6 Journal research area: Whole Plant and et al., 1998; Hemamalini et al., 2000; Li et al., 2001; Xing et al., 2002; Courtois et al., 2003; Xu 123 et al., 2004; Lian et al., 2005; Cui

  • View
    213

  • Download
    1

Embed Size (px)

Text of 6 Journal research area: Whole Plant and et al., 1998; Hemamalini et al., 2000; Li et al., 2001;...

  • Running head: Diversity of biomass traits in rice 1

    2

    Corresponding author: Jan E. Leach, Bioagricultural Sciences and Pest Management, Colorado 3

    State University, Fort Collins, Colorado, 80523-1177 4

    5

    Journal research area: Whole Plant and Ecophysiology 6

    7

    Plant Physiology Preview. Published on November 9, 2010, as DOI:10.1104/pp.110.165654

    Copyright 2010 by the American Society of Plant Biologists

    www.plantphysiol.orgon June 2, 2018 - Published by Downloaded from Copyright 2010 American Society of Plant Biologists. All rights reserved.

    http://www.plantphysiol.org

  • Jahn et al., 2010 2

    Title: Genetic variation in biomass traits among 20 diverse rice varieties 8

    9

    Courtney E. Jahn1, John Mckay1, Ramil Mauleon2, Janice Stephens1, Kenneth L. McNally2, 10

    Daniel R. Bush3, Hei Leung2, and Jan E. Leach1 11

    12

    1Bioagricultural Sciences and Pest Management and Program in Molecular Plant Biology, 13

    Colorado State University, Fort Collins, Colorado, USA 80523-1177 14

    2International Rice Research Institute, DAPO 7777, Metro Manila, Philippines 15

    3Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort 16

    Collins, Colorado, USA 80523-1878 17

    18

    www.plantphysiol.orgon June 2, 2018 - Published by Downloaded from Copyright 2010 American Society of Plant Biologists. All rights reserved.

    http://www.plantphysiol.org

  • Jahn et al., 2010 3

    Financial source: Jahn was supported by a Colorado Center for Biorefining and Biofuels-19

    Chevron fellowship (www.C2B2web.org). Leach and McKay were supported by The Colorado 20

    Agricultural Experiment Station. This research was supported by grants from the U.S. 21

    Department of Agriculture-CSREES (2008-35504-04852), Office of Science (BER), US 22

    Department of Energy (DE-FG02-08ER64629), and Colorado State Universitys Clean Energy 23

    Supercluster. 24

    25

    Corresponding author with e-mail address: Jan Leach, Jan.Leach@colostate.edu 26

    27

    www.plantphysiol.orgon June 2, 2018 - Published by Downloaded from Copyright 2010 American Society of Plant Biologists. All rights reserved.

    http://www.plantphysiol.org

  • Jahn et al., 2010 4

    Abstract 28

    Biofuels provide a promising route of producing energy while reducing reliance on 29

    petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major 30

    challenge and will require significant breeding efforts to maximize plant biomass production. Our 31

    approach to elucidating genes and genetic pathways that can be targeted for improving biomass 32

    production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza 33

    sativa). In this study, we analyzed a diverse set of 20 recently re-sequenced rice varieties for 34

    variation in biomass traits at several different developmental stages. The traits included plant 35

    size and architecture, above ground biomass, and underlying physiological processes. We 36

    found significant genetic variation among the 20 lines in all morphological and physiological 37

    traits. Although heritability estimates were significant for all traits, heritabilities were higher in 38

    traits relating to plant size and architecture than for physiological traits. Trait variation was 39

    largely explained by variety and breeding history (advanced vs. landrace), but not by varietal 40

    groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall 41

    composition varied significantly among varieties. Surprisingly, photosynthetic rates among the 42

    varieties were inversely correlated with biomass accumulation. Examining these data in an 43

    evolutionary context reveals that rice varieties have achieved high biomass production via 44

    independent developmental and physiological pathways, suggesting there are multiple targets 45

    for biomass improvement. Future efforts to identify loci and networks underlying this functional 46

    variation will facilitate improvement of biomass traits in other grasses being developed as 47

    energy crops. 48

    49

    www.plantphysiol.orgon June 2, 2018 - Published by Downloaded from Copyright 2010 American Society of Plant Biologists. All rights reserved.

    http://www.plantphysiol.org

  • Jahn et al., 2010 5

    Introduction 50

    Developing a sustainable biofuels program that makes significant contributions to our 51

    current and future national energy budget requires unprecedented inputs of biomass for energy 52

    conversion. Presently, the U.S. fuel-ethanol industry produces its bioethanol from corn grain, 53

    however this is not considered a sustainable source of energy as an increase in demand for 54

    corn-based ethanol will have significant land requirements, compete with food and feed 55

    industries, and reduce exports of animal products (Sun and Cheng, 2002; Elobeid et al., 2007). 56

    Because of these issues, liquid fuel production from plant lignocellulose is considered a better 57

    alternative and is being pursued from both agronomic and engineering perspectives. 58

    Plants display a variety of architectures that encompass branching (tillering) patterns, plant 59

    height, arrangement and size of leaves, and structure of reproductive organs. Widespread 60

    adoption of wheat and rice cultivars with altered plant architecture (semi-dwarf varieties) averted 61

    severe food shortages in the 1960s, and was an essential component of the Green Revolution 62

    (Khush, 1999). Continued use of these semi-dwarf varieties in conjunction with higher rates of 63

    nitrogen application has resulted in doubled grain yields; these gains are due to increased 64

    allocation of resources to grain rather than vegetative tissues, and also greater resistance to 65

    lodging in extreme weather events (Khush, 1999, 2001; Reinhardt and Kuhlemeier, 2002). In 66

    many ways, improvement of plants for both food and fuel or for dedicated biofuel feedstock 67

    purposes will require new breeding and selection emphases that are different from those 68

    targeted during the Green Revolution. Therefore, understanding the genetic and molecular 69

    processes that control key morphological and physiological processes will facilitate the breeding 70

    of high biomass yielding crops. Leaf traits, such as leaf thickness, size and shape, leaf number 71

    and orientation, are key factors influencing biomass formation (Yang and Hwa, 2008). In rice 72

    (Oryza sativa L.), erect leaves have a higher leaf area index that increases photosynthetic 73

    carbon assimilation rates through increased light capture and nitrogen use efficiency (Sinclair 74

    and Sheehy, 1999; Sakamoto et al., 2006). Leaves are the predominant photosynthetic organ, 75

    www.plantphysiol.orgon June 2, 2018 - Published by Downloaded from Copyright 2010 American Society of Plant Biologists. All rights reserved.

    http://www.plantphysiol.org

  • Jahn et al., 2010 6

    and thus, are critical targets for maximizing carbon assimilation by improving morphological 76

    traits and/ or by improving photosynthetic efficiency (Zhu et al., 2010). 77

    Many non-food crops, including perennial C4 rhizomatous grass species, such as 78

    switchgrass (Panicum virgatum) and Miscanthus, have potential to serve as viable, long-term 79

    sources of energy. Rice shares patterns of growth and development (plant architecture, 80

    flowering and maturity timelines, and senescence patterns) and physiological processes 81

    (photosynthetic light reactions, assimilate partitioning, secondary metabolism) with these other 82

    grasses. Unfortunately, many of these perennial grasses have very large genomes, and the 83

    genetic and genomic resources necessary to propel their development forward as biomass 84

    crops do not exist. Rice, in contrast, has all these tools readily available (Bush and Leach, 85

    2007), and, despite large differences between genome size and chromosome number, gene 86

    content and order are well conserved among the grasses (Gale and Devos, 1998; Feuillet and 87

    Keller, 2002; Nazeema et al., 2007). In addition, available rice germplasm collections contain 88

    genetic and phenotypic variation accumulated over years of domestication and selection under 89

    very diverse environments, e.g., well-watered, flooded, water-limited (Leung et al., 2007). Thus, 90

    rice serves as an excellent model grass for biomass gene discovery, and that information can 91

    be transferred to the new energy crops (Bush and Leach, 2007). However, current 92

    understanding regarding the magnitude of genetic variation for biomass traits in all plants is 93

    limited, including the variability in rice. 94

    Here we investigate biomass variation in the OryzaSNP set (Table I), a collection 20 rice 95

    varieties that are genetically and agronomically diverse, and which were re-sequenced for the 96

    purpose of identifying single nucleotide polymorphisms (SNPs) (McNally et al., 2009). This 97

    diversity set contains varieties that are widely used in a number of international breeding 98

    programs, and that are representative of the two major lineages, indica and japonica. The set 99

    also includes aus, deep water and aromatic rice groups. The OryzaSNP set also can be divided 100

    into two varietal classes based