research to food security gains:\u00a0 An interview with Jan Leach<\/a>\u201d by Julie MacCartee; June 2, 2013<\/li>\n<li>Lignin Levers\u00a0<a href=\"http:\/\/www.c2b2web.org\/3RGrants.php\" target=\"_new\">funding announcement<\/a><\/li>\n<li><a href=\"http:\/\/biomassmagazine.com\/articles\/1900\/csu-receives-grant-to-study-rice-as-a-feedstock\" target=\"_new\">Biomass magazine<\/a>\u00a0story on Department of Energy grant<\/li>\n<li><a href=\"http:\/\/www.today.colostate.edu\/story.aspx?id=6043\" target=\"_new\">Today @ ColoState\u00a0<\/a>Department of Energy grant announcement<\/li>\n<li><a href=\"http:\/\/www.news.colostate.edu\/Release\/5760\" target=\"_new\">Clean Energy Supercluster grant announcement<\/a><\/li>\n<\/ul>\n\n<\/div>\n<!-- END block -->","protected":false},"excerpt":{"rendered":"<p>One aspect of research in the Leach Lab has focused on biomass and bioenergy and how plants can be optimized for food, forage, and energy. 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