Estimating canopy cover from color digital camera image of rice field

Canopy cover (CC) is a good predictor variable for plant growth parameters such as leaf area index and aboveground biomass. A nondestructive, low-cost, and convenient method is presented for estimating CC using digital camera image analysis. CC was estimated by the ratio of plant pixels to total pixels of digital camera image of rice field. To determine the criteria for segmenting the rice plant from variable soil background, three mosaic images for rice plant, flooded/bare soil, and algae-infested background were prepared from digital camera images that were taken in various field conditions. An image analysis program was developed in Visual Basic to extract red, green, and blue (RGB) features from the mosaic images, calculate RGB-based color indices, and compute the minimum segmentation error for separating rice plant from background. When judged by the segmentation error, modified excessive green index (MEGI) showed the highest potential for segmenting rice plant from flooded/bare soil background, followed by normalized green (g) and excessive green index (EGI). At the threshold MEGI value of 0.03, the segmentation error was the lowest as 0.13%. Any single index considered was not satisfactory in segmenting rice plant from algae-infested background. However, a discriminant function of 1.2553EGI + 0.01735G − 0.01474B was successful in segmenting rice plant from flooded/bare soil and algaeinfested background with segmentation errors of 0.34 and 1.17%, respectively. CC for four rice varieties from tillering to booting stage was estimated based on the threshold value of MEGI and discriminant function and also manually using commercial software. Both estimates of CC showed good relationship of r² = 0.94, suggesting that a digital camera could be used efficiently for measuring the CC of rice field.     

Viewpoints on synergising ASEAN academic visibilities through research collaboration and the establishment of an ASEAN Citation Index Database1

This opinion article expresses two key viewpoints regarding the options for Association of South‐East Asian Nations (ASEAN) universities in pursuit of fulfilling the demand for greater research visibility and academic reputation. The first viewpoint outlines the importance of promoting research collaboration among ASEAN researchers and their international peers in increasing the visibility and impact of ASEAN research. The second viewpoint examines the ASEAN research characteristics, the challenges and existing best practices of its journal publishing landscape, the potential role of non‐ASEAN international journals in improving the profile of ASEAN research and explores the needs and benefits of establishing an ASEAN Integrated Journal Publishing Network (IJPN). It is through these combined approaches, we believe, that effective policy change, the standardisation of publishing structure, procedures, and systems to drive journal development, improvement of journal quality, and establishment of a consistent framework for measuring researcher performance will result. This article also includes a proposal for the IJPN structure and implementation plan, and highlights the key benefits of taking a collaborative approach to achieving this common goal.     

Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia

Very rare cases of human T cell acute lymphoblastic leukemia (T-ALL) harbor chromosomal translocations that involve NOTCH1, a gene encoding a transmembrane receptor that regulates normal T cell development. Here, we report that more than 50% of human T-ALLs, including tumors from all major molecular oncogenic subtypes, have activating mutations that involve the extracellular heterodimerization domain and/or the C-terminal PEST domain of NOTCH1. These findings greatly expand the role of activated NOTCH1 in the molecular pathogenesis of human T-ALL and provide a strong rationale for targeted therapies that interfere with NOTCH signaling.     

Three AFLP markers tightly linked to the genic male sterility <Emphasis Type="Italic">ms</Emphasis><Subscript><Emphasis Type="Italic">3</Emphasis></Subscript> gene in chili pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) and conversion to a CAPS marker

Genic male sterility (GMS) has long been used as a tool for hybrid seed production in chili pepper (Capsicum annuum L.). We developed DNA markers linked to the GMS ms ₃ gene in a segregating population using bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) techniques. The segregating population was subjected to BSA-AFLP with 512 primer combinations. Three AFLP markers (Eagg/Mccc₂₇₆, Eagc/Mctt₁₇₈, and Ecag/Mtgc₂₀₄) were identified as tightly linked to the ms ₃ locus. Among them, we converted the AFLP marker Ecag/Mtgc₂₀₄ to the cleavage amplified polymorphic sequence (CAPS) marker, named GMS3-CAPS, based on sequencing analysis of internal and flanking regions for the markers between male-fertile and sterile plants. This marker will be useful for pepper breeding using the GMS system.     

Genetic variant BDNF (Val66Met) polymorphism alters anxiety-related behavior

A common single-nucleotide polymorphism in the brain-derived neurotrophic factor (BDNF) gene, a methionine (Met) substitution for valine (Val) at codon 66 (Val66Met), is associated with alterations in brain anatomy and memory, but its relevance to clinical disorders is unclear. We generated a variant BDNF mouse (BDNF(Met/Met)) that reproduces the phenotypic hallmarks in humans with the variant allele. BDNF(Met) was expressed in brain at normal levels, but its secretion from neurons was defective. When placed in stressful settings, BDNF(Met/Met) mice exhibited increased anxiety-related behaviors that were not normalized by the antidepressant, fluoxetine. A variant BDNF may thus play a key role in genetic predispositions to anxiety and depressive disorders.     

Genetic, agronomic and quality comparisons of two 1AL.1RS. wheat-rye chromosomal translocations

The 1AL.1RS wheat-rye chromosomal translocation originally found in ‘Amigo’ wheat possesses resistance genes for stem rust, powdery mildew and greenbug biotypes B and C, but also has a negative effect on wheat processing quality. Recently, a second 1AL.1RS translocation carrying Gb6, a gene conferring resistance to greenbug biotypes B, C, E, G and I, was identified in the wheat germplasm line ‘GRS1201′. Protein analytical methods, and the DNA polymerase chain reaction were used to identify markers capable of differentiating the 1RS chromosome arms derived from ‘Amigo’ and ‘GRS1201′. The secalin proteins encoded by genes on 1RS chromosome arms differed in ‘Amigo’ and ‘GRS1201′. A 70 kDa secalin was found in the ‘Amigo’1AL.1RS, but did not occur in the ‘GRS1201’1AL.1RS. Polymorphisms detected by PCR primers derived from a family of moderately repetitive rye DNA sequences also differentiated the two translocations. When ‘GRS1201’was mated with a non-1RS wheat, no recombinants between 1RS markers were observed. In crosses between 1RS and non-1RS parents, both DNA markers and secalins would be useful as selectable markers for 1RS-derived greenbug resistance. Recombination between 1RS markers did occur when 1RS from ‘Amigo’ and 1RS from ‘GRS1201’were combined, but in such intermatings, the molecular markers described herein could still be used to develop a population enriched in lines carrying Gb6. No differences in grain yield or grain and flour quality characteristics were observed when lines carrying 1RS from ‘Amigo’ were compared with lines with 1RS from ‘GRS1201′. Hence, differences in secalin composition did not result in differential quality effects. When compared with sister lines with 1AL.1AS derived from the wheat cultivar ‘Redland’, lines with ‘GRS1201’had equal grain yield, but produced flours with significantly shorter mix times, weaker doughs, and lower sodium dodecyl sulphate sedimentation volumes.     

Estimating water footprint of paddy rice in Korea

The purpose of this article is to examine the issues of low grain self-sufficiency and the high portion of agricultural water use in South Korea, and to trace the water footprint (WF) of rice products. In this study, different types of water use were described as green, blue, and gray WFs and were analysed using suitable estimation methods to determine irrigation water requirements in South Korea. Virtual water (VW) import and export of rice product were calculated based on international trade statistics during 2004–2009, and the WF of the national consumption was estimated. The WF of rice was 844.5 m³/ton, and green, blue, and gray water accounted for 294.5, 501.6, and 48.4 m³/ton, respectively. The VW import and export were 404.17 and 2.03 Mm³/year, respectively, against an import 199.5 times that of the export. Three countries (China, USA, and Thailand) accounted for over 95 % of the total VW imports of rice products into South Korea. The total WF was 5,712.08 Mm³/year, thus the WF per capita for rice was estimated at 118.1 m³/year. The internal WF of rice consumption was 5,308.05 Mm³/year, and the external WF was 404.03 Mm³/year. The WF of total agricultural water use should be analyzed for sustainable agricultural production and water management, and these results should be applied in establishing long-term policies for agricultural water resources.     

Analysis of Variation in Anthocyanin Composition in Korean Coloured Potato Cultivars by LC-DAD-ESI-MS and PLS-DA

Anthocyanin concentration and composition and the effect of steaming and baking on these were evaluated in tubers of Korean red- and purple-fleshed potato cultivars and breeding clones using liquid chromatography with diode array detection and electrospray ionization-mass spectrometry (LC-DAD-ESI-MS). Twenty-six anthocyanins were isolated, of which 24 were identified. Remarkably, five cis isomers were identified, of which four, viz., cis-petanin, cis-peonanin, petunidin 3-cis-caffeoylrutinoside-5-glucoside, and petunidin 3-cis-feruloylrutinoside-5-glucoside, are reported for the first time. Moreover, pelargonidin 3-p-coumaroylrutinoside-5-glucoside (pelanin), peonidin 3-p-coumaroylrutinoside-5-glucoside (peonanin) and petunidin 3-p-coumaroylrutinoside-5-glucoside (petanin) were identified as the principal anthocyanins. We found that the total anthocyanin content of coloured potatoes was decreased by steaming and baking compared with the raw state. In addition, we performed partial least square discriminant analysis (PLS-DA) to discriminate between the analyzed anthocyanins. Cis isomers seemed to play a vital role as a biomarker in the PLS-DA model based on the type of processing and colour of the tubers.