The Experts below are selected from a list of 294 Experts worldwide ranked by ideXlab platform
Anjan K. Banerjee - One of the best experts on this subject based on the ideXlab platform.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops
BMC Genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Background Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs ( StBEL5 and POTH1 ) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Results Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5- , PTB1/6- and POTH1 -like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Conclusions Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1 - like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops.
BMC genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
Kirtikumar R. Kondhare - One of the best experts on this subject based on the ideXlab platform.
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Mobile RNAs and proteins: Prospects in storage organ development of tuber and Root Crops.
Plant science : an international journal of experimental plant biology, 2019Co-Authors: Bhavani Natarajan, Kirtikumar R. Kondhare, David J. Hannapel, Anjan BanerjeeAbstract:Abstract Storage tuber and Root Crops make up a significant portion of the world’s subsistence food supply. Because of their importance in food security, yield enhancement has become a priority. A major focus has been to understand the biology of belowground storage organ development. Considerable insights have been gained studying tuber development in potato. We now know that two mobile signals, a full-length mRNA, StBEL5, and a protein, StSP6A, play pivotal roles in regulating tuber development. Under favorable conditions, these signals move from leaves to a belowground modified stem (stolon) and regulate genes that activate tuberization. Overexpression of StBEL5 or StSP6A increases tuber yield even under non-inductive conditions. The mRNAs of two close homologs of StBEL5, StBEL11 and StBEL29, are also known to be mobile but act as repressors of tuberization. Polypyrimidine tract-binding proteins (PTBs) are RNA-binding proteins that facilitate the movement of these mRNAs. Considering their role in tuberization, it is possible that these mobile signals play a major role in storage Root development as well. In this review, we explore the presence of these signals and their relevance in the development and yield potential of several important storage Root Crops.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops
BMC Genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Background Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs ( StBEL5 and POTH1 ) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Results Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5- , PTB1/6- and POTH1 -like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Conclusions Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1 - like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops.
BMC genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
David J. Hannapel - One of the best experts on this subject based on the ideXlab platform.
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Mobile RNAs and proteins: Prospects in storage organ development of tuber and Root Crops.
Plant science : an international journal of experimental plant biology, 2019Co-Authors: Bhavani Natarajan, Kirtikumar R. Kondhare, David J. Hannapel, Anjan BanerjeeAbstract:Abstract Storage tuber and Root Crops make up a significant portion of the world’s subsistence food supply. Because of their importance in food security, yield enhancement has become a priority. A major focus has been to understand the biology of belowground storage organ development. Considerable insights have been gained studying tuber development in potato. We now know that two mobile signals, a full-length mRNA, StBEL5, and a protein, StSP6A, play pivotal roles in regulating tuber development. Under favorable conditions, these signals move from leaves to a belowground modified stem (stolon) and regulate genes that activate tuberization. Overexpression of StBEL5 or StSP6A increases tuber yield even under non-inductive conditions. The mRNAs of two close homologs of StBEL5, StBEL11 and StBEL29, are also known to be mobile but act as repressors of tuberization. Polypyrimidine tract-binding proteins (PTBs) are RNA-binding proteins that facilitate the movement of these mRNAs. Considering their role in tuberization, it is possible that these mobile signals play a major role in storage Root development as well. In this review, we explore the presence of these signals and their relevance in the development and yield potential of several important storage Root Crops.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops
BMC Genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Background Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs ( StBEL5 and POTH1 ) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Results Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5- , PTB1/6- and POTH1 -like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Conclusions Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1 - like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops.
BMC genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
Amit Kumar - One of the best experts on this subject based on the ideXlab platform.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops
BMC Genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Background Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs ( StBEL5 and POTH1 ) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Results Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5- , PTB1/6- and POTH1 -like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Conclusions Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1 - like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage Root Crops.
BMC genomics, 2018Co-Authors: Kirtikumar R. Kondhare, David J. Hannapel, Amit Kumar, Anjan K. BanerjeeAbstract:Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and Root Crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and Root growth. Storage tubers and Root Crops are important sustenance food Crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of Root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage Root Crops as well. Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage Root Crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage Root Crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and Root tissues of these five storage Root Crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage Root Crops exhibited differential accumulation patterns in leaf and storage Root tissues. Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage Root Crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in Root Crops.
Antoine Champagne - One of the best experts on this subject based on the ideXlab platform.
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Diversity of anthocyanins and other phenolic compounds among tropical Root Crops from Vanuatu, South Pacific
Journal of Food Composition and Analysis, 2011Co-Authors: Antoine Champagne, Laurent Legendre, Ghislaine Hilbert, Vincent LebotAbstract:To study the composition and amounts of phenolic compounds in ten tropical Root crop species consumed daily worldwide and particularly in South Pacific, acidified aqueous extracts were analyzed. Among 134 samples, 78 components were found. Among total peaks detected from these fractions, 3 anthocyanins (peonidin-caffeoyl-feruloylsophoroside-5-glucoside, petunidin-3-glucoside and pelargonidin-3-glucoside), 5 flavonols (hyperoside, isorhamnetin-3-glucoside, kaempferol-3-glucoside, quercetin-3-glucopyranoside and quercetin-3′-glucoside,6′-acetate), 3 flavanols (catechin, epicatechin and epicatechin-3-gallate), and 3 phenolic acids (caffeic acid, chlorogenic acid and 3,5-dicaffeoylquinic acid) were tentatively identified by HPLC-DAD. Although many compounds remain to be identified, results suggest that these tropical Root Crops are good sources of anthocyanins and phenolic compounds. The greater yam (Dioscorea alata) had the highest anthocyanin content (up to 93.3 mg CGE/100 g DW), while taro (Colocasia esculenta) had the widest range of flavonols (up to 326.7 mg QGE/100 g DW). Cultivars of these staples should be exploited in breeding programs for the development of varieties with enhanced health and nutritional benefits.
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Chemotypic variation explaining traditional selection of tropical Root Crops in Vanuatu, South Pacific
2009Co-Authors: Antoine ChampagneAbstract:In Vanuatu, Melanesia, Root Crops (aroids, cassava, sweet potato and yams) are staples. Several methods exist and are employed to process and cook these foods such as boiling, roasting or baking on hot stones. In Vanuatu, unlike other Melanesian and Pacific countries, these starchy foods are processed into the traditional dish called laplap, which is a pudding-like dish prepared from hand-grated fruits, corms, Roots or tubers. The raw paste is wrapped in Heliconia indica leaves and slowly steamed in a ground-oven. Producers and consumers alike are unanimous to state that some cultivars are suitable for laplap while others are not. It is still unknown what the chemical characteristics of so-called “good” varieties are and how chemotypes are traditionally selected.
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Development of a methodology for the on-farm conservation of Root Crops diversity
2006Co-Authors: Antoine ChampagneAbstract:Many developing countries have found great difficulty in sustaining the conservation and genetic improvement of Root Crops. Conservation is fraught with difficulty: ex situ collections are expensive to maintain and methods for on-farm conservation have not been studied. This project is testing the hypothesis that the geographical distribution of allelic diversity can represent an efficient and practical alternative to present conservation and use activities.
