C2 Cotton

Farm to fibre: Impact of hybridisation and molecular cloning on cotton and cotton growers

C2.1 Introduction

Look at what you and others around you are wearing. It is very likely that the clothes you are wearing are made, at least partially, of cotton. Cotton is central to Indian agriculture and clothing, and India is one of the largest producers of cotton globally.

Cotton belongs to the Gossypium genus in the family Malvaceae. The Gossypium genus has 50 species and the four species from which cotton fibre is derived are Gossypium hirsutum, G. arboreum, G. barbadense and G. herbaceum. Cotton naturally grows in tropical and sub-tropical regions of the world. The plant requires a period of frost-free growth, ample sunshine and a dry climate. Agriculturally it develops best when air temperatures range between 21 and 32°C. It can also survive for short periods at higher temperatures (~37°C). This means that the sub-tropical agricultural zones of India are ideal for its growth, and the three main regions in India are the north zone (Punjab, Haryana, Rajasthan), central zone (Maharashtra, Gujarat, Madhya Pradesh) and south zone (Karnataka, Tamil Nadu).

alluvial soils
Very fertile and porous soil deposited on the banks of rivers, in floodplains, and in deltas by flowing water.
black soils
Mineral soils enriched in organic carbon, making them fertile and productive.

The growth cycle of the plant from planting to harvest is about five to six months and it requires about 500 mm of rain. It grows in all kinds of soil that are well drained from alluvial soils in North India to the black soils found in south India.

For several centuries cotton has been a driving force of India’s economy due to the large number of people involved in cotton production and processing. Indian cotton weaving is known around the world, from the ikat weavers of south India to the finest muslin of eastern India. See Figure C2.1 for some fine examples of Indian cotton fabrics produced 2 to 3 centuries ago.

Cotton fabrics in pre-colonial India – photograph of a seventeenth century hand-painted cotton robe.

Figure C2.1a Seventeenth century hand painted cotton robe.

Cotton fabrics in pre-colonial India – photograph of an early eighteenth century palampore wall hanging.

Figure C2.1b Early eighteenth century palampore wall hanging made for the export market.

crop yield
The amount of a crop produced per unit of agricultural area for that crop.
recombinant DNA
A DNA molecule artificially developed through the combination of genes from at least two different sources.

The importance of cotton to the economy has led to a great deal of government focus on making improvements to cotton yield via cotton hybrids, investment in fertilisers and pest control, and improved irrigation practices. More recently, recombinant cotton varieties have led to tremendous changes in farming practices.

In this chapter we explore the history of cotton growing in India and understand its centrality to Indian agriculture. We will review how colonial powers attempted to change farming practices in India, and their effect on cotton farming and weaving. By the end of the history section, you will understand how biological, agricultural, cultural, and economic factors decide the success or failure of a crop.

Government focus on increasing cotton yields post-independence led to a large programme on cotton breeding. Such efforts led to the first cotton hybrid ever being produced in India in 1953. In order to study cotton hybrids, we first study the botany of cotton: its physiology and growth characteristics. You might be familiar with some aspects of this from the plant biology you studied in school.

Bacillus thuringiensis (Bt) is a soil bacterium whose proteins are toxins. These have been expressed in crop plants to confer pest resistance.

Studying the biology of hybrid cotton allows us to touch upon many core biological themes and concepts, from classical botany to molecular biology. We study Hybrid-4, the first cotton hybrid that was commercially grown. Hybridisation is widely used in agriculture for improving crop and livestock characteristics. Learning about hybrid production allows us to understand the large-scale increases in crop yields that have been possible in the last 100 years.

We continue to look at scientific advances to cotton growing by studying Bt cotton. Recombinant DNA is now a routine part of basic and applied biology, and the introduction of Bt cotton to India in 2003 has transformed cotton farming. Using the case of Bt cotton, we will understand how this technology first came about and how it is used to produce a recombinant organism. This is one of the scientific techniques that you need to learn from this chapter, as it is based on molecular biology.

The introduction of Bt cotton cannot be separated from the controversy of whether it has benefitted Indian farmers or not. This makes it a good case study for assessing new technology in terms of its benefits and drawbacks to society.

A technology cannot be separated from the claims it makes, and we will therefore learn to evaluate claims in science critically. For this purpose we will use published data on growth of Bt cotton to examine the pros and cons of recombinant DNA technology beyond the simple dichotomy presented in popular media.

The different aspects of cotton growing from its history to scientific advancements are rich in educational and learning potential. In this chapter, we focus on a few of these to enhance capacities in particular areas.

Critical thinking Scientific process

Why do you think India attained high proficiency in cotton fabric manufacture?

Think of the timescale of the history of our civilisation.

C2.2 Brief history of cotton growing in India

Bridging science, society and the environment

Old World
Referring to the continents of Asia, Africa, and Europe.

Cotton in India has a history that goes back at least 4500 years. There is evidence that the Indus Civilisation used cotton fabric. In medieval times, Indian cotton fabric (woven and printed) was famed throughout the Old World. Indian cotton might have accounted for 25% of global industrial output in the Mughal era.1 Travellers such as Marco Polo, Tavernier and the Greeks praised the high quality of desi cotton fabrics.

The pan-Indian cotton industry was thriving and had great value in international trade. A ninth century Arab trader named Sulaiman records, ‘speaking of the town of Calicut … the garments are made in so extraordinary a manner that nowhere else are the like to be seen. These garments are for the most part round, and wove to that degree of fineness that they may be drawn through a ring of middling size’.2

These records and actual fabrics collected by museums and private collectors show that Indian farmers and weavers were skilled in cotton growing, weaving, dyeing and embroidering. Over centuries, farmers honed indigenous methods to cultivate cotton. They carefully selected seeds from plants that could withstand local climatic conditions and pests. Farmers used organic farming techniques to reduce vulnerability to pests while providing high yields.

The resulting fibre produced textiles that were unique to regional climate and culture, and yet had global appeal. Small-scale weavers used techniques specific to their location to clean the cotton, spin the fibres within their own households, and make cloth of varying fineness, depending on the end use. Different regions were known for specific varieties of fabric, from the fine muslins of Bengal to the bright dyed cottons of South India.

The first stage in cotton cloth production – photograph of two women carrying bales of raw cotton on their head.

Figure C2.2a Cotton in colonial India – cotton bales being taken from the fields after harvest (1930).

Unknown author, Wikimedia commons, public domain.

The second stage in cotton cloth production – illustration of a woman extracting cotton lint on a hand–wound ginning machine.

Figure C2.2b Cotton in colonial India – cotton hand-ginning to extract lint.

Unknown author, Wikimedia commons, public domain.

The third stage in cotton cloth production – illustration of a woman wearing fine cotton clothes reclining on a bolster and smoking a hookah.

Figure C2.2c Cotton in colonial India – woman wearing fine cotton fabric.

Fransesco Renaldi, Wikimedia commons, public domain.

Cotton production during colonial rule

cotton gin
A machine used to separate cotton fibres from cotton seeds.

Colonial rule in India coincided with the Industrial Revolution. In the seventeenth century, before the colonial era, the East India Company had been importing quantities of Indian cotton cloth, such as calico and chintz, and generating large profits. The Industrial Revolution during the eighteenth century produced the cotton gin – (gin is a contraction of engine), which allowed large volumes of cotton fibre to be separated from seeds and prepared for further processing. Other machines could spin larger quantities of fibre into yarn, and cotton mills could weave the yarn into a variety of textiles.

With these technological advancements, the British could produce cotton textiles on a far faster scale than had been done before. They began to meet internal demand for cotton fabric through industrially manufactured cloth and also explored new markets for their cotton products. Newer markets meant the British were keen to scale up the production of cotton to meet the demand from English mills. The main source of raw cotton for the British were their colonies in North America and Egypt. They also looked for alternative sources of raw cotton, including in Africa and the West Indies. By the mid-nineteenth century most of the cotton for global demand came from the United States.

Gossypium hirsutum, the cotton species grown in the United States, was not native to the country. Over the course of 150 years, it had acclimatised to the southern states of America. (G. hirsutum is native to Central America.)

The start of the American Civil war stopped cotton production, and British traders turned to other regions of the world for cotton. British traders looked to India for cheaper and larger quantities of cotton.3

staple length
The average length of a group of fibres.

Before the colonial period, Indian farmers grew varieties of Gossypium arboreum and G. herbaceum, which were all short staple length cotton. These indigenous varietes were known as desi cotton. The short staple length, cultivation and trade practices could not supply the large volumes required by cotton gins.

Many attempts were made to replace desi varieties of arboreum and herbaceum cottons with American varieties, mainly Gossypium hirsutum. From the 1790s to well into the nineteenth century, trials with American varieties persisted and failed consistently. American plantation owners also came to India to teach their growing and harvesting techniques to colonial officers, without much success. Some varieties like the Dharwar American did get acclimatised and were grown in South India. In the 1920s and 30s British agricultural officers also worked on improving local varieties, mainly with a view to increasing staple length. To maintain seed purity so as to ensure long staple length of certain varieties, mixed cultivation of varieties was banned. But at the time of independence, the arboreum and herbaceum varieties of cotton were still the major types grown in India, with hirsutum providing only 3% of total yield.4

Critical thinking Scientific process Bridging science, society and the environment

What factors need to be taken into account when deciding what species or strain of cotton should be planted? Is there always a balance to be achieved between economics and environmental impact?

Think about how farming was done 50 to 70 years ago and the kind of economic system that was prevalent then.

By the late nineteenth century, India stopped exporting textiles and supplied only raw cotton. British-controlled centralised mills and those set up by Indian industrialists demanded large quantities of raw cotton, and farmers (via traders) increasingly relied on them to buy their cotton harvest. The fact that mills preferred long stapled cotton meant that farmers increasingly shifted to these varieties and the state actively promoted them.

Household spinning and weaving almost disappeared over the course of these 100 years. The damaging effects of colonial practices on Indian cotton cultivation persists even today, especially in terms of loss of biodiversity of native species and destruction of the weaving industry.

Post-colonial developments

After independence in 1947, sociopolitical conditions played a key role in driving agricultural policy. There was a strong drive to grow high-yielding varieties (of all crops, not just cotton) to augment overall income. This led to increased cultivation of hirsutum varieties. Research programmes were also launched to generate cotton hybrids in order to increase yields.

The successful generation of hybrids in India and elsewhere did lead to increasing yields. Hybrids, especially hirsutum hybrids, responded well to pesticides and fertilisers, which contributed to increased yields.

capital intensive
Requiring large monetary input.
pesticide resistance
The resistance gained by a pest population that makes it less vulnerable to successive applications of pesticides.

Cotton farming became capital intensive because of the onerous cost of hybrid seeds and increasing usage of pesticides and fertilisers. By the late 1990s, yields had stagnated at values far lower than the rest of the world because cotton farming in India was largely rainfed. Pesticide resistance had become rampant because of indiscriminate application of pesticides. Added to this, exposure to large amounts of toxic pesticides led to environmental poisoning. This led to the introduction of Bt cotton in India with government support as a way to attain pest resistance and improve yields. We will see how the introduction of Bt cotton has changed cotton farming in India in the last 20 years.

Critical thinking Bridging science, society and the environment

How does the historical perspective change your views on the science behind agriculture, especially that of cotton cultivation? Do you think this is important?

Think about how scientific advancements need to be understood in the context of societal and economic movements.


In this section we learned about the history of cotton growing in India in the last two centuries. We saw how developments due to the Industrial Revolution, namely mechanised ginning and spinning techniques, led to increased demands for cotton of a particular kind (long staple cotton). India changed from being an exporter of fine cotton textiles into an exporter of raw cotton. Colonial powers also promoted the cultivation of hirsutum varieties although it was found unsuitable for our environmental conditions.

Post-independence government policies promoted the cultivation of hirsutum varieties, since the spinning and weaving industry was geared to using this variety of cotton. Finally, the push to increasing yields also led to the adoption of Bt cotton in 2003. The section highlights the importance of gaining a historical perspective in order to be able to understand the present day state of cotton production.

C2.3 Agro-botany of cotton

Reading and interpreting

To study the biology of cotton, we first need to be familiar with the cotton plant. Barbara McClintock, a famous plant geneticist, said, ‘I start with the seedling, and I don’t want to leave it. I don’t feel I really know the story if I don’t watch the plant all the way along’.5 Let us follow Professor McClintock’s edict and see if we can study cotton all the way from a seed to the production of cotton bolls.

Morphology and growth

Commercial cotton is primarily derived from one species, G. hirsutum (Upland cotton) with G. barbadense (Egyptian or Sea-island cotton) being grown in relatively minor volumes.

The desi cotton varieties derived from G. arboreum and G. herbaceum are grown in India and parts of Asia and Africa, but in much smaller volumes. India is one of the few countries in the world where all four Gossypium species and their hybrids are grown.

Botanical drawing of Gossypium hirsutum
: Drawing of Gossypium hirsutum cotton plant showing leaves, flowers and cotton bolls.

Botanical drawing of Gossypium hirsutum

The seed with cotton fibres growing from it, as well as the cotton boll are drawn. Reproduced from photographs.

Botanical drawing of Gossypium arboreum
: Drawing of Gossypium arboreum cotton plant showing leaves, flowers and cotton bolls.

Botanical drawing of Gossypium arboreum

The cotton boll and the seed with the cotton fibres are also drawn. Note the difference in the morphology of the flower, leaves, and boll of Gossypium arboreum and Gossypium hirsutum.

Exercise C2.1 It runs in the family

Scientific process

  1. Refer to Figure C2.3 and make a list of similarities and differences between the two cotton species.
  2. Can you list plant species from your locality that are similar to the two cotton species?
  3. Why do you think we have chosen these historical images?

Check your answer

Extra reading Characteristics of the Malvaceae family of plants

  • Commonly called hibiscus or mallow family containing 243 genera with 4225 species of herbs, shrubs and trees.
  • Contains a number of economically important plants such as cotton (Gossypium species), okra/bhendi (Abelmoschus esculentus), cacao (Theobroma cacao, used for making chocolate), Hibiscus and durian (Durio species). (Interesting fact: The African Cola species is also part of this family and the caffeine containing seeds are used to make cola drinks.)
  • Important fibre-bearing plant species such as cotton and kapok (from Bombax species and Ceiba species).
  • Simple leaves (often lobed) arranged alternately and sometimes hairy.
  • Flowers are radially symmetrical, showy with pollen-bearing and ovule-bearing parts. They also have prominent bracts forming an epicalyx. Flowers have a central spot (as shown in the photographs).
a. Photograph of a cotton flower. b. Photograph of a hibiscus flower. c. Photograph of a bhendi flower.

Extra Reading C2.1 Flowers from the Malvaceae family.

a. Kenpei, Wikimedia commons, CC-BY-SA 3.0.
b. Kaustubh Rau.
c. Prenn, Wikimedia commons, CC-BY-SA 3.0.

Gossypium arboreum
: Photograph of a cotton flower.

Gossypium arboreum

Gossypium arboreum (cotton) is native to India and Pakistan.

Hibiscus panduriformis
: Photograph of a hibiscus flower.

Hibiscus panduriformis

Hibiscus panduriformis is a yellow hibiscus shrub found across Africa, Asia, and Australia.

Abelmoschus esculentus
: Photograph of a bhendi flower.

Abelmoschus esculentus

Abelmoschus esculentus (bhendi) grows in tropical and sub-tropical regions. Various parts of the plant are used in food and medicine.

In this section we will study the morphology and growth of Gossypium hirsutum, the long staple cotton that is the dominant species planted worldwide.

This section makes use of several terms in describing the cotton plant. Before reading this section, ask yourself two things:

Plants that have a life cycle longer than two years. See also: annual.
Plants that complete their life cycle in one growing season.

Cotton is a perennial in the wild, meaning that it returns every year in the right season without requiring replanting. It grows as a tree or shrub to 1.5–2 m in height. Commercially it is grown as if it were an annual, so plants are allowed to grow to 1.0–1.5 m and are destroyed after harvesting for fibre and seed.

It has characteristics that are typical of dicots: a taproot, reticulate venation and flowers with five-fold symmetry. Figure C2.4a shows the parts of the flower. Note the similarity and differences between monocot and dicot flowers.

monopodial growth
Growth that occurs when the main stem of a plant grows vertically and new leaves grow at the apex. There is one primary apical meristem (the growing tip of a shoot). See also: sympodial growth.
indeterminate growth (plants)
Growth that occurs throughout a plant’s life and does not stop.

The main stem of cotton is monopodial and indeterminate. Monopodial means single axis, and indeterminate means there is no definite endpoint to growth.

sympodial growth
Growth form characterised by multiple stem branches or apical meristems. See also: monopodial growth.

Lateral branches are produced in a spiral arrangement around the main stem. Lateral branches arise from axillary buds at the base of each leaf and can develop into vegetative or fruiting branches. Fruiting branches develop in a sympodial pattern from vegetative branches and contain flowers. Each sympodial unit consists of a terminal boll‐generating flower, a subtending leaf, and an axillary bud that generates the next sympodial unit. (Refer to Figure C2.4b.)

The number of monopodial to sympodial branches and their branching pattern is important, since the timing of fruiting has to be calculated. The sympodial development of fruiting branches means that the innermost bud of the lowest and oldest branch is the first to open, while the outermost bud of the highest and youngest branch is the last to do so.

A cotton flower cut longitudinally with different parts labelled.

Figure C2.4a Parts of a mature cotton flower.

Cotton plant with sympodial and monopodial branches.

Figure C2.4b Branching pattern on a cotton plant.

Scientific terms are important for scientists to communicate their observations clearly. For example, if you study pollination and fertilisation in cotton plants, you need terms to describe the parts of the flower. Using the terms given above allows you to describe these processes in a concise manner. We should consider our audience when we communicate our work, and use appropriate language.

Critical thinking Scientific process

Watch the video of the life cycle of cotton for a timelapse development of the cotton plant. As highlighted in the video, cotton flowers change colour from white or yellow to pink within 1 or 2 days of blossoming. Why do you think plants undergo floral colour change?

Try to come up with different hypotheses. For example, is it related to pollination, fertilisation, ageing?

Pollination and fibre development

Now that we have the appropriate vocabulary to describe plant structure, let us begin to learn about the development of cotton from seed to cotton boll.

Cotton plants are insect pollinated and the pollen is relatively large, heavy and sticky. The main pollinators are honey bees (Apis dorsata, A. florea, A. indica), bumble bees and leaf-cutter bees. Plants are typically self-pollinated (pollination within the same individual), with cross-pollination varying between 0 and 20%.

Fertilisation takes place about one day after pollination. The corolla, along with anthers and filament, drop from the fertilised ovary. Post fertilisation, the seeds develop inside the fruit, called a boll, along with the characteristic cotton lint (cotton microfibrils). From seeding to boll bursting and fibre maturation takes 140 days. Bolls burst 120 days after shoot emergence.

A panel of images showing the development of cotton seeds into plants, and then on to flowers and cotton bolls. A timeline shows that the entire growth cycle from seed to cotton boll takes 5 to 6 months.

Figure C2.5 Timeline and growth cycle of cotton from seedling to cotton boll.

What is a cotton fibre?

Cotton fibres are single cell extensions of the epidermal layer of the seed which help disperse the seeds. Fibre cells can elongate to 3–6 cm in G. hirsutum, making them some of the largest plant cells in the world!

The period in a plant life cycle when the flower is entirely open and functional.

Cell development and elongation begins as soon as the plant begins to flower. This flowering period is called anthesis. Cell growth is tracked using days post anthesis (DPA) as the measure.

A cotton fibre cell consists of a cuticle, primary wall, secondary wall, and a hollow lumen (Figure C2.6a). The epidermal cells go through a complex series of changes that involve fibre initiation, cell elongation and synthesis of a secondary wall. This secondary wall is several layers thick and made up almost exclusively of cellulose, forming cotton microfibrils or lint. The properties of this secondary layer determine the quality of the cotton fibre used to make yarn.

In the maturation stage the fibre cells die and the mature fibres twist and entangle to form a three-dimensional network. This twisting and entangling helps later in the formation of spinnable yarn. The mature fibre is hollow (‘kidney bean shaped’) and under the microscope has the appearance of a twisted ribbon (Figure C2.6b).

A schematic of the structure of cotton fibre, showing the different layers in both cross section and vertical section.

Figure C2.6a The structure of cotton fibre, with the different layers seen in cross section and vertical section.

Adapted from Yu, C, ‘Natural Textile Fibres: Vegetable Fibres’, in Textiles and Fashion: Materials, Design and Technology, ed. R Sinclair, pp. 29–56, Woodhead Publishing Series in Textiles (ScienceDirect, 2015)

A high magnification image of a bundle of cotton fibres.

Figure C2.6b A scanning electron microscope image of knotted cotton fibres. Note the flattened shape and natural twist of the fibres. The diameter of cotton fibres varies from 11µm to 22µm.

Bruce Ingber, USDA Agricultural Research Service, public domain

Critical thinking Scientific process

Cotton is a perennial plant and yet is grown as an annual. Why do you think this is so?

Think about how cotton is harvested. Also think about what parts a plant allocate resources to as it keeps growing (that is, annual versus perennial).

Pests of cotton

primary pests
Pests that directly feed and breed on whole, undamaged plant parts.
secondary pests
Pests that can only feed on plant parts that have already been damaged by primary pests, or on processed grains.

Over 150 insect species feed on different parts of the plant. Of these only a few can be categorised as pests, in other words, their actions are detrimental to human economic concerns. Two main types of pests attack cotton: sucking pests and bollworms. Cotton pests in India are primarily at the caterpillar stage of the insect life cycle. Caterpillars (which eat the cotton bolls and are called bollworms) are the primary pests, and sap-sucking bugs are secondary pests.

polyphagous insects
Insects that feed on plants of diverse taxonomic groups. They are voracious feeders and multiply in large numbers. See also: oligophagous.
Feeding on a diverse set of foods. See also: polyphagous insects.

The primary pests that cause the most damage in India6 are the polyphagous Helicoverpa armigera, or American bollworm (ABW, an Old World species) and the oligophagous Pectinophora gossypiella, or pink bollworm (PBW). Sap-sucking bugs suck sap from leaves, and more than 150 species attack cotton.

Pest attacks have a large economic impact for cotton farmers and the cotton industry. Pesticides have contributed to increasing cotton production. However, pesticide resistance has also developed in many pests, meaning that newer pesticides need to be designed to combat this resistance. Methods we have developed to combat these pests may have inadvertently created more problems than they have solved.

Caterpillars from the moth family that are major pests of cotton plants are shown.

Figure C2.7 Lepidopteran pests of cotton. Caterpillars from the bollworm family are the most destructive pests.


In this section we learned about the characteristics of the cotton plant. Cotton shows several characteristics of the family Malvaceae, particularly the large showy flowers and lobed leaves. We learned about the characteristics of pests that plague cotton; information that is linked to the next section on genetic improvements to cotton.

C2.4 Genetic improvements to cotton

Scientific process Scientific tools

Early in the twentieth century, the rediscovery of Mendel’s laws, which showed how traits were passed from parent to offspring, provided impetus for research in plant hybrids. University agricultural programmes were launched to generate hybrids for several important crops, including cotton. Let us study one of the first such efforts to produce a cotton hybrid.

A cell containing more than two chromosomes per homologous pair of chromosomes. See also: haploid and diploid.
allotetraploid genome
The genome of a hybrid in which each parent contributes a homologous pair of chromosomes instead of a single chromosome. The hybrid has twice as many chromosomes as its diploid counterpart.
The enhancement of traits in a hybrid offspring that occurs from the mixing of the parents’ genes. Also known as: hybrid vigour.

G. hirsutum and G. barbadense are polyploid, which means they have several copies of each chromosome in every cell. By contrast, humans are diploid, since we have two chromosomes per homologous pair in our genome. G. hirsutum and G. barbadense have an allotetraploid genome, with four sets of chromosomes. This double-duplicated genome provides some advantageous characteristics such as heterosis and gene redundancy (Refer to Figure C2.8).

dominant gene
A gene in which only one allele for a character is expressed in a heterozygote.
Breeding between individuals of different species or genetically distinct individuals such as varieties of the same species.
gene redundancy
Presence of more than one gene that can be expressed to carry out the same function.

Heterosis or hybrid vigour happens because of the accumulation of favourable dominant genes. Hybridisation is the process by which plants cross-breed within the same species or different species. In addition, in a tetraploid genome, gene redundancy allows duplicated genes to be used for other functions, producing advantageous phenotypes.

The long staple length of fibres in the hirsutum and barbadense varieties results from the tetraploid genome. These long staple lengths produce spinnable fibres, which was a major driver for the domestication of these two species. Disadvantages to having a polyploid genome include high pest susceptibility, as seen in cotton.

A flowchart showing how domesticated Gossypium hirsutum with long fibre length developed from ancestral cotton species with shorter fibre length. The domesticated species acquired a tetraploid genome via duplication along the way.

Figure C2.8 Fibre phenotypes of domesticated allotetraploid cotton (G. hirsutum L. acc. TM-1), wild cotton (G. hirsutum L. acc. yucatanense), and their two closest extant progenitors, G. herbaceum and G. raimondii (scale bar, 10 mm). Note the difference in fibre length between herbaceum and the domesticated tetraploid species (AADD).

Adapted from Zhang, T et al., ‘Sequencing of Allotetraploid Cotton (Gossypium Hirsutum L. Acc. TM-1) Provides a Resource for Fiber Improvement’, Nature Biotechnology 33, no. 5 (2015): 531–537, doi: 10.1038/nbt.3207, CC-BY-NC-SA 4.0.

Crop hybridisation takes advantage of heterosis or hybrid vigour. All domesticated varieties of plants and animals result from hybridisation carried out by farmers and livestock owners for thousands of years. More recently, scientific production of plant and animal hybrids has led to tremendous gains in agriculture and livestock farming in terms of yield, disease resistance and other factors.

In plants the procedure for hybridisation is still the same as Gregor Mendel’s famous studies of pea plant crosses. Conventional hybridisation is the method largely used for producing hybrid cotton seeds.

Agricultural scientists in India and elsewhere explored cotton hybrid production in order to increase yield and fibre quality. The first cotton hybrids in the world were produced in India from the late 1950s. We will look at how Hybrid-4, a well known cotton hybrid, was produced.

Producing cotton Hybrid-4

The original research on producing hybrid cotton was carried out by Prof. C. T. Patel at Gujarat Agricultural University.7 Professor Patel produced three different cotton hybrids, of which Hybrid-4 was a line that was commercialised successfully.

Patel crossed two hirsutum varieties. For the female parent he chose a long-staple Indo-American variety called Gujarat 67. For the male parent he chose an exotic hirsutum variety called American Nectariless. The male parent lacked nectaries, the glands that produce nectar for attracting insects for aiding pollination.

Prof. Patel’s procedure was as follows:

  1. The plants were grown in separate plots of female and male parents in the proportion of 5 : 1. The sowing time was adjusted so that flower production of both parents was synchronised.
  2. Prof. Patel emasculated flowers on each female parent plant using Doak’s method.8 In this method, field workers remove the bracts (see Figure C2.4a) by hand. Then, using their thumbnails, they remove the petals along with entire anther sacs. They are careful not to damage the stigma, style or ovary. The emasculation is done in the morning before anther sacs burst. Field workers cover emasculated flowers with a red bag to prevent fertilisation from unwanted pollen, and also for easy identification (see Figure C2.9b).
  3. Field workers collect flower buds from male plants before they open and remove the bracts and petals. They keep the bud in the sun, allowing the anther sacs to burst open.
  4. Field workers pollinate between four and five emasculated female flowers with each male flower. The stigma produces a sticky substance that signals its receptivity for pollination (usually between 09:00 and 11:00 in the morning). After cross-pollination, field workers cover the female flowers with a white bag to prevent cross-contamination.
  5. They make sure that no open flowers remain on the female plant after crossing as this hinders the development of crossed bolls. Similarly, all male flowers are plucked post pollination in order to prevent contamination by natural outcrossing.
grow out test
A test of genetic purity in which a large number of plants are grown from hybrid seeds to evaluate whether desirable traits in the hybrid are reproducibly inherited.

Prof. Patel and his group found that 40% to 50% of their attempted crosses were successful. Seeds were certified by testing for germination and a grow out test to check for genetic purity.

Hybrid-4 expressed a high degree of heterosis, as seen by its high productivity (yield). It had extraordinary bearing capacity, bigger boll size, and profuse and continuous flushes (flowering) that overlapped with each other. Importantly, yields were 216% higher than a parent line under optimised conditions.

Black-and-white photograph of a pot containing a cotton plant with many cotton bolls. The cotton plant is the first successful cotton hybrid produced in India.

Figure C2.9a Hybrid-4, produced by Gujarat 67 (female) × American Nectariless (male).

Patel, CT, ‘Evolution of Hybrid-4 Cotton’, Current Science 50, no. 8 (1981): 343–346.

An illustration of Doak’s method for producing cotton hybrid plants.

Figure C2.9b Doak’s method of hybridisation.

Subsequent to the development of Hybrid-4, many other cotton hybrids were developed by different agricultural universities in India. The excellent performance of the hybrids led to large increases in yield in the years following the green revolution (discussed in the next section).

Critical thinking Reading and interpreting

Natural hybridisation occurs across many plant families. How do plants maintain species purity?

Think about reproductive isolation barriers and how they might be used to maintain species purity. Also consider whether hybrids can be fertile or sterile.


This section discussed the process of hybridisation with special focus on the first cotton hybrid. We saw how the hybridisation programme, based on Mendel’s research, resulted in a more productive cotton crop. This experiment is an excellent example of the scientific enterprise. One set of results builds on previous work, which is sometimes a century and thousands of miles away! Cotton hybrids in India subsequently used the success of the Hybrid-4 for the production of many other hybrids.

Exercise C2.2 Hybridisation of cotton

Reading and interpreting Scientific process

  1. Divide your class or study circle into groups and draw a flow diagram showing the steps Patel followed when he produced Hybrid-4 cotton plants.
  2. What are the advantages of hybridisation in crop plants? Might there be disadvantages, too? Randomly divide the groups into pro-hybridisation and anti-hybridisation groups. How will you convince other groups of the advantages or disadvantages of hybridisation in crop plants? What types of information sources will you rely on to construct your argument?
  3. Summarise the advantages of Hybrid-4 in cotton production.

Check your answer

C2.5 Genetic improvements in cotton: producing Bt cotton

Scientific process Reading and interpreting

As seen in the previous section, a cotton hybrid was first produced in India. With the advent of the green revolution in the late 1960s to early 1970s, the use of fertilisers and pesticides for increasing yields became common practice in agriculture.

molecular cloning
A procedure used to replicate recombinant DNA within a host. See also: recombinant DNA and vector (biotechnology).

Chemically intensive agriculture spread to cash crops like cotton. By the 1980s, pesticide resistance was increasing worldwide to a wide range of pests, with cotton pests proving to be particularly resistant. Scientists turned to the emerging technology of molecular cloning to produce a better plant with improved pest resistance. In this section we will go into the development of Bt cotton in depth.

Introduction to recombinant DNA: processes of science

animal cell culture
Animal cells grown in controlled, artificial environments.

Recombinant DNA technology began in Paul Berg’s laboratory at Stanford University. Berg had worked in Rennato Dulbecco’s lab, which had pioneered techniques of animal cell culture.

vector (biotechnology)
A DNA molecule, like a plasmid, used to carry foreign genes into a cell so that they can be expressed in that cell. See also: host.

The Dulbecco lab had shown that viruses could induce cancerous states in cells they infect by integrating themselves into the host genome, causing it to make more copies of the virus. Drawing on this, Dr Berg wondered whether the virus SV40 could be used as a vector to carry foreign DNA into mammalian cells.

Berg and co-workers carried out a historic experiment in gene splicing in 1971. In the experiment, two different pieces of viral DNA – simian virus 40 (SV40) and the bacterial virus, lambda (λ) – were mixed and joined together to form modified SV40. Dr Berg’s idea was to infect bacteria with modified SV40. The infected bacteria would reproduce, amplifying the modified SV40.9

The experiment hinged on three enzymes that had been previously discovered:

Enzymes that cut DNA.
restriction enzymes/restriction endonucleases
Enzymes that cleave the DNA strands at specific recognition or restriction sites.
DNA ligase
An enzyme essential for DNA replication that attaches DNA fragments together and facilitates the formation of the phosphodiester bond in the backbone of the DNA strand.
terminal transferase
A type of DNA polymerase that facilitates attachment of nucleotides to the 3’ end of a DNA strand.

The experiment scheme is shown below in Figure C2.10.

sucrose gradient column
A column consisting of layers of sucrose representing differing densities used to separate small molecules like nucleic acids and proteins.
  1. The endonuclease EcoRI was used to produce breaks in SV40 and bacterial virus λ to make two linear DNA molecules.
  2. Terminal transferase then added deoxynucleotides, namely triphosphate adenine (dATP) or thymine (dTTP), to SV40 to produce a polynucleotide tail at the 3’ end.
  3. The complementary nucleotide (either dATP or dTTP) was added to virus λ to again produce a polynucleotide end.
  4. These DNA molecules were then incubated together with DNA ligase. The enzyme joined DNA fragments due to hydrogen bonding of complementary nucleotide ends.
  5. The recombinant DNA molecule (SV40 + λ) was expected to be longer than the original SV40 molecule, and this was confirmed on a sucrose gradient column.
A drawing showing the steps involved in producing recombinant DNA.

Figure C2.10 Schematic of method for recombinant DNA production.

Jackson, DA, Symons, RH, and Berg, P, ‘Biochemical Method for Inserting New Genetic Information into DNA of Simian Virus 40: Circular SV40 DNA Molecules Containing Lambda Phage Genes and the Galactose Operon of Escherichia Coli’, Proceedings of the National Academy of Sciences 69, no. 10 (1972): 2904–2909, doi: 10.1073/pnas.69.10.2904.

Hear about making the first recombinant DNA molecule from Berg himself, in this video.

Berg’s technique produced a recombinant DNA molecule and showed it could be taken up by bacteria. This process is called transformation.

To familiarise yourself with some of the terms used in this section please take a look at the primer on molecular biology.

Boyer and Cohen (1973) extended Berg’s procedure in a second landmark experiment. Dr Boyer’s lab had originally supplied Paul Berg with the restriction enzyme EcoRI to do the recombinant DNA experiment.10

Boyer and Cohen recognised that EcoRI produced DNA breaks only at a specific sites. They extended Berg’s experiment by recombining genes from two different bacterial strains into one DNA molecule and using it to transform a bacterium. Because they knew that the restriction enzyme made cuts in the DNA at specific sites, they did not need to add complementary nucleotides as Berg had done in his experiment. As shown in Figure C2.11, they essentially ‘cut’ plasmid DNA with EcoRI and ‘pasted’ different bits together with DNA ligase. They then inserted this recombined DNA molecule into E. coli bacteria, allowing it to express the recombined DNA.

Boyer and Cohen’s work benefited from two recent developments in molecular biology:

A flowchart with drawings showing the steps involved in production of recombinant bacteria.

Figure C2.11 Schematic representation of recombinant bacteria production

Single-celled or multicellular organism whose cell contains a distinct nucleus surrounded by a membrane.

A year later, Cohen’s lab combined a plasmid pSC101 along with DNA from the African clawed toad Xenopus laevis to produce a plasmid containing eukaryotic DNA.11 Previously, they had shown that bacteria could replicate a recombinant plasmid. Cohen’s experiments showed that recombinant technology was feasible across biological domains. Many labs from around the world immediately began to work on this technology.

You should take away two main points about the processes of science from this section:

  1. All of our scientific knowledge is essentially produced as a result of teamwork. This team stretches across humanity and time.
  2. It is important to make connections across disciplines. Discovering that viruses could lead to cancer (a bad outcome for human health), actually led to a whole new field: biotechnology.

Critical thinking Scientific process

Multiple outcomes are possible for Boyer and Cohen’s experiment with cutting and pasting DNA. Can you think of some?

Think of ways for the experiment not to work.

Recombinant DNA technology in plants

The Cohen and Boyer experiment led to the birth of the biotech industry, as it showed a robust method to produce recombinant DNA. Plant scientists recognised the potential of using this technology to confer pest resistance on plants. They began to explore ways to introduce these pest resistence genes into economically important plants.

An important early report on the introduction and expression of foreign genes in plants, that also led to the development of Bt cotton, is the paper ‘A Simple and General Method for Transferring Genes into Plants’.12

This paper described a plasmid and vector system for transforming tomato, petunia and tobacco plants in order to confer antibiotic resistance to them. The scientists chose to introduce antibiotic resistance genes into these plants as proof-of-concept. The paper also showed that these changes were heritable. In this experiment, a soil bacterium called Agrobacterium tumefaciens was the vector used to deliver foreign genes into the target plants.

Agrobacterium tumefaciens is a bacterium species that causes crown gall disease in a wide variety of plants. It can insert a T-DNA (transfer DNA, a short segment of DNA) from the Ti plasmid into the plant host. The T-DNA can then become incorporated into the host genome.

The Ti plasmid is a versatile system that contains a variety of genes both for virulence and for metabolic activity of the bacterium. It is a large plasmid of 200 kilobases (kb) and about 200 genes. Table C2.1 summarises the gene regions found in the Ti plasmid and their functions.

A region of DNA that precedes a DNA sequence that is going to be expressed. Specific proteins bind to the promoter to initiate transcription of the sequence.
A diagram of a plasmid shown as a circle, with various important genomic regions marked on it, including the origin of replication, virulence region and border regions.

Figure C2.12 Schematic of Ti plasmid. Typically a 35S cauliflower mosaic virus promoter is used in front of the gene of interest, as it is a strong promoter.

A plant hormone that is primarily responsible for root and shoot growth through cell elongation, but has other functions too.
A plant hormone that regulates cell division, among other functions.
Ti region Function
T-DNA region Genes for auxin (aux) and cytokinin (cyt) and opine synthesis (ocs). Auxin and cytokinin are plant hormones.
Virulence region Genes responsible for excision, transfer and integration of T-DNA into the plant genome.
Opine catabolism region Genes responsible for catabolism of opines, a class of amino acids that serve as a source of nitrogen and carbon for the bacterium.

Table C2.1 Regions and functions of the Ti plasmid.

origin of transfer
A region of DNA that is transferred along with the DNA sequence when DNA from one host is introduced into another, as is done during molecular cloning.

Apart from these three main regions, the plasmid also contains an origin of transfer (oriT). The T-DNA region uses the phytohormones auxin and cytokinin to induce uncontrolled cell division in the host plant cell. The right border sequence is important for inducing virulence.

Recombinant DNA experiments modify the Ti plasmid by deleting the T-DNA region. This ensures that the bacterium cannot induce uncontrolled growth due to hormone production in the host. The virulence region is maintained so that integration into the host is achieved. The gene of interest (GOI) is inserted between the right and left border sequences of the T-DNA region. This creates a new Ti plasmid that is capable of entering and integrating with the host genome but is avirulent, thus allowing for transfer of DNA between organisms.

In a natural environment, A. tumefaciens enters the host plant at a wound site. (We normally see gall tumours on leaves or trunks.) For producing an engineered plant, A. tumefaciens is grown in the lab on petri dishes. A plant part which can be a leaf, root or stem, depending on the plant, is kept in contact with the bacterial plate for up to 24 hours. It is then transferred to a new plate that contains an antibiotic that acts as a selectant.

A mass of undifferentiated plant cells whose growth can be artificially induced in the lab.

Only plants that have taken up the Ti plasmid containing the antibiotic resistance gene are able to grow on this plate. Then these calluses (developing plant embryos) are transferred to media that induce shoot and root growth, leading to the development of an engineered plant.

A drawing showing how the Agrobacterium tumefaciens can enter a host plant at wound sites and use the Ti plasmid to propagate itself.

Figure C2.13 Schematic of Agrobacterium tumefaciens inoculation and engineered plant growth.

Critical thinking Scientific process Scientific tools

How will you get rid of unwanted genes in a plasmid?

Think about how mutations arise (and get removed) from bacteria.

Recombinant DNA technology has evolved for many applications, from medicine to agriculture to biofuel production. The fact that all living things share the same language – the sequence of nucleic acids – to store information means that practically any gene can be taken from one organism and transferred to another. While this should invoke a sense of wonder in how interconnected all life is, it should also serve as a warning to us about how easy it is to modify living things and their traits. Think about why this last point is important.

Development of Bt cotton

Over 150 insect species attack cotton plants. These insects can attack different parts of the plant, at different growth stages. The cotton bollworm complex is particularly harmful to the crop as the pests bore into the cotton boll, ruining the most economically valuable part of the plant.

The only way to control this pest is through several rounds of pesticide application. This is not financially viable for farmers, especially in India with its small land holdings. Pesticides also lead to tremendous ecological damage by persisting in the environment for many years.

Recombinant DNA technology and pest resistance in cotton

Genetically engineered cotton, resistant to bollworm attack, has great potential in insect control since it does away with the problems accompanying pesticides. In this section we will discover how Bacillus thuringiensis (Bt), a gram-positive bacterium, was exploited using recombinant DNA technology to create pest resistant cotton.

Bt is largely soil dwelling, but also grows on leaf surfaces and has been found in flour dust. It is found almost everywhere in the world and there are several hundred Bt strains. The bacterium causes disease or death in various insect species and it began to be used as a pesticide as early as the 1930s. Bt was particularly effective against the destructive larval stage of pest insects.

An insecticidal toxin produced by B. thuringiensis and expressed in Bt cotton.

Scientists have discovered many strains of Bt, capable of producing over 700 different toxins. Bacterial spores produce crystal proteins that contain the toxin (δ-endotoxin) (see Figure C2.14). Scientists identified the genes for producing these crystal proteins and found that they occur on plasmids. Their function was therefore related to bacterial resistance and survival.

Industrial agriculture from the 1950s onwards led to increasing amounts of fertilisers and pesticides being used in food production. By the 1980s, pesticide resistance was a known phenomenon and Bt sprays gained popularity. Bt was seen to be an ‘organic’ method for controlling pests.

A pesticide is used against all pests such as fungus, bacteria and insects. An insecticide is specifically used against insects. Based on the study we cite, we have used the word chosen by the authors.

Timeline of discoveries related to Bacillus thuringiensis.

Figure C2.14 Timeline of discoveries related to Bacillus thuringiensis.

Critical thinking Scientific process

Why would a soil bacterium produce toxins harmful to insects?

Think about the life cycle of the bacterium and environmental stability.

A diagram showing the shape of the Bacillus thuringiensis cells and the spores inside the cells.

Figure C2.15 Cells of Bt containing Bt spores and crystals

Cry toxins and insecticidal action

The lifecycle of Bt has two phases: vegetative cell development/growth and spore development. The vegetative cell is rod shaped (1–2 μm length, 0.5 μm width) and divides into two symmetric daughter cells, as is typical of bacterial cell division.

Spore development occurs when vegetative cells form spores during unfavourable environmental conditions (such as desiccation or high heat). It involves asymmetric cell division and has a complex cycle with different stages. The spore is a dormant stage in the life cycle of the organism.

When Bt spores start developing, the bacterium synthesises crystal proteins as inclusions (see Figure C2.15). Crystal proteins can constitute up to 50% of the cell’s dry weight. We do not completely understand why Bt strains produce these crystals during spore formation.

cry genes
A family of genes in Bacillus thuringiensis that produce cry proteins which act against specific insect taxa.
cry proteins
Proteins produced by the cry genes from Bacillus thuringiensis that form toxins that result in the death of the target insect.

While many Bt crystal proteins have insecticidal action, others have no effect on insects. Scientists have identified around 500 cry genes that encode information to make crystal proteins. The Cry proteins produced by cry genes target specific insects.

Insects normally ingest bacterial spores containing a large amount of Cry protein when feeding on leaves or other plant parts. Digestion and breakdown of Cry proteins in the high pH environment of the insect gut releases the Cry protoxin.

The Cry protoxin, which is a precursor of the Cry protein, binds to specific receptors on the cell membrane of the insect gut. The Cry protoxin is then inserted into the cell membrane and subsequently, pores form. The pores allow bacterial spores to enter the insect digestive tract and multiply. Bacteria in the insect gut eventually kill the larva. The whole process takes between one and two days, during which time the larva stops feeding.

a. Image of a large bollworm larva on a normal cotton boll. b. Photograph of a small bollworm larva grown on cotton bolls with Bt proteins.

Figure C2.16 Effect of Bt crystal proteins on cotton pests.

Peggy Greb, USDA Agricultural Research Service, public domain.

Effect of normal diet
: Image of a large bollworm larva on a normal cotton boll.

Effect of normal diet

Cotton bollworm 12-day old larva raised on a control diet. The larva is large and healthy.

Effect of Bt diet
: Photograph of a small bollworm larva grown on cotton bolls with Bt proteins.

Effect of Bt diet

Cotton bollworm 12-day old larva raised on a diet containing Bt proteins. The size of the worm is significantly reduced compared to the control worm.

Cry toxins have several features that make them advantageous as insecticides for agriculture:

Critical thinking Scientific process Reading and interpreting

The pH of the human gut is 2, while that of the insect gut is 10. How do you think these two different environments will affect the action of the Cry proteins?

How does the chemical environment affect protein shape and function?

Development of transgenic cotton

The advantages of Cry proteins led to great interest in their use for pest resistance, and especially for the use of Bt toxins in developing transgenic plants. Bt protein cry1Aa was successfully cloned and expressed in E. coli in 1981. The protein retained its insecticidal activity. A truncated version of the protein was also expressed in E. coli and also retained its insecticidal activity.

in planta
Within the plant, instead of using tissue cultures.

Initially, Bt proteins were poorly expressed in plants and the plants did not have significant insect resistance. Scientists solved this problem by making a synthetic Bt gene that was truncated by deleting a sequence of DNA. Protein expression increased and in planta synthetic gene expression was first reported in cotton. Synthetic Bt genes gave greater insect protection to transgenic plants than to control plants.

After several years of testing, Monsanto, an agrochemicals company, decided to develop transgenic Bollgard cotton varieties. This cotton line (Bollgard I) was transformed with a vector containing a synthetic Cry1Ac-like Bt coding sequence. Bollgard II cotton, a second-generation product, contains two cry genes that express Cry1Ac and CryIIAb proteins. The dual gene cultivars were expected to provide broader control over a wide variety of insects.

More recently, several new cotton varieties have been introduced that have three Cry proteins in them, using a technology called gene stacking.


While journeying through the story of recombinant DNA technology, we learned about how science is actually an endeavour that connects all of us. Scientists build on each other’s experiments, across space and time. We then learned about seminal work that eventually led to the establishment of a new field of biology: biotechnology. This led to the development of Bt cotton, a pest resistant crop that could help farmers increase their yield while lowering their insecticide. Next we will try to evaluate this new technology by assessing its long-term impact.

Exercise C2.3 Understanding Berg’s experiment

Scientific process

  1. What was the impetus for Paul Berg’s experiment?
  2. Berg and Cohen used plasmids from two different E. coli strains for their experiment. One plasmid carried the gene to confer resistance to the antibiotic kanamycin, and the other plasmid carried the gene conferring resistance to tetracycline. What do you think they did to check if their recombinant strategy worked?
  3. Make a flowchart to show the process of how Bt toxins infect cells.

Check your answer

C2.6 Impact of Bt cotton in India

Bridging science, society and the environment

Belonging to or being owned by an entity.

In the previous section, you learned about the molecular basis for Bt cotton pest resistance. Bt cotton was officially introduced in central and southern India in 2002, and in northern India in 2005. By 2011, 93% of cotton cultivated in India was Bt cotton. The Bt gene is proprietary to Monsanto, a multinational company that operates in India through its local subsidiary, Mahyco Monsanto Biotech (MMB). Since Monsanto owns the intellectual property describing the gene, the company receives royalties for every seed containing the gene that is sold.

How do we assess a technology?

Opinions on the success of Bt cotton lie between two extremes. At one extreme, farmers are thought to have achieved moderate to high increases in yield, accompanied by economic stability. At the other extreme, it is thought that Bt cotton has directly or indirectly led to several farmer suicides due to the increased capital investment required and decreasing farmer profit. However, these impacts, positive and negative, are strongly debated.13 14 15

The opposing narratives are illustrated in Figure C2.17. As you can see, each narrative stems from different origins and concerns. This immediately raises larger questions about sources of knowledge, how we collect evidence, its social context, authenticity and interpretation.

A flowchart that shows how different actors such as NGOs/environmental activists and industry–supported commentators and applied economists look at the issue of Bt cotton. The non-governmental organisations and civil society view it as a failure while the industry and economists see it as a triumph of science and technology.

Figure C2.17 Two branches of narratives on the success of Bt cotton. How does one decide which narrative to believe when each has its own inherent bias?

Figure C2.17 presents claims for and against Bt cotton. To evaluate the claims, we need to study data and reach our own conclusions. Figure C2.18 shows a graph of cotton yields in million tonnes between 1950 and 2010. Also plotted is the percentage area under Bt cotton cultivation from 2003 to 2010 (so this graph has two y-axes). We see that a rise in the percentage of Bt cotton area coincides strongly with a rise in cotton yield.

Critical thinking Quantitative skills

What conclusion would you draw from Figure C2.18 regarding the success of Bt cotton in increasing yield?

Bear in mind that cause and correlation are two different relationships.

At first glance, one might conclude that an increase in Bt cotton area caused (or at least is strongly correlated with) a strong increase in cotton yield. How can we verify this hypothesis?

A graph that shows the annual cotton production and Bt cotton areas from 1950 to 2010. Both graphs rise steeply after 2002.

Figure C2.18 Production area for Bt cotton and cotton production from 1952 to 2010. Note that the figure has two y-axes.

Adapted from Kranthi, KR and Stone, GD, ‘Long-Term Impacts of Bt Cotton in India’, Nature Plants 6, no. 3 (2020): 188–196, doi: 10.1038/s41477-020-0615-5.

Investigating the relationship between Bt cotton area and cotton production

Figure C2.18 clearly shows a strong increase in the area under Bt cotton and cotton production after 2002. Here, we will evaluate the relationship between area under Bt cotton and cotton production through systematic critique. Each observation raises follow-up questions which explore possible bias in the data.

Potential critique Follow up question Bias
Are all farmers who adopted Bt cotton equivalent in wealth, land area, level of education, or any other socioeconomic measure? Are all treatments of Bt cotton vs. non Bt cotton equivalent? Selection bias
How did the yield on the same plots differ before Bt cotton adoption and immediately after? Did farmers plant Bt cotton seeds (which are more expensive and from which higher yields were thought possible) on the same plots or did they select their ‘best plots’ (the plots that were most fertile for example). Cultivation bias
The plot shows a strong increase in yield up to 2010 after the 2002 introduction of Bt cotton. How has the yield changed since 2010? If long-term yields have changed is it because of Bt or other practices (e.g. use of pesticides or fertilisers)? Time-term bias

Table C2.2 Investigating biases.

Adapted from Kranthi, KR, and Stone, GD. ‘Long-Term Impacts of Bt Cotton in India’, Nature Plants 6, no. 3 (2020): 188–196, doi: 10.1038/s41477-020-0615-5.

Each of the questions in Table C2.2 reveals potential biases that Figure C2.18 obscures. Therefore, Figure C2.18 cannot directly address our hypothesis. Furthermore, Figure C2.18 does not reveal whether there is any variation across the country. Since the cultivation methods, climate and soil conditions vary considerably across India, the impact of the environment on yield is also relevant.

We now turn to a study on the long-term impacts of Bt cotton in India. The researchers have systematically addressed the biases mentioned in Table C2.2 to reach a verifiable conclusion.

Has Bt cotton increased yield or not?

longitudinal data
Data taken from a single sample or site that is studied over time.

Kranthi and Stone used longitudinal data over 20 years (3 years preceding the introduction of Bt cotton, and 17 subsequent years) of cotton yield.6 They recognised that within India, government regulations, climate, farming practices and other environmental conditions may vary. Therefore, rather than pooling data from all states that grow Bt cotton, they conducted a comparative study across different states.

Exercise C2.4 Quantitative reasoning to understand effects of individual versus pooled data

Scientific process Quantitative skills

Look at the table showing figures for cotton production for three states and for all of India for the years 2017 to 2018. The data shown is for two states that are among the biggest cotton producers (Gujarat and Maharashtra) and for one minor producer (Punjab).16

State Cotton area (lakh hectares) Cotton yield (lakh bales) Cotton productivity (kg/hectare)
Punjab 2.91 11.5 671
Gujarat 26.23 104 674
Maharashtra 42.07 85 343
All India 124.44 370 505.46
  1. What percentage do Gujarat and Maharashtra contribute to the All India cotton area under cultivation?
  2. Compare Gujarat and Maharashtra’s yields. How much greater is Gujarat’s yield than Maharashtra’s?
  3. What percentage is Maharashtra’s productivity compared to Gujarat’s? Why might Maharashtra have such low productivity?
    1. Calculate Punjab’s area under cotton cultivation as percentage of the All India total.
    2. Calculate Punjab’s percentage of the total yield.
    3. Speculate on why Punjab’s cotton productivity is among the highest among all states.

Check your answer

Examining state-wise data allows us to determine the differences between different cotton-growing regions and think about what could be contributing factors to these differences. It follows that response to new technologies (for example, hybrids and fertilisers) will also differ across these regions.

Figure C2.19 uses two y-axes to present two sets of data as a function of time. The figure documents the yield (black lines), and the percentage of cotton farmland that had adopted Bt cotton across several cotton-growing states. Using two y-axes on the same graph allows the authors to superimpose two sets of data to see if there is any relationship between yield and percentage of Bt cotton area.

Critical thinking Quantitative skills

Study the data in Figure C2.19 and compare the data between states. Do you see any trends? Is it as clear as the trend we saw in Figure C2.18?

  • Is there an increase in cotton area in all the states? Is there an increase in yield in all the states?
  • If there is an increase in either cotton area or yield, is the increase gradual or does it increase quickly and steeply after the introduction of Bt cotton?
  • If there is an increasing trend in both variables, did the trend coincide with the introduction of Bt cotton in 2002?
a. Graph showing cotton yields and % area under Bt cotton cultivation for the time period 2000 to 2018 for Gujarat. b. Graph showing cotton yields and % area under Bt cotton cultivation for the time period 2000 to 2018 for Punjab c. Graph showing cotton yields and % area under Bt cotton cultivation for the time period 2000 to 2018 for Andhra Pradesh and Telangana.

Figure C2.19 Cotton yield in kg/hectare and area under Bt cotton cultivation between 2000 and 2018 in three states: a. Gujarat. b. Punjab. c. Andhra Pradesh and Telangana.

Adapted from Kranthi, KR and Stone, GD, ‘Long-Term Impacts of Bt Cotton in India’, Nature Plants 6, no. 3 (2020): 188–196, doi: 10.1038/s41477-020-0615-5.

: Graph showing cotton yields and % area under Bt cotton cultivation for the time period 2000 to 2018 for Gujarat.


Figure C2.19a

: Graph showing cotton yields and % area under Bt cotton cultivation for the time period 2000 to 2018 for Punjab.


Figure C2.19b

Andhra Pradesh and Telangana
: Graph showing cotton yields and % area under Bt cotton cultivation for the time period 2000 to 2018 for Andhra Pradesh and Telangana.

Andhra Pradesh and Telangana

Figure C2.19c

Pattern observed in descriptive, numerical or graphical data.

The data shown in Figure C2.19 do not show the same ‘clean’ trend that is observed in Figure C2.18. Can we conclude that Bt cotton has not impacted yield at all? Can we conclude that Bt cotton has negatively impacted yield?

The answer to both these questions is no! (Note: we can conclusively say that after 2006, almost 100% of the cotton-producing land in the three states was under Bt cotton cultivation.)

The only tentative conclusion we can draw is that other factors may also be influencing the yield of cotton. Such factors could include fertiliser use, pesticide use, increase in acreage of cotton plantations, or changes in technology, to name a few.

Kranthi and Stone also considered the changing nature of pest resistance and insecticide spraying as well as the changing dynamics of fertiliser use and technological advances in irrigation. These farming practices could significantly impact yield and farmer investment.

Indeed, Kranthi and Stone point out a few important facts that emerge from this data:

A graph showing pesticide expenditure for spraying for lepidopterans and sucking pests of cotton plants from 1999 to 2018. Expenditure for lepidopteran pesticides decreased up to 2012, then increased after pesticide resistance emerged. Expenditure on spraying for sucking pests has increased consistently since 2006.

Figure C2.20 Annual pesticide expenditure in US dollars per hectare for lepidopterans and sucking pests, 1999 to 2018.

Adapted from Kranthi, KR and Stone, GD, ‘Long-Term Impacts of Bt Cotton in India’, Nature Plants 6, no. 3 (2020): 188–196, doi: 10.1038/s41477-020-0615-5.

a. Graph showing fertiliser use and Bt cotton yield for Gujarat for the years 1999 to 2015. The line for fertiliser use tracks the line for Bt cotton yield in all states. b. Graph showing fertiliser use and Bt cotton yield for Punjab for the years 1999 to 2015. The line for fertiliser use tracks the line for Bt cotton yield in all states. c. Graph showing fertiliser use and Bt cotton yield for Andhra Pradesh/Telangana for the years 1999 to 2015. The line for fertiliser use tracks the line for Bt cotton yield in all states.

Figure C2.21 State-wide fertiliser use and Bt cotton yields between 2000 and 2015. a. Gujarat. b. Punjab c. Andhra Pradesh and Telangana.

Adapted from Kranthi, KR and Stone, GD, ‘Long-Term Impacts of Bt Cotton in India’, Nature Plants 6, no. 3 (2020): 188–196, doi: 10.1038/s41477-020-0615-5.

: Graph showing fertiliser use and Bt cotton yield for Gujarat for the years 1999 to 2015. The line for fertiliser use tracks the line for Bt cotton yield in all states.


Figure C2.21a

: Graph showing fertiliser use and Bt cotton yield for Punjab for the years 1999 to 2015. The line for fertiliser use tracks the line for Bt cotton yield in all states.


Figure C2.21b

Andhra Pradesh and Telangana
: Graph showing fertiliser use and Bt cotton yield for Andhra Pradesh and Telangana for the years 1999 to 2015. The line for fertiliser use tracks the line for Bt cotton yield in all states.

Andhra Pradesh and Telangana

Figure C2.21c

These figures show that something else is going on apart from pest resistance that contributes to improved yield. Kranthi and Stone conclude that increased fertiliser use and irrigation has had a greater impact on improving cotton yields than Bt cotton.

Increased use of Bt seeds increased predation by non-lepidopteran pests. This, combined with rapidly spreading Bt resistance in the pink bollworm, led to increased expenditure on pesticides than before Bt seed adoption. Therefore, it seems that Bt cotton has made cotton farming capital intensive rather than providing any agronomic benefit.

study design
The methodology used to obtain and analyse data.

Many studies preceding Kranthi and Stone’s research had found that Bt cotton had benefited the economy and small-scale farmers.17 Each study uses (1) data derived from different sources, (2) collected over different periods of time, and (3) with varying study designs (that is, the different types of trials and experiments involving combinations of variables). These three factors can dramatically influence the conclusion of the study. Therefore, researchers need to carefully consider possible biases in order to reach an objective conclusion. Take a moment to revisit Table C2.2 on possible biases while designing studies.

Bt cotton is not the only Bt product in India. Other crops include Bt brinjal on which active trials are ongoing. If you had to design agricultural policies relating to the regulation of Bt cotton and other Bt products in the country, what action would you take? What factors would you take into account? We will leave this as an open question for you to think about, and independently form your opinion.

The point of changing pest resistance from lepidopteran to non-lepidopteran and the rise in pink bollworm resistance also highlights the fact that insect populations can adapt to changing conditions extremely rapidly, and there can be a switch in the pest population distributions. Changing this distribution may in turn influence organisms that predate on those pests and thus may lead to cumulative effects. Indeed, altering one component of any ecosystem can have long-term consequences over large spatial scales.

There may never be a final answer to the question of Bt cotton’s usefulness. A variety of factors influence Bt cotton yield, profit, and consequent environmental impact. These factors are dynamic, for example pest resistance may emerge, market demands may change, or technology may advance. It is difficult to come to a permanent conclusion about the usefulness of Bt cotton. Our answer may change as time passes and leads us to be cautious in our claims when adopting new technology.


In this section we learned how to evaluate a new technology and ask questions regarding its advantages and disadvantages. We saw, using the example of a recently published study, that we need to consider several aspects when evaluating the use of Bt cotton. We need to be very careful about off-target impacts in assessing a new technology.

Some impacts can be non-biological, such as farmers rapidly and illegally adopting Bt seeds for cultivation. Since no safety measures were taken while planting, this led to contamination of non-Bt plants with Bt genes via cross-fertilisation.

Another effect was that hybrid Bt seeds needed large inputs of fertiliser and pesticides for good yields. Such effects were not considered when the technology was approved. This means that the scientific validity of new technology is only one aspect to be considered when certifying it for public use.

C2.7 Quiz

Question C2.1 Choose the correct answer(s)

Cotton belongs to the _____ family whose flowers show the following characteristics:

  • Asteraceae: solitary, showy, coloured
  • Malvaceae: large, axillary, solitary, showy, coloured
  • Liliaceae: inflorescence, six-segmented flowers
  • Poaceae: inflorescence, wind pollinated
  • Asteraceae are characterised by composite flowers. Cotton has simple flowers.
  • Cotton has large, solitary, showy flowers. It belongs to the family Malvaceae.
  • Liliaceae have an inflorescence with flower parts in multiples of three. Cotton has solitary flowers with flower parts in multiples of five.
  • Poaceae have an inflorescence and are wind–pollinated. Cotton has a simple flower that is insect–pollinated.

Question C2.2 Choose the correct answer(s)

Gossypium hirsutum, the dominant cotton species grown worldwide, has an allotetraploid genome. This means that the plant has:

  • two copies of each gene
  • a duplicated genome
  • four copies of each gene
  • extra alleles of each gene
  • This is the normal condition for a diploid organism (2n).
  • In some sense it has a double duplicated genome since there are four copies of each gene.
  • This is partially true for tetraploid hybrids. There are 26 A chromosomes and 26 D chromosomes, each coming from the hybridisation event between the two Gossypium species.
  • Although technically true, it is possible that all alleles have a function.

Question C2.3 Choose the correct answer(s)

Bar graph comparing cotton yield in kilogram per hectare. Cotton yield in Maharashtra and All India was 332 and 525 respectively in 2012–13, 341 and 566 respectively in 2013–14, 316 and 504 respectively in 2014–15, 396 and 541 respectively in 2016–17, 344 and 524 respectively in 2017–18.

Cotton yield in Maharashtra and All India from 2012 to 2018.

The bar graph shows cotton yield in kg/hectare for Maharashtra and All India over several years. Which of the sentences below describe the data accurately?

  • Cotton yields in Maharashtra increased in 2017–2018 compared with 2012–2013.
  • Bt cotton was responsible for the increase in yields for Maharashtra.
  • All India cotton yields showed no clear trend over the surveyed period.
  • Maharashtra yields are an accurate representation of All India yields.
  • There is an increase of 6% for the years shown.
  • No statements can be made about use of Bt cotton and its contribution to yield.
  • For the time period shown, the yield has fluctuated around an average of 525 kg/hectare.
  • Maharashtra yields are less than the All India figures, so this statement is not true.

Question C2.4 Choose the correct answer(s)

The pink bollworm is extremely harmful to cotton plants because:

  • in the adult stage it feeds voraciously on cotton leaves
  • at the caterpillar stage it attacks the cotton boll and feeds on the seed
  • at the caterpillar stage it feeds on the plant roots
  • the caterpillar is toxic to cotton farmers
  • Helicoverpa armigera (pink bollworm) is a moth in its adult stage which is not harmful to cotton plants.
  • The caterpillar bores into the cotton boll at the first stage in its growth (instar) and feeds on the seeds as it grows, destroying the cotton boll.
  • The caterpillar doesn’t feed on the roots.
  • The insect is not known to be toxic to humans at any stage.

Question C2.5 Choose the correct answer(s)

The Agrobacterium tumefaciens Ti plasmid contains the following regions:

  • T-DNA, Antibiotic resistance gene, Opine catabolism region
  • Virulence region, T-DNA, Antibiotic resistance region
  • T-DNA, Virulence region, Opine catabolism region
  • Antibiotic resistance region, Virulence region, Opine catabolism region
  • The Ti plasmid doesn’t contain an antibiotic resistance gene.
  • The Ti plasmid doesn’t contain an antibiotic resistance region.
  • T-DNA region contains plant hormone genes; Virulence region contains genes responsible for excision, transfer and integration of T-DNA into the plant genome; Opine catabolism region contains genes for catabolism of opines, a class of amino acids that serve as a source of nitrogen and carbon for the bacterium.
  • The T-DNA region is missing in this choice.

Question C2.6 Choose the correct answer(s)

If you want to introduce a new gene in a plant, inoculation with the Ti plasmid should be done in _________.

  • seed
  • callus
  • germ cells
  • mature plant
  • It will be difficult to introduce the Ti plasmid into a seed, which is a well protected structure.
  • A callus is plant tissue at a very early stage of growth, so inoculating with the Ti plasmid is easy to do under laboratory settings in a controlled fashion.
  • Germ cells participate in fertilisation and are haploid. Their isolation is difficult and they will still need to be fertilised before they develop into a mature plant.
  • You want transformation to appear in every cell of the plant, which will not happen in a mature plant.

Question C2.7 Choose the correct answer(s)

Plants are bagged during artificial hybridisation for the following reason:

  • to prevent self-pollination
  • to prevent cross pollination
  • to prevent contamination with foreign pollen
  • to maintain optimal conditions in the hybridised plan
  • Self pollination could be a problem for bisexual flowers but usually self-pollination doesn’t occur in an open flower.
  • Uncontrolled cross pollination will interfere with artificial hybridisation.
  • Contamination with pollen from unselected flowers is a major problem in artificial hybridisation. Hybridised plants need to be protected so that there is no dilution of the desired traits by foreign pollen landing on the stigma of the female plant.
  • No special conditions need to be maintained post hybridisation.

Question C2.8 Choose the correct answer(s)

You carry out an experiment with SV40 and λ DNA using EcoRI to produce cuts in the two DNA species. You then mix the two DNA species with DNA ligase to produce recombinant DNA. However, you find when you run a gel that λ DNA has not been incorporated into the SV40. Assuming you have followed the protocol, what could have happened to produce such a result?

  • SV40 does not have a restriction site for EcoRI
  • λ DNA does not have a restriction site for EcoRI
  • DNA ligase cannot repair cuts made by EcoRI
  • SV40 can be rejoined by DNA ligase without incorporating λ DNA
  • It is known that SV40 has a restriction site for EcoRI. That was the reason for Paul Berg and co-workers using EcoRI.
  • λ DNA has a restriction site for EcoRI.
  • DNA ligase can repair cuts made by EcoRI.
  • We have to consider the possibility that SV40 can reseal without incorporating the λ DNA. Normally, we prevent this possibility by removing the phosphate group at the cut end.

Question C2.9 Choose the correct answer(s)

Gossypium arboreum and G. herbaceum fibres are not suited to making yarn because:

  • the short staple length is not conducive to being processed in industrial ginning and milling machines
  • the lint quality is poor
  • the diameter of the fibre is not optimal
  • these species are difficult to grow
  • The staple length is the deciding factor for processing cotton fibre into yarn. The long staple length of G. hirsutum is well suited for industrial ginning and spinning machines.
  • The lint quality of both these species is excellent and fetches a premium in the market.
  • The fibre diameter of all species is suitable for making yarn.
  • G. arboreum and G. herbaceum grow naturally over large parts of India.

Question C2.10

The cotton fibre is a kind of ______ that is almost completely made of _______

  • germ cell; lignin
  • trichome; lignin
  • epidermal cell; cellulose
  • sclerenchyma; cellulose
  • Germ cells would typically occur inside the seed.
  • The cotton fibre could be thought of as a kind of trichome, but based on function it is classified as an epidermal cell (rather than a more specialised trichome).
  • Epidermal cells in the seed wall extend to form the fibre. The cell wall synthesises cellulose during the secondary phase of cell wall growth.
  • Sclerenchyma tissue is composed of cellulose and lignin but the cotton fibre isn’t part of this tissue.

C2.8 References

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  11. Morrow, JF, Cohen, SN, Chang, AC, Boyer, HW, Goodman, HM and Helling, RB, ‘Replication and Transcription of Eukaryotic DNA in Escherichia Coli’, Proceedings of the National Academy of Sciences of the United States of America 71, no. 5 (1974): 1743–1747, doi: 10.1073/pnas.71.5.1743. 

  12. Fry, JE, Hoffman, NL, Eichholtz, D, Rogers, SG and Fraley, RT, ‘A Simple and General Method for Transferring Genes into Plants’, Science 227, no. 4691 (1985): 1229–1231, doi: 10.1126/science.227.4691.1229. 

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  14. Gutierrez, AP, Ponti, L, Herren, HR, Baumgärtner, J and Kenmore, PE, ‘Deconstructing Indian Cotton: Weather, Yields, and Suicides’, Environmental Sciences Europe 27, no. 1 (2015), doi: 10.1186/s12302-015-0043-8. 

  15. Shiva, V, ‘Toxic Genes and Toxic Papers: IFPRI Covering up the Link between Bt Cotton and Farmers Suicides’, Research Foundation for Science, Technology and Ecology (20 December 2008). 

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