Saturday, November 01, 2014

Breeding for Nutrient Efficiency: A Model for the Future


Having identified a plethora of putative QTLs that contribute to nutrient use efficiency, the logical next step is to design appropriate selection strategies for improving genotype efficiency against low nutrient stress. However, not-so-significant effects of the identified QTLs are a serious concern in designing robust MAS strategies, since QTL-by-environment interaction may jeopardize the selection process. Further, the arcane effects of the identified QTLs confound the scientific soundness of the selection programmes. It is unlikely that many major-effect QTLs may emerge for nutrient use efficiency in future. This reduces us to the option of using small effect QTLs for future rice improvement.

One of most encouraging observations in the abiotic stress breeding so far is the interoperability of abiotic stress resistance across the causative factors. Armed with strict phenotyping tools, it is likely that an integrated approach of marker assisted selection may help us in improving abiotic stresses together, rather than the individualistic approach for each causative factor. I prefer to propose a model of recurrent selection for improving nutrient use efficiency, by channelizing the genotypes that has been selected for drought, salinity, submergence, and for nutrient use through an integrated breeding programme that also select for N and P use efficiency together. This process offer the advantage of including any new genotype in the breeding chain at any time, while a new genotype can emerge at any stage that are suitable for various target environments. This program will be more resource abundant, including beneficial gene flow, which is otherwise not the case in targeted breeding programmes for individual stress resistance.

Tuesday, October 28, 2014

The Need for Nutrient Efficient Crop Varieties


Since the birth of genetics as a science almost one and a half century ago with Gregor Mendel’s classical pea hybridization experiments, plant breeding has taken leaps and bounds to reach modern day crop varieties that sustain humanity. Genetic improvement of crop varieties has scaled from introduction of ‘good’ and ‘tasty’ food species from wild and the selection for the ‘best’ crops under domestication to vistas of hybridization for developing superior recombinants and robust hybrids. Development of genetics, always paved new ways and means for crop improvement. Past the discovery of DNA and more clearer understanding of the genes, genetic manipulation has turned to molecular levels from mere visual (qualitative) and measurable (quantitative) selection. The growing food needs for the expanding world population, has always been driving the need for sustained development of high yielding crop varieties.

Corresponding to the development of better crop varieties, agricultural practices had taken new dimensions and methods to support large scale food production. The rapid developments in crop management and crop improvement which ran mutually complimenting paved way to ‘green revolution’ in several key food crops which almost eradicated famines from the face of earth. However, the best agro-management always required large quantum of agronomic inputs such as fertilizers. The modern varieties need high positive nutrient balance in the soil to throw their best yields. Currently, indiscriminate chemical inputs into agriculture either as fertilizers or pesticides has been recognized as an environmental hazard, with respect to varying adverse consequences such as residual toxicity, pest resurgence, development of pathotypes through inadvertent mutations, biohazards, eutrophication, volatilization, acid rains, ozone depletion and so forth. Another major concern with the major fertilizers is that almost all of them are resourced from natural rocks and deposits that are non-renewable. Continuous mining of these resources is depleting their natural reserves so fast that none of these may exist beyond next 500-600 years.

Crop plants require sixteen elements for their survival and growth, of which three essential elements, carbon, hydrogen and oxygen are sourced through water and air. Of the remaining thirteen, three mineral elements, nitrogen, phosphorus and potassium are required in large quantities (major nutrients), and others are either required in minor quantities (secondary nutrients) or in micro quantities (micronutrients). Nitrogen fertilizers are required by crop plants in large quantities followed by phosphatic and potash fertilizers. Chemical synthesis of nitrogen fertilizers uses ammonia produced through Haber-Bosch process that consumes huge quantity of petroleum and natural gas, the major natural non-renewable energy reserve. Whereas, phosphatic fertilizers are exclusively sourced from phosphate rock reserves and potassium fertilizers depend on large deposits of potassium salts. Overdependence of mineral fertilizers for agricultural production envisions problems such as, (a) soil nutrient deficiency caused by continuous crop removal and fixation through soil chemical processes, (b) loss of significant amount of nutrients through crop harvests and food chain that are non-recycled, (c) significant loss of applied nutrients through leaching and volatilization due to poor nutrient use efficiency of crops, (d) nutrient pollution in the water bodies resulting in eutrophication and life-threatening algal bloom toxicity in the aquatic ecosystems, (e) atmospheric pollution causing ozone depletion and green-house effects, (f) faster depletion of non-renewable natural resources for fertilizer production, (g) geographic confinement of most of the natural fertilizer resources (especially phosphate rock) instill global overdependence on few countries that may create unhealthy monopolistic situation, (h) booming fertilizer costs in the wake of diminishing production and increasing demand is making cost of cultivation to go up, (i) unavailability and constrained affordability of fertilizers by the marginal farmers are rendering more agricultural areas nutrient deficient worldwide, and finally (j) unavailability of alternate fertilizer resources other than the natural sources is a serious threat to the future sustenance of agriculture.

To sustain agriculture in future, we need to preserve environmental and soil health by preventing undesirable nutrient drainage from soil and also need to prolong the supply of natural nutrient resources. This implies that there is an immediate need for reduction in soil nutrient input. Although skipping chemical fertilization altogether may not be possible in modern agriculture, input reduction is a feasible alternative. Modern organic agricultural systems advocate skipping of inorganic fertilization, with the objectives of maintaining biodiversity at soil, crop, field, seasonal and landscape level with a greater focus on integration of crop and livestock production systems and by using organic fertilization1. However, in the current agricultural scenario, fertilizer reduction may lead to serious crop production loss and may accelerate negative nutrient balance in soil. Therefore a more sustainable approach is to develop crop varieties that respond well to low fertilizer doses and are high uptake efficient even under reduced nutrient conditions. Use of low input happy varieties can go in tandem with fertilizer reduction and organic fertilization. The reduced availability of bio-available nutrients in the soil, a common phenomenon under soil nutrient deficiency, occurs either through fixation of available nutrients into bio-unavailable forms or due to depletion. Either cases levy tremendous stress of nutrient starvation in plants. Ability of plants to withstand nutrient starvation is leveraged by a variety of mechanisms such as deeper and wider root system for nutrient harvest from soil, root exudations to solubilize fixed nutrients into available forms, root microfloral symbiosis to promote nutrient availability and better nutrient transport systems2.

Crop responses to nutrients and their genetics differ fundamentally under nutrient sufficiency and deficiency. Nutrient sufficiency does not produce any stress on the plants unless it is excess to the toxic levels, whereas nutrient starvation does incite a stress response. Estimates of genotype response to applied nutrients, nutrient use efficiency (NtUE) is basically done under nutrient sufficient conditions therefore does not have any stress response component attached to it. Conventionally, NtUE is defined as the quantum of economic output realized per unit nutrient applied. Thus scope of this estimate is confined to nutrient responding genotypes of the high yielding category because it cannot rank genotypes that are low nutrient tolerant. Therefore NtUE is a term that should be limited to nutrient sufficient conditions, and for nutrient starved situations terms such as ‘low nutrient tolerance’, ‘nutrient starvation tolerance’ or ‘nutrient efficiency (NtE)’ may be more appropriate. The term NtE is suggested because the low nutrient response and its consequences fundamentally include all mechanisms of nutrient homeostasis comprising of low nutrient signaling and responses, active recovery, uptake and assimilation. May be new indices are needed to define various components of NtE and to identify the genetic mechanisms underlying low nutrient tolerance. This should also take into consideration of the soil nutrient status before and after the application of fertilizer, temporal soil nutrient fluctuation and plant biomass assimilation rate. In systems such as organic farming wherein organic fertilization alone is done, temporal soil nutrient fluctuations may be very important in defining the NtE, because it will help in accommodating the effects of slow release organic fertilizers. Further, nutrient fluctuations also occur when fixed soil nutrients are released either through root solubilization activity or by native root microbial symbiosis or through addition of bio-fertilizers. Other components of NtE are maintenance of photosynthesis, nutrient-uptake, nutrient-utilization and translocation under nutrient stress. Hence quantum of economic output yielded per unit net soil available nutrient throughout the cropping season may be a better index in identifying low nutrient tolerant genotypes.

Plant nutrient homeostasis depends on uptake and utilization processes, which are different for different nutrients and vary between phonological stages. At this point, both NtUE and NtE share common components such as uptake efficiency (UpE) and utilization efficiency (UtE). UpE is predominantly related to rhizosphere processes regulating better foraging for nutrients in the soil, in association with efficient uptake and transport mechanisms of nutrient ions into the plants. It is apparently important that UpE under relatively lower nutrient availability is to be considered as an important trait for developing nutrient efficient varieties. Balanced internal nutrient mobilization and assimilation is essential to maintain UtE, and nutrient efficient genotypes should therefore have efficient uptake in harmony with internal assimilation processes. Considerable genetic variations are reported for low nutrient responses in various crops, although a clear practical differentiation between UpE and UtE is still lacking. Therefore it is essential to develop phenotyping protocols, agronomic, biochemical and physiological to distinguish UpE and UtE. Since the genetics of NtUE and NtE are different, it may be possible to combine both the traits to develop widely adapted varieties that may perform well under both nutrient deficient and sufficient conditions, although not at the same performance level. Selection for NtUE in crop plants has been hugely successful and is responsible for green revolution in major staple crops. However in this process, many low nutrient responsive genes got inadvertently unselected and lost. Therefore, sourcing of nutrient starvation tolerance genes from the modern cultivated high yielding germplasm is likely to go unsuccessful and therefore old traditional varieties and landraces may be potential sources of such genes. Several instances of better performance of landraces and traditional varieties under low nutrient soils have been reported in rice, wheat, tomato, cauliflower etc., than the modern cultivars. Therefore, it is essential that older germplasm be screened for nutrient starvation tolerance genes.

Unlike that of breeding for NtUE, recent studies show that NtE has very low heritability and is likely to give little progress through conventional breeding. Hence more direct genetic approaches such as marker assisted selection or genetic transformation may be required to manipulate NtE in crops. Although indirect selection is advocated in conventional breeding under low heritability situations, to take advantage of correlated selection responses under contrasting environments3, relative gain towards NtE may likely to be low as most of the low nutrient response genes are already lost in the elite germplasm. Molecular dissection of phenotype performance is now possible in almost all major food crops that may aid largely in identifying genomic regions that are responding to low nutrient exposure. Several such regions and QTLs have been reported in crops like rice, wheat, maize, barley etc. Molecular isolation of large effect QTLs for phosphorus starvation tolerance and the gene responsible for the root proliferation under low phosphorus conditions, PSTOL1 (phosphorus starvation tolerance 1) has been reported in rice4. Identified from a traditional indica variety Kasalath5, the quantitative trait locus (QTL) containing PSTOL1, known as Pup1, has already been used for marker assisted transfer of the gene imparting low phosphorus tolerance in sensitive varieties6. Likewise, many QTLs for low nitrogen response have also been mapped in major staple crops, rice and wheat. Apart from nitrogen and phosphorus, works are progressing for identifying tolerance for reduced levels of other nutrient elements such as zinc, sulphur and potassium. It is likely that several improved varieties with better NtE would be developed using modern molecular breeding technology in the days to come.

1. van Bueren, E.T.L., Jones, S.S., Tamm, L., Murphy, K.M., Myers, J.R., Leifert, C. and Messmer, M. M., The need to breed crop varieties suitable for organic farming, using wheat, tomato and broccoli as examples: A review. NJAS – Wagen. J. Life Sc., 2011, 58, s 193–205
2. Gregory, P. J., Crop root systems and nutrient uptake from soils. In The molecular and physiological basis of nutrient use efficiency in crops (ed. Hawkesford M. J. and Barraclough, P.), John Wiley & Sons, 2011, pp. 21-45.
3. Falconer, D.S. and Mackay, T. F. C., Introduction to Quantitative Genetics, 4/e. Longman, 1996.
4. Gamuyao, R., Chin, J. H., Pariasca-Tanaka, J., Pesaresi, P., Dalid, C., Slamet-Loedin, I., Tecson-Mendoza, E. M., Wissuwa, M. and Heuer, S., The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature, 2012, 488, 535-539
5. Wissuwa, M., Yano, M. and Ae, N., Mapping of QTLs for phosphorus-deficiency tolerance in rice (Oryza sativa L.). Theor. Appl. Genet., 1998, 97, 777-783
6. Chin, J. H., Gamuyao, R., Dalid, C., Bustamam, M., Prasetiyono, J., Moeljopawiro, S., Wissuwa, M. and Heuer, S., Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application. Plant Physiol., 2011, 156, 1202–1216.

Tuesday, September 09, 2014

Some interesting rice facts


Rice is a semiaquatic annual grass belonging to the genus Oryza and has two cultivated and 22 wild species. The cultivated species are Oryza sativa and O. glaberrima. O. sativa is grown all over the world while Oryza glaberrima has been cultivated in West Africa for about 3500 years. There are more than 120,000 varieties of cultivated rice. Cultivated rice is diploid (2n=24) and belong to AA genome. O. sativa has two subspecies O. sativa ssp. indica and O. sativa ssp. japonica. A less prominent intermediate O. sativa ssp. javonica is also available.

Rice was domesticated more than 10,000 years ago is possibly one of the oldest domesticated species. Huke and Huke (1990) observes that the domestication of rice ranks as one of the most important developments in history, for this grain has fed more people over a longer period of time than has any other crop. Rice is the staple cereal for more than 50% people (~3.25 billion) around the world, cultivated in about 9% of the earth's arable land, which is the largest single use of land for producing food. Rice provides 25 to 85 percent of the calories in the daily diet and 15% of per capita protein. In Asia, where rice is the major energy providing food, it accounts for 50-80% of daily caloric intake, especially among the poor. Unlike other major cultivated grains like wheat and corn which are also used for feeding livestock, rice is exclusively used for human consumption.

With China, India and Indonesia producing the most of the world’s rice, Asia accounts for over 90% of the world's production of rice. Only 6-7% of the world's rice crop is traded in the world market. Production of rice in The United States accounts to 1.5% of the world's production, with Arkansas, California and Louisiana producing 80% of the U.S. rice. Thailand, Vietnam, China and the United States are the world's largest exporters.

Rice is the only cereal that can be grown for long period in standing water. Even though predominantly semi-aquatic, rice is grown under many different conditions and production systems, including upland and dry conditions. 57% of the world’s rice is grown on irrigated land, 25% on rainfed lowland, 10% on the uplands, 6% in deepwater, and 2% in tidal wetlands. The flooded rice paddy sustains rich aquatic biodiversity, providing a home for fish, plants, amphibians, reptiles, mollusks, and crustaceans.

Rice has many characteristics, making it useful in various ways to be included in cereals, snack foods, brewed beverages, flour, oil, syrup, flakes and religious ceremonies. Rice grains can be short, medium and long or waxy (sticky) or non-waxy. Some are aromatic, some are colored including brown, red, purple and black and some are of medicinal value. The variation in characteristics makes one variety more popular in one region of the world than another.

Wednesday, July 09, 2014

Nitrogenomics: Is the term worth science?


Anyone searching the internet for the term 'nitrogenomics', chances are that you will be taken to a page describing,

Nitrogenomics as the branch of the study of genomics pertaining to nitrogen utilisation and assimilation in organisms. Nitrogen is a primary nutrient essential for sustaining the life of every organism. Nitrogen is freely available in the atmosphere and Earth's crust and is generally assimilated by plants and microorganisms, then moved to higher organisms through the food chain. Genomics of nitrogen assimilation lie at different levels of organisms, from microbes to higher organisms, where different genetic controls regulate the actual assimilation.

This term nitrogenomics was not available before April 2004, when I made the posting of this term for the first time in Wikipedia. The growing awareness of genomic sciences and their enormous application potential, led me to think of a specialised term for the molecular genetics and genomics of the nitrogen utilisation in the organic world. It rather amused me that the words 'nitrogen' and 'genomics' fused well. Though I coined the term without much thinking of its potential as a branch of science, I now feel that the science which is described within this term can be the science of life itself.

Nitrogen is as essential as carbon, hydrogen and oxygen in the organic world, as it forms the primary component of amino acids which makes proteins, the building and guiding blocks of organic life. But the most intriguing part of the story is that nitrogen is not freely available as in the case of other primary elements of life. In fact it is mostly available abundantly in the unavailable forms. So how then nitrogen comes into life? Its an intricate cycle that involves enormous microorganisms, entire plant kingdom and the whole animal kingdom or every living organisms in interaction with the forces of nature! The science behind this is immense.

I learned the indispensable requisiteness of this science when I started working on the genome mapping of nitrogen assimilation genes in our staple food crop, rice. By this time, more than one and a half centuries had passed since we started adding nitrogen fertilisers into agriculture. More and more nitrogen added gave more and more food grains, enabling us to feed millions of mouths that were born in the world. Indiscriminate fertiliser usage had started to take its toll through irreversible damage to the ecosystems, nitrate poisoning, eutrophication of the water bodies so on and so forth... How are we going to cope up to this situation? One way is by regulating the usage of inorganic nitrogen sources while we look for better living environment with sufficiency of food. Here we require the science I am talking of....nitrogenomics. I am convinced...are you?

Monday, July 08, 2013

Behavior of wheat awn


Recently, an interesting discussion was active in GrainGenes mailgroup, describing about an unusual behavior of wheat awn asking for further explanation on the phenomenon. The story went like this:
During a recent trip Mr Norman Rossen and colleagues met a lady who was a worker at a US Department of Agriculture facility where she did chemical research on wheat components. Mr Rossen happened to relate an experience about wheat to this lady which she never had heard and did not believe. When he was a young boy, while traveling with his dad along rural Pennsylvania they happened to stop along a wheat field. His father broke off an awn of wheat, put it on his bare, but hairy, forearm and told him to watch what happened. The head of wheat very slowly moved up his fathers arm. He recalls that the same movement repeated when they put the head of wheat on his not-quite-so-hairy arm too.

I believed this is a common phenomenon with dry awns of many grass species, especially the ones which make longer awns. I have seen kids playing with some grass species whose awns are long and 'L' shaped which spin around when they wet them. Such grass species are common in tropical South India, which is not a wheat growing region. Nevertheless the phenomenon was very similar to what Mr Norman experienced with the wheat awn.

The reason for the movement is nothing but moisture. The dry awn must be having its cells under tension because of the loss of moisture and when it absorbs water it probably must be expanding causing the movement. For the grass awns, wetting is must for the rotation. So the movement Mr Nornam observed on his dad's and his arms could have been caused by the perspiration which the wheat awns absorbed causing the movement.

Dr Maarten van Ginkel of the Plant Genetics and Genomic Division of the Primary Industries Research Victoria (PIRVic) says he has regularly demonstrated this phenomenon to interested parties using wild oats. Hold the separated seed-filled floret by the tip of the L shaped twisted awn, wet the twisted region at the base of the awn with some spittle and the floret will make a 360-degree turn in the air and sometimes more as the awn unwinds. The assumption is that lying on the ground the L-shaped tip is lodged in between some rocks or soil clods, and when the first rains set in or even excessive dew, the seed drills itself into the soil by the spring-loaded action of the trapped awn unwinding. The tips of wild oat seeds are heavily bristled forming an arrow-shaped projectile of the glumes closely adhering to the seed. Thus a handful of oat seeds (rather seeds plus fused-glumes) on the open soil one day the next morning can have fully drilled themselves into the soil, leaving no trace.

In a recently published article in Science Elbaum et al., (2007) explains the phenomenon of movement of the awns. The dispersal unit of wild wheat bears two pronounced awns that balance the unit as it falls. They discovered that the awns are also able to propel the seeds on and into the ground. The arrangement of cellulose fibrils causes bending of the awns with changes in humidity. Silicified hairs that cover the awns allow propulsion of the unit only in the direction of the seeds. This suggests that the dead tissue is analogous to a motor. Fueled by the daily humidity cycle, the awns induce the motility required for seed dispersal.

Elbaum,R., Zaltzman,L., Burgert,I., Fratzl,P. (2007) The Role of Wheat Awns in the Seed Dispersal Unit. Science 316: 884 - 886

More references:

Peart, M.H. 1979. Experiments on the biological significance of the morphology of seed dispersal units in grasses. J. Ecol. 67: 843-163.
Peart, M.H. 1981. Further experiments on the biological significance of the morphology of seed dispersal units in grasses. J. Ecol. 69:425-436.
Peart, M.H. 1984. The effects of morphology, orientation, and position of grass diaspores on seedling survival. J. Ecol. 69:425-436.

Saturday, January 26, 2013

A tribute to Nikolai Ivanovich Vavilov (1887-1943)


I thought my next post should be a tribute to Nikolai Ivanovich Vavilov. Today (26 Jan 2013) marks the 70th death anniversary of this legend. The great who led us to the depths of origin of cultivated species... A great warrior like Gregor Mendel, who lost to the bureaucracy of science. Did he really lose?

Nikolai Ivanovich Vavilov (1887 - 1943)

A pioneer geneticist and the person who organised the earliest potato-collecting expeditions to the Andes after 1926, when many species and varieties were lodged in the then Horticultural Research Institute of St. Petersburg, where he and others carried out genetic analyses and field trials.

Founder-Director of the Soviet Academy of Agricultural Sciences

From 1920 to 1930, Vavilov organised and participated in several scientific expeditions to collect culturally important and cultivated plants from Afghanistan, Japan, China, Central and South America, Europe, North Africa, the Middle East, Ethiopia, Eritrea and Yemen. After 1938 he collected widely in the then U.S.S.R. By 1940 some 200 thousand plant species had been lodged in Russia, many sown annually in some 150 field research stations, some outside Russia.

A pioneer plant geographer, Vavilov published in 1924 a very important work The Centres of Cultivated Plant Origins - today known to biographers as "The Vavilov Centres", seven in number, and essentially the origins of most important agricultural plants. There are a few smaller centres recognised. Thus it was with great gratitude that in 1991 the writer received both membership of the then U.S.S.R. (Soviet) Academy of Agricultural Sciences and, the foundation gold Vavilov medal, a likeness of Vavilov. My own major is also in Biogeography, but the honours bestowed on me by the Academy are for my publications in Permaculture (1978 - 2000), as pioneer work on the conscious design of sustainable agricultural systems. A brief biography of Vavilov, forwarded to me by Bogdan Popov of Kiev, who was my student and interpreter for courses in Russia and elsewhere (abridged here) follows:

Vavilov was born in Moscow, his family were merchants. An elder brother was the famous physicist Sergei Ivanovich Vavilov. In 1906 Vavilov graduated from the Moscow College of Commerce, then joined the Moscow Agricultural Institute under the scientists K.A. Timiryasev, D.N. Pryanishnikov and V.R. Villiamo. At this Institute Vavilov studied in diverse disciplines, and published on the molluscan predators (snails, slugs) of plants in the Moscow province. He graduated in 1911 and worked on plant breeding, then transferred to the Bureau of Applied Botany (Director R.E. Regel) and the Laboratory of Mycology and Phytopathology (Director A.A. Yachevskiy).

From 1913 to 1914 Vavilov studied at the University of Cambridge in England under Prof. W. Bateson, and at the John Innes Horticultural Institute in London, a centre of composting research. There he published on the development of plant immunity to fungal diseases. In 1914, he went to France to study at the seed company of Vilmorin, and then to Germany ( E.Gekkel). At the outbreak of war he left Germany after great difficulty and returned to Russia, there publishing on plant immunity to viral infections.

In 1916, collecting in Fergana, Northern Iran, and the Pamirs, his material allowed him to discover the laws of homological series, hence to trace the origins of the cultivated varieties of plants. In 1917, Vavilov became Professor of Botany at the University of Saratov, but in 1921, he and colleagues moved to St. Petersberg where they set up the Horticultural Research Institute specifically intended to centre the collection of the species of cultivated plants in the world. Accessions were available for growing trials and genetic studies in the U.S.S.R. and elsewhere, but the collections have never been equalled.
In 1929 Vavilov and others founded the Lenin Academy of Sciences in Agriculture, forerunner of the U.S.S.R. Academy of Agricultural Sciences, and finally (after Glasnost) the Russian Academy of Agricultural Sciences. Vavilov was founder-president.

In the mid 1930s, Lysenko and his supporters developed a group of "Agro-biologists" who promised rapid crop improvement; their theories attracted Stalin and his secret police chief Beria, so that the "neo-Lamarkians" were in fact destroying support for Soviet genetic sciences in the scientific mode. Lysenko was able to instigate the arrest of Vavilov and his friends on 6th August, 1940, when he was collecting in the western Ukraine.

In prison, Vavilov was subjected to severe interrogations - a total duration of 1,700 hours - and was eventually sentenced to death in July 1941, later reduced to twenty years in a death cell, underground and without windows. There he contracted scurvy and developed severe dystrophy, dying on the morning of January 26th, 1943, still in Moscow. His family nearby were not told of his fate.

As a member of the Royal Society of London, he and others published The Origin, Variation, Immunity and Breeding of Cultivated Plants, translated and edited by K.S. Chester (English edition 1951).

All evidence of Vavilov's tenure at the Moscow headquarters of the Academy was removed by his fellow scientists on his arrest, and remained hidden until Stalin had died and Beria was replaced in the 1950s.

Today, Academy members (Nikinov was President in my day) speak openly and with great affection of Vavilov; Lysenko and his works are buried. The K.G.B. (then N.K.V.D.) destroyed Vavilov's manuscript A World History of Agricultural Development in 1941 as being of no value to his case!

So, a true world patriot and pioneer plant explorer was killed, aged 66 years, by jealous and vicious enemies, isolated from friends and family. He is survived by his successors and the seven hundred members of the Academy. Many scientists starved to death among the bags of grain and potatoes at the Academy in St. Petersburg during the 900-day seige by the Nazis. They died, preserving for the future the seeds of survival. We owe them all our thanks.

Vavilov died because he asserted the truth.

The Vavilov Centres

From Symons (1967) Agricultural Geography pp 11 to 12:

Vavilov listed eight independent centres of origin of the world's most important cultivated plants, based on expeditions he and other Russian scientists made throughout the world between 1916 and 1934:

1. China: The earliest and largest independent centre . . . consists of the mountainous regions of central and western China, together with the adjacent lowlands. Vavilov credited this region with important millets, buckwheat, soya beans, legumes and fruits and listed 136 endemic species.

2. India, including Burma and Assam, excluding north west India: 'India is undoubtedly the birthplace of rice, sugar cane, a large number of legumes and many tropical fruit plants, including the mango and numerous citrus plants. . .' Pulses, gourds and vegetables including cucumber, lettuce and radish were among the 117 listed species.

Also, the Indo-Malayan centre, including Indonesia and the Philippines: 55 species were listed by Vavilov.

3. Central Asia, including north west India, Afghanistan, Tadjikistan, Uzbekistan and western Tian-Shan: To this region were attributed a range of wheats, important legumes including peas, lentils and beans, and cotton. 42 species were listed.

4. The Near East, including the interior of Asia Minor, Transcaucasia, Iran and the highlands of Turkmenistan: Nine botanical species of wheat and rye, the grape, pear, cherry, fig, walnut, almond and alfalfa were among the 83 species listed.

5. The Mediterranean: home of the olive and many vegetables, was an important secondary source, in which man's part in selecting the more promising varieties for cultivation is particularly notable. 84 species were listed.

6. Ethiopia: Vavilov's expedition in 1927 established the importance of this area as an independent centre of origin, important especially for varieties of wheat, barley, sorghum and millet. 38 species were listed.

7. South Mexico and Central America (including the Antilles): Here was placed the primary centre of maize (corn), the sweet potato and upland cotton, and 49 endemic species were listed.

8. South America: The Russian expedition of 1932-1933 stressed the importance of the high mountainous area of Peru, Bolivia and part of Ecuador, remarkable for its endemic plants, notably numerous species of potato. Other centres distinguished were the island of Chiloe and the Brazilian-Paraguayan area. A total of 62 species were listed.

Major N.I.Vavilov's Expeditions

Expedition to Iran (Hamadan and Khorasan) and Pamir (Shungan, Rushan and Khorog).

Acquaintance trip to Canada (Ontario) and USA (New York, Pennsylvania, Maryland, Virginia, North and South Carolina, Kentucky, Indiana, Illinois, Iowa, Wisconsin, Minnesota, North and South Dakota, Wyoming, Colorado, Arizona, California, Oregon, Maine).

Expedition to Afghanistan (Herat, Afghan Turkestan, Gaimag, Bamian, Hindu Kush, Badakhshan, Kafiristan, Jalalabad, Kabul, Herat, Kandahar, Baquia, Helmand, Farakh, Sehistan), accompanied by D.D. Bukinich and V.N. Lebedev.

Expedition to Khoresm (Khiva, Novyi Urgench, Gurlen, Tashauz).

Expedition to Mediterranean countries (France, Syria, Palestine, Transjordan, Algeria, Morocco, Tunisia, Greece, Sicily, Sardinia, Cyprus and Crete, Italy, Spain, Portugal, and Egypt, where Gudzoni was explored by Vavilov's request) and to Abyssinia (Djibouti, Addis Ababa, banks of Nile, Tsana Lake), Eritrea (Massaua) and Yemen (Hodeida, Jidda, Hedjas).

Exploration of mountainous regions in Wuertemberg (Bavaria, Germany).

Expedition to China (Xinjiang - Kashgar, Uch-Turfan, Aksu, Kucha, Urumchi, Kulja, Yarkand, Hotan) together with M.G. Popov, then alone to Chine (Taiwan), Japan (Honshu, Kyushu and Hokkaido) and Korea.

Expedition to USA (Florida, Louisiana, Arizona, Texas, California), Mexico, Guatemala and Honduras.

Trip to Canada (Ontario, Manitoba, Saskatchewan, Alberta, British Columbia), USA (Washington, Colorado, Montana, Kansas, Idaho, Louisiana, Arkansas, Arizona, California, Nebraska, Nevada, New Mexico, North and South Dakotas, Oklahoma, Oregon, Texas, Utah); Expedition to Cuba, Mexico (Yucatan), Ecuador (Cordilleras), Peru (Lake Titicaca, Puno Mt., Cordilleras), Bolivia (Cordilleras), Chile (Panama River). Brazil (Rio de Janeiro, Amazon), Argentina, Uruguay, Trinidad and Porto Rico.

Systematic explorations of the European part of Russia and the whole regions of the Caucasus and the Middle Asia.

(partially adapted from

Wednesday, July 25, 2012

Gene transformation and chromosomal translocation – A plant breeder’s vista

K.K.Vinod, Neway Mengistu, Nicholas Adam Crowley and Jeffery Ryan Sullivan

(This was the subject of a threaded discussion at University of Nebraska-Lincoln)

When a breeder is looking to incorporate “alien” genes into a line, two good choices he has are translocation and transformation (transgenic events). With a little luck, time, and effort their results can show great benefit to commercial crops. The two methods are similar because you are adding DNA segments to an existing genome without conventional breeding methods. Both of these methods are used to add a desired gene(s) to a crop which lacks the gene of interest. Chromosome translocation is caused by the interchange of parts between non-homologous chromosomes. Transgenic inserts add new, although more controllable segments, to an existing genome. The two methods require selfing and selection to be successful.

Translocation mostly gives a successful result in polyploid crops. It has been tried in wheat and rye to transfer disease resistant genes from their wild relatives. Moreover, translocation lines are more acceptable in polyploidy systems, wherein other chromosomes in the genome can compensate for a lost arm/part of chromosome eventuate in translocation events. Chromosomal translocations are random events. Translocations therefore differ from crossing over by randomness of insertion points. Any chromosomal segment can get attached to any arm of another chromosome. Classical examples are random translocations caused by transposable elements. When a chromosomal fragment carrying a desirable gene is getting translocated to a cultivated variety, the event may result in transferring of some other unknown alleles along with the gene of interest. For example, if a chromosomal segment from a wild relative carrying a disease resistance gene is translocated into a cultivated variety, it may also carry some undesirable wild traits into the cultivar. In the earlier days translocation was not much utilized in crop improvement due to this impediment. Nowadays, by use of transposable elements translocations and insertions are being utilized for site directed mutagenesis and random transfer of genetic elements.

Transformation techniques use biolistics/particle bombardment or Agrobacterium tumefaciens to insert a gene. These transformation techniques are “quick” means to introduce a gene into the plant of interest. Transformation events, try to incorporate new resistance, tolerance, or quality traits. Examples of transgene insert performed in soybean (RoundupReady® soyaben), cotton (Bt-cotton), rice (golden rice - enriched with vitamin A) etc., give a good reasoning to suggest that it can work. However, most of the traits are novel, which produce a function beneficial to humankind/cropping systems and the genes responsible are not found in that specific crop or any of its relatives. Transferring a trait using transgene insert can be manipulated by genetic engineering techniques to isolate the gene and manipulate it through cloning. In the case of a transgene, the insertion is a random event and can occur any where in the genome. This will result in hemizygosity for the transgene.

Although the advantages of these two methods are a great benefit to breeders, both have their own considerations when using them for adding desirable genes to a crop. The translocated disease resistant gene would contain surrounding chromosome segments from the wild relative. The surrounding genome would likely be undesirable since it is being donated by a distant relative to the crop. Moreover, it may take longer years to find a stable line that contain the disease resistant gene. In theory, transgenic events seem simple, and scientists/geneticists have found ways to make it as easy as it sounds, but when breeders work with translocation lines, it is hard to get everything seem simple. One case in which the breeders/scientists have used to make this technique easier is the Ph mutant in wheat. This mutation allows homoeologous pairing and crossing over between alien chromosome and its crop homoeologue, allowing transfer of chromosome segment containing the alien gene. And also if the crop is a kind of polyploid chromosomal translocation may be preferred than transgene insert - because of better tolerance of the new chromosome fragment in polyploids. On the other hand, many diseases are controlled by a single gene resistance which may not justify transfer of a chromosome fragment. A transgene insert may accomplish the job very well. However, transgene methods are still questionable by some and this must be measured when developing transgenic crops. Transgenic methods must also be isolated and sequenced for the desired gene.

Notwithstanding the fact that these methods have similarities and differences, both techniques can be used for transferring desirable traits like disease resistance. The similarity between the translocation and transgene lies in the hemizygosity it produced. Since corresponding allele(s) from the translocated fragment are not found in the homologous pair, or transgene is attached only to one chromosome, hemizygosity produces a situation where only one allele is present in excess on one chromosome, while it is totally absent on its pair. As breeders, hemizygosity is not a desirable situation as we have the threat of missing the event upto 50% among gametes. The best solution is to self the plants to generate a homozygous line for the transferred gene. This homozygous line can be used for further breeding programmes. Another similarity can be from incorporation of many novel genes from translocation and transformation. Translocation between species can provide more than one beneficial gene. This is also the case in transformation; a good example is YieldGuard® plus corn hybrids. These incorporate herbicide resistance, and various insecticide genetic events to produce a corn hybrid that is beneficial to the farmer.

One way, in which these methods differ, lie in the mode of prediction of the gene transformation event itself, i.e. marker. In the case of transformation, an antibiotic resistance, herbicide tolerant or gus gene is added for easy phenotypic identification in early stages of development. In translocation crosses, phenotypic markers that may be by chance linked to the gene being transferred need to be looked to identify the plant with the alien translocation.

The major difference between a transgene insert and the translocation event is that, we know the number and nature of the genes inserted in the transgenic event, while we are unsure of the number and nature of alleles inserted through a translocation event. Shorter the translocation insert more stable will be the translocated event, while the question of stability of the transgene is still not resolved. Depending upon the length of the translocated fragments, the number of alleles will vary which may comprise of many introns and exons. Transgene insert usually has gene of interest along with antibiotic or herbicide resistance markers and/or gus markers plus the promoter regions and plasmid fractions.

When using the translocation technique in a breeding program, a breeder must consider the difficult task of achieving fertilization from the parents and possible seed abortion and using embryo rescue. In the case of transformation this is not a problem. Transformation can cause problems when the gene of interest is placed in an existing gene for interest and produces a mutant or lethal plant.

Monday, December 12, 2011

My Professor's Dilemma

K.K.Vinod and M. Maheswaran

Yesterday my Professor, Dr M Maheswaran wrote me after reading the book “Emperor of All Maladies- A Biography of Cancer” by Siddhartha Mukherjee.

He wrote,

Genes talk to genes and pathways to pathways in perfect pitch, producing a familiar yet foreign music that rolls faster and faster into a lethal rhythm.

If the data did not fit the dogma then the dogma, not the data, needed to be changed.

After reading the book and understanding the biological causes behind the cancer genetics I felt very bad about things what we are teaching and doing in understanding the genetics of many of the traits we deal with crops and exploit the results in practical plant breeding. Many of the concepts of predictions we make based on the classical genetics, whether it is Mendelian or Galtonian, remain irrelevant considering the biological implications on a particular phenotype. For example, p53 gene, an unassuming name, has major role in the development of human cancer than any other component of the genome. The gene get its name from the product it encodes, p53, which is a polypeptide having a molecular weight of 53 kilo Daltons. p53 was thought for number of years to be a dominantly acting oncogene, but in 1990, it was recognized as the tumour suppressor gene that, when absent, is responsible for a rare inherited disorder called Li-Farumeni syndrome, whose victims are affected with a very incidence of certain cancers, including breast cancer and leukaemia (though there are separate and specific genes for breast cancer and leukaemia). Like individuals with the inherited form of retinoblastoma, persons with Li-Farumeni syndrome inherit only one functional copy of the p53 tumour suppressor gene and are thus highly susceptible to cancer as the result of random mutations that knock out the function of the remaining copy of the gene. Further, if we see the development of cancer in humans (for any type of cancer development), the possible sequence of genetic changes in a cell lineage are given below.

The complexity of cancer can be better understood if you read the above book. But in plant genetics we decide the genes based on the prediction methods and most of the gene predictions are based on the “breeder friendly phenotyping methods (whatever be the trait we have the simple means and many models to predict the genes). The advent of molecular marker technology made this simpler. Once there is co-segregation of DNA marker, the gene discoverer assumes he/she got gene for the phenotype (some where I read that there are 83genes identified for resistance to rice blast disease and we have 26 genes for brown plant hopper resistance in rice- just go back and read the situation of gene for Li-Farumeni syndrome). Gene identification based on breeder friendly phenotyping and pyramiding of those genes without knowing the functionality of the genes is a wasteful exercise. In recent times people started asking questions whether it is good to pyramid dominant genes or recessive genes without understanding the situation of obscurity prevailing over dominance or recessiveness. This can be remedied if every gene discoverer realizes the importance understanding the biology behind each of the phenotypes instead of evolving prediction methods.

My Professor stops his letter by saying “Predictions are always based on perceptions”.

Concern of my professor was of a genuine teacher, who attach paramount importance to imparting current and competitive knowledge to his students. He laments that except a very few teachers of plant genetics, none are ready to change the way science unfolds life’s mysteries. So instead of changing the dogma, we are often bending the data fit the dogma. Are we ruthlessly incompetent because we are afraid of deviating from the conventions?

Saturday, December 03, 2011

A tribute to Damodar Dharmananda Kosambi


Scientists and students of genetics studying linkage and recombination are familiar with Kosambi’s mapping function. Chances are that they never had heard of Kosambi before. The reason - Damodar Dharmanada Kosambi was not a geneticist by training and profession, but a mathematician. He was also a statistician, historian, marxist, linguist, writer – he was everything – a multi-faceted scholar. His famous mapping function was published in 1944, in Annals of Eugenics (Kosambi, 1944). How he got into this work is not known, but Kosambi’s works generally spanned across many disciplines from mathematics to children’s literature. At the time of this publication he was teaching mathematics at Fergusson College, Pune.

Recently, Professor Kosambi’s birth centenary was celebrated, in Pune mainly by the historians and scholars. I as a student of genetics, came to know more about Kosambi after this celebrations. Ignorant of a great scientist, whose name I would have used thousands of time while doing genetic map constructions, I decided to put this tribute.

Kosambi’s mapping function estimates the recombination fraction (c) between two loci as a function of the map distance (m) between the loci, by allowing some interference, as
c = ( e4m -1) / 2( e4m +1)

The estimate of the map distance between two loci can be obtained from
m = ln [ (1+2c)/(1-2c) ] /4

Kosambi’s function go intermediate between actual recombination fraction taken as map distance (no interference) and Haldane’s map function (Haldane, 1919), closely predicting recombination fractions especially when the loci are linked.

My article on Kosambi and the mapping function was published in the popular science journal Resonance in its Kosambi commemorative issue in June 2011. This article can be accessed from this link

Damodar Dharmanand Kosambi (D.D. Kosambi) was born at Goa on 31 July 1907 to Acharya Dharmananda Damodar Kosambi and Balabai. After his early schooling, young Kosambi moved to Cambridge, MA (USA) and studied grammar and Latin. After successful schooling at Cambridge, he joined Harvard University in 1924 studying mathematics. He discontinued his studies for a brief period and returned to India, again to join back in 1926, where he was awarded with Bachelor of Arts degree. Returning to India soon after, he joined Banaras Hindu University as a professor, teaching German and mathematics. Here he started his personal research and started publishing his findings. He got married in 1931 with Nalini, and in the same year joined Aligarh Muslim University as the professor of mathematics. He continued his mathematical research more vigorously here, and publishing his papers regularly in European languages.

Two years after he joined Fergusson College in Pune, and continued to teach mathematics. His two daughters Maya and Meera were born here. It was during this period his famous paper on mapping function was published in 1944. Kosambi had done extensive research on many areas of mathematics and published many papers. However, many of his publications went unnoticed by Indian scholars and eventually a great scientist and a historian was getting ignored to a great extend. No students of genetics were told Kosambi was an Indian scientist.

It was probably Homi J Bhabha, who recognised his talents and made him to join Tata Institute of Fundamental Research (TIFR) in 1945. He was professor of mathematics and worked there for next 17 years. During this period, Kosambi published 40 research papers, mostly on mathematics. However, his interest was shifted to history and social sciences in the later years, extensively researching on ancient Sanskrit works, numismatics and ancient history of India. Probably these later works made him to be remembered as a historian rather than a mathematician.

Kosambi authored 9 books including edited ones and 127 articles. But this number is not authentic as there are many childrens’ stories written by him. As a prolific writer, thinker, mathematical genius, linguist and historian Professor Kosambi, as Dale Riepe wrote, ‘deserves to be remembered as one of the highly gifted and versatile scientific workers and indefatigable scholars of modern India for whom a relentless search for the highest human values was the only natural way of life’.

After leaving TIFR, in 1964, Kosambi was appointed as a Scientist Emeritus of the Council of Scientific and Industrial Research (CSIR) and worked in Pune. He got involved in many historical, scientific and archaeological projects, including stories for children. But most of his works that he produced in this period could not be published during his lifetime.

Professor Kosambi died at Pune, at the age of 59, on June 29, 1966. He was posthumously decorated with the Hari Om Ashram Award by the government of India's University Grant Commission in 1980.
A biographical sketch of Prof DD Kosambi written by Chintamani Deshmukh can be downloaded from here.

References (Click on the title to download)

Friday, July 03, 2009

Marker Assisted Selection

K K Vinod

Primary objective of any plant breeding programme is selection of the best genotype from an array of breeding lines (genotypes). Conventionally, selection involves various traits that are expressed in plants (phenotypes) and the selection tools employed by the breeders involve qualitative (visual or perceivable traits) and/ or biometrical (quantitative) traits. However, since gene expression is always modified by the environment due to several adaptive reasons, selection of traits is not always as successful as it should be. This led to the thinking of selecting directly for the genes themselves, as the genes are coded on the DNA molecules that are free of environmental interference. However, selection of genes was not an easy job as it appeared to be, because of their obscure locations on the genome. Hence, this is achieved indirectly by selecting detectable DNA variations in the individual genomes, which are either associated or closely linked to the target genes, as detected by the co-segregation of these fragments with phenotype. Such detectable DNA fragments are called markers. Use of these molecular markers has opened a novel way for selection known as marker assisted selection or marker aided selection (MAS). Extensive use of molecular markers by the present day breeders has opened up a separate field of study, the molecular breeding.

Principles of MAS

As the name indicates, MAS is not a breeding method but markers are used as a selection aid. We consider that traits may be typically controlled by single or many genes. Although in strict sense no trait is controlled by a single gene but a group of genes, the practical consideration of mono, oligo and polygenes revolves around the number of genes that produce the perceivable quantum effect of the trait. Any detectable DNA fragment lying around or within these genes can report the presence of this gene in its carrier. This forms the fundamental idea behind MAS. MAS therefore can involve in selection for both qualitative and quantitative characters. However, MAS is not generally advocated for the selection of easily selectable traits, especially those qualitative traits with high heritability and penetrance, while for traits with low heritability and low expressivity MAS may be a good option.

Since markers tag for genes, MAS is useful mostly in transfer of genes from a donor to a recipient. Therefore the donor should have a distinguishable marker allele that is linked to the target gene. This marker allele should be distinctly different from the allele produced by the same marker in the recipient genotype. Now while crossing both donor and recipient it is easy to determine which progeny carry the gene by identifying the linked marker allele. The target allele of the gene may be either a dominant one or recessive. Most commonly used procedure in transfer of single gene from donor to recipient is backcross breeding. Since the recipient genotype is used repeatedly in crossing steps in the backcross process it is also called recurrent parent (RP). Using markers, the backcross breeding proceeds by selecting progenies that are carriers of the target allele until a stable homozygous genotype is obtained which has almost entirely of the recipient genome carrying the target allele. This is called marker assisted backcross breeding (MABB). Depending on the transfer of dominant or recessive allele backcross procedures may suitably vary.

Sunday, March 02, 2008

Basic Concepts of Selection in Plant Breeding


Generally breeders in two ways can change variability in their working population. Firstly by allowing individuals to produce next generation within limits of breeders preference or by natural choice in which which some of these individuals may be allowed to produce many offsprings and some of which may be allowed to produce which few or no offsprings. This non-random reproduction in a breeding population is called selection. The two agencies involved in the selection, one is by the natural choice is called natural selection and the other that is done by the breeder is the artificial selection. Secondly, breeders can decide how the selected individuals will be mated to each other either by inbreeding and cross-breeding.

Following basic principles operates on selection:

1. Selection works only on heritable variation
Variation that is governed by genetic makeup of the individual alone can be recovered in the progenies, not the variation that is environmentally dependent.

2. Selection works only in existing variability ie., it cannot create new variation. 
Hence, selection can only shuffle the variation and also can combine variations of different individuals of the population, which is however, pre-exist within the population itself.

3. Selection works by providing preference to certain individuals to reproduce, therefore certain set of genes get preferential inheritance at the expense of the unselected genes. Asa consequence gene and genotypic frequency  get altered. 

4. Continuous selection leads to loss of variability, because unselected genes get eliminated in the course of generation advancement.

5. When a new variability is created in a population either by mutation or by movement of genes from outside (from another unrelated population), new selection pressure is generated on the introduced genes.

6. Purpose and consequence of selection varies from type of selection, individual genes, mating methods etc.

Plant breeding employs artificial selection to generate plant populations that are cultivated for the benefit of the mankind. Artificial selection is fundamentally aimed at the following facts:

1. To change the phenotype of the selected individual in the most desired way to the man
2. To bring down the variability in the selected population
3. To increase uniformity in the selected population
4. To increase number of populations with different level of variability between them
5. To increase the range of uniform populations

Various artificial selection methods used in plant breeding are, 

In self pollinated crops,
1. Mass selection
2. Pureline selection
3. Pedigree selection

In cross pollinated crops,
1. Mass selection
2. Progeny selection (ear to row methods, modified ear to row methods etc)
3. Family selection (half sib, full sib family selection and their modifications)
4. Recurrent selection

Clonally propagated crops,  
1. Clonal selection.

Thursday, January 10, 2008

Crop improvement in Para rubber tree (Hevea brasiliensis)


Para rubber tree (Hevea brasiliensis) belong to Euphorbiaceae. It is the major source of natural rubber in the world. The genus Hevea occurs naturally through out the Amazon basin and in parts of Matto Grosso, Upper Orinoco and the Guianas (Schultes, 1970). Hevea brasiliensis (2n = 36) is a monoecious perennial tree belonging to Euphorbiaceae. There are ten species recognised under this genus, H. brasiliensis, H. benthamiana, H. camporum, H. camargoana, H. nitida, H. pauciflora, H. guianensis, H. microphylla, H. spruceana and H. rigidifolia. These species are highly cross-pollinated and putative hybrids of natural intercrossing between the species occur in the natural habitat. Experimental crosses between species show no hybridisation barriers (Webster and Paardekooper, 1989).

Genetic resources

Though there are few reports of introduction of rubber plants to other areas of the world, all of them lack evidence to substantiate such claims. Recorded history of introduction the rubber from its natural habitat starts with the collection of rubber seeds by H.A. Wickham near Santarem during 1872. In 1876, Wickham collected about 70,000 seeds of H. brasiliensis from near Boim on the Rio Tapajoz and from the well-drained undulating areas near Rio Madeira and despatched them to Royal Botanic Gardens at Kew, England. About 2800 seedlings raised at Kew, 2397 were despatched to Sri Lanka and few to Malaysia, Singapore and Indonesia. Virtually all the rubber trees cultivated in Asian countries originated from this collection.

After Wickham, there were several attempts to introduce H. brasiliensis to Asian countries, but these introductions were confined to very few in number did not contribute much to the introduced genetic base. Later wild species and few cultivated cloned were introduced to Rubber Research Institute of Malaysia from Brazil. Besides few other organised attempts by International Rubber Research And Development Board (IRRDB), a major collection of wild Hevea Germplasm was carried out in 1981 by IRRDB team of scientists from major member countries, in collaboration with Brazil collected 64736 seeds from the states of Acre, Rondonia and Mato Grosso and budwoods from 194 high yielding trees free of major diseases like abnormal leaf fall (Phytophthora sp.) and South American leaf blight (SALB) caused by Microcyclus ulei (Ong et al., 1983). Of these collections, India introduced about 9000 accessions from Malaysia, of which about 6000 are surviving and being conserved in ex situ gardens. Besides, India also introduced 127 commercial clones from other countries where Hevea is grown on commercial scale.

Apart from H. brasiliensis, SALB affects only three more species, H. benthamiana, H. guianensis and H. spruceana (Langford, 1945; Chee and Holliday, 1986). Others species are free from infection. Eleven physiological races are reported to be identified for this disease. Though H. brasiliensis is totally affected by this disease immune reactions are shown by some H. benthamiana, H. spruceana and H. pauciflora derivatives. Sporadic attempts to use these immunities, by crossing with H. brasiliensis had produced clones with transient and non-durable resistance (Simmonds, 1989). Evaluation of wild Hevea germplasm for sources for biotic and abiotic stresses are in progress at major rubber growing countries.

Crop improvement

The rubber tree is introduced into cultivation very recently. The genetic base of the cultivated germplasm is very narrow, converging to a very few seeds collected from upper Amazon basin near river Tapajos in Brazil. Though rubber tree is infected by many diseases, the plantation industry suffers mainly from only one really devastating pathogen causing South American leaf blight (SALB). This disease in still confined to American sub-continent and all the rubber growing areas of South and Southeast Asia are free from it. However, it is already proved that none of the cultivated varieties in Asia are resistant to this disease when tested at various locations of South America. However, in recent years, another disease Corynespora leaf fall (CLF) has gained importance for wiping out entire RRIC 103 plantations of Sri Lanka, which had almost gained its name SALB of Asia.

Clonal selection is the most important procedure followed in breeding rubber. Clones can be evolved at any stages of different breeding steps. Usually selective hybridisation of promising parents is done among themselves and also with wild germplasm lines. The progenies are directly selected from seedling nurseries and cloned for further evaluation. Also, natural seedling population or half-sib population are also screened for desirable characters including resistance. Susceptible and poor performing clones are generally discarded. Polycross gardens comprising of pre-potent clones are also utilised and the selection is generally exercised in the polyclonal seedling orchards, even at the stage of maturity. The selections are directly carried forward for clonal evaluation and selection. A general scheme of rubber improvement is provided in Fig.

A general scheme of Hevea breeding

The major thrust of quality improvement in Hevea does not orient to the quality of rubber, but on the quality of secondary products like Hevea wood. Rubber trees produce enormous quantity of semi-hardwood at every replanting cycle. The shrinking availability of natural timber from the forests has made this so valuable. The wood on appropriate chemical treatment could be used as a best substitute for timber for furniture making and for similar uses. The treated wood is now being used to produce very high quality furniture, panel boards, house-hold articles and for flooring purpose.

Owing to the growing importance of rubber wood, the improvement in the direction of developing timber – latex clones is in progress. The clones combining better yield, high vigorous growth, short life span, high quality strong wood, free from diseases and with good branching habits are preferred.
Rubber tree is a prolific producer of honey. Honey is produced on extrafloral nectaries located on the Hevea leaves. High honey production can give additional income to plantation sector, and population that yield more honey are preferred.

Though rubber products are being used for so many decades, recently, the problem of latex protein allergy has emerged mainly in America. The allergy is reported to be caused by the proteins present in the latex, which are found in traces in the finished products. However, the allergy reported is mainly of type IV allergy of cutaneous origin. There are several processing methods available for the deproteinization of the rubber products. However, it would be better to look out for genotypes, which do not accumulate harmful proteins in the latex.

Biotechnology rubber crop improvement

The one area of biotechnology with clear applications in rubber is that of molecular markers. Marker-assisted selection offers prospects of accelerating the process of long term breeding objectives offered by the conventional approaches. An important first step towards developing linked markers is the construction of a linkage map. Maps have been published for rubber (Seguin et al, 1996). A map allows the selection of markers which are evenly distributed over the genome, thus enhancing the probability of finding markers linked to quantitative trait loci (QTL). Molecular markers that are linked to these QTL will co-segregate with the genes involved in desirable traits and could be used efficiently to follow introgressions and accumulation of favourable traits during recombination cycles.

Besides, interfering with the biochemical pathway are also being contemplated, in producing many biomolecules including antibiotics. However, the lesson is that a single, apparently simple, change in a synthetic pathway may have unexpected side effects. Successful transformation programmes have been those where the transformation work is integrated into a conventional breeding programme, allowing individuals with the required phenotype to be developed from a range of transformants.


Chee, K.H. and Holliday, P. (1986) South American leaf blight of Hevea rubber. Malaysian Rubber Research and Development Board, Kuala Lumpur. 50p.
Langford, M.H. (1945) ) South American leaf blight of Hevea rubber trees. USDA Technical Bulletin, 882: 31.
Ong,S.H., Ghani, M.N.A. and Tan, H. 1983. New Hevea germplasm: Its introduction and potential. Proceedings of the RRIM Planters Conference, Kuala Lumpur. pp. 3-17.
Seguin, M., Besse, P., Lespinasse, D., Lebrun, P., Rodier-Goud, M., and Nicolas, D., 1996. Hevea molecular genetics. Plantations, Recherche, Développement 3(2): 77-87 
Shultes RE (1970) The history of taxonomic studies in Hevea. Bot. Rev., 36: 197-276.
Simmonds, N.W. 1989. Rubber Breeding. In: Rubber (C.C. Webster and W.J. Baulkwill, eds). Longman Scientific and Technical, U.K. pp. 85-124.
Webster,C.C and Paardekooper. 1989. Botany of the rubber tree In: Rubber (C.C. Webster and W.J. Baulkwill, eds). Longman Scientific and Technical, U.K.