Genetic and Phenotypic diversity of cultivated Robusta coffee (Coffea canephora Pierre) in Uganda and effect of environmental factors on quality
Abstract
Cultivated Coffea canephora in Uganda has low productivity with unknown quality trait
variability. At present in Uganda, improvement of quality aspects of the Coffea
canephora that would directly translate to increased incomes is hindered by the lack of
information on the extent of the genetic and phenotypic diversity of the cultivated C.
canephora and the effects of environmental influence on the coffee quality. The
objective of this work was to evaluate the genetic and phenotypic diversity of cultivated
C. canephora and assess the effects of the environmental influence on quality traits.
Genotypic variation, morphological and green bean physical characteristics, biochemical
compounds and organoleptic cup attributes present in the local landraces were evaluated.
The effects of environmental factors such as soil elements and texture, locations, altitude,
rainfall and temperature at different bean development stages were also assessed.
In the experiments reported here, a total of 265 Robusta coffee genotypes collected from
farmer fields in 13 traditional growing districts were analyzed using 32 Simple Sequence
Repeats and were compared with 84 on station germplasm collections. SSRs efficiency
and reliability was reflected by the low values for quality index and average minimum
variance, detection of abundant and rare alleles to the extent of differentiation
exemplified by allelic drift. Three genetic diversity groups with a mean genetic distance
of 0.60 were different from those from Western and Central Africa possibly due to
isolation or controls were few. Genetic diversity values were not antagonistic as all
relationships were positive. High genetic variability among cultivated Robusta coffee
was demonstrated by the high Polymorphic Information Content (PIC) of 0.55 to 0.93
with a mean of 0.75 for 18 selected markers. The 54.05% within individual variability
implied that genetic selection for desirable traits should be based on individual plants.
Fairly polymorphic change over generations was revealed by the genetic differentiation
value of 0.17 and gene flow mean value of 0.7±O.09 that caused exchange of one migrant
between populations in each generation. The germplasm collection had fewer alleles,
effective alleles, PIC, allele frequency and rare alleles as compared to accessions from
farmer fields reflected limited variability among the few genotypes in the collection.
Research controlled hybrid crosses and commercial varieties though genetically and
morphologically, had limited genetic variability as each type confined to single groups.
Evaluation of morphological characters for 476 Ugandan farm Robusta coffee accessions
showed that farmers cultivate predominantly 88% "uganda" and "erecta" landraces with
improved types constituting 12%. Though 'uganda' and 'erecta' types were not
genetically defined, were morphologically close and significantly different. The 206
Robusta coffee green bean physical characters evaluated using International Coffee
Organization (ICO) criteria showed that 61.27% were of average screen size 15 and 19%
larger beans.
The 16 accessions caffeine content analyzed using both Near Infra Red Spectroscopy
(NIRS) and High Performance Liquid Chromatography (HPLC) methods were
insignificantly different making NIRS technique better option because is fast and
economically viable. Ugandan Robusta coffee biochemical compounds were aggregated
independently from that of CIRAD data base possibly because it was CIRAD's first
encounter with Ugandan accessions and the possibly high species biochemical compound
variability. The high fat (10.44 to 15.94 % dry matter) and chlorogenic acid (10.88 to
15.64 % dry matter) with a wide range of sucrose content (2.48-7.34% dm) indicated that
Ugandan Robusta coffees are diverse with high fragrance, aroma and flavour. Other than
potential to serve many markets, quality improvement and conservation purposes, the 4
multivariate groups were significantly different for dry matter and caffeine, implying it
possible to select for dense beans with low caffeine to reduce bitterness in coffee brew.
Genotypes in the three major genetic diversity groups distributed differently in the four
multivariate green bean biochemical compounds diversity groups most likely due to the
influence of environment on the latter. Lack of genetic diversity relationships with
locations where they were grown meant that trait variations were strongly influenced by
genotypes.
Evaluating roasted coffee green beans using the sensory technique developed by The
Coffee Quality Institute of America (CQIA) alongside Uganda Coffee Development
Authority, showed that the evaluator organoleptic cup trait rating was significantly
different implying that individuals perceive cup taste differently. Positive correlation
among organoleptic cup attributes implied that they complimented each other instead of
antagonizing. Cup balance regression coefficient of 0.90 rated it as most important in
overall cup evaluation. About 84% of Ugandan Robusta coffee brew was premium
reflecting high quality. Acidity was least rated as average while other cup attribute rating
ranged from premium to specialty grade pointing out that Robusta coffee can have as
good cup as Arabica coffee with medium acidity. Fragrance, aroma and flavour
attributes could easily be selected from the 4 multivariate groups because because the
attributes were significantly different. The present study has estimated optimum
expression of different phenotypic quality traits at 30 to 35 years at a height of 1200
m.a.s.L The genetic diversity and multivariate variability derived from this study offer
numerous opportunities to select for breeding materials to develop diverse flavours that
serve different markets, enrich existing germplasm collection, design further desirable
trait studies and advice policy makers and coffee industry stakeholders. Cultivating at
1201-1300 m above sea level, use of "uganda" and "erecta" landraces, selecting trees of
31-40 years are some of the genotypic and environmental management practices that
could be used to improve cup acidity.
Soil, leaf and green bean essential elements were detected and quantified using Energy
Disperse X-Ray Florescence. Calcium, manganese, iron, zinc and lead mean content
were higher in the soil and lowest in the green beans implying that not all the soil
elements were taken up by plant. Potassium content in coffee was highest in the green
bean because of its involvement in the metabolism and translocation of compounds such
as oil, proteins and carbohydrates that influence cup quality. Although calcium is known
to influence fruit ripening and quality, its content was highest in the leaves possibly
because it's a major constituent of cell walls and its content, involved in crucial functions
such as cell division, root and leaf development, various enzymatic functions and
transport carbohydrates.
Multivariate analysis of the effects of phenotype and environmental factors on quality
traits revealed none of the variables was explained 100% by a single or a combination of
phenotypic traits, elements, rainfall and temperature bean development stages suggesting
that this trait is complex to select. Soil, leaf and bean elements explained most variability
in organoleptic cup attributes (6.3 to 22.1%), bean physical characters (24.3 to 50.9%)
and morphological characters (13.9 to 44.4%), possibly because elements are responsible
for plant functions, vegetative development and constitute substances in cells based on
genotypes. The highest chemical compound variability of 3.7 to 35.5% that was
explained by rainfall and temperature bean development stages may have been a
requirement for moderating plant function and facilitating access and movement of
elements from the soil and in the plant. Most desirable bean size was average screen size
15 which more sucrose and less dry matter, caffeine and trigonelline content with better
aftertaste, acidity, flavour.
This thesis evaluated cultivated C. canephora from traditional growing areas for genetic
and phenotypic variability as well as influence of some environmental factors on quality
traits. Information that has been derived is important not only in the identification of
needed future research goals but the analysis of such diversity also goes a long way to
contributing to an improved national economy and to raising the living standards of
small-scale farmers of Uganda. Although all methods that have been used to assess
quality traits are important, in case of meager resources and limited time, genetic
diversity studies on quality can be complemented with fast, easy to use NIRS technique
validated by organoleptic cup assessment which determines acceptability.
Citation
Aluka Pauline (2013). Genetic and Phenotypic diversity of cultivated Robusta coffee (Coffea canephora Pierre) in Uganda and effect of environmental factors on quality. Doctor of Philosophy in Plant Breeding and geneticsPublisher
University of Nairobi