Cotton Trait Ontology

The lack of a common, structured vocabulary to describe cotton phenotypic traits is an obstacle for researchers wanting to understand the work of colleagues as well as for integration of QTL associated with these traits into CottonGen.  Here we present a Cotton Trait Ontology (a set of standardized and structured vocabularies for cotton traits) which aims to provide a central location with controlled vocabulary for phenotypic traits to improve discussion and collaboration among research groups within the cotton community.  The terms in the Cotton Trait Ontology were developed from trait evaluation data within five germplasm collections from four countries and from QTL-trait association data obtained from over one hundred peer-reviewed publications.  The vocabulary was established by CottonGen with input from Drs. Lori Hinze, Richard Percy, and Russell Kohel (USDA-ARS, College Station, TX).

Click to view Standardized Descriptors and Rating Scale used for the US National Cotton Germplasm Collection

Root Term Sub-root Term Phenological Term Abbreviation Definition
Quality fiber length 2.5 span length SL2.5 The length at the 2.5% of fibers in an array are that long or longer
Quality fiber length 50 span length SL50 The length at the 50% of fibers in an array are that long or longer
Quality fiber length fiber length FL Fiber length is measured on a beard of cotton fibers on HVI systems and is reported in hundredths of an inch and equivalent staple length in thirty-seconds of an inch
Quality fiber length fiber length by number FLN Using AFIS to measure the mean length of fibers calculated by number
Quality fiber length fiber length by weight FLW Using AFIS to measure the mean length of fibers calculated by weight
Quality fiber length fiber mean length ML The average length in inches of all fibers longer than 1/4 inch
Quality fiber length short fiber content SFC The percent of the fibers, calculated by number, that are less than 0.50 in
Quality fiber length short fiber index SFI It is defined as fibers shorter than 0.5 inch or 12.7 mm.
Quality fiber length upper half mean length UHML Upper half mean length is the average length of the longer one-half of the fibers (inch)
Quality fiber length upper quartile length by number UQLN Using AFIS to measure the length which is exceeded by 25% of the fibers by number
Quality fiber length upper quartile length by weight UQLW Using AFIS to measure the length which is exceeded by 25% of the fibers by weight
Quality fiber instrument color fiber color grade FCG Color grade refers to the gradations of reflectance (Rd) and yellowness (+b) the cotton.
Quality fiber instrument color reflectance CRD Colorimeter Rd, the percentage of reflectance
Quality fiber instrument color yellowness CB Colorimeter +b. Yellowness indicates how much yellow color is in the sample
Quality fiber maturity/fineness Arealometer A AREOA Arealometer A measures the external surface area of the fibers of a given volume of material, expressed in square mm per cubic mm of fibrous material.
Quality fiber maturity/fineness Arealometer AH AREOAH Arealometer AH measures specific area, which is an arealometer A determined at high pressure
Quality fiber maturity/fineness Arealometer D AREOD Arealometer D is the difference between specific area determined at high pressure and standard pressure. D is presumably a measure of flatness of the fiber ribbon.
Quality fiber maturity/fineness fiber cell wall thickness WALL Using either Arealometer (t) or AFIS to measurement the fiber cell wall thickness
Quality fiber maturity/fineness fiber fineness FF Using AFIS to measure the mean fiber fineness (weight per unit length)
Quality fiber maturity/fineness fiber immature content FIM The immaturity ratio is a dimensionless number which describes a physical characteristic of the fiber cross section.
Quality fiber maturity/fineness fiber mature content FM Arealometer M, the simple linear regression prediction of caustic soda percent maturity from Hertel and Craven Textile Research Journal 21: 765-774,1951.
Quality fiber maturity/fineness fiber perimeter FP Arealometer p, a measure of the perimeter, is defined as the distance around the outside wall of the fiber cross section.
Quality fiber maturity/fineness micronaire MIC The fineness of the sample taken from the ginned lint, measured by a Fibronaire and expressed in standard (curvilinear scale) micronaire units
Quality fiber maturity/fineness weight fineness WTFN Arealometer w, is defined as the mass per unit length of fiber
Quality   fiber uniformity FU The ratio between the mean length and the upper half mean length of the fibers expressed as a percentage
Quality   fiber elongation FEL Elongation is the degree of extension of the fibers before a break occurs when measuring strength
Quality   fiber strength FS The fiber strength of a bundle of fibers measured on a Stelometer
Quality   fiber spin consistency index FSCI  
Quality   coefficient variation of length by number LNCV The coefficient of variation (CV) of fiber length by number (Ln, AFIS measurement)
Quality   fiber quality score QS Fiber quality score (Qscore), very similar to a selection index, adds the weighted values of selected fiber traits (length, mic, UI, strength) to provide a single measure (0-100) of desirable fiber qualities
Quality   trash content TRASH Trash content is a measure of the non-lint particles (like leaf, bark) in the cotton
Biochemical seed kernel composition seed oil content SOC Percentage of oil by weight in 10 gram sample of dehulled seeds.
Biochemical seed kernel composition seed protein content SPC Protein weight per 100 kernels
Biochemical seed kernel composition seed gossypol content SGC gossypol or free gossypol contents in seed kernel
Biochemical seed kernel composition seed nitrogen content SNC The nitrogen in fuzzy seeds expressed as a percentage of nitrogen in the mass of fuzzy seeds. The percentage of nitrogen multiplied by 6.25 is an approximation of the percentage of protein.
Biochemical seed kernel composition seed arginine content AAARG The amount of total cotton seed protein that is composed of arginine
Biochemical seed kernel composition seed aspartate content AAASP The amount of total cotton seed protein that is composed of aspartate
Biochemical seed kernel composition seed cysteine content AACYS The amount of total cotton seed protein that is composed of cysteine
Biochemical seed kernel composition seed glycine content AAGLY The amount of total cotton seed protein that is composed of glycine
Biochemical seed kernel composition seed isoleucine content AAILE The amount of total cotton seed protein that is composed of isoleucine
Biochemical seed kernel composition seed leucine content AALEU The amount of total cotton seed protein that is composed of leucine
Biochemical seed kernel composition seed phenylalanine content AAPHE The amount of total cotton seed protein that is composed of phenylalanine
Biochemical seed kernel composition seed serine content AASER The amount of total cotton seed protein that is composed of serine
Biochemical seed kernel composition seed valine content AAVAL The amount of total cotton seed protein that is composed of valine
Biochemical seed kernel composition seed linolenic acid content FALIN The amount of total cotton seed oil that is composed of linolenic acid
Biochemical seed kernel composition seed oleic acid content FAOLE The amount of total cotton seed oil that is composed of oleic acid
Biochemical seed kernel composition seed palmitic acid content FAPAL The amount of total cotton seed oil that is composed of palmitic acid
Biochemical seed kernel composition seed stearic acid content FASTE The amount of total cotton seed oil that is composed of stearic acid
Agronomical yield lint index LI The weight of lint per 100 seed
Agronomical yield lint percent LP The weight of lint ginned from a sample of seed cotton expressed as a percentage of the weight of seed cotton.
Agronomical yield lint yield LY The mean production of the plots harvested, expressed in weight of lint of each plant/plot/area
Agronomical yield seed cotton yield SCY weight of harvested cotton seed by each plant/plot/area
Agronomical yield seed index SI The mass of 100 fuzzy seeds, in grams  
Agronomical yield component boll number BN number of mature bolls per plant
Agronomical yield component fruit branch node number FBNDN The average nodes of the fifth to eighth fruit branches.
Agronomical yield component fruit branch number FBN the number of fruiting branches
Agronomical yield component productiveness PRODUCT Relative assessment of the productivity of an accession by observing the boll load on a single plant
Agronomical yield component seed cotton weight per boll BWT The average weight in grams of a boll
Agronomical yield component seed number per boll SNPB Number of seeds per boll is a calculated estimate of the actual number of seeds in a boll.
Agronomical stature or vigor first fruit branch internode length FFBNDL first fruit branch internode length
Agronomical stature or vigor first fruit branch position FFBH first fruiting branch position measured by number of stem node or height
Agronomical stature or vigor fruit branch internode length FBNDL Calculated by dividing fruit branch length by fruit branch nodes.
Agronomical stature or vigor fruit branch length FBL The mean length of fruit branches
Agronomical stature or vigor fruit branch length to plan height ratio RFBLPH The ratio of fruit branch length to plant height
Agronomical stature or vigor plant height PH Height of the plant at maturity
Agronomical stature or vigor stem height to node ratio RPHND The ratio of dividing the plant height by the total number of nodes on the plant.
Agronomical stature or vigor stem node number STEMNNN number of nodes on main stem
Biotic stress bacterial disease bacterial blight resistance BBR Resistance to bacterial blight [Xanthomonas citri pathovar malvacearum (Xcm) or Xanthomonas axonopodis pv. malvacearum (Xam)]
Biotic stress virus disease cotton leaf crumple virus resistance GBR Resistance to cotton leaf crumple virus (CLCrV, family Geminiviridae, genus Begomovirus)
Biotic stress fungal disease anthracnose resistance ANR Resistance to anthracnose (Coletotrichum gossypii)
Biotic stress fungal disease fusarium wilt resistance FWR Resistance to fusarium wilt (Fusarium oxysporum)
Biotic stress fungal disease southwestern cotton rust resistance PCR Resistance to southwestern cotton rust (Puccinia cacabata)
Biotic stress fungal disease verticillium wilt damage VWD Damage caused by verticillium wilt (Verticillium dahliae)
Biotic stress fungal disease verticillium wilt resistance VWR Resistance to verticillium wilt (Verticillium dahliae)
Biotic stress insect pest aphid resistance APR Resistance to aphid (Aphis gossypii)
Biotic stress insect pest red bollworm resistance RDBWR Resistance to red bollworm (Disparopsis spp.)
Biotic stress insect pest cotton bollworm resistance CTBWR Resistance to cotton bollworm (Helicoverpa gelotopoeon)
Biotic stress insect pest corn earworm resistance CEBWR Resistance to corn earworm (Helicoverpa zea)
Biotic stress insect pest tobacco budworm resistance TBBWR Resistance to tobacco budworm (Heliothis virescens)
Biotic stress insect pest African bollworm resistance AFBWR Resistance to African bollworm (Helicoverpa armigera)
Biotic stress insect pest South American bollworm resistance SABWR Resistance to South American bollworm (Sacadodes pyralis)
Biotic stress insect pest pink bollworm resistance PKBWR Resistance to pink bollworm (Pectinophora gossypiella)
Biotic stress insect pest pink spotted Bollworm resistance PSBWR Resistance to pink spotted Bollworm (Pectinophora scutigera)
Biotic stress insect pest spider mite resistance SPMR Resistance to spider mite (Tetranychus spp.)
Biotic stress insect pest boll weevil resistance BWVR Resistance to boll weevil (Anthonomus grandis)
Biotic stress insect pest leaf worm resistance LFWR Resistance to leaf worm (Alabama argillacea or Cosmophila auragoides or C. Flava)
Biotic stress insect pest plant bug resistance PTBR Resistance to plant bug (Lygus lineolaris or L. hesperus Knight)
Biotic stress insect pest sweet potato whitefly resistance SPWR Resistance to sweet potato whitefly (Bemisia tabaci)
Biotic stress nematode pest Columbia lance nematode resistance NCLR Resistance to columbia lance nematode (hoplolaimus columbus sher)
Biotic stress nematode pest reniform nematode resistance NRFR Resistance to reniform nematode (Rotylenchulus reniformis)
Biotic stress nematode pest rootknot nematode resistance NRKR Resistance to root-knot nematode (Meloidogyne spp.)
Biotic stress nematode pest sting nematode resistance NSTR Resistance to sting nematode (Belonolaimus spp.)
Abiotic stress   acidity tolerance ACIT  
Abiotic stress   cold tolerance CLDT  
Abiotic stress   drought tolerance DRTT  
Abiotic stress   hot tolerance HOTT  
Abiotic stress   salinity tolerance SALT  
Abiotic stress   wet tolerance WETT  
Morphological   boll color BOLLCL Boll color (NCGC rating scale)
Morphological   boll gossypol glands BOLLGL Gossypol gland density on bolls (NCGC rating scale)
Morphological   boll length BL Length of boll from base to tip
Morphological   boll nectaries BOLLNT The presence of nectar glands on the base of the boll or calyx (NCGC rating scale)
Morphological   boll opening BOLLOP Boll opening degree from tight to loose
Morphological   boll pitting BOLLPIT The depth and density of pitting associated with glands of the boll wall of the mature but non cleft bolls (NCGC rating scale)
Morphological   boll point BOLLPNT Degree of tapering of the boll tips (NCGC rating scale)
Morphological   boll shape BOLLSP General description of degree of roundness to the boll shapes (NCGC rating scale)
Morphological   boll size BS Relative size of bolls
Morphological   boll width BW Cross section at widest part of boll
Morphological   bract color BRACTCL The degree of red coloration to the bracts (NCGC rating scale)
Morphological   bract nectaries BRACTNT The presence of nectar glands on the base of the bracts on the outside or abaxial side.
Morphological   bract shape BRACTSP  
Morphological   bract size BRACTSZ  
Morphological   bract teeth number BRACTTN Relative number of bract teeth to what is typically seen for cultivars of G. hirsutum
Morphological   bract teeth size BRACTTSZ Bract teeth size (NCGC rating scale)
Morphological   bract type BRACTTP Bract type (NCGC rating scale)
Morphological   fruit branch angle FBA The angle between the fruit branch and the main stem
Morphological   fruiting type FRTP Pattern of boll formation on branches
Morphological   leaf color LFCL Coloration of mature leaf (NCGC rating scale)
Morphological   leaf gossypol glands LFGL Gossypol gland density on leaf
Morphological   leaf nectaries LFNEC Commonly observed nectar glands on the undersides of the leaf (NCGC rating scale)
Morphological   leaf shape LFSP The shape and structure of leaf (NCGC rating scale)
Morphological   leaf size LFSZ Leaf size (NCGC rating scale)
Morphological   lint color LINTCL Coloration of mature fiber (NCGC rating scale)
Morphological   locule number per boll LCLNPB  
Morphological   petal color PETALCL Flower petal pigmentation (NCGC rating scale)
Morphological   petal spot PETALSP Red coloration at base of flower petals, creating the effect of a spot in the center of the flower (NCGC rating scale)
Morphological   plant color PCL Plant pigmentation
Morphological   plant shape PS The shape and structure of plant
Morphological   pollen color POLLENCL Pollen pigmentation (NCGC rating scale)
Morphological   root fork number RF  
Morphological   root length RL  
Morphological   root surface area RSA  
Morphological   root tip number RT  
Morphological   root volume RV  
Morphological   seed coat index SCI Weight in grams of seed coats per 100 seeds
Morphological   seed color SDCL  
Morphological   seed fuzz color SDFZCL Observe seed fuzz color on the seed surface
Morphological   seed fuzz content SDFZCT  
Morphological   seed fuzz grade SDFZGD Observe seed fuzz on the seed surface and rate the density of fuzz
Morphological   seed kernel content SKC The weight of kernel over weight of whole seed
Morphological   seed kernel index SKI Weight in grams of kernel per 100 seeds
Morphological   seed type SDTP The clustering of the seed in the boll
Morphological   stem color STEMCL  
Morphological   stem gossypol glands STEMGL  
Morphological   stigma exsertion STGMTP The classified length of the stigmatic column in relation to the antheridial cone (NCGC rating scale)
Morphological   trichome density on calyx DTC The degree or relative density of trichome on calyx
Morphological   trichome density on leaf DTL The degree or relative density of trichome on leaf
Morphological   trichome density on plant DTP The degree or relative density of trichome on plant
Morphological   trichome density on stem DTS The degree or relative density of trichome on stem (NCGC rating scale)
Phenological   boll rate BOLLRT the avg number of bolls formed per day in a selected time period
Phenological   days emergence to flower bud DOS Number of days from seedling emergence to flower bud
Phenological   days emergence to maturity DOG Number of days from seedling emergence to boll opening
Phenological   days flower bud to flowering DOB Number of days from flower bud emergence to flowering
Phenological   days flowering to boll open DOFB Number of days from flowering to boll opening
Phenological   days to 50% boll opening BOLL50 Number of days between emergence and the first boll opening for 50% of the plants
Phenological   days to 50% emergence DOE50 Number of days to 50% emergence of cotton seedlings
Phenological   days to 50% flowering FLW50 Number of days between emergence and the first flower for 50% of the plants
Phenological   flower date FLWDT Flowering or anthesis time
Phenological   flower rate FLWRT flowering percentage during certain time period
Phenological   fruit node rate FBNDRT the number of fruit nodes formed per day during selected time period
Phenological   maturity group PM Relative maturity of entries when earliest cotton had all bolls open
Phenological   photoperiod FLWSC Indication of the flowering of the plot in relation to daylength
Physiological   canopy temperature CT The canopy temperature. The surface temperature of the canopy is related to the amount of transpiration resulting in evaporative cooling.
Physiological   canopy type CNPTY  
Physiological   leaf chlorophyll content CHL The amount of chlorophyll normally found in a plant under normal environmental conditions
Processing   waste WASTE The difference in mass, expressed as a percentage of the fed stock and delivered stock
Processing   yarn elongation YE  
Processing   yarn strength YS  
Processing   yarn tenacity YT