Association between alleles of the waxy gene and traits of grain quality in Philippine Seed Board rice varieties

The association between alleles of the Waxy gene, defined by the number of CT repeats on exon 1, and traits of grain quality was carried out using 47 Philippine Seed Board rice varieties. The major alleles of the Waxy gene in the set of 47 were (CT), (CT) (CT)and (CT)20. Varieties were divided into four clusters based on the metric of each trait of grain quality. (CT) (27-32% amylose content (AC)) and (CT) (22-30% AC) were mainly in clusters 3 and 4 (hard texture), and (CT) (20-24% AC) and (CT) (18- 27% AC) were exclusively in grain quality cluster 1 (soft texture) and 2 (medium texture). (CT) associated negatively with AC in this set. Only six (CT) and one (CT) rices were in cluster 4 (high-AC low-GT) and had high RVA consistency (final viscosity - trough viscosity) > 200 RVU. (CT) seemed to be the preferred source of low-intermediate AC in the Philippine rice breeding program, followed by (CT)

Efforts to capture high amylose in rice

Screening of wild and cultivated rice in IRRI germplasm collection revealed that majority have intermediate apparent amylose content. It appears that ancient farmers selected rice based on texture of the lower amylose varieties, considering that the majority of rice consumers today prefer intermediate to soft-textured rice. Furthermore, 30% seems to be the natural upper natural limit of amylose levels in wild-type rice. If this is the case, the rich biodiversity of rice has been subjected to the bottleneck of domestication to select for grains that have superior cooking and eating but not nutritional or satiating qualities considering that the majority of rice consumers today eat rice three times a day. On the other hand, the amylose content of available rice mutants with deficient SBEIIb or an over-expressed GBSSI also revealed amylose levels of around 35% which is significantly lower by comparison with other high amylose cereals, whose amylose content ranges from 70–90%. Hence, to produce the high amylose phenotype in rice, one might need to target different sets of enzymes or regulatory pathways. Since increasing the amylose levels in rice might mean a concomitant increase in its resistant starch content and in its levels of satiety, and a decrease in its glycemic response, developing high amylose rice by biotechnology is imperative. This type of rice will be important not only in addressing the growing obesity epidemic which now also affects the developing countries but also as a basis of novel degradable biopolymers and for further elucidating the mechanisms of starch synthesis in the cereal endosperm. In this paper, we also present the status of our research project which aims to silence the expression of SBEIIa, SBEIIb and SSIIa singly or in combination using microRNA and RNAi silencing technologies with the aim of increasing the amylose levels in rice beyond its natural limits

Balancing the double‐edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms

Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS contributes to a lower glycemic index. A genome‐wide association study coupled with targeted gene association studies was conducted utilizing a diverse panel of 281 resequenced Indica rice lines comprising of ~2.2 million single nucleotide polymorphisms. Low‐to‐intermediate RS phenotypic variations were identified in the rice diversity panel, resulting in novel associations of RS to several genes associated with amylopectin biosynthesis and degradation. Selected rice lines encoding superior alleles of SSIIa with medium RS and inferior alleles with low RS groups were subjected to detailed transcriptomic, metabolomic, non‐starch dietary fibre (DF), starch structural and textural attributes. The gene regulatory networks highlighted the importance of a protein phosphatase alongside multiple genes of starch metabolism. Metabolomics analyses resulted in the identification of several metabolite hubs (carboxylic acid, sugars and polyamines) in the medium RS group. Among DF, mannose and galactose from the water‐insoluble fraction were found to be highly associated with low and medium RS lines, respectively. Starch structural analyses revealed that a moderate increase in RS is also linked to an elevation of amylose 1 and amylose 2 fractions. Although rice lines with medium RS content negatively affected textural and viscosity properties in comparison to low RS, the textural property of medium RS lines was in the same acceptable range as IR64, a rice mega variety popular in Asia

Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing

The inactivation of starch branching IIb (SBEIIb) in rice is traditionally associated with elevated apparent amylose content, increased peak gelatinization temperature, and a decreased proportion of short amylopectin branches. To elucidate further the structural and functional role of this enzyme, the phenotypic effects of down-regulating SBEIIb expression in rice endosperm were characterized by artificial microRNA (amiRNA) and hairpin RNA (hp-RNA) gene silencing. The results showed that RNA silencing of SBEIIb expression in rice grains did not affect the expression of other major isoforms of starch branching enzymes or starch synthases. Structural analyses of debranched starch showed that the doubling of apparent amylose content was not due to an increase in the relative proportion of amylose chains but instead was due to significantly elevated levels of long amylopectin and intermediate chains. Rices altered by the amiRNA technique produced a more extreme starch phenotype than those modified using the hp-RNA technique, with a greater increase in the proportion of long amylopectin and intermediate chains. The more pronounced starch structural modifications produced in the amiRNA lines led to more severe alterations in starch granule morphology and crystallinity as well as digestibility of freshly cooked grains. The potential role of attenuating SBEIIb expression in generating starch with elevated levels of resistant starch and lower glycaemic index is discussed

Vegetation analysis of the understory of a residual dipterocarp forest at the National Botanic Garden (Real, Quezon).

The trees and other woody perennials were the most dominant group of understory vegetation. They were predominated by the secondary forest species represented by Ficus botryocarpa, Connarus semide—candrus, Guioa sp. x and y, Canthium sp., and Syzygium sp. The primery forest species were represented by the dipterocarps Hones philippioensis and Parashorea malaanonan. The most common herbaceous plants are Mapania cuspidata and a species belonging to family Zingiberaceae. Crudia sE. was the dominant vine species present. The number of species encountered was higher during the dry than the rainy season. There were 42 new species observed during the dry season while 20 species present during the rainy season were absent in the dry season. Forty two species were observed common to both seasons. Variation in microenvironmental conditions were also noted between seaso,3. The indices of divert, and evenness were relatively high while dominance was low. Thi3 would imply species richness in the community and the adaptability the environment for the growth of a large number of species population.

Analysis of impacts of migrant settlers\u27 activities on forest ecosystem of the UP Quezon Land Grant Real, Quezon.

The interactions between the social system of the migrant farmers and the forest environment of the UP-Quezon Land Grant in Real, Quezon was evaluated using the conceptual framework of human ecology. The socio-economic characteristics and forest resource uses of the migrant farmers were obtained from interview of 56 farmer respondents and five key informants. The impacts of kaingin activities were assessed by comparing the newly-opened, one-year old, two- year old, three-year old and five-year old kaingins with a secondary forest as baseline. Fifty nine percent of the respondents were forest product gatherers while forty one percent were non-forest product gatherers. Charcoal-making and carabao logging were the main income sources from the forest. The other forest products obtained as sources of income were wild fruits, wild animals, firewood and rattan. The presence of ready market, the huge demand for forest products, lack of alternative sources of income and low farm productivity have strengthened the settlers\u27 dependence on forest product gathering. Forest product gathering was associated with absence of off-farm income and forested farm location. The age of the kainginero, educational attainment, perception of the forest value, size and number of land parcels, previous residence, previous occupation, knowledge of forestry laws and soil conservation and household size were not related to forest product gathering. Occupancy of the land grant and the use and condition of its forest and land resources have changed the settlers\u27 lifestyle, affected their income, nutrition and health conditions and impacted on community relationships as well as on the University of the Philippines\u27 administration of the area. Deforestation through kaingin-making, charcoal-making and carabao-logging has resulted in the changes in microclimatic conditions. Cultivation decreased soil pH, organic matter content and total nitrogen and available phosphorus and potassium of the soil. Kaingin-making has resulted in the lowering of species diversity and change in growth form and species composition from woody to herbaceous and from forest to grass-dominated stands.Very crucial issues for effective management of the UPQLG are the settlement of the land tenurial disputes and proper mix and balance of biophysical, social, political, incentives, technical and locational factors. This would entail a comprehensive survey of the area\u27s existing human and natural resources. Rational land use evaluation and allocation are imperative as well as the screening for occupants. Existing resource maps have to be updated and the boundaries should be properly marked. Identification and immediate segregation of critical watershed, forest and wildlife protection area and sanctuary are highly recommended to preserve the ecological integrity and uniqueness of the area. The National Botanic Garden should be kept intact and its activities should be enhanced through appropriate support-mechanisms