INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGYARUNA ASAF ALI MARG, NEW DELHI - 110067

Consortium Leader

NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGYPUSA CAMPUS, NEW DELH I- 110012

UNIVERSITY OF AGRICULTURAL SCIENCESDHARWAD - 580005

GENOMICS OF COTTON BOLL

AND FIBRE DEVELOPMENT

National Agricultural Innovation Project(Indian Council of Agricultural Research)

OBJECTIVES Identification of genes in the developing boll that are highly influenced under Bollworm

attack and drought and nutritional stresses. Construction of EST database of Gossypium hirsutum from tissues derived from various

stages of boll development. Assignment of functions to key genes involved in cotton fibre length and quality. Isolation and characterization of promoters for the genes expressed specifically in bolls and

are strongly up regulated.

In the recent years, rapid development of genomic tools and resources such as expression profiling of elongating fiber cells has provided clues to facilitate the understanding of cotton production. This opens up opportunities to isolate genes encoding fiber quality and strength. Efforts to isolate these genes will facilitate our ability to manipulate fibre characters that the textile industry is looking forward. Promoters that are highly active during boll development will sustain the expression of foreign proteins such as Bt toxins in the bolls providing effective protection against Cotton bollworm and Pink bollworm. Similarly, boll-specific promoters will facilitate hyper-expression of osmotolerant genes in developing bolls thus imparting protection to the physiological and biochemical processes involved in fibre development.

Cotton is the most important fibre crop in India occupying 9 mha area which represents world highest acreage of 34 mha under cotton. In four of the cultivated cotton species, two are A-genome diploid species (Gossypium arboretum L. and G. herbaceum L.) and two are allotetraploid AD-genome species (G. barbadense L. and G. hirsutum L.). G. hirsutum L. is the most widely cultivated species and accounts for more than 90% of the world cotton lint production.

Cultivated Species

Fibre morphogenesis can be divided into four overlapping development stages: Fibre initiation, Primary cell wall synthesis (fibre expansion and elongation), Secondary cell wall synthesis and Maturation. The growth and development of cotton plant is highly influenced by both biotic and abiotic factors and directly influence the fibre yield and quality.

Insects Drought

Abiotic factorsBiotic factors

National Agricultural Innovation Project (NAIP) of Indian Council of Agricultural Research (ICAR) accords high priority to generation and transfer of innovative agricultural technologies. The overall objective of the NAIP is to facilitate an accelerated and sustainable transformation of the Indian agriculture, so that it can support poverty alleviation and income generation through collaborative development and application of agricultural innovations by the public organizations in partnership with farmers, the private sector and other stakeholders. The specific objective of the NAIP under the component 4 is to build capacity to undertake basic and strategic research in frontier areas of agricultural sciences. Present project is funded by the NAIP to develop cotton genotypes with good quality fiber and insect resistance.

Different boll developmental stages

Isolate proteins from various stages of fiber development

2DE

Gel spots

Trypsinfragments

MALDI-TOF: Peptide mapping Masspec data Proteome and EST data bases, genome analysis

Towards this objective novel approaches will be followed which include:

Studies on the influence of various factors during the boll development can provide vital information on the expression profile of various genes and their role at molecular level that is necessary for understanding the cotton fibre formation and its development under various adverse conditions. The project envisages identification and isolation of genes and promoters involved in fibre development and characterization of their responses to biotic and abiotic stress factors.

The deliverables: Genes and promoters that are specific to boll development. Genes associated with fiber development. Genes and promoters that are expressed in response to biotic and abiotic stress factors during boll

development. Validated boll-specific promoters useful for the development of transgenic cotton Novel methods for the genomic analysis.

Expected output and impact of the project: The most important outcome of the project is a fundamental understanding of gene expression during flower, square, boll and fiber development in cotton. The knowledge thus gained will have profound implications in applied cotton breeding, transgenic development and biotechnology of cotton leading towards trait introduction and improvement. Expression of insecticidal proteins such as Bt toxins under the control of boll-specific promoter will sustain their expression thus providing effective control of cotton Bollworms. The project will generate fundamental knowledge about the gene function and the influence of biotic and abiotic factors on fiber development.

•Global expression profiling of boll-specific ESTs under biotic and abiotic stress conditions. •Identification of the corresponding gene sequences by bioinformatics tool•PCR-based genome walking to isolate boll-specific and high expressing promoter sequences and validation using reporter gene expression in cotton. •Development of cotton boll proteome database and identify proteins whose accumulation is influenced by abiotic and biotic factors using mass spectrometric analysis.•Functional validation of candidate genes involved in the fibre development using expression and gene silencing approaches in cotton.

• Execution of the programme will help identify and isolate genes and respective promoters that will lead to better fiber quality, improved marketability and value to the farmer.• Well-trained human resource in the frontier technologies such as functional genomics through DNA microarrays, proteomics and transcriptomics.• The novel genes and promoters identified will be protected in the form of patents by the NAIP.

Name of the member University/ Institute

Email Phone

Dr V Siva Reddy, CL

Dr. M K Reddy, CCL

Dr. S. Leelavathi, CCL

ICGEB, Aruna Asaf Ali Marg, New Delhi-67

vsreddy@icgeb.res.in

reddy@icgeb.res.in

sadhul@icgeb.res.in

011-26741358

Dr P. Ananda Kumar, CCL NRCPB, IARI, New Delhi

polumetla@hotmail.com 011-25848783

Dr I S Katageri, CCL

Dr. H. M. Vamadevaiah, CCL

UAS, Dharwad-580004, Karnataka

ikatageri@yahoo.com 0836-2447874

GENOMICS OF COTTON BOLL AND FIBER DEVELOPMENT

ICGEB, New DelhiProteome analysis:* Global analysis of protein expression during boll development under normal and stress conditions* Validation of genes/promoters

NRCPB, New DelhiTranscriptome analysis:* Global analysis of gene expression during boll development under normal & stress conditions* Validation of genes/promoters

UAS, Dharwad Production of cotton plants under biotic and abiotic stress conditions for

proteomic and transcriptomic studies Isolation of transcripts & cDNA for transcripome studies Validation of genes/promoters

Estimated total cost of the project : Rs. 755.50 lakhs

CONSORTIUM IMPLEMENTATION COMMITTEE

CONSORTIUM ADVISORY COMMITTEE

Prof A. R. Reddy, Chairman-CAC,Vice-Chancellor, Yogi Vemana University, Kadapa, A.P.(Expert on functional genomics of crop plants)Prof Amit Ghosh, Director, Indian Institute of Advanced Research, Gandhinagar(Expert on Microbial genetics and molecular biology of Vibrio cholerae)Dr B. M. Khadi, Director, Central Institute of Cotton Research, Nagpur(Expert on cotton breeding and biotechnology)