Ligenioides:Indian Coffee Selection-11

December 22, 2017

Coffee for a consumer means its fine aroma, flavor and taste that contribute to the cheer of the day. These are the hallmark characters of a beverage brewed from the roasted and ground beans of a single species of the genus Coffea, namely Coffea arabica1,2. This is one unique species of the genus and there are over a hundred other species that are also members of this genus3. The genus Coffea belongs to the flowering plant family Rubiaceae7. Coffea arabica was the only species of the genus to be cultivated until the early 20th Century on account of the quality attributes mentioned above. In the last decade of the 19th Century the cultivated Arabica coffee came under severe attack by the disease caused by the fungus Hemileia vastatrix. This led to the devastation of flourishing coffee plantations of Sri Lanka and Indonesia4,5. This is when the world started looking for alternatives to Arabica coffee and other species started being described and some of them were brought into cultivation by progressive growers. Among those that were introduced to cultivation the most prominent is Robusta (Coffea canephora) and the second species of import is Liberica (Coffea liberica)6. Until then, there was no organized effort to conduct research on the coffee plant.

It is important to understand the biological nature of any important plant in the context of its genetic improvement. At this juncture, it is not out of place to remember that all the organisms are endowed with characters determined by genes that are borne on their chromosomes. Each of the species is characterized by a unique chromosome number8. This number is usually an even number because most of the higher organisms are diploid in nature. The term diploid is derived from Greek “diplous” which means double (written as 2n). Thus, all diploid organisms carry two complete sets of chromosomes, each being contributed by one of the parents. This diploid number is reduced to half in the formation of germ cells like sperms and ova of animals and pollen and egg cells of plants through the meiotic cell division that is also known as the reduction division25. This reduced half number of chromosomes is termed haploid, again derived from Greek “haploos” that means single (written as 1n or n). This haploid set of chromosomes carries all the genes that determine the characters of an organism and is generally characteristic in most of the species of a genus and sometimes even of the family to which a genus belongs. This set is also often called as the base genome of the genus. Such basic set of chromosomes is sometimes referred to as the base number of chromosomes in the genus and/or family (written as x). As already said coffee plants of all species belong to the genus Coffea of the family Rubiaceae. Base number of chromosomes in this family is 11. This is written as n=x=119.

Upon cellular examination of different species of Coffea, it was found that C. arabica carries 44 chromosomes in its cells and all other species including C. canephora and C. liberica have 22 chromosomes in their cells. Thus, C. arabica is a tetraploid carrying four sets of the basic haploid set of chromosomes. This means that each parent of any Arabica coffee plant contributes 22 chromosomes which is the haploid set for this species and the diploid number is 44. However, this diploid number is multiplied four times of the basic haploid set and hence it is considered a tetraploid (written as 2n=4x=44). Further, it is considered an allo-tetraploid, derived by the hybridization of two progenitor species and doubling of chromosomes in their allo-diploid hybrid (allo is a greek word that means combing from different organisms/species). The two progenitor species were identified as C. eugenioides being the female progenitor and C. canephora as the male progenitor, each contributing a complete set of their chromosomes. By an extension of the same line of argument, the diploid chromosome number of all other species of Coffea is 2n=2x=22.

In an evolutionary context, each of the species of various organisms is characterized by a unique chromosome number as already mentioned. However, different species of the same genus may carry the same basic set of chromosomes. They become unique, showing different characters by way of differentiation of chromosome structure within the basic set. This may involve different mechanisms like duplication of some parts of certain chromosomes, deletion of small segments of some chromosomes, inversions of some stretches of chromosomes and sometime translocation of segments of chromosomes from one to another chromosome. These changes can ordain the expression of genes to be different between species leading to the observed differences between them. This chromosomal differentiation can be of an order that can prevent intercrossing of related species, i.e. crossing of such differentiated species would not result in viable hybrids. In such cases the species are said to be reproductively isolated10. Thus, chromosomal structural re-organization could be a powerful isolating mechanism in the context of evolutionary species formation. In some cases, differentiation of chromosomes may be of a lower order. In these cases, apparently different species can cross to produce moderately fertile and viable hybrids. These hybrids are an important source of new genes and new combinations of genes for genetic improvement of a related species that may be important for human consumption.

In the genus Coffea, the various diploid species which manifest large differences in morphology and other characters can cross to produce moderately or fairly fertile hybrids11,12,13. Some diploid species can also cross with C. arabica and give rise to triploid hybrids which are moderately fertile and can be used in back crosses to C. arabica to transfer the genes of interest from diploid species to the tetraploid Arabica14. This is because the differentiation of chromosomes among the species of Coffea is not so complete as to reproductively isolate them15. Thus, different species of Coffea carry weakly differentiated chromosomes of the basic set. Thus, chromosomes of different species of Coffea carry large homologous segments which are also homosequential16. This means that the order of genes on these homologous segments of chromosomes is the same among the apparently different species. This situation auger well for the transfer of genes between different species of Coffea and is very useful in the improvement of the commercially very important C. arabica17.

In the mid and late 20th Century, research efforts were devoted to understand the genetic relationships among the apparently different species of Coffea through interspecific hybridization. These studies led to the classification of the different species of Coffea into three sections in the context of Arabica coffee breeding18. Thus, the various varieties of Arabica that cross well within themselves and the tetraploid Arabicoid interspecific hybrids used in Arabica breeding19 were placed in the primary gene pool. So far, this is the main source of genes for all the coffee breeding programmes. The diploid species of Coffea that cross well with C. arabica to produce moderately fertile triploid hybrids were placed in the secondary gene pool. These triploid hybrids can be back crossed with Arabica to evolve synthetic types carrying the characters of Arabica and the diploid species that can be stabilized as varietal characters through appropriate selection and breeding techniques. Coffea canephora and C. liberica and several other species like C. racemosa, C. eugenioides and C. excelsa are in this section. The third section includes C. stenophylla, C. salvatrix and some others that do not cross with C. arabica. However, these species can cross with some species of the secondary gene pool to produce fertile or moderately fertile hybrids which can be used in Arabica breeding. Application of cytogenetic techniques and skills is needed to handle the transfer of genes from diploid species to tetraploid Arabica.

In India, efforts to understand genetic relationships of Coffea species began in 1950s and 1960s when initial crossing of various diploid species was conducted. One of the crosses is between the diploid species C. liberica and C. eugenioides with C. liberica as the mother parent11,15. One of the plants in this line of hybrids has given rise to a sucker which manifested Arabica-like characters12,20. This was found to be tetraploid with 44 chromosomes in its cells20. This sucker was utilized to develop four plants by vegetative propagation. The four clones were fertile and produced seed upon self pollination. Further propagation of these plants was by seed. This was named as Ligenioides21, combining the specific epithets of the two parent species. This is an event of natural doubling of chromosomes in a hybrid of C. liberica and C. eugenioides, the two diploid species. Resemblance of these plants to C. arabica, their self-compatibility and beverage quality of their seed prompted the breeders to propose that C. arabica might have arisen by a hybridization of the species C. liberica and C. eugenioides in the evolutionary past26,27.

This material was given for cultivation as Selection-11 in the late 1970s in India. This selection possesses strong resistance against leaf rust and white stem borer. However, bean size of this selection is small and this has not become popular with growers on account of this. Even so, beverage quality of Ligenioides is found to be good with FAQ and above score24. To improve bean size, Ligenioides was crossed with Hibrido de Timor which was also manifesting high resistance to coffee leaf rust. In the first generation and backcross progenies, an improvement of bean size was recorded. Rust resistance in these hybrids also remained high. Yield and quality of these hybrids are also impressive over several years of observation. A comprehensive study of these materials indicated that Ligenioides could be a source of new genes for breeding Arabica varieties resistant to rust22. It is also possible to incorporate resistance to white stem borer through Ligenioides23.


  1. Van der Vossen HAM. 2009. The cup quality of disease resistant cultivars of Arabica coffee (Coffea arabica). Expl. Agric. 45: 323-332.
  2. Leroy T, Ribeyre F, Bertrand B, Charmetant P, Dufour M, Montagnon C, Marraccini P, Pot D. 2006. Genetics of coffee quality. Braz. J. Plant Physiol. 18: 229-242.
  3. Bridson DM, Verdcourt B. 1988. Flora of Tropical East Africa (Part 2). Balkema, Brookfield, Rotterdam.
  4. Ram AS. 2013. Coffee Breeding. Lambert Academic Publishing. Saarbrücken, Germany.
  5. Cramer PJS. 1957. A Review of Literature of Coffee Research in Indonesia. Inter-American Institute of Agricultural Sciences. Turrialba.
  6. Ram AS, Sreenivasan MS, Naidu R. 1994. Exploitation of Coffee Germplasm in India- II. Diploid species. J. Coffee Res. 24: 107-114.
  7. Chevalier A. 1947. Les caféiers du globe. III. Systematique des cafeiers et faux cafeiers. Maladies et insectes nuisibles. Paul Lechevalier, Paris.
  8. Darlington CD, Wylie AP. 1956. Chromosome Atlas of Flowering Plants. MacMillan, New York.
  9. Homeyer H. 1932. Zur zytologie der Rubiaceen. (Vor. 1 # uf: Htt) Planta 18(3): 640. (as cited in Cramer, 1957).
  10. Stebbins GL. 1950. Variation and Evolution in Plants. Colombia Biological Series XVI. Second Indian Reprint, Oxford & IBH, Calcutta.
  11. Narasimhaswamy RL, Vishveshwara S. 1961. Report on hybrids between some diploid species of Coffea Indian Coffee 25: 104-109.
  12. Narasimhaswamy RL, Vishveshwara S. 1967. Progress report on hybrids between diploid species of Coffea Turrialba 17: 11-17.
  13. Carvalho A, Monaco LC. 1967. Genetic relationships of selected Coffea Ciencia e Cultura 19: 151-165.
  14. Sreenivasan MS. 1987. Cyto-embryological studies of Robusta-Arabica coffee hybrids. Ph.D. Thesis. University of Mysore, Mysore.
  15. Reddy AGS. 1976. Cytomorphological studies in three diploid species of Coffea and their hybrids and hybrid progeny. Ph.D. Thesis. University of Mysore, Mysore.
  16. Kammacher P. 1977. Utilisation des ressources genetiques du genre Coffea pour l’amelioration des caféiers cultives. In: VIII International Scientific Colloquium on Coffee. pp. 335-358. ASIC, Paris.
  17. Kammacher P, Capot J. 1972. Sur les relations caryologiques entre Coffea arabica et canephora. Café Cacao The 16: 289-294.
  18. Medina-Filho HP, Carvalho A, Sondahl MR, Fazuoli LC, Costa WM. 1984. Coffee breeding related evolutionary aspects. Plant Breeding Reviews 2: 157-193.
  19. Sreenivasan MS, Ram AS, Prakash NS. 1993. Tetraploid interspecific hybrids in coffee breeding in India. In: XV International Scientific Colloquium on Coffee. pp. 226-233. ASIC, Paris.
  20. Reddy AGS, Raju KVVS, Dharmaraj PS. 1987. Allopolyploidisation in a spontaneously doubled hybrid of two diploid species of Coffea. In: PLACROSYM VI (Ed. Sethuraj MR), pp. 31-39. Oxford & IBH, New Delhi.
  21. Reddy AGS, Raju KVVS, Dharmaraj PS. 1985. Breeding behavior of “Ligenioides”, a spontaneous amphiploid between Coffea liberica and eugenioides. J. Coffee Res. 15: 33-37.
  22. Ram AS, Ganesh D, Srinivasan CS, Reddy AGS. 2004. Ligenioides-A source of new genes for Arabica coffee breeding. In: PLACROSYM XVI. J. Plantn. Crops 32(Suppl.): 5-11.
  23. Ram AS, Sabir RK, Mythrasree SR, Seetharama HG, Rao RV. 2008. White stem borer resistance in coffee: Perspectives on breeding, management and consumption. In: XXII International Scientific Colloquium on Coffee. pp. 1323-1335. ASIC, Paris.
  24. Ram AS. 2005. Quality improvement in Arabica coffee: Relevance of Ethiopian germplasm. J. Coffee Res. 33: 15-33.
  25. Garber ED. 1974 Cytogenetics. Tata Mc-Graw Hill, New Delhi.
  26. Narasimhaswamy RL. 1962. Some thoughts on the origin of Coffea arabica Coffee 4: 1-5.
  27. Ram AS, Sreenivasan MS. 1981. A chemotaxonomic study of Coffea arabica In: Genetics, Plant Breeding and Horticulture (PLACROSYM IV). pp. 368-374. Indian Society of Plantation Crops, Kasaragod.




Robarbica (Robusta x Arabica) Hybrids: Indian CoffeeSelection-6

December 22, 2017

Arabica coffee (Coffea arabica) possesses the quality characteristics of fine aroma, flavour and taste. Hence, it is commercially very important. However, this species is also the most susceptible to pests and diseases. Of the hundred species of Coffea, only two other species, C. canephora (Robusta) and C. liberica (Liberica) were of some commercial interest. These species produce coffee deficient of quality attributes. Of these two, Robusta is more popular and is produced by many coffee-growing countries. This species possesses resistance to some very important adversaries of Arabica such as leaf rust (caused by Hemileia vastatrix), white stem borer (Xylotrechus quadripes) and root lesion nematode (Pratylenchus coffeae)(Anonymous, 2000). On account of these characters, Robusta is considered an important source of resistance genes for improving Arabica. Arabica is a tetraploid carrying four sets of chromosomes (character bearers) while Robusta is a diploid with only two sets of chromosomes (C. arabica, 2n=4x=44; C. canephora, 2n=2x=22). This is an important and significant difference between these two species (Ram, 2001). Another important difference is that Arabica is self-fertile; producing seed upon self-pollination while Robusta is self-sterile producing hardly any seed when self-pollinated (DeVreaux et al., 1959). These differences render hybridization of these two species very difficult. However, small numbers of hybrid seed were obtained in various efforts of interspecific hybridization across the world (Sybenga, 1961). These seeds produced triploid plants with an imbalanced chromosome complement (2n=33). The crossing was said to be more successful in producing seed when Arabica is involved as the seed bearing mother plant (♀ parent) and Robusta as the pollen donor (♂ parent).

Breeding Efforts to Develop Robusta-Arabica Hybrids

As mentioned above, Robusta carries active and expressing genes conditioning resistance to important adversaries, but does not possess quality attributes. Another important aspect of Robusta is that it has greater caffeine content in its beans. These biological differences besides the others mentioned above render the interspecific hybridization efforts very difficult. However, these differences are useful in setting the breeding priorities and goals to produce synthetic types. Thus, the evolution of an Arabica type plant that produces coffee with the outstanding quality attributes besides possessing the resistance characters of Robusta and even possibly its productivity became the goal of all these exercises. Breeding efforts to evolve Robusta-Arabica hybrids were made with these objectives since the first half of 19th Century in Indonesia, India and Brazil. Later, this line of work was also taken up in Ivory Coast. These efforts can be classified into two major types: the first is prospecting for natural hybrids of Robusta-Arabica parentage and the second is artificial hybridization of Robusta and Arabica in reciprocal combination.

Prospecting for Natural Robusta-Arabica Hybrids

The early work in Indonesia was primarily prospecting for natural hybrids of Robusta-Arabica parentage. The earliest report on such hybrids mentions “Arla” hybrids discovered in Indonesia. However, not much attention was given to these hybrids and their further improvement as Indonesian coffee industry moved towards total Robusta cultivation (Cramer, 1957). Other interspecific hybrids like “Kawisari” (Arabica-Liberica parentage) also faded into history.

Devamachy hybrids discovered in India in 1949 are also considered to be of Robusta-Arabica parentage. These are utilized in the breeding programme to evolve Selection-5 that is commercially exploited in India (Srinivasan and Vishveshwara, 1980; Srinivasan and Ramachandran, 1997).

The most important natural hybrid of Robusta-Arabica parentage is Hibrido de Timor (HDT) discovered in Portuguese Timor. Hibrido de Timor (HDT) introduced into the germplasm bank of Central Coffee Research Institute (CCRI), India in 1961 originated in a C. arabica field on the Timor Island in 1917 (Bettencourt, 1973). HDT is known to manifest resistance to all known races of the rust fungus and is classified as “Type-A” (Rodrigues et al., 1975). It is a putative interspecific hybrid of Arabica (C. arabica L.) and Robusta (C. canephora Pierre ex Froehner) and is referred to as an Arabicoid (Eskes, 1989; Ram and Sreenath, 2000). HDT produces segregates manifesting a spectrum of resistance reactions (Bettencourt et al., 1992). These segregates are susceptible to a few races of the rust but manifest resistance to many races, especially the prevalent ones.

Artificial Hybridization of Robusta and Arabica

In India, the first crossing of these species was effected in 1937 with Robusta as the mother parent (♀) and Kents Arabica as the pollinator (♂). The few F1 hybrids obtained were all found to be triploid and the progeny highly sterile (Sreenivasan, 1987). This F1 was repeatedly backcrossed to the Arabica parent as shown in the genealogy chart. Of the three backcross progenies BC-II was found to possess an optimal combination of characters of both parents such as high resistance of Robusta and quality attributes of Arabica. However, the plants of BC-II were still unstable with a variety of cytological and reproductive abnormalities (Sreenivasan, 1987). Self- and open pollinated seed from the selected individual plants of BC-II were utilized to raise succeeding generations. An F2 descendant line S.2357 (F2 of BC-II) possessing high resistance to leaf rust and good cluster characters as well as the cup quality characters similar to Arabica was distributed to growers. Two progenies of the third generation derived from S.1156 line of BC-II (S.2827 and S.2828) were also found to be morphologically similar to Arabica carrying the high rust resistance and tight fruit cluster characters similar to Robusta with cup quality character of Arabica. Seed from these lines was also distributed for field trials as Selection-6 and its productivity and quality were assessed over the past many years. In the course of this time, this selection was adopted by several growers who, in turn, aided its evolution into a perfect material for commercial exploitation. This document enumerates the experiences of those growers with this material and its evolution under varied cultural practices.

Artificial interspecific hybrids involving C. arabica and induced autotetraploid C.canephora were produced in Brazil as early as 1950 (Monaco, 1977).

Selection of Parents and Breeding Protocol

Breeders at CCRI selected S.274 1/11 (Robusta) as the mother plant (♀parent) on account of the high yield of this plant (double the yield of family mean), its bold fruits and beans (a character that is said to be inherited from the ♀-parent in coffee) and wide adaptation of S.274. The Kents Arabica was selected as the pollen donor (♂parent) on the basis of the quality character and high yield potential.

An important difference between the interspecific hybrid programme of India and other coffee coffee growing countries of the world is that in India, a diploid plant of Robusta was involved in crossing as the mother parent in its native chromosome condition (2n=22) while in Brazil, Ivory Coast and other countries the Robusta parent was rendered tetraploid (2n=44) by colchicine treatment before it is used as the male parent in crossing. On account of this, the Robarbica hybrids of India are different from the Icatu hybrids of Brazil and Arabusta hybrids of Ivory Coast as they carry the cytoplasm of Arabica. Indian Robarbicas carry the cytoplasmic endowments of Robusta and are likely to be important in specific breeding contexts like the resistance against coffee berry disease (CBD). However, the apprehension that beverage quality of interspecific hybrids is compromised stands void as can be seen from the literature (Narasimhaswamy, 1960; Ganesh et al., 2002; Petracco, 2000; Bertrand et al., 2003; Fazuoli et al., 1977).

Backcross breeding method was adopted as it leads to the restoration of the genotype of the recurrent parent by the third backcross generation to an extent of 93% with the introgression of a variable proportion of genes from the donor parent. This variable proportion usually does not exceed 5-7% in the case of normal crossings (diploid-diploid crosses).

Pedigree of Robarbica (Selection-6)

Robusta (S.274 1/11) x Arabica (Kents)

Triploid F1 (S.594)

BC-I Tetraploid (S.905)
BC-II Tetraploid (S.1156)

1st Generation        S.2088                                        S.2089                                     S.2090

2nd Generation      S.2399                                         S.2383                                     S.2386

S.2354                                       S.2384


S.2357 (Distributed to growers)

3rd Generation     S.2828 (Distributed to growers)

4th Generation     S.4374   S.4376


Hibrido de Timor (HDT)  S.2769 x S.2828  >>> S.4369, S.4375

S.2828 x S.1156   >>>>  S.4370, S.4371, S.4372, S.4373

Agro-Climatic Requirements of Sln.6

Sln.6 being an interspecific hybrid of Robusta and Arabica possesses wide ranging adaptability in different agro-climatic conditions. Arabica, in general, prefers high altitude, cooler conditions with high relative humidity and hence is grown under the shade canopy of tall trees. Whereas, Robusta thrives well and is cultivated successfully at lower elevations with warm and humid conditions. The hybrid Sln.6 has the advantage of the genetic contributions of both these species and this is responsible for the adaptability of this selection to different conditions. An elevation of 2800 to 3200 ft. above M.S.L is found to be highly suitable for an adequate vegetative growth and moderate to high crop of this selection. It is also observed that this selection performs well under low rainfall of 40-60” as well as high rainfall of 100-125”. This selection is best grown under medium shade to maintain its vigour, productivity and resistance/tolerance to leaf rust.

Soils and Soil Management

Selection-6 has shown better growth and yield potential in deep, well-drained and fertile soils. Soil pH ranging from 5.8-6.8 is considered ideal for the successful cultivation of this selection. In case of higher acidity (pH 5.0 –5.5), application of lime (1.0 to 5.0 tons per ha.) has improved the yield. Cover digging (to a depth of 15-18”) at the end of monsoon (October – November) is advised for young clearings. On steep slopes, opening cradle pits is found to be more useful to conserve moisture as well as weed control. Scuffling is practiced in plantations to control weeds and to provide aeration to the sub-surface soil.


Spacing provides the criterion to judge the performance of a variety in a given location and climatic conditions by assessing the yield and resistance to pests and diseases under a specific regime of nutrition.

Sln.6 is a tall variety of coffee that has a higher plant vigour and wider bush spread. This necessitates wider spacing like 7×7 ft. or 7×8 ft. for good growth, adequate aeration and light to the bush. A spacing of 6×6 ft. is also adopted when the soil is not rich enough or if the plot is located in a marginal area.


Healthy plants with vigorous growth, dark green foliage and thick stem are selected for planting in the field. Pits of 45x45x45 cm were opened at the required spacing and are filled with topsoil. Insecticide Thimet-10G or Chlorpyriphos is also added to the pit to protect the plants from cockchafers and cut worms that prevail in new clearings. Six-month old seedlings are preferable for new planting to establish a vigorous and healthy plantation. Planting older plants (18-month old) may lead to the development of bent root and other similar phenomena resulting in poor and slow growth, moisture stress during dry period and exhaustion of the plants even when their crop is not heavy.


Conservation of moisture in a coffee plantation is of paramount importance in the establishment of young plants and maintaining the established plantations in a good condition. Mulching is the practice of covering the drip circle area of the plant with leaf litter at the end of monsoon. This is done in bearing as well as non-bearing areas of the plantation to conserve moisture and add organic matter to the soil to make it porous and fertile. Mulching is practiced for all coffee varieties and suits well for Sln.6 also.


There are two modes of weed control: manual weeding and chemical weeding. For Sln.6, three to four rounds of manual weeding are useful for better growth and yield. Use of weedicides is generally practiced during the initial years of establishment (1-5 yrs).

Case Studies of Planters Growing Sln.6 in Considerable Area

Sln. 6 is the Indian equivalent of Hibrido de Timor that was extensively used in the Arabica Coffee breeding programmes all over the world as a source of rust resistance genes. Of the various F2 and F3 lines derived from BC-II, two lines became commercially important. These are S.2357 and S.2828. S.2357 is a large spreading bush while S.2828 is relatively compact.  These lines became popular on account of their high rust resistance and high yield with acceptable quality.  A case study of the performance of this selection was carried out in six estates growing it on a reasonably large scale.

Table 1. Sln. 6 materials grown in the sample Estates  

Average Rainfall Age of plants Estate Name Identity of the material Elevation from MSL
60” 1972-75 Swarnagiri Estate, Sidapur S. 2828 2900-3000 ft.
50” 20 Years Chowdirange Estate, Sidapur S. 2828 2850 ft.
100-120” 22 Years Raxidi Estate, Hanbal S. 2828 3200 ft.
90” 19 Years Divangudda Estate, Sakleshpur S. 2357 2900-3000 ft.
90-100” 19 Years Basaveshwara Estate, Jambandi S. 2357 3200 ft.
60 “ 25 Years Coodanhally Estate, Balagodu S. 2357 3000 ft.

Data presented in Table-1 shows that Sln. 6 is in Coffee growing areas located in a range of elevations (2850-3200 ft. from MSL) with different rainfall patterns (50-120”/annum).  Best performance of Sln. 6 in these locations with overlapping climatic and edaphic characters required for Robusta and Arabica cultivation is an indication of the adaptation of this selection in Robusta as well as Arabica growing areas.

Table 2. Disease control in the Case Study Estates 

Estate Name Important diseases Main Control Measures Other methods of Disease control
Swarnagiri Leaf Rust on about 5% plants No chemical control was applied No other methods also were used in disease control
Chowdirange Leaf Rust on about 1% plants After 1999 chemical controls stopped completely No other methods also were used in disease control
Raxidi Leaf Rust on about 2% plants 0.5% Bordeaux spray in 2 rounds (pre and post-monsoon) No other methods were used in disease control
Dewangudda Leaf Rust on

10-20 % plants

1 % Bordeaux spray on pre-monsoon application Systemic fungicide Contaff spray in 2 rounds
Basaveshwara Leaf Rust on

10-15 % plants

0.5 % Bordeaux spray in 2 rounds (pre and post-monsoor) Systemic fungicide Bayleton spray in 2 rounds
Coodanhally Leaf Rust on

5-10 % plants

0.5 % Bordeux spray in 2 rounds (pre and post-monsoon) Systemic fungicide Contaff spray in 1 round (post-monsoon)

 Note : Black rot, the other disease of considerable spread is found to be infecting Sln. 6 also.  However, it could be effectively controlled by cultural operations like centring and handling.

From the above table, it can be seen that the incidence of leaf rust in Sln. 6 is only on a small percentage of plants (1-5 % in S.2828/2827 and 10-20 % in S.2357). However, many of the susceptible plants are highly susceptible like Kents that is one of the parents of this selection. These plants can be converted into resistant and productive ones through top working.  Such an exercise leads to a minimization of the requirement for fungicide sprays and finally its total elimination as practiced in Swarnagiri and Chowdirange Estates.

Table 3. Yield and Quality details

Estate Name Yield of Clean Coffee/acre % of A-grade % of Pea berry Cup Quality Out turn Processing method
Swarnagiri 680-700 kg 64-65 % 11-13 % FAQ Fruit  38% Parchment-Bean 84 % Wet
Chondirange 750 kg 64-65 % 10-15 %  – Fruit 38 % Parchment Bean 84 % Wet
Raxidi 740-800 kg Wet + Dry
Dewangudda 650-700 kg 50-55 % 45-48 % & 85 % Wet + Dry
Basaveshwara 750 kg 60-65 % 45 & 85 % Wet
Coodanhally 750 kg 40 % Wet
CCRI 750-800 kg 60-65% 10-15% FAQ 45% & 85% Wet

Agro-techniques adopted for Sln. 6

Estate Name Fertilizer dosage Weed Control Shade pattern Pest Control  Organic manures Irrigation Desuckering/Cemting/Pruning
Swarnagiri                            NPK/acre in 2 rounds Manual Medium Tracing for WSB incidence 3-4 plants/acre removed in a year Only to support blossom showers, if inadequate 2 times/year Light pruning after harvest in December to remove whippy wood
Chondiragi 60:40:60 kg NPK/acre/year. N and K applied in 3 splits while P is applied once as broad cast Manual Medium Tracing for WSB incidence 3-4 plants/acre removed in a year 8 kg/plant Only to support blossom showers, if inadequate 2 times/year Light pruning after harvest in December to remove whippy wood
Raxidi 110:112:96 kg NPK/acre/year in 2 rounds Manual Medium Lindane spray stopped since 3 years.  Borer incidence on 0.2-0.3 % plants      
Diwangudda 103:97:150 kg NPK/acre/year in 2 rounds Manual Medium 3-4 % plants infested (Lindane spray not done due to low prices) Poultry manure Irrigation during march every year Handling in 4 rounds pruning once
Basaveshwara 126:126:126 kg NPK/acre/year in 3 rounds Manual Medium to low 2 Plants/acre removed due to borer 200 gms Akshya/plant Irrigated Higher harvest reported  
Coodanhally 80:80:80 kg NPK/acre/year in 4 rounds (reduced to 40:40:40 in 2 rounds for the past 2 years Manual Medium 0.2-0.3 Not irrigated Light handling once in year (Pruning/handling became irregular due to price situation)

Breeding Efforts to Further Improve Robarbica

A generally reported shortcoming of Selection-6 is its relatively poor out-turn. This is a result of the presence of empty locules in the fruits of this selection of interspecific hybrid descent. Empty locules in the produce can be reduced through selection and presently, efforts are devoted to identify mother plants that produce least empty locules (i.e. under 5%), low peaberries (also under 5%) and triage (2-3% or less). This selection is expected to improve out-turn of the Selection-6 in just one generation of advancement as the presently exploited materials are in F2 and F3 generations.

Further, crosses were effected to render this selection more resistant to leaf rust as follows:

New Crosses of Selection-6

Sl. No. Parentage Accession No.
01 S.1156 10/4 (BC II ) x  S.2769 25/16  (HDT) S.4369
02 S.1156 10/4  x S.2828-5 S.4370
03 S.2828-5 x S.1156 10/4 S.4371
04 S.1156 10/4  x S.2828-33 S.4372
05 S.2828-33 x S.1156 10/4 S.4373
06 S.2828-5 x S.2828-33 S.4374
07 S.2828-33 x S.2769 25/16 S.4375
08 S.2828-33 x S.2828-5 S.4376

Plants obtained from the above crosses were vigorous and spreading types. They manifest high resistance to leaf rust in the field. Productivity of S.4369 and S.4375 is reasonably high. Individual plants in these progenies were marked for further breeding.


Anonymous. 2000. Coffee Guide. Central Coffee Research Institute, India.

Bertrand B, Guyot B, Anthony F, Lashermes P. 2003. Impact of the Coffea canephora gene introgression on beverage quality of C. arabica. Theor. Appl. Genet. 107: 387-394.

Bettencourt AJ, Lopes J, Palma S. 1992. Factores geneticos que condicionum a resistencia as racas de Hemileia vastatrix Berk. et Br. dos clones tipo dos grupos 1, 2 e 3 derivados de Hibrido de Timor. Broteria Genetica XIII (LXXX): 185-194.

Bettencourt AJ. 1973. sCpnsideracoesn gerais sobre o Hibrido de Timor. Instituto Agronomico, Campinas, Sao Paulo, Brazil.

Cramer PJS. 1957. A Review of Literature of Coffee Research in Indonesia. Inter American Institute of Agricultural Sciences, Turrialba.

DeVreaux M, Vallayes G, Pochet P, Gilles A. 1959. Recherches sur l’autosterilite du cafeier robusta (Coffea canephora Pierre). INEAC Serie Scientifique 78. 48p.

Eskes AB. 1989. Resistance. In: Coffee Rust: Epidemiology, Resistance and Management. (Eds. Kushalappa AC, Eskes AB), pp. 171-292. CRC Press, Boca Raton.

Fazuoli LC, Carvalho A, Monaco LC, Teixeira AA. 1977. Qualidade de bebida do café Icatu. Bragantia 36: 165-172.

Ganesh D, Ram AS, Prakash NS, Mishra MK, Ahmed J, Jagadeesan M, Reddy AGS, Srinivasan CS. 2002. Evaluation of Coffea liberica x Coffea eugenioides and its progenies for yield, leaf rust resistance and quality. In: PLACROSYM XV (Eds. Sreedharan K, Vinod Kumar PK, Jayarama, Basavaraj MC), pp. 72-77. Central Coffee Research Institute, India.

Monaco LC. 1977. Consequences of the introduction of coffee rust in Brazil. Annals New York Acad. Sci. 287: 57-71.

Narasimhaswamy RL. 1960. Arabica selection S.795: Its origin and performace – A study. Indian Coffee 24: 197-204.

Petracco M. 2000. Organoleptic properties of espresso coffee as influenced by botanical variety. In: Coffee Biotechnology and Quality (Eds. Sera T, Soccol CR, Pandey A, Roussos S), pp. 347-353. Kluwer Academic Publishers, Dordrecht, London, Boston.

Ram AS, Sreenath HL. 2000. Genetic fingerprinting of coffee leaf rust differentials with RAPD markers. In: Coffee Biotechnology and Quality (Eds. Sera T, Soccol CR, Pandey A, Roussos S), pp. 197-208. Kluwer Academic Publishers, Dordrecht, London, Boston.

Ram AS. 2001. Breeding for rust resistance in coffee: The gene pyramid model. J. Plantn. Crops. 29(1): 10-15.

Rodrigues Jr. CJ, Bettencourt AJ, Rijo L. 1975. Races of the pathogen and resistance to coffee rust. Annu. Rev. Phytopathology 13: 49-70.

Sreenivasan MS. 1987. Cyto-embryogical studies of Robusta-Arabica coffee hybrids. Ph.D. Thesis. University of Mysore, Mysore.

Srinivasan CS, Ramachandran M. 1997. Selection 5B – S.2931 (S.333 x Devamachy Hybrid) – An old Arabica hybrid rediscovered with promising features. Indian Coffee 61(11): 4-6.

Srinivasan CS, Vishveshwara S. 1980. Selection in coffee: Some criteria applied and results obtained in India. J. Coffee Res. 10: 53-62.

Sybenga J. 1960. Genetics and cytology of coffee: A literature review. Bibl. Genet. 19: 217-316.


Re-Creating Coffea arabica

March 12, 2017

I have read the stories of possible extinction of the species Coffea arabica by about 2080 A.D. This was predicted on the basis of climatic changes associated with increasing temperatures and global warming1. Scientific efforts at saving this plant are important for the survival of innumerable small farmer families involved in growing coffee and the economic well being of over 80 developing countries involved in supplying this commodity to the consumers all over the world. From what I read, these efforts can be classified into two categories.

The first category of efforts is directed at conserving the wild coffee plants by shifting them to the higher elevations in the montane forests of Ethiopia, the homeland of Arabica coffee1,2. This is very important in the context of high value39 of these genetic resources and also the fact that only a small fraction of the complete gene pool of this species is utilized in the evolution of commercial coffee cultivars40. Recalcitrance of the seed of coffee for conservation in seed banks leaves the only option of maintaining these plants in the form of an orchard that involves not only considerable expenditure but also serious commitment and a variety of plantation management skills3,4.

The second category of efforts is directed towards re-creating Arabica coffee by interspecific hybridization of its putative progenitor species2, a commendable approach undertaken by some scientists at the World Coffee Research. I have been thinking about the proposed action that involves hybridizing C. canephora and C. eugenioides, the species that are perceived to be the progenitors9,13,14,15 involved in giving birth to C. arabica, the lone tetraploid species of the genus Coffea. It is believed that C. eugenioides is the female progenitor and C. canephora is the male progenitor in the origin of C. arabica. The proposed approach is to involve many plants of these two species in hybridization to include as much genetic diversity as possible, as the current perception is that only single plants of these two species are involved in the origin of C. arabica2. If this perception is true, how can we explain the large diversity observed in the wild C. arabica populations. The morphological diversity of the samples drawn from these wild populations is considerably large to think that all of it is derived from just two parent plants5,6,7,8. So, I would like to think that the origin of this important species involved several hybridizations and interbreeding of those hybrids, even if it was between only two species. There are other possible pathways also that could have involved in the birth of original archetypal Arabica.

The origin of C. arabica was considered to have taken place in the Pleistocene period of the Quaternary9, a time when agriculture has not yet begun. Thus, any hybridization events were spontaneous and survival of the hybrid species was solely through positive Natural Selection. Early thinking on the origin of C. arabica also suggested that C. eugenioides10,11,12,13,14,15,16,19 could be the female progenitor. However, the male progenitor was thought to be C. canephora13,14,15,19, C. congensis11,14, C. liberica10,12,19  C. dewevrei12,17,18, C. racemosa24 or C. kapakata25 by different investigators on the basis of certain characters observed in C. arabica. If these perceptions were considered to be true, we have to visualize a scenario of these species coexisting in a population that might have got separated from the centre of origin and diversity of Coffea in a remote area (probably, present equatorial Africa) and found itself in a hostile and inhospitable climate. This could have been a consequence of one of the glaciations events of Pleistocene. That probably triggered a new evolutionary trend through inter species hybridization and spontaneous tetraploidization20,21. Even in this case, assuming a single hybridization event between single plants of any two species severely restricts the diversity that a species needs to survive so many millennia of time in an environment that has been undergoing change constantly42. Our present knowledge of the family Rubiaceae and the species C. arabica indicates that the family probably originated in the Eocene period22 and C. arabica in the Pleistocene (late Pleistocene or early Holocene?)9. This means that the species has survived, at the least, 12000 years or more up to about 2.5 million years. This survival demands that the organism should carry adequate genetic diversity and plasticity to adapt to the contemporary and changing climatic conditions. Its solo existence in Ethiopian high lands and Boma Plateau, its wide adaptation in the various locations of introduction and its capability to accept genes from the related species suggest that it could be a compilospecies20,21. This means that re-creating it should involve more than two species.

Another series of thoughts on the origin of C. arabica propose that this species originated by autotetraploidy of other Coffea species. Particularly, C. eugenioides was thought to have given rise to Arabica by autotetraploidy because of the morphological resemblances of its autotetraploid13. Support for this argument was provided by the similarity of mitochondrial genomes of C. arabica and C. eugenioides23.

The species C. arabica was not known to man until a few hundred years ago26. Its discovery by man and his development of a taste for it led to all the developments that we knew and finally to the possibility of its extinction in the next 50-60 years. Even after coffee came into world trade, Arabs controlled the coffee trade until the 18th century when plant breeding was not a scientific art, meaning that all deleterious developments happened in the last one hundred years. Thus, re-creating this species requires considerable deep thinking and sincere efforts with perceptions that should not go wrong.

Considering the climate of Quaternary that is also called the Ice Age27, large areas of the earth were covered by glaciers in the Pleistocene, the first epoch of the Quaternary. These ice sheets started melting with increasing temperatures towards the later part of that epoch and the glaciation events were linked to the origin of Arabica coffee during this period9. Considering its wild existence in the upper montane forests of Ethiopia, a plausible assumption is that the nascent allotetraploid was adapted to a climate that was the colder even at that time. Thus, if we wish to re-create Arabica from the same progenitor species, we should also have a similar climate for its adaptation. This scenario appears to be a very difficult one to create. Over the several millennia of Quaternary, some of the other species of Coffea were found to be adaptable in much harsher climates. Some of these species were found to be crossable with C. arabica and were used in its improvement and some were thought to be involved in its origin as already mentioned. There is also considerable understanding of the crossability relationships among the species of Coffea15,16. There were reports of spontaneous hybridization between species giving birth to Arabicoids with introgressed genes28,43 from some of these species and even a case of allopolyploidy16. All these natural hybrids and the allopolyploid were used in improving Arabica for disease and pest resistance29,30,44. An important point is that all of them were created in the contemporary climate of the recent past and all of them closely resemble Arabica in their morphology. Thus, thoughts on re-creating Arabica may have to be re-oriented to include the many species of the diploid gene pool that manifest considerable resistance to the many adversaries of Arabica coffee in the current climate. This leads to the creation of a gene pyramid34 that helps the new arrival to resist the adversaries for a considerably long time.

Why should we include the other species that were known to produce beans that give a poor quality beverage? What are the genetic implications for quality and adaptation?

In the context of these questions, I would like to address the matter of adaptation first. The events of Pleistocene that led to the first appearance of C. arabica and its survival until now would have included resistance to the contemporary pests and diseases in all likelihood as this determines the fitness to survive41. That resistance has seen the species through the so many centuries that it has been existing before its discovery by man and his manipulations to produce it on a commercial basis. The pests and diseases that infest the various varieties of Arabica coffee, now-a-days is attributed to the lower genetic diversity in the gene pool of cultivated Arabica initially35 and this observation got extended to the wild forms also ain a recent study of the germplasm collections maintained in Costa Rica as mentioned in an internet story2. One limitation of this germplasm study could be that the explorers who collected these materials depended primarily on the morphological characters and the genetic diversity of collections may be very low in the modern context of molecular biology. Sampling of the early collections also would have been random. Thus, this could be a profound reflection of the Founder effect. Also, it is possible that the disease and pest organisms evolved into forms that can overcome the innate resistance of original Arabicas. Some of the modern hybrids carrying the introgressed genes from diploid species are manifesting resistance to some of the disease and pest adversaries and promise to be of value in cultivation31,35,43. Considering these facts, it may be pragmatic to think of re-creating C. arabica by involving different diploid species carrying resistance to nematodes, leaf miners, stem borers and the diseases like leaf rust, berry disease and bacterial blight. A basic concept for creating novel allotetraploid germplasm to be used in Arabica coffee breeding was posted on this blog sometime earlier. In the present scenario of pest and disease infestation32,33, re-creating C. arabica from such diverse allotetraploids makes better sense than the suggested path of hybridizing C. canephora and C. eugenioides.

The question of coffee quality has been debated hotly for many decades. The intrinsic elements that condition the taste and flavour of the consumed beverage are described as fair average quality and can be realized in most of the coffee produced anywhere in the world. Our concern in the context of possible extinction of the coffee plant should be in preserving the coffee plants that can produce beans with this basic quality standard. The early period coffee tasters were of the belief that the best quality is realized from the Arabica coffee plants whose breeding history does not involve any diploid species36,37. But then, dealing with adversaries like coffee leaf rust, coffee berry disease and stem borers and leaf miners made it necessary to involve the diploid species like C. canephora, C. liberica, C. racemosa  and others in evolving Arabica coffee varieties. Beverage quality of these varieties was considered inferior to that of pure Arabicas for a considerable time. However, literature of the more recent times indicates that some of these hybrids are not simply good but better in quality over the conventional Arabica in beverage quality38. All these facts suggest that basic beverage quality does not suffer because of introducing genes from other Coffea species into C. arabica. On the other hand, it seems to improve. A natural allotetraploid derived by spontaneous doubling of chromosomes in a hybrid of C. liberica and C. eugenioides also produced beverage of good quality indicating tetraploidy may be at the root of Arabica’s quality. Genetic basis of such beverage quality characters was well explained in literature26. These aspects have to be seriously considered when we propose to re-create Arabica.

On the whole, re-creating Arabica coffee is important but requires to internalize many aspects as narrated above to evolve a new species (shall we call it C. arabica?) that can effectively replace the old C. arabica and survive for, at least, another 15000 years.


  1. Davis AP, Gole TW, Baena S, Moat J. 2012. The impact of climate change on indigenous Arabica coffee (Coffea arabica): Predicting future trends and identifying priorities. PLoS ONE 7(11): e 47981. Doi:10.1371/journal.pone.0047981.
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  6. Balami S. 2007. Genetic diversity analysis of the wild Coffea arabica populations from Harenna forest, Bale mountains of Ethiopia, using inter simple sequence repeats (ISSR) marker. M.Sc. Thesis. Addis Ababa University, Addis Ababa, Ethiopia.
  7. Montagnon C, Bouharmont P. 1996. Multivariate analysis of phenotypic diversity of Coffea arabica. Genetic Resources and Crop Evolution 43: 221-227.
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  11. Raina SN, Mukai Y, Yamamoto M. 1998. In situ hybridization identifies the diploid progenitor species of Coffea arabica (Rubiaceae). Theor Appl Genet 97:1204-1209.
  12. Narasimhaswamy RL.1962. Some thoughts on the origin of Coffea arabica Coffee 4(12):1-5.
  13. Thomas AA. 1944. The wild coffees of Uganda. Genetics 40: 563-
  14. Cramer PJS. 1957. Review of literature on coffee research in Indonesia. Miscellaneous Publication # 15. IICA, Turrialba.
  15. Carvalho A, Monaco LC. 1967. Genetic relationships of selected Coffea Ciencia e Cultura 19(1): 161-165.
  16. Narasimhaswamy RL, Vishveshwara S. 1961. Report on hybrids between some diploid species of Coffea. Indian Coffee 25: 104-109.
  17. Fernie LM. 1966. Impression on coffee in Ethiopia. Kenya Coffee 31: 115-121.
  18. Mendes AJT. 1949. Observaçoes citologicas em Coffea. XII: Uma nova forma tetraploide. Bragantia 9: 25-34.
  19. Sybenga J. 1961. Genetics and cytology of coffee: A literature review. Bibl. Genet. XIX: 217-316.
  20. Ram AS. 2004. Coffea arabica L – A compilospecies: Implications for Breeding. Proc. XX International Colloquium on Coffee Science, pp. 740-746. Association Scientifique Internationale du Cafe, Paris, France.
  21. Ram AS. 2008. Speciation of Coffea arabica: Implications for genetic improvement. J Plantation Crops 36: 79-85.
  22. 2017. Rubiaceae.
  23. Berthou F, Trouslot P, Hamon S, Vedel F, Quetier F. 1980. Analyse en electrophorese du polymorphisme biochemique des caféiers: variation enzymatique dans dix-huit populations sauvages; variation de l’ADN mitochondrial dans les especes canephora, C. eugenioides et C. arabica. Café Cacao Thé 24: 313-326.
  24. Medina DM. 1963. Microsporogenese em um hibrido triploide de Coffea racemosa x Coffea arabica L. Bragantia 22: 299-318.
  25. Monaco LC, Medina DM. 1965. Hibridacoes entre Coffea arabica e Coffea kapakata. Analise citologica de um hibride triploide. Bragantia 24: 191-201.
  26. Ram AS. 2005. Quality improvement in Arabica coffee: Relevance of Ethiopian germplasm. J. Coffee Res. 33(1&2): 15-33.
  27. Live Science. 2017. Quaternary period: Climate, animals and other facts.
  28. Bettencourt AJ. 1973. Consideracoes gerais sobre o Hibrido do Timor. Circular # 23, Instituto Agronomico, Campinas, Brazil.
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  30. Ram AS, Ganesh D, Reddy AGS, Srinivasan CS. 2004. Ligenioides – A source of new genes for Arabica coffee breeding. Proc. PLACROSYM XX. J. Plantn. Crops. 32 (Suppl.): 5-11.
  31. Ram AS. 2005. Breeding coffee for leaf rust resistance: The Indian experience. Indian Coffee 69(4): 10-13.
  32. Ram AS. 2015. Plant breeding: Importance for coffee industry in India. J. Dev. Social Change 11(4): 91-96.
  33. Avelino J, Cristancho M, Georgiou S, Imbach P, Aguilar L, Bornemann G, Laderach P, Anzueto F, Hruska AJ, Morales C. 2015. The coffee rust crisis in Colombia and Central America (2008-2013): impacts, plausible causes and proposed solutions. Food Sec. 7: 303-321.
  34. Ram AS. 2001. Breeding for rust resistance in coffee: The gene pyramid model. J. Plantn. Crops. 29(1): 10-15.
  35. Lashermes P, Andrzejewski S, Bertrand B, Combes MC, Dussert S, Graziosi G, Trouslot P, Anthony F. 2000. Molecular analysis of introgressive breeding in coffee (Coffea arabica). Theor. Appl. Genet. 100: 139-146.
  36. Van der Vossen HAM. 2008. Disease resistance and cup quality in Arabica coffee: The persistent myths in the coffee trade versus scientific evidence. In: XXII International Scientific Colloquium on Coffee. pp. 1351-1360. ASIC, Paris.
  37. The cup quality of disease resistant cultivars of Arabica coffee (Coffea arabica). Exptl. Agric. 45: 323-332.
  38. Sobreira FM, Oliveira ACB, Pereira AA, Sakyiama NS. 2015. Potential of Hibrido de Timor germplasm and its derived progenies for coffee quality improvement. Aus. J. Crop Sci. 9(4): 289-295.
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Pre-emptive Breeding – The case for Coffee

September 7, 2013

High value of coffee in international trade and domestic economies of the many producing countries is well known. It is also well known that most of world’s coffee is produced in the poor and under-developed countries. This is a beverage being consumed across the world for almost four centuries and most of the consumption is in the affluent western countries. Possibly, it is on account of these facts that very little effort is directed towards the pre-emptive breeding of this important crop plant to achieve resistance against various adversaries.

If we take a look at the history of the various diseases and pests of coffee, it becomes clear that these various adversaries became prominent in different crisis times. Like all other internationally traded commodities, coffee has also been passing through ‘boom and bust’ cycles, leading to financial crises in the lives of farmers producing this crop. When the price of coffee is very low in the markets, its direct impact is on the maintenance of coffee plantations that get neglected. This leads to the more severe occurrence of diseases, of which coffee leaf rust is the most prominent. Leaf rust is a defoliating disease that predisposes the coffee plant to many other adversaries that take advantage of the situation. Defoliation leads to debilitation of the plant as its photosynthetic and other biosynthetic processes carried out by leaves get compromised opening an advantageous situation for the adversaries. Evolution of new races of coffee leaf rust that can defeat the resistance achieved by incorporating newer genes is known to be considerably rapid.

All this is true in the context of Arabica coffee that is susceptible to the pests and diseases. We have known resistance to a variety of adversaries like nematodes, insects and diseases in the various species of the diploid gene pool of coffee. Diploid species like Robusta and Liberica were utilized in a modest way towards improving leaf rust resistance of the coffee plant and Arabica – Robusta hybrids are also known to possess some resistance to the nematodes. Also, it is known that several diploid species cross well with the lone tetraploid Arabica to yield moderately fertile hybrids. Also, it is known that diploid species of coffee naturally cross to give rise to natural interspecific hybrids. These innate potencies of the coffee plants should be exploited to transfer the requisite resistance to the species of choice to create germplasm that can be used in long term breeding exercises to evolve coffee plants resistant to the various adversaries.

This is a long term exercise in breeding that also demands special skills in cytogenetics and chromosome manipulation to achieve positive and stable results that benefit the coffee farmers over long periods of time. Conceptual background for this effort comes from the fact that diploid species of coffee naturally and freely cross among themselves and also with Arabica to yield fertile or moderately fertile hybrids. As explained in the concept paper posted a few days earlier, scientists at different coffee research stations in Africa as well as other countries where some species are available in the gene banks should create diploid-diploid and diploid-tetraploid interspecific hybrids that should be handled appropriately to evolve tetraploid Arabicoids that constitute novel germplasm for breeding Arabica coffee in the future, against a variety of adversaries like newer diseases, nematodes and possibly abiotic factors arising out of climate change.

Concept Paper for Project on Novel Coffee Germplasm

August 18, 2013

Coffee is the largest exported agricultural product of Tanzania and contributes about US$115 million to their foreign exchange earnings and supports the livelihoods of about 400,000 small farmer families and many more in the processing and trading sectors26. Thus the importance of coffee for Tanzanian economy cannot be overemphasized. A similar situation can be expected in the context of the many coffee producing countries of Africa.


Coffea arabica the lone tetraploid (2n=4x=44) species of the genus Coffea was considered to have been derived from two diploid species of the same genus by spontaneous hybridization and doubling of chromosomes in the interspecific hybrid. Many researchers agree and sought evidence to prove this hypothesis. Presently, it is accepted by scientists that C. eugenioides could be the possible evolutionary female progenitor of C. arabica, having contributed one set of 22 chromosomes (2n=2x=22) and its cytoplasm. The other set of chromosomes appear to have been contributed by C. canephora (Robusta) or C. congensis or even by C. liberica, the species that were proposed to be the possible evolutionary male progenitor of C. arabica1-12. There is evidence that C. arabica could be a species that has inherited genes from other diploid species like C. racemosa13 or even C. stenophylla and C. excelsa (unpublished data). However, all schools agree that C. eugenioides is the putative female progenitor. This implies that most of the Arabicas carry the cytoplasm of C. eugenioides, but possibly the genes of several species, a situation akin to the nature of ‘compilospecies’14,19. This also calls for the understanding that simple breeding techniques would not lead to dependable results in resolving the complex problems of susceptibility to diseases like leaf rust, CBD, stem borer and leaf miner, the major biotic adversaries of coffee claiming over 50-60% of production cost. Observed resistance to most of these adversaries in the diploid species of Coffea and the compilospecies nature of C. arabica21,22 indicate that breeding involving interspecific hybridization is the only way to achieve resistance in C. arabica. In this context, some unique germplasm generated in the Indian coffee breeding programme, such as Devamachy (Natural hybrid of Robusta and Arabica), Robarbica (Artificial hybrid of Robusta and Arabica), Racemusta (Artificial hybrid of C. racemosa x C. canephora) and Ligenioides (Amphiploid from the artificial hybrid of C. liberica x C. eugenioides) hybrids have proven to be of value24,25. These germplasm were created as part of a long term exercise in coffee breeding in India and the initial efforts took place in the 1930s. Present proposal is with the idea of creating such germplasm in Tanzania and possibly other African countries where some of the 100 known species of Coffea are native.

Tanzania is home for 16 diploid species of Coffea. Some of the species are C. racemosa, C. sessiliflora, C. kimbozensis, C. eugenioides, C. zanguebariae, C. fadenii, C. charrieriana and C. anthonyi. These species constitute the secondary gene pool carrying important traits for the improvement of C. arabica. As C. arabica is tetraploid, and these species are diploid, it becomes necessary that these species be hybridized and diploidized to render the hybrids tetraploid and be able to cross with C. arabica and transfer the genes of interest to that species.

In the genus Coffea, the reproductive isolation barriers are incomplete and allow the intercrossing of diploid species. In fact, interspecific hybrids appear spontaneously when two or more species are growing together in any location. During the current project, it is proposed to collect as many Tanzanian diploid species of Coffea as possible through seeds and establish a germplasm bank at the University of Dodoma and possibly Tanzania Coffee Research Institute to eventually generate hybrids from all possible combinations of these species. As Coffea species are perennial plants, their initial establishment is expected to take, at least, 3-4 years and the generation of hybrids can be done in the subsequent period of another 4-5 years. Thus, the proposed project takes about 10 years to realize the proposed products. However, genetic, cytological, biochemical and molecular characterization of these species can be carried out in the course of establishing the germplasm bank itself and the study of hybrids commences after their being generated.

A situation of considerable relevance is that of Maize. During 1960s, cytoplasmic male sterile (CMS) lines were extensively used in USA to produce hybrid seed that helped in doubling the corn production. However, during early 1970s, all these hybrids fell susceptible to southern corn blight (caused by Helminthosporium maydis). It was found that a particular CMS line from Texas was involved in the derivation of all the hybrids rendering the cytoplasm of all the hybrids uniform. Later, this cytoplasm was named as T-cytoplasm. This exerted the selection pressure on the pathogen and resulted in the evolution of a single race (race-T) that could cause devastation of the entire lot of hybrids20. We have an analogous situation, in that most of the Arabica coffees carry the cytoplasm of C. eugenioides. According to the available information, the earliest appearance of CBD was also on C. eugenioides17. Later, it has spread to most Arabicas. This is further supported by the fact that CBD resistance is found only in the interspecific hybrids like Hibrido de Timor (HDT). Rume Sudan Arabica that possesses resistance was also shown to be distinct from pure Arabicas and closer to some lines of HDT by DNA fingerprinting studies13. Maize hybrid seed production in USA could be continued using diverse CMS lines other than Texas and a similar exercise of Arabica coffee breeding involving the cytoplasm of other species is most likely to lead to positive results. In the proposed project, tetraploid genotypes carrying diverse cytoplasmic endowments of the diploid different species will be combines with a tetraploid nucleus that can transfer genes to C. arabica will be created and will prove to be of great value in breeding this important crop plant.

On account of the value of C. arabica to the economy of all African coffee producing countries and the value of these species to the breeding of this important cash crop, the project is justified. C. arabica is susceptible to diseases like coffee berry disease (CBD), coffee leaf rust (CLR) and pests like coffee berry borer (CBB) and stem borer and innate genetic resistance to these adversaries is resident in the diploid species proposed to be collected. At present, over 50% of production cost is towards the control of these adversaries and resistant plants are expected to reduce the cost of production considerably.

Apart from the utilization of this germplasm in African countries, it can also be shared with other coffee producing countries, on mutually agreed terms to derive IPR benefits for the Institutions and to the countries of origin23.



  1. Carvalho, A., Monaco, L.C. 1967. Genetic relationships of selected Coffea species. Ciencia e Cultura 19: 151-165.
  2. Narasimhaswamy, R.L., Vishveshwara, S. 1961. Report on hybrids between some diploid species of Coffea L. Indian Coffee 25:104-109.
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Coffea arabica is a compilospecies

August 17, 2013

There are two schools of thought regarding the origin and evolution of Coffea arabica L. the world’s most important non-alcoholic stimulant beverage. The first or conventional school of thought based their inference on the evidence raised from observations on morphological, cytological, biochemical and reproductive biological features. The school proposes that C. arabica evolved by spontaneous hybridization of C. eugenioides with C. canephora, C. congensis or C. liberica and doubling of the chromosomes in the natural hybrid. An interesting offshoot of this thought is the belief that C. arabica is a segmental allotetraploid. The second or technological school of thought hypothesizes that natural hybridization of C. eugenioides or a sub-species by an unreduced gamete of C. canephora and spontaneous stabilization of chromosome number in the progeny of triploid hybrid resulted in the evolution of C. arabica on the basis of evidence from molecular marker studies. Evidence from some of the marker studies also suggests that C. arabica may be sharing considerable genomic homologies with C. racemosa and C. congensis. Molecular cytogenetic evidence also supports that C. eugenioides and C. congensis are the probable evolutionary parents of C. arabica. The distribution of C. arabica outside the area of distribution of all diploid species was attributed to the events of Pleistocene glaciation. Both schools agree that C. eugenioides or a sub-species of it is the most probable female progenitor of C. arabica. While they differ in the matter of male progenitor, in that, a species of the canephoroid group or liberio-excelsoides group is considered to be the likely male progenitor of C. arabica. Considering the genetical evidence from plant breeding studies, the disease resistance genes of C. liberica and C. canephora are inherited by C. arabica. All these available evidence points to the possible compilospecies nature of C. arabica. This has strong implications for the breeding practices, as inheritance patterns in compilospecies are considerably different from those observed in diploids and allopolyploids. These aspects are discussed and a possible breeding model with integration of vegetative selection to maintain traits of interest in the commercially exploited arabicoid derived materials is suggested. Utilization of unique tetraploid hybrids of interspecific origin like Ligenioides, Racemusta and Robarbica are proposed for use in breeding for resistance to coffee berry disease, insects and nematodes on the basis of their cytoplasmic genetic endowments.

This is the summary of a paper presented at the XX International Conference on Coffee Science, ASIC, pp. 740-746. (Bangalore, 11-15 October, 2004) and has implications for future breeding efforts and the large role that African countries can play.

New Assignment

March 1, 2012

I have taken up a new assignment as Associate Professor of Genetics at the University of Dodoma in Tanzania. I hope to put my research background to utility in developing models for coffee improvement using the genetic resources available in this country.
Coffee is very important as a large foreign exchange earner for Tanzania and Tanzania is home to 16 of the over 100 known species of Coffea that can be used to improve Arabica coffee through developing interspecific hybrids to transfer genes that condition resistance many biotic adversaries.