Research & Development:

CASSAVA

Starch Biosynthesis

Compared with other starchy plants, very limited amount of information on starch biosynthesis in cassava is available. To expand the knowledge, we focus on the two important aspects of starch biosynthesis in cassava: (i) the sucrose partitioning and sucrose-to-starch conversion pathway and (ii) the biosynthesis of storage starch.
At the beginning, the main focus of our research is to identify and characterize genes known to play roles in sucrose and starch metabolic pathways. From this, a collection of full-length cDNA clones participating in the sucrose and starch metabolic pathways have been created. Subsequently, functional roles of some of these candidate genes have been studied by transforming cassava, and also potato, with RNA interference and/or over-expression constructs. At present, we have obtained a number of transgenic lines, some of which are currently grown in the greenhouse for phenotypic evaluation.
With the presence of cassava genome sequence database (http://www.phytozome.net/cassava), collaboration with systems biologist from King Mongkut’s University of Technology Thonburi has allowed us to further investigate the starch biosynthesis pathway in cassava at transcriptomic, proteomic and metabolomic levels. With this approach, it has opened an opportunity to see how the starch biosynthesis pathway is regulated, and how genes or enzymes might interact either with each other or with those in other metabolic pathways.
The knowledge gained from these studies should extensively broaden our understanding on starch biosynthesis in cassava allowing us to efficiently and purposely produce cassava cultivars with a wide range of desirable starch traits.

Somatic embryogenesis development

Due to the lack of an efficient transformation and regeneration system in cassava, application of genetic engineering to study function of homologous and/or heterologous genes in cassava has been extremely challenging. Development of somatic embryo culture and genetic transformation system in various Thai cassava cultivars has become one of our research areas. We have successfully established the system to produce somatic embryogenesis and organogenesis of Thai cassava cultivars and implemented them in gene transfer platform. Various functional analysis tools, including gene suppression by RNA interference and gene over-expression approach, have been employed to monitor the effect of the genes of interest on the properties and quantity of the storage starch as well as various aspects of storage root development. Moreover, attempts are also being made to hunt for tuber-specific promoters and to develop a cultication technique to ensure tuberous root formation. This would lead to the generation of genetically modified cassava clones with improved starch quantity and quality, which will in turn help expand the use of cassava starch in the food and non-food industries.

Storage Root Development:

With a constant increase in the demand of cassava starch to accommodate for rapid urbanization and growth of industrial markets, there is an urgent need to increase and stabilize cassava yields. One approach is to achieve higher cassava productivity by placing particular emphasis on higher storage root yields. In this respect, improvement of the agronomy practice over the years, together with conventional breeding has contributed a great deal to help increase cassava storage root productivity. However, these approaches have their limits and it has become increasingly more difficult to better the currently in-use cassava cropping system or to develop higher yielding lines by conventional breeding. Biotechnology offers a new and attractive mean to improve plant traits. However, this requires a prerequisite knowledge of the genetic network regulating the trait of interest. In the case of storage root formation and development, the gene cascades underpinning the process remain largely uncharacterized. Thus at present, research inputs are much needed to gain the founding knowledge of the genetic networks behind the initiation and growth of storage roots in cassava. The information obtained would be invaluable in helping us getting a clearer view of the process which could allow one to generate cassava elite lines with enhanced storage roots.

Cassava Active Germplasm Collection
In vitro multiplication and maintenance system has been implemented for Thai cassava cultivars. Field evaluation revealed that these tissue culture-derived plants performed equally as well as normally propagated cassava plants. These disease-free cassava plants serve as a seed stock resource for long-term germplasm maintenance of elite Thai cassava cultivars and also future mass multiplication of selected cultivars with enhanced storage root yield for distribution to Thai farmers throughout the country.

RICE
Male sterility used for hybrid seed production of rice
Rice hybrids showed 15-30 % higher yields than inbred varieties. Hybrids have also demonstrated an ability to perform better under adverse conditions, such as drought and high salinity. The development of hybrid rice also improves several other desirable traits, including grain quality, and disease and pest resistances. The temperature-sensitive genetic male sterility (TGMS) system, two-line hybrid, provides a great potential for improving food production by hybrids. The use of TGMS system is simple, inexpensive, effective, and eliminates the limitations of the conventional three-line system.


We evaluated exotic TGMS rice lines controlled by 3 tgms genes obtained from the International Rice Research Institute (IRRI) for their potential use for hybrid production by studying their fertile and sterile conditions, and their adaptability to Thai environments. The promising TGMS lines were used as female parents for 2-line hybrid production. Currently, several hybrids generated from the exotic TGMS lines were planted for yield evaluation in several Rice Researcher Centers. In addition, the exotic tgms genes were used to generate new TGMS lines, which are now using as female parents in 2-line hybrid production. Using gene-specific markers, we also study genetic diversity of 101 rice lines, including 27 Thai commercial cultivars, 11 Thai landraces, 5 species of wild rice, 57 germplasms having desirable traits obtained from IRRI, and a well known japonica (Nipponbarea). The information obtained is used for selecting parents used for two-line hybrid production.

Marker Assisted Selection and cultivar identification
Using information available in public databases, we located 3 tgms genes in rice genome and developed closely linked markers to these genes. We identified a 70 kb deletion in TGMS line, controlled by tms2. The candidate gene and the gene flanking the deletion were used to develop linked markers for selection of this gene. Specific markers linked to the other two tgms genes are also developed.
In addition, we generated single nucleotide polymorphism (SNP) and short insertion/deletion (indel) markers, and applied these markers for cultivar identification. Using 8 of these markers, we are ale to differentiate all 27 commercial Thai rice lines such as, KDML105, Phathumthani 1, Chai Nat 1, Suphanburi 1, Suphanburi 90, Pisanulok 2, Surin 1, RD 7, RD 23, and RD 27. Furthermore, molecular markers such as SSR and AFLP are used for DNA fingerprinting of hybrids and their parents. The cultivar-specific markers are useful for detection of seed purity, protection of breeders’ rights, and accelerating plant breeding programs.

Characterization of Genes Controlling Flower and Seed Development under Abiotic Stresses
Drought, salt, and high temperature are major abiotic stresses limiting rice growth and productivity. Changes in gene expression are important factors for adaptations leading to tolerance, or failing to adapt to the stress resulting in yield reduction or death of the plants. Using published information, we study expression of several selected genes in panicles of several drought/salt sensitive and tolerant rice lines. In addition, we identified proteins/genes controlling flower and seed development under high temperature based on proteomic analysis. The results gained from our studies could be used in traditional breeding as marker assisted selection and/or in genetic engineering for development of cultivars having desirable traits.

Plant Genetic Engineering

Understanding gene function is important for crop improvement. Genetic manipulation is critical for understanding gene function used for improvement of agronomic traits. Currently, we are using RNAi and miRNA to test function of interested genes

Tissue-Specific and Inducible Promoters

We are searching for tissue-specific expression and inducible promoters. Such promoters could be used to regulate gene expression. Currently, we identified a panicle specific and drought inducible promoter from a rice cultivar. We are searching for panicle specific and ethanol inducible promoters. In the near future, transformation using inducible promoter will be one of our major works to confirm function of genes controlling desirable agronomic traits.

National Center for Genetic Engineering and Biotechnology (BIOTEC)
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