Constitutive and inducible promoters from coffee plants

Details Constitutive and inducible promoters from coffee plants Constitutive and inducible promoters from coffee plants

2000-04-07

2002-08-27

Fox, David T. (Department: 1638)

Multicellular living organisms and unmodified parts thereof and

Method of introducing a polynucleotide molecule into or...

C536S023600, C536S023200, C536S024100, C435S469000, C435S470000, C435S411000, C435S412000, C435S414000, C435S415000, C435S416000, C435S417000, C435S419000, C435S427000, C435S252200, C435S232000, C435S252300, C800S293000, C800S294000, C800S298000, C800S320200, C800S320300, C800S320000, C800S314000, C800S322000, C800S320100, C800S317200, C800S313000, C800S305000, C800S306000

Reexamination Certificate

active

06441273

ABSTRACT:

FIELD OF THE INVENTION
This invention relates to the identification and isolation of DNA promoters from coffee. The invention also relates to a method of protein expression in transgenic plants.
BACKGROUND OF THE INVENTION
Coffee is an agricultural commodity that plays a significant role in the economies of many developing countries. In Colombia, coffee cultivation is restricted to mountain areas with altitudes between 1200 and 1400 meters above sea level. It is especially concentrated in the central region, in an area called the Coffee Zone. With a total annual yield of around 12 million bags, Colombia is ranked second in world production. Of this production, 26% is used for domestic consumption, and the rest is exported to Europe (6 million bags), United States (3 million bags), and Asia (1 million bags), with an average annual market value (1991 to 1995) of $1.6 billion (Banco de la Republica,
Indicadores Economicos NI
828 Banco de la Republica, Bogota, Colombia (1996)).
The genus Coffea belongs to the Rubiaceae family which includes other important plants, such as ipecacuanha (
Cephaelis ipecacuanha
) and cinchona (Cinchona spp.). The genus contains about 70 species, most of them trees and shrubs growing at low altitudes in the tropical rain forests of Africa and Asia (Sondahl et al., “Coffee,”
Biotechnology of Perennial Crops CAB International
, Wallingford, UK (1992)). Only two species are widely cultivated,
Coffea arabica
and
Coffea canephora
. All known species are diploid (2n=2X=22 chromosomes) and obligate outbreeders with self-incompatibility systems, except for
C. arabica
which is tetraploid (2n=4X) and self-fertile.
The species
Coffea arabica
L probably originates from a relatively recent cross between
C. eugenoides
and
C. canephora
, a hypothesis supported by random amplified polymorphic DNA's (RAPD) (Lashermes et al., “Use of Amplified DNA Markers to Analyze Genetic Variability and Relationships of Coffea Species,”
Genetic Resources and Crop Evolution
40:91-99 (1993)) and chloroplast restriction fragment length polymorphism (RFLP) analyses (Lashermes et al., “Inheritance and Restriction Fragment Length Polymorphism of Chloroplast DNA in the Genus Coffea L.,”
Theoretical and Applied Genetics
93:626-632 (1996)). The nuclear DNA content of
C. arabica
, as determined by flow cytometry, is 2.4 pg/interphase nucleus, or n=2X=1158 Mb (Arumuganathan et al., “Nuclear DNA Content of Some Important Plant Species,”
Plant Molecular Biology Reporter
9:208-218 (1991)). It is cultivated in 75% of the coffee plantations around the world. The quality of the beverage is potentially excellent, being known in the trade as “mild coffee.” The most important pests affecting this species are coffee rust (
Hemileia vastatrix
), coffee berry disease (CBD,
Colletotrichum coffeanum
), and coffee berry borer (
Hypothenemus hampei
, Coleoptera). Worldwide, these three pests cause an estimated crop loss of 14.8%, or about $1 billion annually (Oerke et al., “Estimated Losses in Major Food and Cash Crops,”
Crop Production and Crop Protection
, Elsevier, New York, U.S.A. (1994)).
Several cultivars have been described for
C. arabica
, but because of the narrow genetic base of the species, they are due mainly to single gene mutations. The commonly grown varieties, Tipica and Bourbon, can grow up to 6 m tall under natural conditions. Coffee trees grow well at tropical elevations, ranging from 300 to 1200 m above sea level, with a mean annual temperature of 18 to 21° C.
C. arabica
cv. Caturra is a mutant of the Bourbon cultivar, which was discovered in Brazil in 1949 and has been extensively grown in Colombia. The main characteristic of this cultivar is the dwarf phenotype resulting from the action of a dominant gene that reduces the internode distance (Orozco, “Descripcion de Especies y Variedades de Café,”
CENICAFE
Chinchiná, Caldas (1986)). Use of this phenotype has allowed planting densities to increase from 2500 plants to 10,000 plants/h, which, in turn, has increased bean yields from 5000 kg to about 8000 kg/h.
The species
Coffea canephora
Pierre ex Froehner, also known as
Coffea robusta
Linden, is the diploid species most widely cultivated around the world. It is self sterile and cross pollinated and therefore much more variable than
C. arabica. C. canephora
is better adapted to humid-hot climates and is frequently cultivated in low to medium altitudes. The quality of the beverage made from
C. canephora
is usually regarded as inferior to that made of
C. arabica
. However,
C. canephora
is more resistant to coffee rust and CBD.
Traditionally, Tipica, Bourbon, and Caturra were the
C. arabica
cultivars grown in Colombia. These varieties produce a high quality coffee, but they are very susceptible to pests which are not held in balance by natural biocontrol. Although South America was free of the most important coffee pests for many years, threats became real with the appearance of coffee rust in Brazil in 1970 and in Nicaragua in 1976. This disease finally arrived in Colombia in 1983. In anticipation, the Colombian National Center of Coffee Research (CENICAFE), a organization of Colombian coffee growers, began a breeding program for resistance to coffee rust in 1968. The purpose was to create a cultivar of
C. arabica
that preserves the traditional cup quality, but incorporates increased genetic diversity, durable resistance to the coffee rust, phenotypic homogeneity, and productivity (Castillo et al., “La Variedad Colombia: Selección de un Cultivar Compuesto Resistente a la Roya del Cafeto,”
CENICAFE
Chinchiná, Colombia, 171 p. (1986)).
Timor hybrid was chosen as the resistant parent of the new cultivar since no germplasm of
C. arabica
was known to contain durable resistance genes against coffee rust. Timor hybrid is a natural interspecific hybrid between
C. arabica
and
C. canephora
found in 1917 on the island of Timor, Indonesia. Used in Africa and India for many years, it showed broad resistance against the local rust races. In the Colombian breeding program, the recurrent quality parent of the new cultivar was
C. arabica
cv. Caturra, which in addition to providing the characteristics of dwarfism and good beverage quality, was a familiar cultivar among the growers. The result was the release in 1980 of the Colombia cultivar, a composite cultivar made up by the mixture of seeds coming from the best F5 and F6 progenies resistant to coffee rust and with optimal adaptation to the climate and soils of the Colombian coffee zone (Castillo et al., “La Variedad Colombia: Selección de un Cultivar Compuesto Resistente a la Roya del Cafeto,”
CENICAFE
Chinchiná, Colombia, 171 p. (1986)).
Components of the Colombia cultivar are continuously tested for their resistance against coffee rust and other diseases. When a component is found susceptible, it is withdrawn from the mixture. In the same way, new selected components can be added to the cultivar. This procedure provides a dynamic update of the cultivar in its resistance against coffee rust. Seed production and distribution of the Colombia cultivar are carried out exclusively by the National Federation of Coffee Growers. This maintains a diversity in resistance to coffee rust as well as the phenotypic homogeneity, yet results in low seed prices for the farmers.
In contrast to many other crops, coffee has not been the subject of extensive research in molecular biology. This may be due to factors such as the long life cycle, the difficulty of maintaining plants out of the tropical environment, and the lack of resources from countries that cultivate coffee. Nevertheless, some advances are being made in this field.
Several proteins, especially those involved in the resistant interaction with coffee rust have been studied. Kinetics and differential expression of phenylalanine ammonia lyase (PAL) (Almario, “Study of the Activity of the Phenylalanine Ammonia Lyase in the Presence of the Pathogen in Coffee Varieties Resistant and Susceptible to
Hemileia vastatrix
Ber & B

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