Nomenclatures

  • Country and State Abbreviations to be used with site names
    Source: International Organization for Standardization, document ISO 3166-1
    This table lists country abbreviations
    This table lists Chinese province abbreviations
    This table lists US state abbreviations
     
  • 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 listed as two digits
    For example: AD_chr.01, D_chr.12
    This table lists tetraploid cotton chromosome numbers (current and historic) with associated CottonGen format.
     
  • 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 had the number of digits in their names standardized (decided by the size of the marker dataset).
    This table lists marker prefixs with standardized digit numbers for each marker set.
     
  • QTL Names in CottonGen are assigned using an "A.B-C_Da-E*.Env*.N*", where:
    A = CottonGen QTL Symbol. It consists of the letter 'q' and the 'Abbreviation' name (listed in Cotton Trait Ontology table) for the QTL trait (for example: qSL2.5).
    B-C = Population information. B is the initials of the parents of the mapping population and C is the population type (F2, RIL, etc; for example T3-RIL).
    D-E = Chromosome information. D is the chromosome or linkage group name where the QTL is located and E is the index number if the chromosome has multiple linkage groups.
  • Env = Environment information (cotton site code).
    N = if multiple QTL on the same chromosome or linkage group are of the same trait type and from the same environment, N is used as an index for differentiating between those QTL.
    *: only used when relevant information exists
    a: D has to be displayed as a two digit chromosome number (01-26), do NOT use A01-13 or D01-13 in CottonGen QTL symbols