Genetic Variation in Biomass Traits among 20 Diverse Rice Varieties1[W][OA]

Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops.

[1]  T. Chang,et al.  The morphology and varietal characteristics of the rice plant. , 1965 .

[2]  N. Ahmadi,et al.  Genetic basis and mapping of the resistance to rice yellow mottle virus. I. QTLs identification and relationship between resistance and plant morphology , 1998, Theoretical and Applied Genetics.

[3]  Hao Wu,et al.  R/qtl: QTL Mapping in Experimental Crosses , 2003, Bioinform..

[4]  G. Farquhar,et al.  Correlation Between Water-Use Efficiency and Carbon Isotope Discrimination in Diverse Peanut (Arachis) Germplasm , 1986 .

[5]  P. Tranel,et al.  Variability in Photosynthetic Rates and Accumulated Biomass Among Greenhouse-Grown Common Cocklebur (Xanthium strumarium) Accessions1 , 2003 .

[6]  Elizabeth Pennisi,et al.  The Blue Revolution, Drop by Drop, Gene by Gene , 2008, Science.

[7]  Charlotte K. Williams,et al.  The Path Forward for Biofuels and Biomaterials , 2006, Science.

[8]  Markus Pauly,et al.  Cell-wall carbohydrates and their modification as a resource for biofuels. , 2008, The Plant journal : for cell and molecular biology.

[9]  Y. W. Huang,et al.  Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines , 2004, Theoretical and Applied Genetics.

[10]  D. Jiang,et al.  Effects of Nitrogen Deficiency on Gas Exchange, Chlorophyll Fluorescence, and Antioxidant Enzymes in Leaves of Rice Plants , 2004, Photosynthetica.

[11]  Richard A Dixon,et al.  Lignin modification improves fermentable sugar yields for biofuel production , 2007, Nature Biotechnology.

[12]  P. Arruda,et al.  Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. , 2007, The Plant journal : for cell and molecular biology.

[13]  B. Courtois,et al.  Locating QTLs controlling constitutive root traits in the rice population IAC 165 × Co39 , 2003, Euphytica.

[14]  Seth C. Murray,et al.  Genetic Improvement of Sorghum as a Biofuel Feedstock: II. QTL for Stem and Leaf Structural Carbohydrates , 2008 .

[15]  D. Govindaraju.  Genetic Variation: A Laboratory Manual , 2008 .

[16]  K. Vogel,et al.  Impact of reduced lignin on plant fitness , 2005 .

[17]  J. Leach,et al.  Translational Genomics for Bioenergy Production: There's Room for More Than One Model , 2007, The Plant Cell Online.

[18]  Alcalde Rovira Roure.  Plant Breeding and Drought in C 3 Cereals: What Should We Breed For? , 2002 .

[19]  J. Araus,et al.  Plant breeding and drought in C3 cereals: what should we breed for? , 2002, Annals of botany.

[20]  G. Khush.  Green revolution: preparing for the 21st century. , 1999, Genome.

[21]  J. Coors,et al.  Quantitative trait loci for cell-wall components in recombinant inbred lines of maize (Zea mays L.) I: stalk tissue , 2005, Theoretical and Applied Genetics.

[22]  J. Hibberd,et al.  The regulation of gene expression required for C4 photosynthesis. , 2010, Annual review of plant biology.

[23]  Hua Yan,et al.  QTLs for low nitrogen tolerance at seedling stage identified using a recombinant inbred line population derived from an elite rice hybrid , 2005, Theoretical and Applied Genetics.

[24]  Chung-Jui Tsai,et al.  Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees , 1999, Nature Biotechnology.

[25]  Ye Sun,et al.  Hydrolysis of lignocellulosic materials for ethanol production: a review. , 2002, Bioresource technology.

[26]  J. G. Coors,et al.  Quantitative trait loci for cell wall components in recombinant inbred lines of maize (Zea mays L.) II: leaf sheath tissue , 2005, Theoretical and Applied Genetics.

[27]  Xin-Guang Zhu,et al.  Improving photosynthetic efficiency for greater yield. , 2010, Annual review of plant biology.

[28]  Amani Elobeid,et al.  The ethanol outlook for Brazil and the United States and implications for livestock. , 2007 .

[29]  A. Paterson,et al.  Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield. , 2001, Genetics.

[30]  C. Bustamante,et al.  Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome , 2010, PloS one.

[31]  J. Hesketh,et al.  Correlations among leaf CO2-exchange rates, areas and enzyme activities among soybean cultivars , 1981, Photosynthesis Research.

[32]  E. Pang,et al.  An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts , 2005, Euphytica.

[33]  Cris Kuhlemeier,et al.  Plant architecture , 2002, EMBO reports.

[34]  D. Cowan,et al.  Boosting silica levels in wheat leaves reduces grazing by rabbits. , 2007, Pest management science.

[35]  R. B. Austin,et al.  Flag Leaf Photosynthesis of Triticum aestivum and Related Diploid and Tetraploid Species , 1982 .

[36]  K. Devos,et al.  Comparative genetics in the grasses. , 1998, Plant molecular biology.

[37]  X. Yang,et al.  Genetic modification of plant architecture and variety improvement in rice , 2008, Heredity.

[38]  M. Keeping,et al.  Epidermal silicon in sugarcane: cultivar differences and role in resistance to sugarcane borer Eldana saccharina. , 2009 .

[39]  Hongzhang Chen,et al.  Near-infrared analysis of the chemical composition of rice straw , 2007 .

[40]  S. Peng,et al.  Mapping QTLs for seedling characteristics under different water supply conditions in rice (Oryza sativa). , 2007, Physiologia plantarum.

[41]  Yunbi Xu,et al.  Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping , 2009, Theoretical and Applied Genetics.

[42]  R. Fao,et al.  Rice-husk, conversion to energy , 1978 .

[43]  Kenneth L. McNally,et al.  Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes , 2006, Plant Physiology.

[44]  R. Sage.  Acclimation of photosynthesis to increasing atmospheric CO2: The gas exchange perspective , 1994, Photosynthesis Research.

[45]  Beat Keller,et al.  Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. , 2002, Annals of botany.

[46]  J. Boyer.  Plant Productivity and Environment , 1982, Science.

[47]  C. Lin,et al.  A process development for gasification of rice husk , 1998 .

[48]  R. Saxena,et al.  Iron, silica, and aluminum stresses and varietal resistance in rice : effects on whitebacked planthopper , 1992 .

[49]  M. Matsuoka,et al.  Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice , 2006, Nature Biotechnology.

[50]  Yang Xc,et al.  Genetic modification of plant architecture and variety improvement in rice , 2008 .

[51]  Shahab Sokhansanj,et al.  The Potential of C4 Perennial Grasses for Developing a Global BIOHEAT Industry , 2005 .

[52]  S. Hittalmani,et al.  Molecular marker assisted tagging of morphological and physiological traits under two contrasting moisture regimes at peak vegetative stage in rice (Oryza sativa L.) , 2000, Euphytica.

[53]  J. Ehleringer,et al.  Carbon Isotope Discrimination and Photosynthesis , 1989 .

[54]  Cai-guo Xu,et al.  Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice , 2002, Theoretical and Applied Genetics.

[55]  B. Jenkins,et al.  Combustion properties of biomass , 1998 .

[56]  T. Sinclair,et al.  Erect Leaves and Photosynthesis in Rice , 1999, Science.

[57]  Kenneth L. McNally,et al.  Genomewide SNP variation reveals relationships among landraces and modern varieties of rice , 2009, Proceedings of the National Academy of Sciences.

[58]  G. Khush.  Challenges for meeting the global food and nutrient needs in the new millennium , 2001, The Proceedings of the Nutrition Society.

[59]  R. Monson,et al.  Evolutionary and Ecological Aspects of Photosynthetic Pathway Variation , 1993 .

[60]  D. Rockey.  Physician-Scientists at Risk , 1999, Science.