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



September 21, 2009

Name : Akundi Santa Ram

Present Position: Professor and Head, Department of Microbiology Pooja Bhagavat Memorial Mahajana’s Post Graduate Centre KRS Road, Metagalli, Mysore 570016, Karnataka, India

Permanent address : # 51, Block 22, Madhuvana Srirampura 2nd Stage Mysore 570023, Karnataka, India

E- mail:

Phone: 0091-821-2361894 (Res) 0091-94487-53302 (Mobile)

Education:  Ph.D. in Botany (Special training in Cytogenetics, Radiation Genetics and Developmental Morphology of Angiosperms at M.Sc., Phytochemistry and Plant Development at Ph.D.).

Trainings attended: Training in plant regeneration techniques at Indian Institute of Science (Bangalore, India,1986)

Molecular biology and biodiversity conservation techniques at MS Swaminathan Research Foundation (Chennai, India,1997).

Underwent training  in the techniques of Plant Molecular Biology at MS Swaminathan Research Foundation as  a SERC Visiting Fellow (1998).

Underwent training on IPRs at ASCI, (Hyderabad, 2006) and participated in several discussions on the subject and involved in the registration of unique coffee germplasm with the National Bureau of Plant Genetic Resources.

Title of Ph.D. Thesis: Phytochemical and Embryological Studies in some Umbelliferae.

Employment :

Professor and Head of the Department of Microbiology, Pooja Bhagavat Memorial Mahajana Post Graduate Centre, Metagally, Mysore(March 2009).

Head, Division of Plant Breeding and GeneticsIn Central Coffee Research Institute (voluntarily retired in  2008)

Research involvement: Involved with coffee plant breeding since 1980. A variety of research subjects were explored to gain a deep insight into the genetic architecture of the coffee plant and plants in general in order to develop models for plant improvement in coffee.

Total research work can be broadly divided into three major areas: reproductive biology, plant breeding and biotechnology.

Participated in the technical execution of national and international collaborative projects on coffee breeding and biotechnology.

Published over 80 research papers in journals and/or proceedings of National and International seminars/symposia.
List of Publications

Fund Raising: The following funds were raised from National and International nodal agencies for coffee breeding projects .

1. Collaborative project “ Studies on Properties of Wood as Indicators of Coffee White Stem Borer Resistance” in collaboration with Institute of Wood Science and Technology (2005-2008).

Total value: Rs.22.85 lakhs.

Source of Funds: Coffee Board, Bangalore.

2. Collaborative project, “Breeding Coffee for Durable Resistance Against Coffee Leaf Rust and Coffee Berry Disease” in collaboration with Centro Investigacao das Ferrugens do Cafeeiros, Oeiras, Portugal (2007-2010). Total value: Rs. 6.60 lakhs.

Source of Funds: Department of Science & Technology, New Delhi.

3. Collaborative Project “Increasing the Resilience of Coffee Production to Coffee Leaf Rust and Other Diseases in India and Four African Countries” in collaboration with CABI (Commonwealth Agricultural Bureau International), Coffee Research Foundation, Kenya; Coffee Research Institute, Uganda; Coffee Research Station, Zimbabwe and Institut des Sciences Agronomiques du Rwanda, Rwanda.

Total value: US$ 39.88 lakhs. India’s share: US$ 9.11 lakhs.

Source of funds: International Coffee Organization, London and Common Fund for Commodities (CFC), Amsterdam, The Netherlands.

Achievements: An important achievement in the course of my work with CCRI is the development and release of a new variety of coffee plant named as Chandragiri in the year 2007.

Developed model breeding systems for various hybrid lines of coffee in the course of past 28 years.

Current Research Interest: Building  a collection of useful microorganisms (bacteria and fungi) of Karnataka to develop bio fertilizers and bio control agents for promoting sustainable agriculture.

Another area of research interest is identification of elite medicinal plants in the wild plant populations of Mysore district.

Research Guidance: I am a recognized guide for the Doctoral students of Kuvempu University and Mysore University in Karnataka and Tamil Nadu Agricultural University, Coimbatore in Tamil Nadu.

Thus far, two students submitted their Doctoral theses to Kuvempu University and one student submitted the thesis to the Tamil Nadu Agricultural University.

Titles of theses :

1. Ramesh G. 2008. Studies on Combined use of Organics and Inorganic Fertilizers on Growth and Yield of Kalmegh (Andrographis paniculata L.) – Kuvempu University.

2. Dinesh KP. 2008. Morphological, Biochemical and Molecular Characterization of Ethiopian Arabica Coffee (Coffea arabica L.) Germplasm in India – Kuvempu University.

3. Muthuramalingam S. 2008. Characterization of Arabica Coffee (Coffea arabica L.) Genotypes for Yield and Quality – Tamil Nadu Agricultural University.

One student N. Suresh, recently registered for Ph.D. Degree of Kuvempu Unviersity with subject of study, Development of Morphological, Biochemical and Molecular Markers for Disease Resistance in Coffee.

As an accredited research guide I have guided over 30 Master’s students from the various Universities such as University of Mysore, Kuvempu University, Kannur University, Bangalore University, Bharatidasan University and Utkal University in their project work.

Completed Projects

1. International collaborative project “Pathology and Improvement of Coffee for the Main Diseases” funded by European Commission (1990-94) in association with the Centro Investigacao das Ferrugens do Cafeeiros, Oeiras, Portugal.

2. National network project on “Biotechnological Approaches for Coffee Plant Improvement” funded by the Department of Biotechnology (1999-2004).

3. A collaborative project, “Properties of Wood as Indicators of Resistance to Coffee White Stem Borer” in association with the Institute of Wood Science & Technology, Bangalore funded by Coffee Board, Bangalore (2004-2007).

On-going Projects

1. A project on “Increasing the Resilience of Coffee Production to Coffee Leaf Rust and Other Diseases in India and Four African Countries” funded by International Coffee Organization (ICO) and Common Fund for Commodities (CFC).

2. A collaborative research project with the Coffee Rusts Research Centre, Portugal on “Coffee Breeding for Durable Resistance to Coffee Leaf Rust and Coffee Berry Disease” funded by Department of Science & Technology (DST), Government of India.

These projects are now being continued by the Institute since my departure from Central Coffee Research Institute. International Visits In the course of my service, I have had the opportunity to contact and develop rapport with international nodal agencies like the International Coffee Organization, Common Fund for Commodities, European Commission and several others.

My international visits:

1. Kyoto city, Japan to present a paper on Mendelian Genetics of Rust Resistance in Coffee (1995).

2. Kenya and Tanzania for a study of the breeding techniques and genetic resources available in those countries (2003).

3. Centro Investigacao das Ferrugens do Cafeeiros, Oeiras, Portugal as part of a collaborative project on Breeding Coffee Plants with Durable Resistance to Coffee Leaf Rust and Coffee Berry Disease (2007).

Computer knowledge: Trained in the use of word processing, database and numerical and statistical analysis software.

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September 21, 2009

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