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FACTORS INFLUENCING CUP

QUALITY IN COFFEE
Photo Courtesy of SPREAD, Rwanda
Prepared for the Global Coee Quality Research Initiative

Brian Howard
Global Coee Quality Research Initiative Review
Draft Copy
FACTORS INF L U ENCING CUP

Q UALITY IN
COF F EE
Introduction
Photo Courtesy SPREAD Rwanda

Cup qualityincoffee is affectedby agreat
numberoffactors; agronomic, genetic and
production related. In this review the
authorseekstosummarizethemajor@ind
ings of the research that has been con
ducted that is speci@ically related to cup
quality andhow it is affected bytheenvi
ronment inwhichthecoffeetreeisgrown,
thegeneticmakeupofthecoffeeplantitself
andthemannerinwhichcoffeeisprepared
forconsumption. Morethan800aromatic
compounds combine to give acidity, body
andaromatoacupofcoffee. Thesethree
descriptors will serve as the parameters
around which cup quality is described in
thisdocument.
Thequalityofcoffeeisextensiveinitsde@i
nition. Leroy et al, 2006 de@ines coffee
quality ona number oflevels. At the ex

porter or importer level coffee quality is
linked to bean size, number of defects,
regularity of provisioning, tonnage avail
able, and physical characteristics. At the
roaster level coffee quality depends on
moisture content, characteristic stability,
origin,organoleptic(tasteandsmell)quali
ties and biochemical compounds. At the
consumerlevelcoffeequalityisabouttaste
and@lavor, effects on healthand alertness,
geographical origin, and environmental
and sociological considerations. At every
linkinthesupplychainthereistheconsid
erationofprice. In2004theInternational
Organizationfor Standardization (IOS)de
@ined a standard for green coffee quality
which entails defects, moisture content,
size, and some chemical compounds of
beans as well as standardizationofprepa
ration ofa sample from which to perform
cuptasting. AccordingtoBertrand,Arabica
coffee production makes up 70% of the
worldtotal. Consequentlythisreview will
deal mainly withC.Arabicawitha few no
tableexceptionsinthesectionsongenetics
andcrossbreedingfordiseaseresistance.
Agronomy:
SoilNutrition
Coffee can be cultivatedon a wide variety
of soil types, provided theseare at least 2
meters deep, freedraining loams with a
goodwaterretentioncapacityandapH of
56, fertileandcontainnolessthan2%or
ganic matter. High quality, acidic Arabica
coffees tendto beproducedonsoilsofvol
canicorigin.
Van Der Vossen, 2005 expresses concern
that, to sustain economically viable yield
levels, 1 ton green coffee per hectare (4.5
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acres)peryear,largeadditionalamountsof
composted organic matter will have to
comefrom externalsources to meetnutri
entrequirements,especiallynitrogen&po
tassium. Themajority ofsmall landhold
ers will not be able to acquire the neces
saryquantitiesandwillbeconfrontedwith
decliningyields. Organic farmingdoesnot
necessarilyprevent diseaseorpests below
economically harmful thresholds and the
humidconditions of heavily shadedcoffee
mayactuallystimulatetheoutbreakofoth
ers.
Vaast etal, 1998foundthattotaluptakeof
nitrate (N03) and ammonium (NH4), key
nutrients for plant growth and develop
ment and the limiting nutrient in Arabica
Coffee, atanyratio washigherthanthatof
plantsfedsolelywithnitrateorammonium
alone. Anaerobic, lack ofoxygen, soil con
ditionsreducednitrateandammoniumup
takeby50%and30%respectivelyandthe
presence of dinitrophenol almost com
pletely inhibited N uptake in any form.
Vaast suggests that these results indicate
thatArabicacoffeeiswelladaptedtoacidic
soil conditions and can effectively utilize
theseasonallyavailableforms ofinorganic
nitrogen(N). Theseobservationscanhelp
to optimize coffee nitrogen nutrition by
suggestingagriculturalpracticesthatmain
tainrootsystemsinthetemperaturerange
that is optimum for both ammonium and
nitrate uptake. Vaast found that both ni
trateandammonium uptake peaked when
root systems were maintained at 34 de
grees Celsius. Below this temperature
plantcolorindicatedalossofvigor. There
forebothnitrate and nitrite availability in
soi, as well asthe coffeetrees capacityfor
uptakethroughidealtemperatureregimes,
can bemaximized. VanDer Vossen, 2009
notesthatexcessivecalciumandpotassium
in soils produce a hard and bitter tasting
liquor.
Fertilizer
OrganicvsInorganicFertilizer
Organic production of coffee is often
thoughtpreferableduetothestrongpoten
tial of negative environmental impacts
fromfertilizerleachingintosurfacewaters
and groundwater. However, any produc
tion crop signi@icantly depletes its soils
ability to replenish key nutrients and hu
mic matter taken from it in the form of
produce. Inorganic fertilizer is often ap
pliedatratesapproaching100to300kilo
gramsperhectareatsigni@icantexpenseto
producers. (Carvajal,1959)Becauseofthe
preference for organically produced pro
duce, especially in the specialty coffee
market,solutionsforsuchade@icitmustbe
found and implemented in regionally ap
propriateways.
Inthe shaded Indian coffeeterrior of Kar
nataka, India Nagaraj et al., 2006 found
thattheadditionofinorganicpotassiumin
theform ofmuriat ofpotash andsulphate
ofpotashhadtheeffectofincreasedcoffee
yields over the period of four years at a
rateofapproximately15%. Thedifference
between the two treatment methods out
linedbyNagarajnotbeingstatistically sig
ni@icant. Itshouldbenotedthatthesoilsin
whichthiscoffeewereplantedwerereceiv
ingapproximately40to60kgofpotassium
perhectareperyearinleaffall. Thestudy
indicatedthatnoconsistenttrendcouldbe
observed in the cup evaluation report for
three years. Cupquality ofArabicacoffee
was found to be similar in both MOP and
SOP treated plots but that there was a
modest improvement inthe cupquality of
robusta coffee in the sulphate potash
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treated plots compared to muriateof pot
ash applications in the second and third
years.Itshouldbenotedthattherehasnot
beenany evidence of changes occurringin
the @lavour compounds due to agronomic
useofsulphurorotherwise. (Krishnamur
thyRao,1989)StudiesconductedinKenya
by (Njoroge and Mwakha, 1985) did not
noteanydifferenceinliquorqualityofcof
fee between NPK fertilized plots and con
trol treatment over eleven years of re
search.
Cupqualitydifferences havebeenfoundin
studies contrasting organic and inorganic
fertilization. In a 2008 study undertaken
by Malta, et al. no signi@icant differences
were observed on the cup quality among
beans from conventional and organic
plantsinthe@irstyear. Howeverinthesec
ond year, cup quality of some organic
treated plants was superior when com
pared to conventionally treated plants. A
positive effect on sensorial attributes was
observedusingcattlemanure, eitheralone
or associatedwith coffee straw and green
manure.
In Hawaii, Youkhana & Idol, 2009 found
thattheadditionofmulchfrom shadetree
pruning signi@icantly offset net nitrogen
and carbon losses from coffee cultivation.
Improved carbon and nitrogen sequestra
tion in soil was measured over two years
andit was foundthatsoilbulk densitydid
notdeclineinmulchedplotsas opposedto
signi@icant changes in bulk density for un
mulchedplots.
Grossman et al., 2006 found that organic
production standards are being met while
availableNitrogen insoil is supplemented
by nitrogen @ixing shade trees. Biological
NitrogenFixationisfacilitatedthroughthe
useofleguminousshadetreesinthegenus
Ingawiththemostsigni@icantresultsfound
in1to 3yearoldplotsofC. ArabicaandI.

oerstediana. In these young plots it was
found that coffee trees were deriving ap
proximately20%oftheirnitrogenfromthe
biological nitrogen @ixation occurring via
symbiosiswithI.oerstediana. Noestimate
couldbederivedforplotsbetween5and7
years. It is a reasonable assumption to
makethatgreateravailabilityanduptakeof
soil nitrogenhas astrongpositive correla
tion to cup quality via plant health and
beansize.
Environmental Factors
ShadevsSun
Ithasbeenshownthatonthemost appro
priate sites, with intensive management,
selfshadingcoffeemonoculturescangive2
and3 fold increases over more traditional
shadedsystems.(Beer,1987)Shadetends
to reducephotosynthesis, rates oftranspi
ration, plantmetabolismandthusdemand
on soil nutrients. Due to lower nutrient
needs acropcouldpotentiallybe obtained
onmoremarginal soilswithlowerfertility.
Inareas where regular fertilizationcannot
be guaranteed it is recommended that
someshading treesberetainedas ahedge
against uncertain future soil inputs. Dr.
John Beer of CATIE stresses, The funda
mental question, when planning the reno
vationorestablishment ofacoffeeandca
cao plantation is whether the owner has
thesite, educationand resources to main
tainthecropswithoutshade.Coffeeunder
shade willsurvivesetbacks far better than
monoculturesofthecrop.(Beer, 1987)As
important as the question could im
provementsincoffeequalitythroughshade
bemadeinagiven location, thequestion
of whether a farmer should seek to use
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shade in his plantation becomes equally
important. Dr. Beer suggestsanumber of
possible advantages and disadvantages of
suchadecision.
AdvantagesofShadingInclude:
(1)TheSuppressionofWeedGrowth
(2) Potential for Product Diversi@ication
suchasfruitsandtimberalongsidecof
fee
(3) Greater control over crop phenology
suchasfruitsettingandmaturation
(4) Potentialimprovementofcropquality
(5) Reductionofevapotranspirationrateof
theshadedcrop
(6) Removal of excess soil moisture by
transpiration of a heavy shade tree
cover
(7) Potential for increased moisture input
throughhorizontal interceptionofmist
orclouds
(8) Extension of the productive life of the
crop
(9) Reductionoftemperatureextremes
(10)Reductionofdamagecausedbyhailor
heavyrainandwinds
(11)Bettersoildrainageandaeriation
(12)Theprovisionofsoil mulchfromtree
throughfall
(13)Reductionoferosiononslopes, iesoil
conservation
(14) Recycling of nutrients not accessible
tothecrop
(15)Nitrogen@ixationbyshadetrees
DisadvantagesofShadingInclude:
(1) Throughfalldamagetounderstorycrop
(2) Suddendefoliationofshadetreescould
causeashocktothecrop
(3) Additional labornecessaryto maintain
thesameacreage
(4) Mechanizationofthe crop maybe hin
dered
(5) Erosion control structures like terrac
ing would be hampered once shade
treesareplanted
(6) New crop varieties are often bred for

monoculturalconditions
(7) Reduced air movement and humidity
mayencouragefungalgrowth
(8) Shade trees can be other potential
hostsforpestsanddiseases
(9) Reduction of photosynthetically avail
ablesunlight
(10) Shade tree rootcompetition of nutri
ents
(11) Rainfall redistribution could cause
spot erosion or reduce overall soil
moisture
(12) Harvesting of wood or fruit from
shadetreesisanadditionaldrainofsoil
nutrients
Desirable Characteristics for Shade
TreesInclude:
(1) Theability to @ix nitrogen from the at
mosphere
(2) Compatibilitywiththecropinterms of
facilitatingminimalcompetitionforwa
ter,nutrientsandgrowingspace
(3) Strong rooting systems as shade trees
are more exposed to adverse climatic
conditions
(4) Ability to extract soil nutrients which
arenottrappedbythecrop
(5) A light crown that provides regular
mottled shade rather than uniform
shadowandpoorlightquality
(6) Flexiblebranchesandstems
(7) High biomass productivity of recycled
materialinsoil
(8) Absenceofmajordiseasesusceptibility
thatcouldleadtorapiddefoliation
(9) Smallleavestoreduceraindropcoales
cence
(10) Not analternative host forinsects or
pathogens which could endanger the
crop
Bosselmannetal., 2009inHuila,Colombia
found that sensory attributes were in@lu
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encednegatively byshade, andthat physi
calattributeswerein@luencedpositivelyby
altitude. In higher altitudes (approxi
mately1700metersabovesealevel)shade
had a negative effect onfragrance, acidity,
body, sweetnessandpreferenceofthebev
erage, while no effect was found on the
physicalqualityofthebean. Atloweralti
tudes, shadedid not havea signi@icant ef
fect on sensorial attributes, but signi@i
cantlyreducedthenumberofsmallbeans.
At high altitudes with low temperatures
and no nutrient or water de@icits, shade
treesmayhaveapartlyadverseeffectonC.
Arabica cv Caturra resulting in reduced
sensory quality. The occurrence of berry
borer (Hypothenemus hampei) was lower
at high altitudes and higher under shade.
Bosselman goes on to suggest that future
studiesonshadeandcoffeequalityshould
focus on the interaction between physical
andchemicalcharacteristicsofbeans.
A studywasdoneinCostaRicabyVaastet
al., 2005contrastinglight regimes andop
timal coffee growing conditions on dwarf
coffee, CoffeaArabica. Shadewasfoundto
decrease coffee tree productivity by 18%
but reducedalternatebearing. Shadealso
positively affectedbeansizeand composi
tionaswellascupqualityduetoadelayin
berry @lesh ripening by up to a month.
Higher levels of sucrose, chlorogenic acid
and trigonelline in sun grown beans indi
catedincomplete beanmaturation andre
sultedinhigherbitternessandastringency
in cup quality. Higher fruit loads, which
can bemitigatedthroughbranchthinning,
reduced bean size owing to carbohydrate
competition among berries during bean
@illing. Higher taste preferences were
linkedto lower fruitload. Shadewasalso
foundtomitigatenegativeattributesincof
fee quality like bitterness and astringency
while positive attributes like acidity were
found to be signi@icantly higher in shade
grownbeans. A noteworthyaspectofthis
studywasthattheoverallbeveragequality,
higher acidity, lower astringency and
higher preference, was foundto be higher
in the year 2000 when production was
around30%lowerthanin1999.
Geromeletal,2008buildshis studyonthe
effects of shade on the development and
sugar metabolism of Coffea Arabica L. on
the premise that coffee fruits grown in
shadearecharacterizedbylargerbeansize
than those grown under full sun condi
tions. Beansize, as noted,is astrong con
tributor to cup quality. He found that
shade led to a signi@icant reduction in su
crosecontent andto anincrease in reduc
ingsugars. Inpericarpandperispermtis
sues, higher activities of sucrose synthase
andsucrose phosphate synthase were de
tected at maturation in the shade com
paredwithfullsunandthat bothenzymes
alsohadhigherpeaksofactivitiesindevel
oping endosperm under shade thaninfull
sun. Geromel went on to suggest that
metabolic pathways for sucrose needed
further study for identi@ication. Van Der
Vossen concurs that shade has a positive
effect oncoffeequality, particularlyat me
diumaltitudesbutalsoreducesyields. He
alsofoundthatataltitudesabove1800me
tersshadedidnotimprovecupquality.
Muschler, 2001foundacrosstheboardim
provement in organoliptic parameters as
shading increased. A blind tasting experi
ment showed highly consistent shade in
duced improvements in both green and
roastedcoffee. Improvements were made
in both theacidity and body ofthe bever
ageforbothCaturraandCatimorarabicas.
Theonemildlynegativeeffectofshadewas
found to be onthearomaof the beverage
for Catimor. It is thought that in the sub
optimal coffee zone that was studied, the
shadepromotedslowerandmorebalanced
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@illing and more uniform ripening of ber
ries that yielded a better cup quality than
the unshaded coffee plants. (Muschler,
2001)
Above: Quality attributes of green beans of two

varieties of Coea arabica grown without shade
and with dense shade (80% shade) of Erythrina
poeppigiana at a low elevation. Beans were harvested at full maturity. (This figure courtesy of
CATIE)
Rainfall&Irrigation
Van Der Vossen states that rainfall re
quirements for Arabica coffee production
are at least 1200mm per year with a
maximum of 2500mm. He contends that
coffee plants grow and yield better if ex
posed to alternate cycles of wet and dry
seasonsandthataperiodofwaterde@icitis
helpfulinsynchronizing@lowerbuddiffer
entiation. Areas with precipitation inex
cess of2500mmhavethetendencytopro
duce lower quality coffee due to irregular
cherryripeningandpoorbeandryingcon
ditions afterharvesting. Ontheother end

of the spectrum in drought years shoot
diebackandprematureripeningoftheber
ries can result in light beans producing a
liquorwithimmatureandastringentnotes.
Da Silva et al, 2005 investigated thein@lu
enceofenvironmentalconditionsandirri
gation on the chemical composition of
greencoffeebeansandtherelationshipsof
thoseparameterstothequalityofthebev
erageaccordingtobothsensorialandelec
tronic analysis. He found that irrigation
was not a major factor affecting chemical
composition since there were few differ
ences in relation to non irrigated coffee
plants. Hefound theproductionsitetem
peraturedifferentials to bethe mainin@lu
encing factor on biochemical composition.
Thestudywas undertakennearSao Paulo,
Brazil and the major @inding was that cup
quality decreased as air temperature rose
to about 3.5 degrees above the optimum
limit for coffee cultivation at 18 to 21de
greesCelsius. Similar@indingsarereported
byDecazietal.,2003inArgentina.
InastudydoneinAustraliabetween2000
2002by David Peasleyof Rural Industries
Research, irrigation was found to signi@i
cantly increase bean yield as well as pro
duce the following results under interna
tionally recognized SCAA cupping forms.
Thenonirrigatedcontrol cropscoreda69
with the description of low acidity and
mild smoky @lavour and thin body. The
low water stressed irrigated treatment
scored 73 with the description of dull
bakeyaroma,niceacidity,sour,greenapple
@lavor. The medium water stressed irri
gated treatment scored 75.5 with the de
scription of faint but sweet aroma, juicy,
citrus @lavour, OKbody. Eachofthethree
areasreceived1634mmofrainfallwiththe
low water stressed irrigated area having
2100mmofirrigationappliedto it andthe
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highly waterstressedirrigatedareahaving
647mmofirrigationappliedtoit.
Temperature&Altitude
Decazy et al, 2003 found that Honduran
coffees ofsuperior qualitycamefrom high
altitudes, above 1000m, where rainfall re
mains relatively low, that is to say below
1500mm per year. It was found that a
strong inverse relation between rainfall
andfatcontentexistsandthatthisrelation
needs to be consideredin relation to alti
tude because in the sampled regions in
Honduras, rainfallandaltitudewerefound
to be inversely correlated. High altitude
greencoffeebeanshadahigherfatcontent
thanloweraltitudebeansandgaveabetter
cup quality. VanDer Vassen stresses that
highaltitudes arecriticalforthesuccessful
production of highquality Arabica coffees
inequatorialregions. Lowertemperatures,
andtheir longer daily amplitudes, tend to
induce slower growth and more uniform
ripeningoftheberries, andproducelarger
anddenserbeans.Beansizeanddensityis
oftencorrelatedtoaroma,@lavorandsupe
rior beverage quality. Altitude also tends
to have a positive effect on acidity while
reducingbitterness.
Whilefortraditionalcultivarselevationhas
tended to play a signi@icant role in bean
biochemistry and organoleptic qualities,
withchlorogenicacidandfatconcentration
increasingwithincreasingelevation,thisis
not necessarily the case with Arabica hy
bridcultivarsliketheCaturra. ForArabica
hybrids little correlation is foundinvaria
tion in chorogenic acid concentration and
none of the variation in fat can be corre
lated to elevation.. However, Arabica hy
brids were found to have 1020% higher
fatconcentrationsthantraditionalcarieties
atlowelevationsandsimilarfatconcentra
tions at highelevations. Theanalysis con

@irmed homeostasis of the hybrids for
which bean biochemical composition was
onlyslightlyaffectedbyelevationthanthat
of traditional varieties. The cupping per
formed on samples originating from high
elevations showed no signi@icant differ
ences between Arabica hybrids and tradi
tionallines.(Bertrandetal.,2006)
Slope
EastfacingslopeswerefoundbyAvelinoet
al., 2005to yield beverageswith generally
superior attributes, probably because of
superior exposure to morning sunlight.
Thebeveragesfromeastfacingslopeswere
mainlymoreacid, witha score of2.73out
of 5, in the higher quality terriors, as op
posedto 2.36outof5forotherexposures.
In addition a positive relation was found
betweenaltitudeandtasterpreferences.
Laderach&Vaastetal. intheirGeographi
cal Analyses to Explore Interactions be
tweenInherentCoffeeQualityandProduc
tion Environment state that increasing
slope negatively in@luencedthe @inal score
of cup quality from terriores on two test
sitesinColumbiaandNicaragua.
Genetics:
With total economic damage to coffee
crops mounting to an estimated US $22.5
billion annually, coffee leafrust andcoffee
berrydiseaseaffectasigni@icantportionof
thesupplychain. In additiontoincreased
scarcity due to disease and fungus signi@i
cant environmental hazards exist due to
the copper based fungicides used to @ight
Coffee Berry Disease andCoffee Leaf Rust
chemically. (Van Der Vossen, 2009) Ac
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cording to Walyaro, 1997 the aim ofmost
genetic improvement programs is disease
resistance and quality. Determination of
berry and bean characteristics usingplant
breeding is relatively simple, aroma and
@lavor attributes present signi@icantly
greater dif@iculties due to their chemical
complexityandsusceptibilitytoagronomic
variability. Walyaro goes on to postulate
thatthedevelopmentofreliablelabproce
dures which relate individual chemical
compounds to cup quality could have im
portantbearingongeneticimprovementof
cup quality in coffee. It has been shown
that resistance to disease and nematodes
canbeincreasedthroughgeneticexchange
betweenC. ArabicandC.canephora. (Ber
trand et al., 2005, Dessalegn et al., 2008,
Leroyetal.,2006)
The Coffea genus encompasses about 100
different species. Within those species, C.
Arabica and C. Canephora make up ap
proximatley70and30%ofthetotalcoffee
market. Atagenetic level, Arabicaisatet
raploid (2n=4x=44 chromosomes), which
havetheirorigininanaturalcrossbetween
thespeciesC.CanephoraandC.Eugenoides
according to Lashermes et al., 1999, 2000.
Arabica is a self pollinating species which
partially explains its narrow genetic base
andtheensuingdif@iculty withincorporat
ingnewtraits.Robusta,however,isdiploid
(2n=22 chromosomes) and is not self
compatible becauseofa gametophytic sys
temofincompatibilitycontrolledbya sin
gle gene with multiple Salleles whichex
plains the higher genetic diversity within
thespeciesandensuingeaseofgeneticim
provement by conventional breedingtech
niques.Castroetal.,2006)
InC.ArabicaandC. Canephorabeandevel
opmentisalongprocessthatis character
ized by fundamental shifts in the makeup
of the beans tissue. For economically vi
able species ,C. Arabica & C. Canephora, 6
to 8months and 911months arerespec
tivelyrequiredforbeansto reachmaturity.
Fruit development does not occur at the
sametimewithvaryingproportions ofdif
ferent fruit sizes occuring on the same
plant. Despite variation in fruit growth
timing andthe differences inthe lengthof
each species reproductive cycle, the pri
mary steps of seed development are
thought to be identical between commer
cialspecies.(DeCastroetal.,2006)
After fertilization and up to mid develop
mentthefruitisprimarilymadeupofperi
carp and perisperm tissue. In the latter
phases of development the perisperm
graduallydisappearsandisreplacedbythe
endosperm, also knownasthe true seed
whichwasinitiallypresentinaliquidstate.
Theendospermhardensasitripensduring
thematuration phase due to accumulation
of storage proteins, sucrose and complex
polysaccharideswhichrepresenttheseeds
primary energy reserves. The @inal phase
of bean maturation is the dehydration of
theendospermandthecolorchangeofthe
pericarpto adark red color. Key changes
accompany the development of the coffee
cherry whichrequire both quantitave and
qualitativedescriptioninordertofullyde
scribe the growth anddevelopment ofthe
beaninrelationtoitseventualcupquality.
(DeCastroetal.,2006)
CoffeeFruitDevelopment
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C: 120150 days after@lowering: There
maining folded outer perisperm layer is
enclosingthecompletelymilkyendosperm.
Below: Phases of coffee fruit development
(TakenfromDeCastroetal.,2006):
D: 230240days after @lowering: A ma

ture cherryfruithasbeenformedshowing
two developedmatureseedsenclosingone
cotyledonary matureembryo insideofthe
solidendosperm.(Decastro,2006)
PlantResistance
Schematic representation of the tissues present at the mature stage (220-250 days after
fertilization). Photo Courtesy of Nestle Inc.
A: 060days after@lowering: Ovary after

anthesis.Thegrowingperisperntissue,the
integuments and the young embryo sac
thatwillfurtherdevelopintheendosperm
arevisible.
B:60120daysafter@lowering:Theperi
carp and liquid endosperm tissueor true
seedwhich grows by absorbing theinner
perisperm tissue, becomeclearly visiblein
crossection.
According to DeNardi et al., Coffee plants

@ight off pathogenic infections through a
number of strategies, including the
strengthening of cell walls, activating or
synthesizingantimicrobialcompounds(an
tibiotics) and expressing defense
associated proteins like pathogenesis re
lated(PR)proteins. Often, plantswillacti
vateahypersensitiveresponsethatischar
acterizedbythe rejection and deathofin
fected cells as shownby Greenburg, 1997.
A localized response can trigger longer
standingsystemicresponsesknownasSAR
systematic acquired resistance. This re
sponse prepares the plant for resistance
against a large spectrum of pathogens.
Plants express large arrays of resistance
genes (R genes)that guardagainst patho
gens. Thesegenes encode putative recep
tors thatrespondto theproducts ofaviru
lencegenesexpressedbypathogensduring
theinfectionofaplant. Therecognitionof
avirulence genes initiates a downstream
signaling that can render the attempted
infection unsuccessful. Systematic ac
quired resistance (SAR) inducing chemi
cals provide a unique opportunity to view
inducedresistancemechanismsinplantsin
the absence of a biological model system.
S p e c i @ i c a l l y , 2 c h e m i c a l s , 2 , 6
dichloroisonicotinic acid (INA) and benzo
(1,2,3)thiadiazole7carbothionic acid s
methyl ester (BTH), have been demon
10
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stratedto be effective inducers of system
atic acquired resistance in a variety of
plants.Thesecompoundsworktoprotect
plants from pathogenic infections without
having direct microbial activity. Despite
acting downstreamofsalicylic acidinSAR
signaling, they activate the SAR signal
transduction pathway through the same
signaling cascade thus imitating an infec
tionand improving the plants natural de
fenses, making it more resistant to infec
tion in the future. De Nardi went on to
con@irm C arabica showed typical SAR re
sponsesto BTH treatment. Bothrootsand
leaves responded with a shift in metabo
lism from normal housekeeping activity
defensive activity. Unexpectedly, the root
reactionwasfoundtobedifferentthanthe
leafreaction. Theprimaryresponseinthe
leafwasanincreaseinphysical andchemi
cal barriers, along with repression of the
genes involved in photosynthesis andnor
mal metabolic pathways. The enhance
mentofcellwalls appearedtobethemain
response in root systems and the normal
antimicrobial peptides, in the form of
chitinases and peroxidases, were not ob
served. ItispropoundedbyDeNardithat
this approach for mimicking a plant dis
ease or a pest attack is an approach that
canbeappliedtotheproblemofproducing
quality coffee without the use of microbi
cides, insecticides and fungicides while
safeguarding crops from pests and dis
eases.(DiNardietal.,2006)
The greater debate and perhaps of more
importance to the topic of cup quality is
whether this genetic resistance will lower
overall cupquality by necessityandinthe
enddecreaseconsumerexperience.
MajorDiseases:
Coffee leaf rust (CLR) is caused by a

pathogen of the leaf called Hemileia vas
tarix and is characterized by orange rust
postulesontheundersideoftheleaf. This
pathogen causes signi@icant losses as are
sultoflossofleafareaandthecorrespond
ing loss of photosynthesis and leaf drop.
Coffeeleafrusthasnowspreadthroughall
Arabica coffee producing countries in the
worldmaking it asigni@icant issueforthe
coffeeindustry asawholeintermsofsup
plysusceptibility.
Coffee berry disease (CBD) is caused by
Colletotrichum kahawae and is a fungus
that causes dark lesions onthe green and
ripening berries. CBD is unique in that
croplossesduetothefunguscanbesevere.
According to the Coffee Research Founda
tion s annual report for 19871988 in Af
rica as a whole losses can range between
30% and50% during very high precipita
tionyearsevenwithchemicaltreatment.
Fusarium (Giberella) stilboides (Fusar
iumbarkdisease)isapathogenthatcauses
bark lesions which are a result of damage
tothevascularsystem. Vascularwiltoften
resultsinthedeathoftheentiretree. Fu
sariumisreportedtohavealmostkilledthe
entirecoffeeindustryinMalawiinthelate
1970saccordingtoSiddiqi,1980.
Root Knot Nematode (Meloidogyne ex
igua)has been shownto be a huge threat
to ArabicagrowingareasinLatinAmerica.
Coffea Arabicas resistance to M. exigua is
controlled by an single inherited major
gene,Mex1. Alipzaretal.,comparedresis
tant and susceptible pure line cultivars
with clones of hybrid cultivars derived
from crosses between resistant and sus
ceptible lines. The results show that re
production of the nematode was signi@i
cantly higher on the hybrid cultivars than
on resistant pure line cultivars, however
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resistance was much lowerthan ona sus
ceptiblepurelinecultivar. Individual galls
on the root systems of hybrid cultivars
were found to be much smaller than on
susceptiblecultivars. After a4year moni
toring period Alpizar et al. reports that M.
exiguapopulationsinatest@ieldweremul
tiplied by a factor of 14 on susceptible
plantsbuyonlybyafactorof1.9onhybrid
cultivars. Theycometotheconclusionthat
Mex1couldhaveincompletedominantex
pression that allowed nematode penetra
tion, but inhibited the durable reproduc
tionofthenamatode.(Alpizaretal.,2006)
Genetic modi@ications have in some cases
affectedcupquality adversely but in many
caseshavenotadverselyaffectedcupqual
ity andincreasedgeneticresistanceto cof
fee leafrust and M. exigua by introducing
genetic material into the Arabica plant
from C Canephora via the Timor hybrid.
(Leroy et al., 2006) There are regional
variations inresistancetodiseasethatcan
beexploited while maintaining or improv
ingbeveragequalityasisnotedbyAnzueto
et al., 2001. Anzueto remarks that Ethio
pian origins provide resistance to nema
todesandpartialresistancetoleafrustand
likelyimprovebeveragequality.
InhigherqualityC.Arabicastocksthemain
goal seems to be in the area of improve
ment of resistances to pathogens and an
increasing of yield. LeRoyetal., contends
thatintrogressionofaliengeneticmaterial,
materialfromC.canephora, does notseem
to be linked directly to variation in cup
quality.(Leroyetal.,2006)Bertrandetal.,
2003cametosimilarconclusions whenhe
statedthat selectioncanavoidaccompany
ing the introgression of resistance genes
withadropinbeveragequalityduetoposi
tiveresultsinapproximatelyhalfofthetri
als that he carried out dealing with taste
characteristicssuchassucrosecontentand
beverageacidity.
Introgression processes that began in the
1980s to combat the spread of coffeeleaf
rustandrootnematodeswasnotrestricted
toresistancetraits butalso includedgenes
that coffee producers widely contend af
fected cup quality. Most coffee buyers
claimthat newintrogressedvarieties have
apoorercupquality thanthestandardva
rieties, this @indingwascon@irmedby Ber
trand et al., 2003 in the same study in
which he showed that some introgressed
lines were similar to the control and that
cup quality was not necessarily related to
theamount ofintrogressedgenomeofRo
busta. Since the late 1990s, CIRAD and
partnershaveworkedtodevelopagenera
tionofF1hybridvarietiesthatarecrosses
F1 hybridsofC. Arabicawith7to22%ge
neticmaterialfromC.canephorahavebeen
shown by Bertrandetal., 2006to produce
good cup quality under ideal conditions
andinabouthalfofthetestedstrains.
In order to avoid damage to roots from
nematodes, C. Arabica is commonly inter
grafted onto C canephora. The perform
ance of such grafts was evaluated over 5
yearsinCostaRicabyBertrandetal.,2001.
The grafting did not have an appreciable
effectoncaffeine,fatandsucrosecontents.
HowevertheC.Libericarootstocks didsig
ni@icantlyreducearomaandthesizeofthe
bean produced. These de@iciencies were
partially explained however by tissue in
compatibilityatthegraftlevel.
Withapproximatelya10%marketshareof
thetotal coffee consumedworld wide, de
caffeinatedcoffee is being considered as a
genetic trait. Considerationof genetic di
versity andthe correlationofcaffeine con
tentinrelationtocupqualitywaslookedat
speci@icallybyDessalegnet al., 2008. Des
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salegn found that Ethiopian genotypes of
low caffeine content typically showed a
lower cup quality but that there were no
table exceptions. Consequently he con
cludes that simultaneous selectionfor low
caffeine content and good cup quality is
possiblegiventhattherearesourcesofde
sirable genes in terms of cup quality with
relatively low caffeine content that can be
utilizedforresistancebreeding.
Bertrand et al., 2006 in Central America
found homeostasis, stable equilibrium, in
tastecharacteristics ofArabicahybrids for
which bean biochemical composition was
less affected by elevation than that of the
traditional varieties. The organoleptic
evaluation of hybrids, which was per
formed on samples originating from high
elevation, showed no signi@icant differ
ences between Arabica hybrids and tradi
tional cultivars. Bertrandgoes on to note
thatnewhybridvarietieswithhighbever
age quality and productivity potential
should act as a catalyst in increasing the
economic viability of coffee agroforestry
systems beingdevelopedinCentral Amer
ica.
VanDerVossen,2009pointsoutthattradi
tional cultivars of Arabica coffee are sus
ceptibletocoffeeleafrustandcoffeeberry
disease. CLR being of worldwide impor
tance while CBD remains restricted to Af
rica. VanDerVossencontendsthatthereis
a mounting volume of scienti@ic evidence
accumulated over many years showing
that,givenoptimumenvironmentalfactors,
disease resistant cultivars canin fact pro
ducecoffee of equal quality to those from
thebesttraditionalvarieties.
Etienneetal.,2001states thatthemolecu
lar phylogeny of Coffea species has been
established using DNA sequencing. Mo
lecular markers werefoundthat reveal an
extremely reduced genetic diversity in

Coffea Arabica L. in comparison to C
Canephora. Wild accessions found in
Ethiopiaseemto constituteakeygeneres
ervoir for Arabicastocks. The use of Mo
lecular Assisted Selection in coffee breed
ingpromisesto drastically increasetheef
@iciency of breeding programs as a com
pletegenetic linkage map ofC. Canephora
was reportedand additional linkagemaps
areunderconstructionforC.arabica. Eco
nomically crucial genes related to the caf
feinebiosyntheticpathwayorgenesencod
ingforseedstorageproteinshavebeeniso
lated. The high performance already
achievedin the in vitro propagation proc
ess by somatic embryogenesis offers the
possibility to mass propagate superior hy
bridsindifferentregionsforbothCarabica
and C. Canephora. (Etienne et al., 2001)
Initial productionbysomatic embryogene
sisisnowpermittingpreparationfordirect
commercial application. Seedcryopreser
vation enables a routine usefor longterm
conservationofcoffeegeneticresources.
Bertrand et al., in his study of C. Arabica
hybrid performance isolated three key
quality indicators; yield, fertility and
weight and sought to improve plant per
formance. This was done by breeding F1
hybrids derivedfrom South American and
wildSudaneseEthiopianstock. TheAfri
canstock is thoughttoimprovegeneticdi
versity. SudanEthiopian genetic material
carries signi@icantresistanceto root nema
todes and leaf rust and possibly even
brings better beveragequalityto thetable.
Bertrands main objective was to increase
bean quality, plant productivity and to in
troducemorevariationinto a verynarrow
genetic base. His studyfoundthat hybrid
populationsyielded2247%morethanthe
maternal lines but that hybrids showed
signi@icantly more sterility than parental
controllines. Selectioninthehybridpopu
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lationsusing theaforementionedtraitsre
sulted in signi@icant genetic gain for yield
anddryweightof100beanswithinsigni@i
cantgainsinfertility. Whenselectedonthe
basisoffertilityalone,increaseinyieldand
100beanweightwerenotobtainedwithin
thehybridpopulations. Byapplyingselec
tiononyieldand100beanweight,the hy
bridsproduced1147%higher yields than
the best line with signi@icantly higher or
identical 100bean weight and the same
fertilityrates.
Pautigny et al., 2010 propounds the idea
that comparative genomics provides the
opportunity to leverage genetic informa
tion between species using comparative
geneticmapping. He goes on to statethat
pholgenetically, the model species most
closely related to coffee, for which signi@i
cant genetics and genomic resources are
available, is the tomato. Both coffee and
tomato belong to the Euasterid I clade of
@lowering plants and are likely descended
fromasingleancestral specieswithahap
loidnumberofx=11or12. They go onto
produce the@irst comparativemapfor cof
fee and link it to the genetic andgenomic
resources available on tomato and other
Solanaceaespecies.
Photo Courtesy of SREAD, Rwanda
Quality Evaluation
Methods
Thesuccessfulintegrationofgenetictraits,
which addpositive taste characteristics as
well as contribute to robustness against
disease andpests, can yield signi@icant re
sults interms ofsupplychainsecurity and
cupquality. DNA introgressionofalienge
netic material is being carried out world
wide withvarying and highly disputedre
sults. Discussionofvariousqualityevalua
tion methods to determine the extent of
geneintrogressionsuccessisakeycompo
nentofgeneticresearch. Coffeeidenti@ica
tionandclassi@icationservesasameansto
avoidcoffeeadulteration. This is essential
due to the high variability of sale prices
whichare largelydependentoncoffeeori
gin and variety. Prices of pure Arabica
achieve prices upwards of 25% over ro
busta coffees takenas a whole and prices
for the @inest specialty coffees can soar to
upwards of $50 per kilo green for rarities
likethePanamanianEsmerelda.
NearInfraredRe@lectance
Near Infrared Re@lectance (NIRS) is based
ontheabsorptionofelectromagneticradia
tionbymatter. Thismethodofanalysisal
lowsfortheextractionofalargeamountof
information concerning biochemical com
position andisused extensively in a num
ber ofcrops. Theabilityto quicklyextract
a great deal of information makes NIR a
highly cost effective sourceof information
forresearchers,coffeebuyersandroasters.
Intodaysmarketplacecoffeeidenti@ication
andclassi@icationis as crucial to cup qual
ity as it is to consumer requirement for
originandspeciesspeci@ication. Inorder
toobtaintopmarketprices,methodsofef
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@icient, inexpensive, and highly accurate
identi@icationofcoffee origins andcharac
teristicsareparamount.
NIRS is the method that Bertrand et al.,
2005& Posada et al., 2009 have shown to
be ef@icient for determining whether a
green coffee comes from an Arabica tree
that has been introgressed with C.
Canephora genes. Spectra taken from
nearinfrared re@lectance of green coffee
werecapable, by principal component and
factorial discrimination, ofcorrectlyclassi
fyingbeans into categories ofintrogressed
or nonintrogressed with degrees of accu
racy from 92.3%to 94.87%. This type of
analysiscanservecoffeebuyersorroasters
as they seek to distinguish between non
introgressed Arabicas and genotypes car
rying chromosome fragments of C.
Canephora genetic material which could
produce negative affects on cup quality.
Posadaet al., 2009concursthat a near in
frared spectroscopy signature that has
beenacquiredoverasetofharvests canin
facteffectivelycharacterizeacoffeevariety.
Posada hypothesizes that the spectral sig
natureisaffectedbyannual environmental
factors but that through multiple harvest
calibration data can be made useful for
practicalapplicationtobreeding.
The Science of Taste

Chemicalcompositioninrelationtopre
establishedcupquality:
Attributesofgreencoffeebeans,bothbean
densityandvolume, werehigher forsofter
tasting samples as opposed to the rio off
@lavoredsamplesaccordingtoastudydone
byFrancaetal., 2004. Therio samplepre
sentedlowerlipidcontents, mostlikelyas
sociated with the presence of defective

beans. AcidityincreasedandpHlevelsde
creasedascupqualitydecreasedlikelydue
to the effect ofdefective beans which had
undergone fermentation. After roasting,
the rio sample presented higher density
trigonelline levels, indicating that it had
notroastedtothesamedegreeastheother
samplestested.
Each of the main reserve compounds of
the bean (parietal polysaccharids, lipids,
proteins,sucrose)aswellassecondaryme
tabolites (chlorogenic acids, caffein,
trigoneline)play acentral role inchemical
reactions during roasting. Webelievethat
deciphering the correspondent metabolic
pathwaysarethekeytobetterunderstand
ing quality and the use of biomarkers for
breeding. Onthe otherhand, volatilecom
ponents, mainly from phenylpropanoids
andisopropenoids, aresynthesizedduring
beanmaturation. Evenvery lowquantities
(nanomole) might strongly in@luence cup
quality. Wehavetwo ongoingpreliminary
works(to be published) inwhichwehave
been studying the in@luence of environ
ment and genetics on cup quality pro@iles
(metabolic @ingerprints) using the SPME
GCMStechnology.
Dr.ChristopheMontagnonofCIRAD,per
sonalcorrespondence
Joetet al, 2010examinedthein@luences of
environmental factors and wet processing
on the lipid, chlorogenic acid, sugar and
caffeine content of green Arabica beans.
Each of these biochemical markers repre
sentingkeycomponentsofcupquality. He
foundthatchlorogenicacidsandfattyacids
inthebeanwerecontrolledbytheaverage
air temperature during beandevelopment.
However, total lipid, total solublesugar, to
tal polysaccharide and total chlorogenic
acidcontentswerenotallin@luencedbythe
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climate in which beans were produced.
Glucose content was positively affected by
altitude and sorbitol content after wet
processing was directly dependent onglu
cosecontentinfreshbeans.
MolecularMarkers
Molecular markers are widely used,
through traditional chemical analysis, to
investigate canephora and liberica gene
introgressioninto Arabica lines as a resis
tanceboostertopestsanddiseases.Coffee
ampli@ied fragment length, polymorphism
and simple sequence repeats have been
used to analyze the introgressions men
tioned above. Villareal et al., 2009 found
fatty acidsinparticularhave proveneffec
tiveforthediscriminationofArabicavarie
ties andspeci@ic growingterriors. Cropto
cropenvironmental factorswherefoundto
haveasigni@icantimpact onfattyacidcon
tentandthus limit discrimination to mod
erate ef@iciency across a number of years.
Posadaet al., 2009also foundthatcorrect
classi@ication and discrimination among
different varieties of introgressed genetic
material was possible through traditional
chemical analysistothetuneof79%accu
racy. Healsofoundinthesamestudythat
using spectral signatures in green beans
provided 100% correct differentiation
amongvarieties.
Farah et al., 2005 investigated Brazilian
greenandroastedcoffeebeans forcorrela
tions betweencupquality andlevels ofsu
crose, carreine, trigonelline and chloro
genicacids asdetermindedbyHPLCanaly
sis. They found that trigonelline and
3.4dicaffeoylquinic acid levels in green
androastedcoffeecorrelatedstronglywith
highquality. Tosomeextentcaffeinelevels
were found to be associated with good
quality.Theamountofdefectivebeans,the
levelsofcaffeoylquinicacids,feruloylquinic
acids and their oxidation products were
associated with poor cup quality and the
Riooff@lavor. Similar correlations be
tween cupquality and chemical attributes
were observed in green and light roasted
samples which indicates that chemical
analysisofgreenbeans maybe usedasan
additional tool for coffee quality evalua
tion. Lindingeretal.,2009drawsacorre
lationbetweenthefermentedoffnote and
ethylformate.
Harvesting and Post

Harvest Handling
Photo of Washing Station Courtesy SPREAD, Rwanda
Ideal conditionsforcoffeeproductionsuch
as the agronomic factors of soil nutrition,
shading, watering and superior genetics
will not yield highcupquality without op
timal harvesting, processing, storage and
brewing. According to Van Der Vossen,
2009only freshly harvested andfully ripe
berriesshouldbeused in anyofthe three
methods of primary processing. Those
methodsincludewashed,semidryanddry
processing. Hand picking coffee beans is
16
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one method for accomplishing such dis
tinction but there are methods of mecha
nized picking that separate the immature
greenfrom theripecherrybeforeprocess
ing. Unripened coffee beans tend to pro
duce astringent, bitter and off @lavored
beverages but unripened beans can be
sorted before processing to mitigate nega
tive effects on batch quality. Delays in
depulping andprolongedfermentation of
ten lead to onion @lavor or unpleasant
smells. Wetfermentationmayimprove@la
vormarginallyasmaysoakingunderwater
for 24 hours after mucilage removal and
washing.
Below:ASurveyonthelowmolecularsugars
inagreencoffee. The circleisrepresentative
of the low molecular sugars, totaling 7.79%
DM.
Accordingto Bytof et al., 2007thespeci@ic

ambientconditionsofanytypeofposthar
vest processing can have signi@icant im
pacts on the time course ofthe metabolic
reactionsthatoccurduringthatprocessing
period. Theextentandthetimecoursesof
germination in various coffee beans were
foundtobe signi@icantly different between
dryandwetprocessingstyles. Thehighest
germination activity was found to occur 2
days after theonsetofwet processing and
approximately 1 week after the onset of
dryprocessing. Bytofgoesonto conclude
that the substantial differences in @lavor
betweenwetanddryprocessedcoffeesare
the result ofthe differential expression of
germination processes, in other words,
they are the result of differences in the
metabolic activities thattakeplace ineach
typeofprocessing.(Bytofetal.,2007)
Knoppet al., 2005statesthat @lavordiffer
ences inpart have to be attributed to dif
ferencesinthethoroughnessappliedto ei
thermethod ofpost harvest processing as
well asthe factthatonlythefullyripecof

fee cherries are typically used for wet
processing as opposed to dry processing
where fruits of varying stages of ripeness
arecommonly used. In his description of
the In1luence ofprocessing on the content
of sugars in green arabica coffee beans
There is a close correlation between the
type of post harvest processing and the
content of fructoseand glucoseinthe cof
fee bean. While in washed coffee beans
only a small amount of either hexos were
present, those in unwashed coffees were
signi@icantly higher. It has been revealed
thatlowlevelsofbothfructoseandglucose
arearesultofdecreaseinthewetprocess.
Fructoseandglucoselevelsstayednearpre
processing levels throughout dry process
ingaccordingtoKnopp.
Knopp concludes that the decrease inglu
coseandfructoseinwetprocessedcoffeeis
asaresultofafermentationenhancedglu
coseturnoverfromanaerobicfermentation
inthecoffeeendosperm.
(Knoppetal.,2005)
Harvesting
Whenthecoffeebeanis readyfor harvest
ing it turns a dark berry color. This will
typically take place between September
and March in the Northern Hemisphere
andbetweenAprilandMayintheSouthern
17
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Hemisphere. In some countries where
thereislittlecleardistinctionbetweendry
and wet seasons a major and minor crop
may be able to be harvested annually.
Countries on the equator are able to har
vest year round. Harvesting of superior
coffees tends to be done by hand as
mechanized picking can gather over ripe
berries and an acrid taste may affect cup
qualityaccordingtotheFAOof@iceforAsia
and the Paci@ic. (Alastair Hicks) Of the
variousmethodsinpractice, selectivehand
picking best ensures that only fully ripe
beans are taken. However a cost bene@it
analysis will inevitably be undertaken by
coffeegrowersastowhethertheincreased
level of quality found in picking only the
ripest cherries is worth the extra expense
of undertaking multiple harvests in the
sameseason.
Approximatley2025%ofallBraziliancof
feeproductionisaffectedbytheRiooffde
fect. This defect is characterized by a
strong medicinal or iodine or musty and
cedarlike character. Occasionally thisde
fect has beenobserved inother countries.
Spadoneetal.contendthatthis defect isa
resultofwet andhumidconditions during
harvestingandistheconsequenceofatype
offermentationandbacterialgrowthanda
highlevelofcellstructuredegradationthat
ensues. The principle compound associ
atedwiththeRiooff@lavorwasfoundtobe
236 Trichloroanisoleand is only percep
tible at concentrations at or above 8ppm.
(Spadoneetal.,1990)
DryProcessing
Post harvest processes include both dry
and wet methods used to process green
cherrycoffees. Dryprocessing is thesim
plest and least expensivemethod ofcoffee
processing. It tends to produce natural
tastingcoffees andis usedmostlyinWest

ern Africa and Brazil. Harvested berries
are sorted and cleaned to remove dirt,
twigsandleavesbyhand. Berriesarethen
spread out in the sun and raked regularly
to keep fermentation at bay. In the dry
method, coffee beans were dried as a
wholewithpulpandmucilageinthecherry
state. Dry processingis slowandcanlead
to the translocation of chemical constitu
entsfromthepulptotheinnerbeanaswell
as chemical transformation that depends
onambientconditions.
It is noted by Clark, 1985 that naturally,
dry,processedcoffeehasabetterbodydue
to the fact that the bean was in contact
withits mucilagethroughagreaterpartof
theprocessingphase.
Cantergiani et al., in 2001, found that
earthy/moldy off@lavors that were pro
duced in Mexican coffees were likely as a
result of dry post harvest treatment. The
compounds geosmin, 2methylisoborneol
(MIB), 2,4,6trichloroanisole (TCA) were
found to be the main contributors to the
tainted@lavorthoughatthetimeofCanter
gianisstudy themoldy /earthy defect had
not yetbeenfullycharacterized. The con
centrationsfoundinsamplesexhibitingthe
moldy/earthy characteristic were between
100and1000ppm, 58times morethanin
the reference sample. Cantergiani also
identi@iedalkyl methoxy pyrazinesas hav
ing less signi@icantcontributions to theef
fect. 2methoxy3isopropyl pyrazine, 2
methoxy3secbutyl pyrazine and 2
methoxy3isobutyl pyrazine (MiPP, MsBP
andMiBPrespectively)werefoundinboth
reference and tainted samples with the
concentrationbeing only 12 times higher
in tainted samples than in the reference
sample. These chemicals evoke strong
earthy, green and bell pepper notes and
MsBP was detected in this study for the
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@irst time in coffee. (Cantergiani et al.,
2001)
Spadone identi@ied 2,4,6trichloroanisole
as primarily responsible for the Rio off
@lavorincoffee. Vitzthumetal.,propounds
MIBas akeysubstanceresponsibleforthe
earthy tone in Robusta coffee. Rougue et
al., noteshisview that theeffectofMIB in
Arabica coffees can be mitigated using
steamtreatmentandroasting.
begintobecomeactive.Theyeastsgoonto
convert sugar to alcohol but are also me
tabolizing the solid parts of the mucilage
resultinginaromaqualitiesthatcanhavea
negativeimpactoncupquality.Thistaste/
smell characteristic is sometimes referred
toasfruitycoffee.Whencoffeecontinues
in this state even longer under reducing
and acidic conditions, the yeast will con
vertsugarsintoacidsasopposedtoalcohol
resultinginsourtastingcoffee. (Tea&Cof
Below: The concentration of low molecular
sugarsinvariouslyprocessedgreencoffees.
WetProcessing
Inthewetmethodcoffeebeansarepulped,
fruitandskin areremoved, or pulped and
demucilatedandmucilaginousmesocarpis
removed under fermentation. In the wet
method fermentation occurs in water at
controlled temperatures which produce
lower levels of undesirable @lavors. For
thisreasonthewetmethodisoftenassoci
atedwithbettercupquality.GonzalesRios
et al., 2007claim that thequality ofgreen
and roasted coffee, measured by aroma,
wasbetterafterconventional fermentation
thanaftermechanicalmucilageremoval.
Wet coffee readily takes up smells and
aromas.Oilconstitutesamajorcomponent
ofthecoffeebeanscompositionandisable
to takeupandstoresmellsand@lavors be
forereleasingthemduringroastinggreatly
affecting cupcharacteristics. According to
the tea and coffee trade journal most cup
defects arecausedbywrongfermentation.
In fermentation there are primarily two
microorganismsatworktoshapetheeven
tualcupquality, bacteriaandyeasts. Dur
ing proper fermentation the bacteria feed
on sugars inthemucilage. As soon asthe
sugars have been digested and the muci
lage has beenlique@ied, the pH in the fer
mentationtankbeginstodecrease. Itisat
this point of lowering pH that the yeasts
fee, November December, 2005) Rec

ommendations for avoidance of fruity and
sour @lavors include washing of beans as
soonasfermentationhas@inished,whenall
mucilage has been lique@ied. There is no
across the board time frame for develop
mentoffruityandsour@lavorsastempera
ture and altitude play signi@icant roles in
thoseprocesses. Itisnotedthatingeneral
thebestwaytoavoidthesecupdefectsisto
washthe parchment coffeeas soon as fer
mentation has @inished and parchment
feelsroughtothetouch.
Clifford,1985proposesthatWetprocessed
Arabica tends to be aromatic with a @ine
acidity but some astringency while dry
processed Arabica tends to be less aro
matic but produce greater body. This is
largelyduetotheformationofacidsinun
derwaterfermentation.
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GonzalesRios et al., 2006 states that a
comparison of green coffees from the dif
ferenttreatments(wetanddryprocessing)
reveals the importance of mucilage re
moval inwater to obtaincoffees withbet
ter aroma quality. These wet processed
coffees are in fact characterized by pleas
ant and fruity aroma characteristics
whereasthoseobtainedafter amechanical
mucilage removal used in a more ecolo
cial process were characterized by less
pleasantaromaticnotes.
Kleinwachter and Selmar contend that
whenwetprocessedcoffeebeansaredried,
thereensuesadecreaseinthewaterpoten
tial which causes a number of metabolic
responses within the coffee bean. They
foundthatthe contentoffructoseandglu
cosedecreasedsigni@icantlywithinthe@irst
day ofdrying. Thisdecreaseinsugar con
tent, they contend, proves that the lower
contents of glucose and fructose that are
generally found in wet processed coffees
are, at least in part, due metabolic proc
esseswithinthebeanandarenottheresult
of leaching of sugars into the water used
forprocessing. (Kleinwachter andSelmar,
2010)
In2001Mendezetal.foundthatsigni@icant
improvements could be made in customer
receptivity to robusta coffees given high
qualityprocessing.Thestudyrevealedthat
whenroastedat optimum ranges of 225
230*Cfor22to 28minutes andwetproc
essed, acceptance scores increased to
likedslightly& likedmoderatelyonthe
hedonic scale for both aroma and @lavor.
Mendezgoesontomaketheargumentthat
with higher @lavor and aroma scores a
higher percentage ofrobustamay be used
in blended coffees without adverse effects
on customer satisfaction. (Mendez et al.,
2001)
Storage
Signi@icantdefectscanalsoariseasaresult
ofinsuf@icientdryingand/orstoragecon
ditions asitisthedryingprocessthat pre
paresbeansforprocessinglateronaswell
as storage. When beans are insuf@iciently
orunevenlydriedadecreaseincupquality
can occur much more rapidly than with
beansthathaveundergoneanidealdrying
process. Stirling, 1974 shows a rapidde
crease in cup qualitylevel withincreasing
storage time from 6 to 18 months given
various moisture contents. Thedecline in
cupqualityinwetcoffeeisduetomoldand
bacteriaasmoldsandbacteriagrowbestin
moisture richenvironmentsand cupchar
acteristics change as a result of bacteria
andmouldutilizationofsugars inthe cof
feebeanformetabolism. Tea&Coffeerec
ommenda bean moisture content of10 to
12%beforepackagingandstorage.
One key aspect of coffee storage is bean
respiration. Every24hours anaverageof
4.4milligramsofCO2are producedby100
grams of coffee beans andthe 96 calories
ofheatproducedby the4.4mgofCO2 will
raisethetemperatureofthebeans.25o Cel
sius. A highrespirationrate, in combina
tionwithheat generation,cancausealoss
of weight and dry material in the bean as
wellasbeanfatdecompositionwhichplays
akeyroleinthearomaofthecup. (Sivetz
andDosrosier,1979).
Stink coffeecanbe produced as a result
ofexcessive fermentationfromthe normal
microbes that are at work in coffee proc
essing. It is recommended that factory
tanks and machinery be cleaned daily to
ensurethatoldbeans caughtincrevicesof
machinery do not contaminate a later
batchofcoffee. Extremeoverfermentation
20
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can germinate the coffee seed which dies
quickly andleaves ahollow pit in the end
of the bean. The dead bean then very
quickly develops a cheesesmellingtexture
whichishighlydistinctivewhenthebeanis
brokenor cut. A singlebeancancontami
nateand spoil anentire batch of perfectly
goodcoffee.(Coffee&Tea,2005)
Declining of cup quality is inevitable to
some degree during storage. The reason
for this decline, oraging, is surface oxida
tionfrom beans aided bymicroorganisms.
Theagingeffectcanbeminimizedbystor
ing parchment and process beans in low
temperature, low oxygenandlowhumidity
conditions in order to dissuade bacterial,
yeast and mold activity. Damaged beans
tendto bemuchmore subject to agind as
theoilsinthebeanareextrudingfromthe
bean and provide a good growing ground
formoldandbacteria. Moldshavethepo
tentialtogrow ondry surfaces andextract
needed moisture from the air in storage
roomsmakinghumidityakeyissueinstor
agefacilitydesign, maintenanceandrepair.
Onepotentialmitigationoftheagingproc
ess on coffee beans is to utilize hermeti
cally sealed containers or storage silos as
opposed to bags. Such units could mini
mizeoxygenlevelsaswellasmoisturecon
tactmetabolicratesofmicroorganismsand
prolonging the amount of time in storage
that would cause minimal affects on cup
quality. Little information is available
about theeffectofCO2 insuchasystemon
thecupqualityofthecoffeestored.
Green beans can produce a grassy or
harsh@lavorcauseby pickingandprocess
ingimmaturecherries. Lateinthepicking
season many cherries loose their green
color but do not turn completely red.
These unripe cherries will pulp easily but
arefull ofchlorophyll. Thisisreadilyseen
in fresh wet washed parchment which

showsupthecolorofthesilverskinunder
neath.Onesolutionistodundrythecoffee
when weather conditions permit as ultra
violetlightcanbleachoutthegreennessin
the silverskin. A slight degree of green
color will often fade over time, making it
undetectableat the@inal destination, buta
strong degree of unripeness will facilitate
chemical absorptionback into the oilfrac
tionofthe@inalproduct.
Below: Aroma profiles of unstored raw coee
beans (gray line) and coee bean with a water
content of 13.5% stored for 9 months at 40*C
under an atmosphere of 20% oxygen.
Onion @lavor is another potential result of

faultypostprocessing. Onion@lavoroccurs
whentherationofsolublesugarsto proto
pectins (contained in the mucilage) be
comes too low. Theprimaryrapidbuildup
of fermentation bacteria is fuelled by the
relativelyhighlevelofsugarpresentwithin
the ripened mucilage. If excessive fresh
water is used in prewashing of cherries
and during the pulping process, most of
thesesolublesugarsareleachedoutbefore
normal fermentation takes place. Conse
quently, thebene@icialsoftrot bacteriacan
beoverwhelmed later in the fermentation
process not onlyby the yeastsbut also by
bacteriawhichconvertaceticandlacticac
21
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ids to propionic and butyric acids which
cause the onion@lavor. It has been found
that this fault can be minimized by recy
cling of pulping water as maintaining a
highlevelofsugarsandenzymesinthewa
terwillfacilitatenormalbacterialaction.
Scheidig et al., 2007 studied the atypical
odors that develop during the storage of
raw coffee beans and eventually in@luence
thearoma of the coffeebeverage. His re
sults showedstrongincreases indamasce
none (cooked applelike odor), 2methoxy
4vinyphenol(clovelike odor), andmethyl
2methyl and methyl3methylbutanoate
(fruityodor),withanincreasedwatercon
tentand a storage time of9 months at 40
*C. It was also foundthatearthysmelling
3isopropyl2methoxypyrazine as well as
2phenylethanol and 3methozyphenol
remained unchanged during the storage
period. Itwasalsofoundthatapreviously
unknownodorincoffee,theintensesmoky
@lavorcausedby productionof2methozy
5vinylphenol, increased signi@icantly due
to storage. Inconclusion, Scheidig recom
mends a reduction in water content of
green beans in combination with lower
storage temperatures to avoid aroma
changesinrawcoffeebeansoverlongstor
ageperiods.(Scheidigetal,2007)
CafBrittofCostaRica,inconjunctionwith
the Mesoamerican Development Institute,
is experiencing positive results in the de
velopmentofahermeticstorageunit. This
unit facilitates long term storage ofcoffee
in its parchment state without the use of
pesticides, the degradation of cup quality,
aroma, or appearance for a period of @ive
monthsormore. Coffeebeans, evenwhen
properly dried can reabsorb fungus and
bacteria encouraging moisture over time
fromtheatmosphere. Thestorageofgreen
beans can be even more problematic as
they are more susceptible to quality dete

rioration. Hermetic enclosures manufac
tured by Grainpro Inc. inConcord, Massa
chusetts, are being used to store coffee.
These enclosures use ultra violet light re
sistance PVC to provide an environment
that maintains a very low moisture (hu
midity),lowoxygen,highCO2environment.
This type ofenvironment is highly condu
cive to maintaining low levels of bacterial
life, mold, insects and even prevents the
formation of a@latoxins as a byproduct of
molddevelopment. Temperature and hu
midity ranges found in the hermetically
sealed enclosures were also signi@icantly
narrowerthanfor control groups ofbeans
stored in silos or in bags in a warehouse.
Cuppingtestsweredonemonthlyona@ive
point scale and found that after two
months there was a signi@icant change in
quality in beans storedin sacks andinsi
los,from4.0to3.8whilecupqualitystayed
thesamefor beans storedinthe hermetic
enclosure. After a storage of @ive months
cup quality for sacked coffee and coffee
storedinasilohaddecreasedafullpointto
3.0andweredescribedasSlightold@lavor
perceptible in cup, slight harshness,
tainted. The cup quality from beans
stored hermetically was noted as Very
good @lavor despite being from the previ
ous harvest. Slight @loral @lavor. Cupping
was done by Caf Britts cupper Carmen
Lidia Chavarria as well as the cupper for
the Costa Rican Consortium, COOCAFE,
JimmyBonilla.
Roasting
Roasting has been calledthe most impor
tant step in the production of aroma and
taste by Juerg Baggenstoss with the insti
tute of Food Science and Nutrition in Zu
rich. Asbeancolorturnsto brownoreven
black intheroastingprocess brittlenessis
22
Draft Copy
greatly increased which facilitates the
grinding and extraction processes. High
temperatures, above200* C, arenecessary
for the roasting process to occur. Green
beansare especially harddueto unusually
robustcellwallsandalackofintracellular
spaceinherentinthecoffeebean. Asare
sult,coffeebeansareregardedasanaggre
gate of micro reactor units that sustain a
considerable pressure buildup due to the
heat of roasting withtheoretical values of
up to 16 bars being produced within the
cell walls withno evidenceofthecell wall
disruption being observed in scanning
electron microscope investigation. Thisis
thought to be due to the fact that at high
temperaturecoffeecellwallschangefroma
hard glassy state to a more elastic state
which facilitates considerable volume in
creasewithoutrupturing. Ithasbeengen
erallynotedthatconvectiveheattransferis
themosteffectiveforuniformroasting.
Thestateofroastedcoffeeisin@luencedby
theroasting conditions in terms ofdegree
ofroast. Anumberofoptionsexistforde
scription of degree of roast; color devel
opment, roast loss, organic roast loss and
water content. Of these, the color of the
coffee bean or ground coffee is the most
commonly usedindicator ofroast as bean
color intensity has been correlated to
roastingtemperature. Thishowever,isnot
adirectrelationshipascolordoesvaryasa
functionofrawmaterialandprocesscondi
tions.(Baggenstossetal.,2008)
Baggenstoss went on to explore the effect
of roasting onaromaformationunderdif
ferenttimetemperatureconditions. When
compared to low temperaturelong time
roasting, high temperatureshort time
roasting results in relevant differences in
thephysicalpropertiesofaromaformation.
It was found that excessive roasting typi
cally leadto decreasing orstableamounts
of volatiles with the notable exceptions of

haxanal, pyridine, and dimethyl trisul@ide,
whose concentrations increased continu
ally during over roasting. When roasters
wereoperatedinthetemperaturepro@ile
mode, along the identical development of
coffee bean temperature over roasting
time,thekineticsofaromagenerationwere
similarinbothdrumroasterand@luidizing
bedroasterprocesses.
Franca et al., 2009 concludes that caffeine
andpyridinewerethemaindiscriminating
compounds for coffees roasted at high
temperatures andmore intensedegrees of
roast. Although discrimination of coffee
samples roasted to different degrees was
attained by analyzing the effect of hun
dreds of compounds together, the com
pounds that presented the most pro
nounced effect on the discrimination of
roasting degrees and temperatures were
thosegeneratedrightaftertheonsetofpy
rolysis (decomposition brought about by
hightemperatures). Theresultspresented
in this study reveal that color and weight
loss in and of themselves are not entirely
reliableas roastingdegree assessmentcri
teria and the temperature at which beans
areroastedmustalsobetakenintoconsid
eration.
BrewedCoffee
OncecoffeeisbrewedthedeclineofpHand
the quality score were correlated at a
numberofstoragetemperaturesbyRosaet
al, 1989. Roass sensory analysis allowed
de@inition of a lower limit of pH at which
coffees shelflifeended. Sivetz andDesro
sier, 1979 showed that the decline in pH
comesassresultoftheformationofcaffein
andquinicacidsasbreakdownproductsof
chlorogenic acid. This process was found
to accelerate withincreasing storage tem
perature. Resultsshow that coffeequality
23
Draft Copy
remainshighaslongaspHremainshigh,in
the 5.2 range, after brewing and that the
ideal temperature regime for storage is
nearfreezingatapproximately4oC.
The Impact of
Climate Change
Global climate changeinthe comingyears
will have signi@icant impact on the coffee
producing regions of the world. Current
correlations between altitude, tempera
ture, rainfall and cup quality as well as
yieldwillall bemodi@iedto somelesser or
greater extent. It is generally recognized
that higher mean temperatures and
changesinprecipitationregimeswilltypify
the climate changes that we are likely to
see across the globe in the next 50 years
accordingto anumberofglobalcirculation
models(GCMs).
Coffee systems are characterized by long
leadtimesnecessaryfor both farmers and
theirbusinesspartners to makeaccommo
dationforchangeingrowingpatterns,with
an average of 815 years being required
fromdecision to fruition. (Laderachet al.,
2009) Laderachet al., 2008predicts that
climatechangewillshifttheprimealtitude
range to higher elevations over time. He
estimates that in Central America a shift
will occur from 1200m for optimal plant
health and cup quality to 1400m in 2020
and1600min2050.
Overall climatewill becomemoreseasonal
interms ofvariability throughttheyearin
termsoftemperature and precipitationon
the whole with temperature increasing in
South America on the order of 2* C by
2050. Consequently, suitability for coffee
will move upwards on the altitudinal gra
dientwithclimatechange. Loweraltitude
areas will lose suitability due to their
highertemperatures.
24
Draft Copy
The areas that will be highly suitable for
coffee production in 2050 are likely to be
thoseareasthatarehighlysuitabletoday,it
is thelargemarginalareasthatwill proba
bly lose their capacity for coffee produc
tion. Altitudeandtemperaturehavea@ixed
relationcalledthelapseratewhichisequal
to.6*Cper100mofaltitude. Precipitation
inthewettest monthoftheyearandmean
temperature of the coldest quarter of the
yeartendtobethemostdecisivefactorsin
thesuitability ofanareaforcoffeeproduc
tionas stated byLaderach, 2009. Assum
ing that these@indings are widely applica
ble,globalclimatechangewillrequirecof
fee producers to implement signi@icant
strategicplanningtoadjusttheircropsand
production areas inorder to mitigate the
negative affects of changing climate pat
terns.
Conclusions
Whilethedatasupportfewuniversalequa
tions for coffee quality, afewkeytradeoffs
are evident from literature. Firstly, that
there is a tradeoff in perception, if not in
fact, between disease resistance and cup
quality. Furtherstudyhas thepotential to
uncoverthresholdsinproductivityandcup
qualitytradeoffsinthis@ield.Soilnutrition
willalsobeakeyareaoffocus inthecom
ing years as decreasingsoil qualitydue to
consistent high yield output could cause
further constriction of the supply chain
through decreasing yields. This is largely
due to the inability of small land holder
farmerstoprovidetheinputsnecessaryfor
consistent and long term quality harvests.
Larger scale inputs could be facilitated
through larger scale farming techniques
but signi@icant tradeoffs exist due to the

possibility of decreasing quality ofcoffees
picked andprocessedmechanically at one
time as opposed to hand picked beans
pickedattheheightoftheirmaturity. Post
harvest separation of ripe from unripe
beans remains a key quality control that
has the potential to mitigate this issue if
properlyapplied,aspointedoutbyDr.Car
losBrando.
At thispointmajortradeoffsexistfor stor
ageaswell. Increased storage times have
traditionally meant supply chain stability
at the expense of cup quality. However,
technologies are being developed that
could change even this paradigm in the
nearfuture.
Thefutureofcoffeeisbrightgiventhecon
tinued and expanded dissemination and
implementationofcuttingedgeresearchat
the farm level. Working in concert with
one another as an industry to implement
suchresearch,thereisno limittoourcom
binedpotential forproducingcoffeethatis
asexcellent asitisuniqueineconomically
viablequantity.
25
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FACTORS INFLUENCING CUP

Photo Courtesy of SPREAD, Rwanda

Prepared for the Global Coee Quality Research Initiative

Global Coee Quality Research Initiative Review

FACTORS INF L U ENCING CUP

Photo Courtesy SPREAD Rwanda

quality ona number oflevels. At the ex

Global Coee Quality Research Initiative Review

Global Coee Quality Research Initiative Review

in1to 3yearoldplotsofC. ArabicaandI.

Global Coee Quality Research Initiative Review

(6) New crop varieties are often bred for

Global Coee Quality Research Initiative Review

Global Coee Quality Research Initiative Review

Above: Quality attributes of green beans of two

ditions afterharvesting. Ontheother end

Global Coee Quality Research Initiative Review

tions at highelevations. Theanalysis con

Global Coee Quality Research Initiative Review

Global Coee Quality Research Initiative Review

D: 230240days after @lowering: A ma

A: 060days after@lowering: Ovary after

According to DeNardi et al., Coffee plants

Global Coee Quality Research Initiative Review

Coffee leaf rust (CLR) is caused by a

Global Coee Quality Research Initiative Review

Global Coee Quality Research Initiative Review

extremely reduced genetic diversity in

Global Coee Quality Research Initiative Review

Photo Courtesy of SREAD, Rwanda

Global Coee Quality Research Initiative Review

The Science of Taste

sociated with the presence of defective

Global Coee Quality Research Initiative Review

Harvesting and Post

Photo of Washing Station Courtesy SPREAD, Rwanda

Global Coee Quality Research Initiative Review

Accordingto Bytof et al., 2007thespeci@ic

well asthe factthatonlythefullyripecof

Global Coee Quality Research Initiative Review

tastingcoffees andis usedmostlyinWest

Global Coee Quality Research Initiative Review

fee, November December, 2005) Rec

Global Coee Quality Research Initiative Review

Global Coee Quality Research Initiative Review

in fresh wet washed parchment which

Onion @lavor is another potential result of

Global Coee Quality Research Initiative Review

they are more susceptible to quality dete

Global Coee Quality Research Initiative Review

of volatiles with the notable exceptions of

Global Coee Quality Research Initiative Review

Global Coee Quality Research Initiative Review

but signi@icant tradeoffs exist due to the

Global Coee Quality Research Initiative Review

Bertrand, B., Vaast,P., Edgardo,A., Etienne,

Bertrand, B.,Etienne,H., Lashermes,P.,Gu

Cantergiani, Brevard, Krebs, Y., Feria, M.,

Baggenstoss, J., Poisson, L., Kaegi, R., Per

Carvahal, J.F., 1959. Mineral nutrition and

Global Coee Quality Research Initiative Review