Nomenclatures

  • IUPAC codes
    This table lists IUPAC nucleotide code
    This table lists IUPAC amino acid code
     
  • Chromosome Numbers in CottonGen are assigned using an "A_chr.B" system, where:
    A = genome group name
    B = chromosome number lists in two digits
    For example: AD_chr.01, D_chr.12
    This table lists  tetraploid cotton chromosome number that used before and after chromosome pairs identified and the way used in CottonGen
     
  • Map Names of AD genome genetic maps are assigned using an "A-B_C/D" system, where:
    A = initials of the two parents of the mapping population;
    B = population type;
    C = chr + chromosome number;
    D = linkage group name or A or D tetraploid name.

     

  • Marker Names: SSR marker in CottonGen have been standardized by number of digits (decided by the size of marker dataset).
    This table lists marker prefixs with standerdized digit numbers for each different marker data set.
     
  • QTL Names in CottonGen are assigned using an "A.B-C_Da-E*.Env*.N*", where:
    A = CottonGen QTL Symbol. It is consisted of a letter 'q' with the 'Abbreviation' name (has to be listed in Cotton Trait Ontology table) of QTL trait (for example: qSL2.5);
    B-C = Population information. B is initials of the two parents of the mapping population and C is the population type (F2, RIL, etc; for example T3-RIL);
    D-E = Chromosome information. D is Chromosome or linkage group names where the QTL located and E is there number of pieces if the chromosome/linkage_group piece has more than one pieces;
    Env = Environment information (i.e. cotton_site_code).
    N = if the QTL on the same chromosome from the same environment has multi-locations, N is the orders (digit only) along to the chromosome;
    *: only being used when related information exist
    a: D has to be displayed as the 2-digits of chromosome number 01-26, do NOT use A01-13 or D01-13 in CottonGen QTL symbols.