Casuarina Genome initiative - Revision history

Raj at 03:09, 1 July 2010

2010-07-01T03:09:59Z

← Older revision		Revision as of 03:09, 1 July 2010
Line 24:		Line 24:

	=Background CGI=		=Background CGI=
	<~~pre~~>		<nowiki>
	Casuarina, in addition to Eucalyptus, is an important pulp wood species for our paper industry. This is extensively grown in the coastal areas of Andhra Pradesh from where PSPD procures wood for the pulp mill at Bhadrachalam (BCM). Acreage under Casuarina in the core wood procuring area for BCM pulp mill is relatively less in comparison to Eucalyptus. This is mainly due to its adaptability to inland areas that are water-deficient and its coppicing ability. There are several species of Casuarina that differ in their drought tolerance and coppicing ability. Bringing these traits together into a species of Casuarina that also has good growth potential and pulp yield requires a well planned tree breeding programme. Tree breeding is greatly assisted by availability of ‘Genome sequence’ which makes it possible to design and develop of DNA-based markers that speed up informed selection process. Genome sequence also will be essential to understand basic biology of plant regeneration in order to develop technological intervention to improve coppicing ability. Casuarina is species that stands apart from eucalypts and poplar in evolution and feasibility of inferring its gene sequence using information from other species is very low. This makes it imperative to obtain the “Genome Sequence” in order to carry out tree improvement of Casuarina.		Casuarina, in addition to Eucalyptus, is an important pulp wood species for our paper industry. This is extensively grown in the coastal areas of Andhra Pradesh from where PSPD procures wood for the pulp mill at Bhadrachalam (BCM). Acreage under Casuarina in the core wood procuring area for BCM pulp mill is relatively less in comparison to Eucalyptus. This is mainly due to its adaptability to inland areas that are water-deficient and its coppicing ability. There are several species of Casuarina that differ in their drought tolerance and coppicing ability. Bringing these traits together into a species of Casuarina that also has good growth potential and pulp yield requires a well planned tree breeding programme. Tree breeding is greatly assisted by availability of ‘Genome sequence’ which makes it possible to design and develop of DNA-based markers that speed up informed selection process. Genome sequence also will be essential to understand basic biology of plant regeneration in order to develop technological intervention to improve coppicing ability. Casuarina is species that stands apart from eucalypts and poplar in evolution and feasibility of inferring its gene sequence using information from other species is very low. This makes it imperative to obtain the “Genome Sequence” in order to carry out tree improvement of Casuarina.

	There are different species of Casuarina with variation in wood and pulp yield. Casuarina wood has higher density which packs better in the digestor during pulping. In comparison with other species accessed at our pulp mill, at similar age, Casuarina poles are bigger in diameter which makes it easy to debark which is an important criterion at the pulp mill. Currently 25% of the wood consumed at our BCM mill is of Casuarina. Development of Casuarina that is suitable for planting in the core wood procuring area for BCM pulp mill would save Rs. 200/tonne in transportation costs. These are some of the benefits for the business of having a superior planting material of Casuarina that can be planted in the core area.		There are different species of Casuarina with variation in wood and pulp yield. Casuarina wood has higher density which packs better in the digestor during pulping. In comparison with other species accessed at our pulp mill, at similar age, Casuarina poles are bigger in diameter which makes it easy to debark which is an important criterion at the pulp mill. Currently 25% of the wood consumed at our BCM mill is of Casuarina. Development of Casuarina that is suitable for planting in the core wood procuring area for BCM pulp mill would save Rs. 200/tonne in transportation costs. These are some of the benefits for the business of having a superior planting material of Casuarina that can be planted in the core area.

	Genome sequence is a specialized service which is provided by few expert service providers who have prior expertise in this field. We have explored two leading service providers – KeyGene, the Netherlands and BGI, Hong Kong. Both these vendors have extensive experience in genome sequencing as seen by their contribution deciphering the genomes of Cucumber, Panda, Orchids, 1000 animal and plant reference genomes (BGI), Melon, Potato, Tomato, and Brassica (KeyGene). We have had extensive discussions on the technical aspects of Genome sequencing with both the parties. Two representatives from KeyGene visited our Centre in Bangalore on 12 Feb 2010 for discussion. Both the vendors have submitted their quotations detailing the time taken and the costs involved. BGI and KeyGene follow different methods of deciphering the Genome sequence. The costs and time involved are: KeyGene € 957000 and 12 months; BGI $234346 and 7-9 months. BGI’s quote includes annotation (assigning meaning to the sequence) whereas it is not included in KeyGene’s quote.		Genome sequence is a specialized service which is provided by few expert service providers who have prior expertise in this field. We have explored two leading service providers – KeyGene, the Netherlands and BGI, Hong Kong. Both these vendors have extensive experience in genome sequencing as seen by their contribution deciphering the genomes of Cucumber, Panda, Orchids, 1000 animal and plant reference genomes (BGI), Melon, Potato, Tomato, and Brassica (KeyGene). We have had extensive discussions on the technical aspects of Genome sequencing with both the parties. Two representatives from KeyGene visited our Centre in Bangalore on 12 Feb 2010 for discussion. Both the vendors have submitted their quotations detailing the time taken and the costs involved. BGI and KeyGene follow different methods of deciphering the Genome sequence. The costs and time involved are: KeyGene € 957000 and 12 months; BGI $234346 and 7-9 months. BGI’s quote includes annotation (assigning meaning to the sequence) whereas it is not included in KeyGene’s quote.

	Based on the discussions and analysis of data to be carried out and the time taken to complete the project our recommendation would be to go with BGI for sequencing the genome of Casuarina.		Based on the discussions and analysis of data to be carried out and the time taken to complete the project our recommendation would be to go with BGI for sequencing the genome of Casuarina.
	</~~pre~~>		</nowiki>

Raj at 03:09, 1 July 2010

2010-07-01T03:09:14Z

← Older revision		Revision as of 03:09, 1 July 2010
Line 24:		Line 24:

	=Background CGI=		=Background CGI=
			<pre>
	Casuarina, in addition to Eucalyptus, is an important pulp wood species for our paper industry. This is extensively grown in the coastal areas of Andhra Pradesh from where PSPD procures wood for the pulp mill at Bhadrachalam (BCM). Acreage under Casuarina in the core wood procuring area for BCM pulp mill is relatively less in comparison to Eucalyptus. This is mainly due to its adaptability to inland areas that are water-deficient and its coppicing ability. There are several species of Casuarina that differ in their drought tolerance and coppicing ability. Bringing these traits together into a species of Casuarina that also has good growth potential and pulp yield requires a well planned tree breeding programme. Tree breeding is greatly assisted by availability of ‘Genome sequence’ which makes it possible to design and develop of DNA-based markers that speed up informed selection process. Genome sequence also will be essential to understand basic biology of plant regeneration in order to develop technological intervention to improve coppicing ability. Casuarina is species that stands apart from eucalypts and poplar in evolution and feasibility of inferring its gene sequence using information from other species is very low. This makes it imperative to obtain the “Genome Sequence” in order to carry out tree improvement of Casuarina.		Casuarina, in addition to Eucalyptus, is an important pulp wood species for our paper industry. This is extensively grown in the coastal areas of Andhra Pradesh from where PSPD procures wood for the pulp mill at Bhadrachalam (BCM). Acreage under Casuarina in the core wood procuring area for BCM pulp mill is relatively less in comparison to Eucalyptus. This is mainly due to its adaptability to inland areas that are water-deficient and its coppicing ability. There are several species of Casuarina that differ in their drought tolerance and coppicing ability. Bringing these traits together into a species of Casuarina that also has good growth potential and pulp yield requires a well planned tree breeding programme. Tree breeding is greatly assisted by availability of ‘Genome sequence’ which makes it possible to design and develop of DNA-based markers that speed up informed selection process. Genome sequence also will be essential to understand basic biology of plant regeneration in order to develop technological intervention to improve coppicing ability. Casuarina is species that stands apart from eucalypts and poplar in evolution and feasibility of inferring its gene sequence using information from other species is very low. This makes it imperative to obtain the “Genome Sequence” in order to carry out tree improvement of Casuarina.
	There are different species of Casuarina with variation in wood and pulp yield. Casuarina wood has higher density which packs better in the digestor during pulping. In comparison with other species accessed at our pulp mill, at similar age, Casuarina poles are bigger in diameter which makes it easy to debark which is an important criterion at the pulp mill. Currently 25% of the wood consumed at our BCM mill is of Casuarina. Development of Casuarina that is suitable for planting in the core wood procuring area for BCM pulp mill would save Rs. 200/tonne in transportation costs. These are some of the benefits for the business of having a superior planting material of Casuarina that can be planted in the core area.		There are different species of Casuarina with variation in wood and pulp yield. Casuarina wood has higher density which packs better in the digestor during pulping. In comparison with other species accessed at our pulp mill, at similar age, Casuarina poles are bigger in diameter which makes it easy to debark which is an important criterion at the pulp mill. Currently 25% of the wood consumed at our BCM mill is of Casuarina. Development of Casuarina that is suitable for planting in the core wood procuring area for BCM pulp mill would save Rs. 200/tonne in transportation costs. These are some of the benefits for the business of having a superior planting material of Casuarina that can be planted in the core area.
	Genome sequence is a specialized service which is provided by few expert service providers who have prior expertise in this field. We have explored two leading service providers – KeyGene, the Netherlands and BGI, Hong Kong. Both these vendors have extensive experience in genome sequencing as seen by their contribution deciphering the genomes of Cucumber, Panda, Orchids, 1000 animal and plant reference genomes (BGI), Melon, Potato, Tomato, and Brassica (KeyGene). We have had extensive discussions on the technical aspects of Genome sequencing with both the parties. Two representatives from KeyGene visited our Centre in Bangalore on 12 Feb 2010 for discussion. Both the vendors have submitted their quotations detailing the time taken and the costs involved. BGI and KeyGene follow different methods of deciphering the Genome sequence. The costs and time involved are: KeyGene € 957000 and 12 months; BGI $234346 and 7-9 months. BGI’s quote includes annotation (assigning meaning to the sequence) whereas it is not included in KeyGene’s quote.		Genome sequence is a specialized service which is provided by few expert service providers who have prior expertise in this field. We have explored two leading service providers – KeyGene, the Netherlands and BGI, Hong Kong. Both these vendors have extensive experience in genome sequencing as seen by their contribution deciphering the genomes of Cucumber, Panda, Orchids, 1000 animal and plant reference genomes (BGI), Melon, Potato, Tomato, and Brassica (KeyGene). We have had extensive discussions on the technical aspects of Genome sequencing with both the parties. Two representatives from KeyGene visited our Centre in Bangalore on 12 Feb 2010 for discussion. Both the vendors have submitted their quotations detailing the time taken and the costs involved. BGI and KeyGene follow different methods of deciphering the Genome sequence. The costs and time involved are: KeyGene € 957000 and 12 months; BGI $234346 and 7-9 months. BGI’s quote includes annotation (assigning meaning to the sequence) whereas it is not included in KeyGene’s quote.
	Based on the discussions and analysis of data to be carried out and the time taken to complete the project our recommendation would be to go with BGI for sequencing the genome of Casuarina.		Based on the discussions and analysis of data to be carried out and the time taken to complete the project our recommendation would be to go with BGI for sequencing the genome of Casuarina.
			</pre>

Raj at 03:08, 1 July 2010

2010-07-01T03:08:49Z

← Older revision		Revision as of 03:08, 1 July 2010
Line 22:		Line 22:
	# First in the world and no '''entry barrier''' in terms of research		# First in the world and no '''entry barrier''' in terms of research
	# Variety of patent possibilities		# Variety of patent possibilities

			=Background CGI=

			Casuarina, in addition to Eucalyptus, is an important pulp wood species for our paper industry. This is extensively grown in the coastal areas of Andhra Pradesh from where PSPD procures wood for the pulp mill at Bhadrachalam (BCM). Acreage under Casuarina in the core wood procuring area for BCM pulp mill is relatively less in comparison to Eucalyptus. This is mainly due to its adaptability to inland areas that are water-deficient and its coppicing ability. There are several species of Casuarina that differ in their drought tolerance and coppicing ability. Bringing these traits together into a species of Casuarina that also has good growth potential and pulp yield requires a well planned tree breeding programme. Tree breeding is greatly assisted by availability of ‘Genome sequence’ which makes it possible to design and develop of DNA-based markers that speed up informed selection process. Genome sequence also will be essential to understand basic biology of plant regeneration in order to develop technological intervention to improve coppicing ability. Casuarina is species that stands apart from eucalypts and poplar in evolution and feasibility of inferring its gene sequence using information from other species is very low. This makes it imperative to obtain the “Genome Sequence” in order to carry out tree improvement of Casuarina.
			There are different species of Casuarina with variation in wood and pulp yield. Casuarina wood has higher density which packs better in the digestor during pulping. In comparison with other species accessed at our pulp mill, at similar age, Casuarina poles are bigger in diameter which makes it easy to debark which is an important criterion at the pulp mill. Currently 25% of the wood consumed at our BCM mill is of Casuarina. Development of Casuarina that is suitable for planting in the core wood procuring area for BCM pulp mill would save Rs. 200/tonne in transportation costs. These are some of the benefits for the business of having a superior planting material of Casuarina that can be planted in the core area.
			Genome sequence is a specialized service which is provided by few expert service providers who have prior expertise in this field. We have explored two leading service providers – KeyGene, the Netherlands and BGI, Hong Kong. Both these vendors have extensive experience in genome sequencing as seen by their contribution deciphering the genomes of Cucumber, Panda, Orchids, 1000 animal and plant reference genomes (BGI), Melon, Potato, Tomato, and Brassica (KeyGene). We have had extensive discussions on the technical aspects of Genome sequencing with both the parties. Two representatives from KeyGene visited our Centre in Bangalore on 12 Feb 2010 for discussion. Both the vendors have submitted their quotations detailing the time taken and the costs involved. BGI and KeyGene follow different methods of deciphering the Genome sequence. The costs and time involved are: KeyGene € 957000 and 12 months; BGI $234346 and 7-9 months. BGI’s quote includes annotation (assigning meaning to the sequence) whereas it is not included in KeyGene’s quote.
			Based on the discussions and analysis of data to be carried out and the time taken to complete the project our recommendation would be to go with BGI for sequencing the genome of Casuarina.

Raj: /* Need */

2010-01-07T14:38:56Z

Need

← Older revision		Revision as of 14:38, 7 January 2010
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	# Early detection of SEX		# Early detection of SEX
	# PY/WY		# PY/WY
	# Copicing need in C. equisetifolia		# Copicing need in ''C. equisetifolia''

	=Sequencing=		=Sequencing=
	* BGI - estimated size of C. species 340 per haploid genome, so most species will have ~700MB		* BGI - estimated size of C. species 340 per haploid genome, so most species will have ~700MB

Raj at 14:18, 7 January 2010

2010-01-07T14:18:25Z

← Older revision		Revision as of 14:18, 7 January 2010
Line 21:		Line 21:
	# First in the world and no '''entry barrier''' in terms of research		# First in the world and no '''entry barrier''' in terms of research
	# Variety of patent possibilities		# Variety of patent possibilities
	#

Raj: /* Outcome from Bussiness (Kulkarni and Pradeep) */

2010-01-07T14:16:34Z

Outcome from Bussiness (Kulkarni and Pradeep)

← Older revision		Revision as of 14:16, 7 January 2010
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	=Outcome from Bussiness (Kulkarni and Pradeep)=		=Outcome from Bussiness (Kulkarni and Pradeep)=

			=Significance to ITC=
			# Owning genes
			# First in the world and no '''entry barrier''' in terms of research
			# Variety of patent possibilities
			#

Raj: /* Sequencing */

2010-01-07T14:14:33Z

Sequencing

← Older revision		Revision as of 14:14, 7 January 2010
Line 9:		Line 9:
	* BGI - estimated size of C. species 340 per haploid genome, so most species will have ~700MB		* BGI - estimated size of C. species 340 per haploid genome, so most species will have ~700MB
	* Cost today: ~1.5 crores		* Cost today: ~1.5 crores
	* Which species to go in		* Which species to go in?

	=Markers=		=Markers=
	* Apart from PY/WY/drought, what will you address?		* Apart from PY/WY/drought, what will you address?

Raj: /* Sequencing */

2010-01-07T14:14:05Z

Sequencing

← Older revision		Revision as of 14:14, 7 January 2010
Line 9:		Line 9:
	* BGI - estimated size of C. species 340 per haploid genome, so most species will have ~700MB		* BGI - estimated size of C. species 340 per haploid genome, so most species will have ~700MB
	* Cost today: ~1.5 crores		* Cost today: ~1.5 crores
	* ~~which~~ species to go in		* Which species to go in
			=Markers=
			* Apart from PY/WY/drought, what will you address?
			* SEX

	=Outcome from Bussiness (Kulkarni and Pradeep)=		=Outcome from Bussiness (Kulkarni and Pradeep)=

Raj at 14:13, 7 January 2010

2010-01-07T14:13:07Z

← Older revision		Revision as of 14:13, 7 January 2010
Line 6:		Line 6:
	# PY/WY		# PY/WY
	# Copicing need in C. equisetifolia		# Copicing need in C. equisetifolia
	==		=Sequencing=
			* BGI - estimated size of C. species 340 per haploid genome, so most species will have ~700MB
			* Cost today: ~1.5 crores
			* which species to go in
			=Outcome from Bussiness (Kulkarni and Pradeep)=

Raj: Created page with 'Project formulation =Need= # Drought tolerance # Bending - Stem formation # Early detection of SEX # PY/WY # Copicing need in C. equisetifolia =='

2010-01-07T14:08:37Z

Created page with 'Project formulation =Need= # Drought tolerance # Bending - Stem formation # Early detection of SEX # PY/WY # Copicing need in C. equisetifolia =='

New page

Project formulation
=Need=
# Drought tolerance
# Bending - Stem formation
# Early detection of SEX
# PY/WY
# Copicing need in C. equisetifolia
==