Báo cáo khoa học: "A new data processing system for root growth and ramification analysis: description of methods"

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A new data processing system for root growth and ramifi- cation analysis: description of methods Colin-Belgrand H. Joannes 2 4 L. Pages 3 Dreyer M. E. 1 Laboratoire des Sols ef de la Nutrition des Arbres Forestiers, 2 Station de Biom6trie, and 3 Laboratoire de Bioclimatologie et d’Ecophysiologie Forestiere, INRA, Centre de Recherches Forestieres, BP 35, 54280 Seichamps, and 4 Station dAgronomie, INRA, Centre dAvignon, Domaine-de-Saint-Paul, 84000 Montfavet, France acquisition; 2) data storage and Introduction data growth parameter computation; and 3) the integration of the computed parameters Direct observation of root growth in woody into a developmental model (Pages and seedlings is possible using a ’minirhizo- Aries, 1988). The technical prerequisites tron’. Root growth in this device occurs of this processing system are described almost exclusively at the interface be- below. tween the substrate and the lower, trans- parent, rhizotron wall. This method pro- vides a better picture of root morphology and development, but reduces a three- Data acquisition system dimensional root system to a plane. Root growth is generally observed every 2nd day; newly formed roots are traced on a Basic principles for analyzing structural transparent polyethylene sheet with a dif- features of root pictures are the following: ferent color ink for each date. 1) a root is defined as a linear, un- branched structure formed through the Previous studies of root system charac- activity of a single apical meristem; 2) suc- teristics required time consuming manual cessive root orders are defined according processing. To overcome this major limita- developmental terminology (Rose, tion, we have recently developed a semi- to a 1983): the taproot originating from the automated data acquisition system al- hypocotyl is the 1 st order root and bears lowing a quantitative analysis of root 2nd order roots and so on; 3) roots are architecture (Belgrand et al., 1987). This treated as sets of elementary straight seg- new data processing system consists of 3 ments, each being the increment in root successive stages: 1) semi-automated
length between 2 successive observa- hierarchy. Coordinates and ’structural’ tions; 4) each root segment is defined information stored in the data storage are the Cartesian coordinates of some by structure. characteristic points (e.g., terminal points Hardware needed for this processing is (initial and final) and branching points any IBM PC compatible computer equip- where the laterals of the order n +1 ped with a color video screen (EGA or appear); in fact, branching points are also VGA norm) and a graphics tablet. Soft- the initial points of lateral root segments. ware is written in TURBOPASCAL (ver- sion 4.0). Fig. 1 shows a simplified root system with 7 segments belonging to 5 different Digitizing begins at the root origin on the roots, a taproot and 4 laterals. Root seg- hypocotyl (the oldest observation). The ment records are completed with auto- observer provides some information about matically computed information about the the experiment, the dates and associated segment position in the branching system color codes. HEa then introduces with the
mouse the initial point of the 1st Root segment file graphic segment, all the branching points along this segment in an acropetal order and the Each root segment contains time some final point. This procedure is repeated for information (time of emergence), spatial all segments on each date. All structural data (coordinates of its terminal and information about root order, segment branching points) and a set of ’structural’ identification, etc. are automatically com- indexes (Table I): a sequential index spe- puted without any direct intervention. Pro- cifying the order in which the segment was cedures for correction of errors and for digitized (= root segment number); an ori- help in the search for particular points gin index whose value is 1 if the segments (e.g., picture enlarging, etc.) cursor, are is the 1 st one on its root (new root) and 2 also provided. if it is the prolongation of a growing root; a date index; a color code associated with the date, for the video drawing; the coordi- nates of initial and final points (X, Y); a link to the previous segment specifying the Data storage structure sequential index of the segment on which it is inserted; a running index which is the The data storage structure is made up of 3 number of the root to which the segment data sets: a dictionary describing the belongs; the root order; the number of experiment, the root segment records and branching points; a following link index the branching point records. This latter file specifying the sequential index of the seg- contains some redundant information for ment which follows on the same root and, finally, the rank of the branching point redrawing root pictures more swiftly.
giving the position of the branch point on Growth and branching pattern analysis which the segment appeared. Its value is 0 if it is the prolongation of a growing root. Statistical processing of computed coordi- nates allows the calculation of some root architectural characteristics. Each root is Branching point file specified in terms of elongation and ramifi- cation. Some of them are time-indepen- dent, describing branching patterns (e.g., Each branch point record contains: 1) a number of root, number of parent root, sequential index of the root segment to root order, branch angle, Dbase, interbran- which the branch point belongs (sequen- ch distance and time of emergence); the tial index of the parent root); 2) a real la- others evolve with time (e.g., root elonga- teral index: it is 1 if there is a previously tion or velocity of lateral initiation, defined digitized lateral segment and 0 if the by length of the apical non-branching branch point does not yet bear a lateral; 3) zone). virtual segment index: this parameter is a used to help in the search for particular points during digitizing; in fact, branch points are not drawn on the video monitor, Simulation of ra root growing system so, in order to facilitate branch point identi- fication, virtual segments can be intro- duced. When the lateral root segment is This procedure uses a developmental and finally introduced, 4) the virtual segment is deterministic model in which the move- automatically deleted; the coordinates of ment of each root tip is localized in time branch point and of final point of virtual and space (three-dimensionally) (Pages segments; and 5) the rank of branch point. and Aries, 1988). The parameters intro- duced in this mode! are specified for each root order. For oak seedling, taproot elon- Final data structure: resorting root seg- gation is quasilinear (Elong aT+ b) and = ments 2nd order root elongation is exponential (Elong a (1 --); the branching pat- 1 e- b = tern is characterized by 5 parameters In order to facilitate the of computation (basal non-branching zone length, inter- final data storage characteristics, root a branch distance, apical non-branching structure is created by reorganizing root zone length, branch angle and numbers of segments through 3 successive sortings: generators) and geotropism coefficient 1} according to the running index, in other (parameters not produced by the data words, to the root to which they belong; 2) acquisition system). Table II gives numer- according to ascending root order; 3) ical parameters from a simulation of root according to the distance of branching architecture for a 2 mo old oak seedling. point from origin of the parent root (Dbase). This final data organization allows a direct expression of the ’hierar- chic’ position of each root in the ramified Discussion system and speeds up the computing of growth and ramification parameters. Table This new data ;acquisition system allows a I shows the final data structure of the quantitative analysis of root architecture simplified example from Fig. 1.
with all dynamic aspects because the References location of all branches and root tips are Belgrand M., Dreyer E., Joannes H., Velter C. & recorded in space and in each time step. Scuiller 1. (1987) A semi-automated data pro- This method will be very useful for stu- cessing system for root growth analysis: appli- cation to a growing oak seedling. Tree PhysioL dying the changes of root development 3, 393-404 induced by any stress of the substrate Pages L. & Aries F. (1988) Mod6le architectural (e.g., waterlogging, water stress, chemical de base pour 1’6tude de la croissance et du stress, influence of fertilizers). It could be d6veloppement du systeme racinaire. I. Le applied to any ramified structure and mod6le. Agronomie 8, 888-897 allows a detailed analysis of growth and Rose D.A. (1983) The description of the growth branching patterns. of root systems. Plant Soil 75, 405-415 5