Nomenclatures

Index of Nomenclatures used in CottonGen (Click to view details)

• Chromosome Numbers
• Country and State Abbreviations (ISO 3166)
• DNA and Protein IUPAC codes
• Journal Code
• Map Names
• Marker Type/Names
• QTL Names

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 US state abbreviations
• This table lists Chinese province abbreviations
• This table lists India 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 (i.e. AD, A, D, B, G, ...)
• B = chromosome number listed as two digits. AD genome will have both chromosome_number (1-26) and At or Dt 1-13 chromosome number
• For example: AD_ch18_Dt.13; A_01; E12, etc.
• 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 types
• This table lists marker prefixs with standardized digit numbers for each marker set.

QTL Names in CottonGen are assigned using an "A.B-C_D^a-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