**7. Mapping populations for genetic dissection of agronomic and fibre quality traits**

Mapping populations, mainly recombinant inbred lines (RILS), have been developed to genetically dissect the agronomic and fibre quality traits in cotton at several Indian institutes including:


The above said mapping populations are considered as valuable resources for identification of molecular markers linked to key fibre quality traits such as fibre length and strength besides drought tolerance and cotton leaf curl virus disease resistance traits. The major constraint that hampers the precise and early identification of tightly linked markers is the availability of informative polymorphic markers (due to narrow genetic diversity exist in the above men‐ tioned parents; see above) which are essential for the construction of high-resolution genetic map. To overcome this difficulty, a co-ordinated effort is being formulated with a grateful financial support from Department of Biotechnology, Government of India to constitute a network project on developing saturated genetic linkage maps of cotton using different mapping populations available in India and single nucleotide polymorphism (SNP) chip developed at National Botanical Research Institute, Lucknow (Dr. Samir Sawant, personal communication). Development of such saturated genetic linkage map will eventually be utilized for quantitative trait loci (QTL) identification of cotton fibre yield and quality traits.

Among the different types of mapping population, development and employment of RILs is being pursued in selected cotton institutes including TNAU to utilize donor cotton breeding materials for genetic analysis of the desirable characters (see below). Selected superior recombinant line shall be used in enhancement of genetic stocks through molecular breeding and development of more productive and eco-friendly new varieties/hybrids tailored to fit into the future and existing cropping systems.

At TNAU, Coimbatore evolution of new cotton varieties with drought tolerance, jassid resistance and improved fibre quality traits is the major breeding objective. In particular, there is a need to develop ideotype suitable for rainfed cultivation since large cotton cultivating area is under drought conditions. Seed cotton yield under water stress is determined by a combi‐ nation of factors: boll number, boll size, seed number per boll, and fibre/seed. Thus the main features of proposed ideotypes for rainfed cultivation includes, earliness (135-165 days), fewer small and thick leaves, compact and short plant architecture, moderately indeterminate habit, sparse hairiness, medium to big boll size, synchronous boll development, high response to nutrients, tolerance to water stress and tolerance to insects and diseases. The RILs derived from 1) MCU 5 and TCH 1218, 2) SVPR 2 and Suvin and 3) KC 3 and Suvin were evaluated with three different water regimes (irrigated control, managed water stress (by withholding irrigation during flowering phase) and rainfed conditions) at several locations of Tamil Nadu (including TNAU, Coimbatore, Cotton Research Station, Veppanthattai, Regional Research Station, Arupukottai and Maize Research Station, Vagarai) for drought tolerance and fibre quality traits. Linkage map was constructed and used for QTL analysis of fibre quality traits under water stress environment (Boopathi et al; under preparation). The important outcome of these evaluation trials (for above said ideotype characters), is identification of promising lines of mapping populations that were shown superior fibre yield and quality traits under water stress conditions. Such lines have been proposed for further evaluation to release as varieties that are suitable for rainfed cultivation.

and can cause allergies, skin rashes and other related health problems to human beings. Hence, it is preferred to have garments made from natural coloured cotton which is free from the dangerous textile chemicals. This has provoked many cotton workers into developing ecofriendly coloured cotton and has led to the revival of growing naturally coloured cotton. Further, coloured cotton cultivation should also be encouraged since it possesses resistances to many pests, diseases, drought and salinity [26]. In India, coloured cotton can be cultivated in Andhra Pradesh, Karnataka, Madhya Pradesh, Maharashtra and Orissa. Khadi and Village Industries Commission have experimented producing dress material using coloured cotton. The Maharashtra Hybrid Seeds Company (Mahyco), Mumbai, has initiated coloured cotton‐ seed production. However, the share of the colour cotton to the total Indian cotton production

Usefulness and Utilization of Indian Cotton Germplasm

http://dx.doi.org/10.5772/58619

131

Up to the middle of the 20th Century, coloured cotton cultivars *Cocanada 1* and *2* were com‐ mercially cultivated in Andhra Pradesh and exported to Japan. Similarly, cotton with black, brown, creamy white and khaki linted types were grown in Assam. *Kumta* in Karnataka was the home for *G. herbaceum* with dull white colour. Interestingly, globally acclaimed *Dacca muslin* was made from white and colour linted *G. arboreum* [27]*.* However, the main disad‐ vantage of coloured cotton is its lower yield, shorter staple length, weaker fibre strength and undesirable micronaire value when compared with white linted ones, limiting its commercial

Because of the advancement of spinning and textile processing technologies, there is a need for the production of coloured cotton combining high yield and superior fibre qualities. The F1s obtained by crossing brown coloured and white linted lines are intermediate between the two parents for colour intensity and technological properties. Significant numbers of colour cotton genotypes are being maintained in India at CICR, Nagpur, UAS-Dharwad and TNAU, Coimbatore. Nearly 40 colour linted cotton germplasm accessions are being maintained at National Cotton Gene Bank, CICR, Nagpur. Scientists at the CICR laboratories and Cotton Research Station at Khandwa in Madhya Pradesh, University of Agricultural Sciences at Dharwad, Karnataka and Panjabrao Krishi Vidyapeeth, Akola, Maharashtra are investigating the agronomic, economic, and technical attributes of these strains for suitable hybrid produc‐ tion. Such studies have resulted in the identification of six cultures with desirable properties such as moderate resistance to pests, large boll size, and good fibre qualities with shades of brown and green. Studies at UAS, Dharwad indicated that colour development in the fibre occurs between 30 and 40 days after boll formation. A collection of 11 coloured cotton *G. hirsutum* genotypes (Higginbotham, Parbhani American, Brymer brown, Hirsutum Tashkent, Lousiana brown, Nankeen brown, Algerian brown, Russian brown, Red 5–7, Arkansas green and Texas green) and four white linted genotypes (MCU 5, 7, 9 and 12) were evaluated by RAPD markers at TNAU, Coimbatore, India. Cluster analysis showed clear-cut separation of the colour and white lint genotypes [29]. It has been recognized in several occasions that exploitation of heterosis might be an effective method for improvement in yield and fibre

is very negligible (less than 5000 tonnes).

cultivation and utilization [28].

properties in coloured cotton.

In another study, we are trying to identify the QTLs linked to jassid tolerance in cotton using a RILs derived from 1) KC 2 and Suvin and 2) MCU 5 and Suvin. *G. hirsutum* cultivar KC 2 and MCU5 had shown tolerance to jassid [23] but with relatively poor fibre quality. On the other hand, the *G. barbadense* cultivar, Suvin, and *G. hirsutum* cultivar MCU 5 was vulnerable to jassid attack; however, they registered better fibre quality traits with good yield. Based on the variability studies of different leaf anatomical features, diversity, correlation and path coefficient analysis conducted at TNAU, Coimbatore, the following conclusion were made to explain jassid tolerance in cotton: i) pubescent nature indicates jassid tolerance ii) lower palisade cells in leaf lamina act as physical barrier for feeding and oviposition iii) thicker laminar coupled with absence of pubescence or lower palisade depicts susceptibility, but with them confers resistance to jassid and iv) higher cortex cell density is indicative of resistance [24, 25]. Hence, RILs that are developed from both of these interspecific and intraspecific crosses are being used for genetic mapping of jassid tolerance in cotton. In a parallel study, two different RILs developed from MCU 5 and TCH 1218 and P 56-4 and RS 2013 at TNAU, Coimbatore and IARI, New Delhi, respectively were evaluated at four different national partner institutes. Preliminary studies have identified several number of major QTLs linked to fibre yield and quality traits and they are being fine mapped using SNPs.

### **8. Coloured cotton**

The vast majority of cotton grown commercially in the world, including India, has white lint, but recently there is a growing interest in coloured linted cotton. During the process of bleaching and dyeing of white lint cotton to impart colours, dyeing and textile units regularly use several toxic chemicals including heavy metal. The water from these units is a main source of pollution in drinking water, soil and environment. Many of these chemicals are carcinogenic and can cause allergies, skin rashes and other related health problems to human beings. Hence, it is preferred to have garments made from natural coloured cotton which is free from the dangerous textile chemicals. This has provoked many cotton workers into developing ecofriendly coloured cotton and has led to the revival of growing naturally coloured cotton. Further, coloured cotton cultivation should also be encouraged since it possesses resistances to many pests, diseases, drought and salinity [26]. In India, coloured cotton can be cultivated in Andhra Pradesh, Karnataka, Madhya Pradesh, Maharashtra and Orissa. Khadi and Village Industries Commission have experimented producing dress material using coloured cotton. The Maharashtra Hybrid Seeds Company (Mahyco), Mumbai, has initiated coloured cotton‐ seed production. However, the share of the colour cotton to the total Indian cotton production is very negligible (less than 5000 tonnes).

is under drought conditions. Seed cotton yield under water stress is determined by a combi‐ nation of factors: boll number, boll size, seed number per boll, and fibre/seed. Thus the main features of proposed ideotypes for rainfed cultivation includes, earliness (135-165 days), fewer small and thick leaves, compact and short plant architecture, moderately indeterminate habit, sparse hairiness, medium to big boll size, synchronous boll development, high response to nutrients, tolerance to water stress and tolerance to insects and diseases. The RILs derived from 1) MCU 5 and TCH 1218, 2) SVPR 2 and Suvin and 3) KC 3 and Suvin were evaluated with three different water regimes (irrigated control, managed water stress (by withholding irrigation during flowering phase) and rainfed conditions) at several locations of Tamil Nadu (including TNAU, Coimbatore, Cotton Research Station, Veppanthattai, Regional Research Station, Arupukottai and Maize Research Station, Vagarai) for drought tolerance and fibre quality traits. Linkage map was constructed and used for QTL analysis of fibre quality traits under water stress environment (Boopathi et al; under preparation). The important outcome of these evaluation trials (for above said ideotype characters), is identification of promising lines of mapping populations that were shown superior fibre yield and quality traits under water stress conditions. Such lines have been proposed for further evaluation to release as

In another study, we are trying to identify the QTLs linked to jassid tolerance in cotton using a RILs derived from 1) KC 2 and Suvin and 2) MCU 5 and Suvin. *G. hirsutum* cultivar KC 2 and MCU5 had shown tolerance to jassid [23] but with relatively poor fibre quality. On the other hand, the *G. barbadense* cultivar, Suvin, and *G. hirsutum* cultivar MCU 5 was vulnerable to jassid attack; however, they registered better fibre quality traits with good yield. Based on the variability studies of different leaf anatomical features, diversity, correlation and path coefficient analysis conducted at TNAU, Coimbatore, the following conclusion were made to explain jassid tolerance in cotton: i) pubescent nature indicates jassid tolerance ii) lower palisade cells in leaf lamina act as physical barrier for feeding and oviposition iii) thicker laminar coupled with absence of pubescence or lower palisade depicts susceptibility, but with them confers resistance to jassid and iv) higher cortex cell density is indicative of resistance [24, 25]. Hence, RILs that are developed from both of these interspecific and intraspecific crosses are being used for genetic mapping of jassid tolerance in cotton. In a parallel study, two different RILs developed from MCU 5 and TCH 1218 and P 56-4 and RS 2013 at TNAU, Coimbatore and IARI, New Delhi, respectively were evaluated at four different national partner institutes. Preliminary studies have identified several number of major QTLs linked

to fibre yield and quality traits and they are being fine mapped using SNPs.

The vast majority of cotton grown commercially in the world, including India, has white lint, but recently there is a growing interest in coloured linted cotton. During the process of bleaching and dyeing of white lint cotton to impart colours, dyeing and textile units regularly use several toxic chemicals including heavy metal. The water from these units is a main source of pollution in drinking water, soil and environment. Many of these chemicals are carcinogenic

varieties that are suitable for rainfed cultivation.

130 World Cotton Germplasm Resources

**8. Coloured cotton**

Up to the middle of the 20th Century, coloured cotton cultivars *Cocanada 1* and *2* were com‐ mercially cultivated in Andhra Pradesh and exported to Japan. Similarly, cotton with black, brown, creamy white and khaki linted types were grown in Assam. *Kumta* in Karnataka was the home for *G. herbaceum* with dull white colour. Interestingly, globally acclaimed *Dacca muslin* was made from white and colour linted *G. arboreum* [27]*.* However, the main disad‐ vantage of coloured cotton is its lower yield, shorter staple length, weaker fibre strength and undesirable micronaire value when compared with white linted ones, limiting its commercial cultivation and utilization [28].

Because of the advancement of spinning and textile processing technologies, there is a need for the production of coloured cotton combining high yield and superior fibre qualities. The F1s obtained by crossing brown coloured and white linted lines are intermediate between the two parents for colour intensity and technological properties. Significant numbers of colour cotton genotypes are being maintained in India at CICR, Nagpur, UAS-Dharwad and TNAU, Coimbatore. Nearly 40 colour linted cotton germplasm accessions are being maintained at National Cotton Gene Bank, CICR, Nagpur. Scientists at the CICR laboratories and Cotton Research Station at Khandwa in Madhya Pradesh, University of Agricultural Sciences at Dharwad, Karnataka and Panjabrao Krishi Vidyapeeth, Akola, Maharashtra are investigating the agronomic, economic, and technical attributes of these strains for suitable hybrid produc‐ tion. Such studies have resulted in the identification of six cultures with desirable properties such as moderate resistance to pests, large boll size, and good fibre qualities with shades of brown and green. Studies at UAS, Dharwad indicated that colour development in the fibre occurs between 30 and 40 days after boll formation. A collection of 11 coloured cotton *G. hirsutum* genotypes (Higginbotham, Parbhani American, Brymer brown, Hirsutum Tashkent, Lousiana brown, Nankeen brown, Algerian brown, Russian brown, Red 5–7, Arkansas green and Texas green) and four white linted genotypes (MCU 5, 7, 9 and 12) were evaluated by RAPD markers at TNAU, Coimbatore, India. Cluster analysis showed clear-cut separation of the colour and white lint genotypes [29]. It has been recognized in several occasions that exploitation of heterosis might be an effective method for improvement in yield and fibre properties in coloured cotton.

#### **9. Future perspectives**

In India, there is a large scope for cotton genetic improvement for value added traits: an example is cotton for floor coverings. Currently, cotton contributes less than 2% of the fibres used in floor coverings, although this industry represents the largest single end-user of fibres in today's market. What is needed to fulfill this niche in the marketplace is to develop cotton fibres that have (1) more flame resistance to meet strict government standards (2) longer with reduced short fibre content to prevent shredding and (3) improved resiliency. It is also imperative to genetically improve the cotton fibre properties for other value added properties such as improved white brightness, increased postharvest properties such as moisture uptake, dye uptake, binding and/or retention and introduction of novel properties such as naturally coloured fibres and antimicrobial fibres for medical and pharmaceutical use.

are not easily amenable to improvement through transformation. Further, traits that can be routinely modified via conventional breeding need not be targeted for transformation. Availability of molecular markers to track genes controlling complex traits has further reduced the need for transgenic approach to crop improvement. This, however, does not mean that the transgenic approach is unimportant. Since genes can be sourced from any organism for cotton transformation, novel traits can be engineered with ease. Therefore, from a practical viewpoint, deficiencies that severely limit crop production and for which conventional approaches are inadequate, should be accorded high priority for transgenic improvement. At present, almost all of the Indian cotton transgenic technology and products are in private domain. Hence, there is a general worry that the transgenic crops are being promoted solely with profit motive and not for the good of the public. Thus the opposition to transgenic crops is not only on account of biosafety but also due to IPR, ethical, social, economic and moral issues. For technology to

Usefulness and Utilization of Indian Cotton Germplasm

http://dx.doi.org/10.5772/58619

133

progress and reach the farmers, both public and private investments will be essential.

Foregoing section highlighted there are many challenges faced by Indian cotton scientists in creating the next generation of designer cotton plants. Fundamental research is still needed to elucidate biochemical and signalling pathways, as well as acquiring a better understanding of the underlying mechanisms that regulate gene expression in cotton. Further, quick and reproducible protocols for rapid screening of germplasm for biotic and abiotic stress resistance, breeding for drought tolerance, naturally coloured cotton, breeding for cotton varieties that suitable for mechanization and exploiting the genetic potential of wild species require urgent

This work is supported by Department of Biotechnology, Ministry of Science and Technology, Government of India. We sincerely apologize for not citing many research papers due to space

, S. Sathish, P. Dachinamoorthy, P. Kavitha and R. Ravikesavan

**10. Conclusion**

attention.

limitations.

**Author details**

N. Manikanda Boopathi\*

\*Address all correspondence to: nmboopathi@tnau.ac.in

Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India

**Acknowledgements**

Physical and chemical mutagenesis provides a powerful alternative to natural, polygenic variation for identifying functional pathways and complex disease genes and more impor‐ tantly to generate novel cultivars with improved agronomic traits. Though there were some attempts in India, by and large, physical and chemical mutagenesis has not been utilized extensively to create new genetic variation.

The utilization of available germplasm in the national cotton gene bank can be further enhanced by adding the most suitable genetic stocks that can be procured from various international sources. Such activity will be useful in the development of breeding lines by introgressing beneficial alleles from the wild species, races and derivatives. Although elite x elite crosses are typical of traditional plant breeding, interspecific crosses are rarely used in cotton breeding because of numerous barriers. The finding that the *G. hirsutum* allele is favourable at some loci and the *G. barbadense* allele at other loci shows that recombination of favourable alleles from each of these species may form novel genotypes than either of the parental species. Similarly, the genomic exploration of other accessions of these species or other wild tetraploid cottons (*G. tomentosum*, *G. darwinii*, and *G. mustelinum*), maintained at national cotton gene bank could yield additional valuable alleles.

The most important agronomic traits such as biotic and abiotic stress tolerance, plant devel‐ opment and consumer quality aspects are genetically and physiologically complex. Moreover, because of the polyploid nature of cotton, breeding for such traits is time consuming and difficult. Further, the paucity of information about genes that control important traits and the need for more extensive usage of diverse germplasm hinder the genetic improvement of cotton. The rapidly expanding knowledge on gene function and the availability of whole genome structural features of cotton is expected to offer new perspectives to solve these complex problems and future cotton genetic improvement strategy should integrate such knowledge in the breeding program. Taking up of multi-population analyses (such as NAM, MAGIC, four-way cross, etc.) can unambiguously resolve several issues in QTL models and tests of epistatic interactions of QTL with the genetic background and environment.

Currently, the transgenic approach is feasible to engineer traits that are controlled by one or a few major genes. However, it is not a panacea for all the problems. Quantitative traits like yield are not easily amenable to improvement through transformation. Further, traits that can be routinely modified via conventional breeding need not be targeted for transformation. Availability of molecular markers to track genes controlling complex traits has further reduced the need for transgenic approach to crop improvement. This, however, does not mean that the transgenic approach is unimportant. Since genes can be sourced from any organism for cotton transformation, novel traits can be engineered with ease. Therefore, from a practical viewpoint, deficiencies that severely limit crop production and for which conventional approaches are inadequate, should be accorded high priority for transgenic improvement. At present, almost all of the Indian cotton transgenic technology and products are in private domain. Hence, there is a general worry that the transgenic crops are being promoted solely with profit motive and not for the good of the public. Thus the opposition to transgenic crops is not only on account of biosafety but also due to IPR, ethical, social, economic and moral issues. For technology to progress and reach the farmers, both public and private investments will be essential.
