Gene Pyramiding for CLR Resistance

January 24, 2010

J. Plantation Crops. 29: 10-15 (2001).

Breeding for rust resistance in coffee: The gene pyramid model

In the international trade of commodities, coffee occupies a place of pride, next to petroleum, in trade volume and money value. For India, coffee exports earn about Rs.15 billion annually. Many third world economies depend on the earning from this important crop. Leaf rust caused by Hemileia vastatrix is a disease of economic significance on Arabica coffee. About 32 races of this pathogen are known. Almost all coffee research institutions in the world are engaged in breeding rust resistant strains of Coffea arabica. There are nine known genes (symbolized SH1 – SH9), which condition race specific resistance of the host plant. Many combinations of these genes were already known to have been overcome by races of the rust fungus. Hibrido de Timor (HDT) is the singular genotype that remained resistant to all known races. It has a unique genotype (SH6,7,8,9) which is the probable cause of this manifestation. Gene pyramiding is conceived to be able to impart long lasting resistance to this classic disease, and a model combining all known and unknown resistance genes is presented in this paper. Involving a variety of interspecific hybrids manifesting resistance conditioned by the elements of vertical resistance, and wild arabicas with horizontal resistance, and dwarf/semi-dwarf genotypes conditioned by dominant genes, is proposed to derive a resistant plant population carrying the necessary genetic diversity and uniform plant type. Integrating vegetative multiplication in the breeding scheme makes this commercially viable by way of eliminating segregation for plant type as well as resistance.


Biochemical Markers for CLR Resistance

January 15, 2010

Proc. 15th Plantation Crops Symposium PLACROSYM XV (2002). pp. 6-13.

Biochemical Markers for Rust Resistance in Coffee

AS Ram, NP Geetha, KN Amruthesh, KR Kini,D. Ganesh
CS Srinivasa, HS Shetty

Coffee is a great commodity of international trade, sustaining the economies of over eighty developing countries that produce this crop. Commercial coffee is produced from mainly two species of the genus Coffea L. viz. C. arabica L. and C. canephora Pierre. Leaf rust is a devastating disease of coffee causing economically significant crop losses of C. arabica. Thus, achieving rust resistance is one of the major objectives of almost all Arabica coffee breeding programmes of the world. Present study was undertaken with the objective of finding biochemical markers that facilitate the identification of rust resistant plants at an early stage of development (e.g. nursery stage). The enzymes phenylalanine ammonia-lyase (PAL), lipoxygenase (LOX), peroxidase (PO) and chitinase are known for their involvement in plant defense against pathogens. Present study evaluated the constitutive level of activity of these enzymes in progeny populations derived from the cross Ligenioides (natural allo-tetraploid derived from an artificial hybrid of Coffea liberica x C. eugenioides) and Hibrido de Timor (HDT, a spontaneous tetraploid interspecific hybrid of C. arabica and C. canephora) that was manifesting high rust resistance. The study was conducted on Ligenioides, HDT, their F1, F2 and BC progenies. Results indicated that PAL and LOX are good indicators of rust resistance at the constitutive level of activity and can be effectively utilized for the identification of resistant plants. This is a first report of biochemical markers with diagnostic value and utility in coffee breeding. Implications of the utilization of biochemical markers in resistance breeding and propagation and distribution of resistant material for commercial exploitation are discussed.

Systemic Acquired Resistance in Coffee

January 9, 2010

Proc. XX International Conference on Coffee Science, pp. 1272-1276.
(Bangalore, 11-15 October, 2004)

Pathogen-Induced Systemic Acquired Resistance in Coffee


Coffee is the largest traded commodity in the world market after oil and the earnings from coffee trade sustain the economics of many developing countries producing this crop. A major disease causing economical significant crop losses in coffee is leaf rust caused by Hemileia vastatrix. Coffee-leaf rust relationship is one of the well studied host pathogen systems to understand the resistance- virulence interactions. The gene-for gene model was utilized to explain the manifested interactions of coffee and leaf rust. Our recent research revealed interesting deviations from this mechanism. Hibrido de Timor (Spontaneous hybrid of Arabica and Robusta) and other hybrids derived from interspecific crosses were exploited commercially in many coffee-producing countries. New races of rust fungus were reported from these hybrids that express vertical resistance. Present paper describes the incidence and infectivity of a new race on two differential hosts C. congensis and Kawisari and the operation of systemic acquired resistance (SAR) defense mechanism in Coffea was also proposed in the light of these studies. Coffea canephora, C. congensis and C. liberica were believed to have contributed genes to some breeding stocks of C. arabica. In our studies, spores collected from the hostdifferentials, C. congensis (B-type) and Kawisari (Natural hybrid of C. arabica and C. liberica, M-type) failed to re-infect the respective hosts as well as the other differentials carrying the genes from the above mentioned species of Coffea. This is a pointer in the direction of SAR playing an important role in the resistance of coffee to leaf rust. From our various observations in inoculation experiments, it is evident that systemic acquired resistance against leaf rust is operating in the diploid species of Coffea and interspecific hybrids at a higher level than in tetraploid C. arabica. This is the first record of occurrence of SAR in coffee.

Coffee Leaf Rust Resistance

January 8, 2010

Proc. XVI International Scientific Colloquium on Coffee

Kyoto (9th – 14th April 1995).pp.548-556.



Literature on inheritance of resistance to coffee leaf rust is re-examined and lacunae in understanding the mechanism of inheritance are identified as lack of sound genetic assumptions and distorted genetic analysis on the basis of manifestation of resistance or susceptibility rather than actual genotype testing. Assumptions for genetic analysis of inheritance of resistance are laid down and their importance highlighted. The credibility and viability of the suggested model is elucidated by applying it to some of the already published results. The possibility of hitherto unrecorded genotypes of considerable breeding value residing in the progenies of differentials A-, H- and G-types is indicated. Incomplete resistance is indicated to be a Mendelian phenomenon and a manifestation of gene dose effect rather than a quantitative trait.

Evolution of Catimors

January 8, 2010

Catimor is the generic name applied to the coffee hybrids derived by crossing Caturra, a semi-dwarf mutant of Bourbon coffee plant and Hibrido de Timor (HDT, The Timor Hybrid), a natural hybrid of Arabica and Robusta coffee that manifests many characters of agronomic interest like resistance to leaf rust, coffee berry disease (CBD) and nematodes of Meloidogyne sps. These hybrids became popular with the coffee growers across the world on account of their manifested resistance to the above adversaries and consequent lowered cost of production. Besides, these hybrids are also highly productive. On account of their dwarf nature and conical bush shape, they are amenable for high density planting. Above all, Catimors produce beans and beverage of accepted quality. In the recent past, several Catimor-like coffee hybrids found their way into India under the names BBTC Catimor, Brazilian Catimor, Colombian Catimor, Catuai x HDT and Ruiru-II. Present document attempted an appraisal of these materials in terms of their utility to growers, the stability of their manifested plant type, resistance and productivity and finally their possible longevity in the field. A brief summary of the cultivation of these varieties on the basis of field observations and available literature is also included, to be of use to the growers.

The document is available with the author and can be obtained by mail order/request to

San Ramon Hybrids

January 8, 2010

San Ramon

Fruit Clusters

San Ramon Hybrids
San Ramon is a dwarf mutant of Bourbon coffee (Coffea arabica L.) first spotted in Costa Rica. Original San Ramon, thus, is as highly susceptible to leaf rust (caused by Hemileia vastatrix B. et Br.) as Bourbon itself. However, the dwarf stature of San Ramon (Dwarfness and Compactness) permits high density planting. Thus the concept of improving San Ramon by incorporating resistance genes from the then available progenies of S.795 came into being. The first crosses were effected in the year 1958 at the Central Coffee Research Institute (CCRI) of India, to incorporate resistance to the prevalent races I and II conditioned by the gene SH3 available in these materials. Seed from the F1 hybrid lines were given for trials under the name of Sln.7.1. Later, the F1 lines were crossed with Ethiopian Arabica varieties Cioccie and Agaro to obtain resistance against race VIII of the rust fungus conditioned by the gene SH4 available in these collections, in the year 1963. Seed from the resulting hybrid lines was distributed as Sln.7.2. Subsequently, selected plants of Sln.7.2 were crossed with Hibrido de Timor (HDT) to impart maximum possible resistance to leaf rust by transferring the resistance genes of HDT (later identified to be SH6, SH7, SH8 and SH9) in the year 1972. Some efforts were devoted to plant only desirable dwarfs in the progeny plots of this cross. Seed from these hybrids was distributed under the name of Sln.7.3. The cross of Sln.7.3 with selected plants of Sln.6 (Robarbica, an indigenous artificial hybrid of Robusta x Arabica) is aimed at rendering the descendant hybrids extra resistant to leaf rust. This hybrid is named as Sln.7.4. However, there is segregation of resistant and susceptible types in the F3 generation (Resistant 65.6% and susceptible 34.4%). There is also segregation of plant types into tall and dwarf. Among the dwarfs there are four types of plants. These are: a) extreme dwarfs, b) conical shaped dwarfs with short internodes, c) conical shaped plants with slightly longer internodes and d) open type plants with slightly longer internodes. Only the last type of plants in San Ramon hybrids is desirable for cultivation as they are the most amenable for various cultural operations. Presently, seed from resistant plants of this progeny is given out as Sln.7.4.
Improvement of San Ramon mutants has taken place only in India. In the course of improvement of rust resistance, the quality of the produce is not compromised and selection for bold bean size and good cup quality rendered this material resistant to rust as well as producing good quality coffee. The quality aspects and agrotechniques for cultivating this variety are reviewed in the document.
The document is available with the author and can be obtained by mail order/request to

Coffee Breeding- Summary & Contents

October 1, 2009

Summary – Coffee Breeding (A. Santa Ram, 2009)

Coffee is a perennial crop of great significance to the many third world countries that produce this stimulating beverage crop. Arabica and Robusta are the two species of the genus Coffea that provide the consumed coffee. These commercially important plant species are ravaged by diseases and pests that have to be managed and kept to sub-threshold levels to obtain a sustainable livelihood. Breeding to evolve resistant plant materials comprises the first step in managing these adversaries. The book “Coffee Breeding” reviews the existing knowledge on the subject of plant breeding as applied to coffee, summarises the recent advances and presents models for future breeding exercises. The content of the book is presented in three major chapters as follows.

I. The Coffee Plant
II. Coffee Breeding
III. The Future Outlook

The first chapter, “The Coffee Plant” presents details of history of the spread of cultivation of this important beverage crop, the beginnings of research in various countries, reviews knowledge of the taxonomy, physiology, available genetic resources and variability that is the feedstock of breeding exercises, summarises the crop husbandry practices to manage weeds, pests and diseases, reviews knowledge on harvest and processing and culminates in a summary of quality aspects and coffee trade.

The second chapter “Coffee Breeding” begins with a section on the available genetic resources and evaluation of genetic variability providing a detailed insight into the finer aspects of genetic variability and polymorphism and ways and means of utilizing it to evolve the best possible out puts. Reproductive biology of Arabica and Robusta coffees is widely different and thus are dealt in different sections of this chapter.

The section on “Breeding Coffea arabica L.” reviews all available knowledge on the evolution of this species that has important bearing on breeding for various traits of interest and the importance of interspecific hybrids in breeding. The section, breeding for leaf rust resistance provides a deep insight into the variability in the rust fungus as well as the host and physiological specialization of both that leads to an understanding of the types and sources of resistance and the ways and means of utilizing it to the best advantage. This section also provides an insight into the mechanisms of segregation in the progenies and varieties derived from the ancestry of Hibrido de Timor that is extensively utilized as a source of rust resistance genes in the world coffee breeding programmes. Another interesting detail presented in this section is on “Ligenioides”, an amphidiploid of C. liberica and C. eugenioides that crosses well with a variety of Arabicas to yield fertile hybrids. Work done in India on the hybrids of Ligenioides and Hibrido de Timor indicates that this amphiploid could be a new source of genes for breeding Arabica coffee. Mention is made of other similar interspecific hybrids that could be a source of resistance genes for diseases like CBD and the possible use of them in breeding.

This section culminates with a sub-section reviewing the breeding programmes of different coffee producing countries and breeding for resistance to other diseases, yield, productivity and quality.

The section on “Breeding Coffea canephora Pierre ex Froehner”, summarises knowledge of the origin and evolution of cultivated robustas, the self-incompatibility system and related polymorphic genetic structure of the species and its importance in breeding. While yield enhancement was considered the single most important objective of value for Robusta breeding, the other aspects like leaf rust resistance, resistance to tracheomycosis and anthracnose were also reviewed and their importance stressed. Robusta generally manifests a high level of tolerance to pests, but there are specific pests like leaf miner, branch borer and berry borer to which resistance is present in C. racemosa, C.liberica etc. and strategies for transfer are suggested. The quality aspects of robusta breeding terminate the chapter.

The third chapter, “Outlook for the Future” reviews conventional breeding strategies and suggests improvements for the future for Arabica and Robusta separately. The fact that C. arabica is capable of assimilating genes from a many of diploid species and express them has tremendous implications for breeding this important species to evolve disease and pest resistant planting stocks. It is suggested that evolution of C. arabica should be given due importance in the long term breeding exercises. Gene pyramiding leading to multiple resistance and heterosis breeding integrating all the above elements is suggested to achieve positive sustainable productivity. Biotechnological approaches were briefly reviewed and it is apparent that the integration of these elements in breeding may take considerable time.

A review of the breeding strategies in practice for Robusta is presented and the new approaches reciprocal recurrent selection, haplo-diploid hybridization and interspecific hybridization are suggested to obtain value and productivity for this species.

Coffee Breeding – A. Santa Ram



The Coffee Plant
1.1. History
1.1.1. Origin and Spread
1.1.2. Folk Selections
1.1.3. Organized Research on Coffee
1.1.4. Taxonomy
1.2. Plant Improvement
1.2.1. Coffee Germplasm
1.2.2. Breeding
1.2.3. Resistance to Leaf Rust
1.3. Physiology
1.3.1. Photosynthesis
1.3.2. Photoperiodism and Flowering
1.3.3. Metabolism
1.4. Crop Management
1.4.1. Soil and Climate
1.4.2. Seed Selection
1.4.3. Seed bed – Nursery
1.4.4. Planting and After-care
1.4.5. Shade Management
1.4.6. Weed Control
1.4.7. Soil Conservation
1.4.8. Fertilizer Response
1.4.9. Pruning and Training
1.5. Pests of Coffee
1.5.1. Nursery Pests
1.5.2. Plantation Pests
1.5.3. Pest Control
1.6. Diseases of Coffee
1.6.1. Disease Control
1.6.2. Disease Resistance
1.7. Harvesting and Processing
1.7.1. The Dry Processing Method
1.7.2. The Wet Processing Method
1.7.3. Coffee Curing
1.7.4. Grading
1.8. The Coffee Industry
1.8.1. International Coffee Agreement

Coffee Breeding
2.1. Coffee Genetic Resources
2.2. Evaluation of Genetic Variability
2.2.1. Survey and Collection
2.2.2. Morphological Characters
2.2.3. Karyotype
2.2.4. Self-Incompatibility
2.2.5. Genetic and Cytogenetic Polymorphism
2.2.6. Isozyme Polymorphism
2.2.7. DNA Polymorphism
2.3. Coffee Plant Improvement
2.3.1. Breeding Coffea arabica L. (Arabica) Evolution of Coffea Arabica Interspecific Hybrids Breeding Arabica for Leaf Rust Resistance Variability in the Rust Fungus – Physiological Specialization Mechanism of New Race Formation Types and Sources of Resistance Reistance Genes of Coffea arabica and Coffee Differentials Inheritance of Resistance Genes Breeding Programmes
2.3.2. Breeding Coffea arabica for CBD Resistance Resistance to CBD in Coffea Arabica Breeding Programmes – CBD Resistance
2.3.3. Breeding Arabica coffee for Resistance to Other Diseases
2.3.4. Breeding Coffea arabica for Yield and Productivity
2.3.5. Breeding Coffea arabica for Quality
2.4. Breeding Coffea canephora Pierre ex Froehner (Robusta)
2.4.1. Origin and Evolution of Cultivated Robustas
2.4.2. Recent Prospecting for Wild Robustas
2.4.3. Robusta Working Collections
2.4.4. Self-incompatibility, Polymorphism and Genetic Structure
2.4.5. Breeding Robusta Coffee for Yield
2.4.6. Breeding Robusta for Disease Resistance
2.4.7. Breeding Robusta for Resistance to Pests
2.4.8. Breeding Robusta for Quality

Outlook for the Future
3.1. Breeding Strategies for Arabica
3.1.1 Conventional Strategies
3.1.2 Future Strategies
3.2. Breeding Strategies for Robusta
3.2.1. Conventional Strategies
3.2.2. Modern Strategies