Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a custom-designed Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our long-term goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.     

Enhancement of acid phosphatase activity in Capsicum annuum L. plants in response to phosphate deficiency

This study examined acid phosphatase activity in the extracts of Capsicum annuum L. cv. ”︁Sweet Banana” seedlings grown axenically on water-agar medium or plants grown in a hydroponic system with or without phosphate. Initially, no elevated phosphatase activity was detected in the root surface, in root surface extractions or cell-free tissue extracts from plants that were not showing morphological symptoms of stress. Then elevated specific phosphatase activity was evident in all organ tissue extracts of the plants that showed signs of growth inhibition. The increase in specific activity in the cell free extracts of different organs appeared to be primarily the result of increased activity of the dominant isozyme present in all these extracts, instead of due to de novo synthesis of new isozymes. These and other experiments indicate the lack of phosphate starvation-inducible (psi) excreted phosphatase in Capsicum annuum L. cv. ”︁Sweet Banana”. Some limitations with the use of XP, 5-bromo-4-chloro-indolyl phosphate p-toluidine, particularly when incorporated into growth media and buffer with or without phosphate for the study of phosphate starvation-inducible excreted phosphatase activity were noted.     

Locally Grown Oysters in Hawai‘i: Chef Preference and Local Premium?

Locally grown oysters became available in Hawai‘i in 2014, for the first time in decades. It is unclear if these bivalve shellfish will successfully infiltrate the market when imported products similar in nature have long been the only source of fresh, shell stock products. This study investigates chef preferences for oyster attributes to determine marginal willingness to pay for locally grown oysters. A survey containing a questionnaire and a choice experiment was administered to restaurant chefs throughout Hawai‘i who currently offer oysters on their menus. The study examines trade‐offs made between attributes related to price, growout site, freshness, and supply constancy, respectively. Responses were aggregated and data were fit to a random parameters logit model. Results suggest that respondents derive the most utility from oysters that are fresh, grown locally, and supplied on an as‐available basis. The least desired products are, therefore, those that are frozen, imported from foreign sources, and supplied on a set schedule. Chefs are willing to pay an additional $5.25 for one dozen oysters that are grown locally. This evidence of an existing price premium indicates that labeling local oysters as such may be a valuable marketing strategy.     

Rapid Population Analysis of Magnaporthe grisea by Using rep-PCR and Endogenous Repetitive DNA Sequences

ABSTRACT DNA samples from Magnaporthe grisea isolates were fingerprinted by using repetitive element-based polymerase chain reaction (rep-PCR) with two outwardly directed primer sequences from Pot2, an element found in approximately 100 copies in the fungal genome. Variable length fragments, defining the sequences lying between these elements, were generated, and fingerprint patterns specific for individual strains were established. "Long PCR" conditions, including higher pH (9.2) and increased extension time (10 min) were used to amplify DNA fragments ranging from 400 bp to longer than 23 kb. Polymorphisms specific to M. grisea strains were generated, allowing inference of their genetic relationships. Segregation analysis was used to confirm single-locus inheritance for the fragments amplified by rep-PCR. Cluster analysis revealed robust groupings that corresponded to previously determined MGR586 restriction fragment length polymorphism lineages of the rice-infecting strains of the pathogen. We have also demonstrated the utility of rep-PCR to differentiate isolates that infect rice from those that infect nonrice hosts. DNA fingerprinting by Pot2 rep-PCR provides an efficient means to monitor the population dynamics of the blast pathogen. Because of the method's low cost and ease in application, it is now feasible to conduct large-scale population studies to understand the impact of host genotypes on pathogen evolution.     

Detecting the non-breeding region and migration route of Whimbrels(Numenius phaeopus rogachevae)in the East Asian-Australasian Flyway

Determining the migration routes and connections of migratory birds at the population level helps clarify intraspecific differences in migration.Five subspecies...     

Application of the Neospora caninum IgG avidity ELISA in assessment of chronic reproductive losses after an outbreak of neosporosis in a herd of beef cattle.

Point-source infections are most likely the cause for Neospora caninum-induced abortion outbreaks in cattle, whereas an increased annual abortion rate may be a consequence of vertical transmission. The aims of the present study were to examine the reproductive effects of neosporosis in a beef herd for 3 years, after a point-source outbreak and to use IgG avidity serology to examine the chronicity of infections and patterns of transmission. During the study, 76-78% of animals were seropositive for N. caninum. The pregnancy rate varied from 88% to 94%, without any reduction in the pregnancy rate of seropositive cows compared with seronegative cows. The annual abortion rate was 2.5-5.5%, and all but 1 abortion occurred in seropositive dams. The efficiency of vertical transmission was estimated to be 85%. Several calves, born to seronegative dams, were seropositive at 6-13 months of age, indicating a 22% mean annual rate of horizontal transmission. The mean avidity in seropositive cows increased from 30 during the initial outbreak to 74 after 3 years. The mode of IgG avidity was 21-40 during the initial abortion outbreak, 41-60 after 1 year, and 61-80 after 2 and 3 years. The results reveal high annual rates of both vertical and horizontal transmission of N. caninum in a herd of beef cows and provide further validation on the ability of the N. caninum IgG avidity ELISA to accurately assess the chronicity of infection.     

Mapping of leaf and neck blast resistance genes with resistance gene analog, RAPD and RFLP in rice

An F₈ recombinant inbred population was constructed using a commercial indica rice variety Zhong 156 as the female parent and a semidwarf indica variety Gumei 2 with durable resistance to rice blast as the male parent. Zhong 156 is resistant to the fungus race ZC₁₅ at the seedling stage but susceptible to the same race at the flowering stage. Gumei 2 is resistant to ZC₁₅ at both stages. The blast resistance of 148 recombinant inbred lines was evaluated using the blast race ZC₁₅. Genetic analysis indicated that the resistance to leaf blast was controlled by three genes and the presence of resistant alleles at any loci would result in resistance. One of the three genes did not have effects at the flowering stage. Two genes, tentatively assigned as Pi24(t) and Pi25(t), were mapped onto chromosome 12 and 6,respectively, based on RGA (resistance gene analog), RFLP and RAPD markers. Pi24(t) conferred resistance to leaf blast only, and its resistance allele was from Zhong 156. Pi25(t) conferred resistance to both leaf and neck blast, and its resistance allele was from Gumei 2. In a natural infection test in a blast hot-spot, Pi25(t) exhibited high resistance to neck blast, while Pi24(t) showed little effect. This revised version was published online in August 2006 with corrections to the Cover Date.     

Solute redistribution during normal freezing

Mathematical models used in metallurgy to describe solute partitioning are applied to solute distribution in ice crystals. Results demonstrate that the model developed under the assumption of ideal directional freezing can be used to estimate distribution coefficients from experimental data. The deviation of experimental results from normal freezing theory is consistent with the Burton-Slichter film theory model.