Effect of Geographical Indication Information on Consumer Acceptability of Cooked Aromatic Rice.

Geographical indication (GI) labeling is used to represent information about specific geographical origins of target products. This study aimed at determining the impact of GI information on sensory perception and acceptance of cooked aromatic rice samples. Ninety-nine participants evaluated cooked rice samples prepared using each of three aromatic rice varieties both with and without being provided with GI information. Participants rated the acceptance and intensity of the cooked rice samples in terms of appearance, aroma, flavor, texture, and overall liking, and also reported how important the GI information was to them. The results showed that consumers rated the cooked rice samples higher in appearance and overall liking when provided with GI information. Interestingly, participants who valued "state-of-origin" information more highly exhibited increased hedonic ratings of cooked rice samples when provided with GI information, but not when no GI information was given. Participants provided with GI information rated flavor or sweetness intensities of cooked aromatic rice samples closer to just-about-right than those without such information. This study provides empirical evidence about how GI information modulates sensory perception and acceptance of cooked aromatic rice samples. The findings will help rice industry, farmers, and traders better employ GI labeling to increase consumer acceptability of their rice products.

Morphology of Rice Seed Development and Its Influence on Grain Quality.

Various quality attributes of rice seed are affected by the wide array of biochemical products accumulated during the course of reproductive development and the environmental conditions which impact the grain composition. The staging of rice plant reproductive development is needed in experiments to define phase transitions of seed biology. The application of the nomenclature and criteria of the rice growth staging system can facilitate recording the reproductive development by distinct stages. The meaningful progression from one stage to another in time can then be evaluated in a tabular or graphic manner. In order to determine the developmental stages of rice in experiments, it is desirable to select a representative group of plants and to record the development of those plants. We provide procedures for efficiently (1) observing and recording development of rice plants and (2) collecting, storing and seperating seed by developmental stages. It is necessary to divide seeds into differing groups to track development from fertilization until maturity. The earliest seeds to be fertilized on a panicle are superior grains and the latter seeds to develop are inferior grains. In some cases, it is necessary to divide individual seeds into the aforementioned groups and the different stages of development for various analyses. A procedure for dividing seeds into differing stages of development is presented to more appropriately select seeds for further analysis. The developmental record can then be statistically and graphically analyzed to better understand responses to treatments and interactions among treatments, years, and locations.

Identification of candidate genes associated with positive and negative heterosis in rice.

To identify the genes responsible for yield related traits, and heterosis, massively parallel signature sequencing (MPSS) libraries were constructed from leaves, roots and meristem tissues from the two parents, 'Nipponbare' and '93-11', and their F1 hybrid. From the MPSS libraries, 1-3 million signatures were obtained. Using cluster analysis, commonly and specifically expressed genes in the parents and their F1 hybrid were identified. To understand heterosis in the F1 hybrid, the differentially expressed genes in the F1 hybrid were mapped to yield related quantitative trait loci (QTL) regions using a linkage map constructed from 131 polymorphic simple sequence repeat markers with 266 recombinant inbred lines derived from a cross between Nipponbare and 93-11. QTLs were identified for yield related traits including days to heading, plant height, plant type, number of tillers, main panicle length, number of primary branches per main panicle, number of kernels per main panicle, total kernel weight per main panicle, 1000 grain weight and total grain yield per plant. Seventy one QTLs for these traits were mapped, of which 3 QTLs were novel. Many highly expressed chromatin-related genes in the F1 hybrid encoding histone demethylases, histone deacetylases, argonaute-like proteins and polycomb proteins were located in these yield QTL regions. A total of 336 highly expressed transcription factor (TF) genes belonging to 50 TF families were identified in the yield QTL intervals. These findings provide the starting genomic materials to elucidate the molecular basis of yield related traits and heterosis in rice.

Root distribution and potential interactions between allelopathic rice, sprangletop (Leptochloa spp.), and barnyardgrass (Echinochloa crus-galli) based on ¹³C isotope discrimination analysis.

Weed-suppressive rice cultivars hold promise for improved and more economical weed management in rice. Interactions between roots of rice and weeds are thought to be modulated by the weed-suppressive activity of some rice cultivars, but these phenomena are difficult to measure and not well understood. Thus, above-ground productivity, weed suppression, and root distribution of 11 rice cultivars and two weed species were evaluated in a drill-seeded, flood-irrigated system at Stuttgart, Arkansas, USA in a two-year study. The allelopathic cultivars, PI 312777 and Taichung Native 1 (TN-1), three other weed-suppressive cultivars, three indica-derived breeding selections, and three non-suppressive commercial cultivars were evaluated in field plots infested with barnyardgrass (Echinochloa crus-galli (L.) Beauv.) or bearded sprangletop (sprangletop, Leptochloa fusca (L.) Kunth var. fascicularis (Lam.) N. Snow). The allelopathic cultivars produced more tillers and suppressed both weed species to a greater extent than did the breeding selections or the non-suppressive cultivars. (13)C isotope discrimination analysis of mixed root samples to a depth of 15 cm revealed that the allelopathic cultivars typically produced a greater fraction of their total root mass in the surface 0-5 cm of soil depth compared to the breeding selections or the non-suppressive cultivars, which tended to distribute their roots more evenly throughout the soil profile. These trends in root mass distribution were apparent at both early (pre-flood) and late-season stages in weed-free and weed-infested plots. Cultivar productivity and root distribution generally responded similarly to competition with the two weed species, but barnyardgrass reduced rice yield and root mass more than did sprangletop. These findings demonstrate for the first time that roots of the allelopathic cultivars PI 312777 and TN-1 explore the upper soil profile more thoroughly than do non-suppressive cultivars under weed-infested and weed-free conditions in flood-irrigated U.S. rice production systems. They raise the interesting prospect that root proliferation near the soil surface might enhance the weed-suppressive activity of allelochemical exudates released from roots. Plant architectural design for weed suppressive activity should take these traits into consideration along with other proven agronomic traits such as high tillering and yield.

Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.).

Harvest index is a measure of success in partitioning assimilated photosynthate. An improvement of harvest index means an increase in the economic portion of the plant. Our objective was to identify genetic markers associated with harvest index traits using 203 O. sativa accessions. The phenotyping for 14 traits was conducted in both temperate (Arkansas) and subtropical (Texas) climates and the genotyping used 154 SSRs and an indel marker. Heading, plant height and weight, and panicle length had negative correlations, while seed set and grain weight/panicle had positive correlations with harvest index across both locations. Subsequent genetic diversity and population structure analyses identified five groups in this collection, which corresponded to their geographic origins. Model comparisons revealed that different dimensions of principal components analysis (PCA) affected harvest index traits for mapping accuracy, and kinship did not help. In total, 36 markers in Arkansas and 28 markers in Texas were identified to be significantly associated with harvest index traits. Seven and two markers were consistently associated with two or more harvest index correlated traits in Arkansas and Texas, respectively. Additionally, four markers were constitutively identified at both locations, while 32 and 24 markers were identified specifically in Arkansas and Texas, respectively. Allelic analysis of four constitutive markers demonstrated that allele 253 bp of RM431 had significantly greater effect on decreasing plant height, and 390 bp of RM24011 had the greatest effect on decreasing panicle length across both locations. Many of these identified markers are located either nearby or flanking the regions where the QTLs for harvest index have been reported. Thus, the results from this association mapping study complement and enrich the information from linkage-based QTL studies and will be the basis for improving harvest index directly and indirectly in rice.

Utilizing the genetic diversity within rice cultivars.

Plant breeding of rice emphasizes improvement in yield, disease resistance, and milling quality. Numerous other traits (e.g., bran carotenoids) that historically have not been selected for could provide added value in expanding niche markets, as well as be useful tools for understanding the genetic control of these traits. Residual heterozygosity is present in many rice cultivars; therefore, it is possible to select for different alleles within an existing cultivar. By identifying and using cultivars with high levels of variability for a trait, we were able to develop separate lines from single cultivars that showed high and low levels of that trait. The rice cultivar RU9101001 and the warm- and cold-sprouting lines that were derived from it were used to demonstrate that residual heterozygosity was present within a cultivar and that the original heterozygosity was separated in the derived lines. Rice simple sequence repeat markers were heterozygous in the parent RU9101001 cultivar, but the cold-sprouting lines were homozygous for one set of alleles and the warm-sprouting lines were homozygous for the other set. Through detailed phenotypic screening, we developed lines that exhibited low and high levels of the following traits in the specified cultivars: cold-sprouting from RU9101001 and Bonnet 73, postharvest yellowing from Tominishiki, early tillering from Hei Jaio and Tominishiki, and bran carotenoid levels from Spring. If variability exists in a cultivar, then utilization of residual heterozygosity may provide a quicker and more efficient means to develop lines with special characteristics using cultivars that are already agronomically valuable or to develop near isogenic lines for genetic and biochemical investigations.

Mapping QTLs for improving grain yield using the USDA rice mini-core collection.

Yield is the most important and complex trait for genetic improvement in crops, and marker-assisted selection enhances the improvement efficiency. The USDA rice mini-core collection derived from over 18,000 accessions of global origins is an ideal panel for association mapping. We phenotyped 203 O. sativa accessions for 14 agronomic traits and identified 5 that were highly and significantly correlated with grain yield per plant: plant height, plant weight, tillers, panicle length, and kernels/branch. Genotyping with 155 genome-wide molecular markers demonstrated 5 main cluster groups. Linkage disequilibrium (LD) decayed at least 20 cM and marker pairs with significant LD ranged from 4.64 to 6.06% in four main groups. Model comparisons revealed that different dimensions of principal component analysis affected yield and its correlated traits for mapping accuracy, and kinship did not improve the mapping in this collection. Thirty marker-trait associations were highly significant, 4 for yield, 3 for plant height, 6 for plant weight, 9 for tillers, 5 for panicle length and 3 for kernels/branch. Twenty-one markers contributed to the 30 associations, because 8 markers were co-associated with 2 or more traits. Allelic analysis of OSR13, RM471 and RM7003 for their co-associations with yield traits demonstrated that allele 126 bp of RM471 and 108 bp of RM7003 should receive greater attention, because they had the greatest positive effect on yield traits. Tagging the QTLs responsible for multiple yield traits may simultaneously help dissect the complex yield traits and elevate the efficiency to improve grain yield using marker-assisted selection in rice.

Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection.

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.

Rice amylopectin fine structure variability affects starch digestion properties.

UNLABELLED: The possibility to identify or develop new rice cultivars with low glycemic response was investigated. Twelve rice cultivars with a narrow range of amylose contents were selected based on their wide variation in rapid viscoanalyzer (RVA) pasting breakdown to study the relationship between starch digestibility and amylopectin fine structure and pasting properties. Rice flour samples were cooked for in vitro digestibility analysis using the standard Englyst assay. RVA was performed for pasting properties of starches. Results showed that rapidly digestible starch (RDS) was highly and negatively correlated (r = -0.86, p < 0.01; r = -0.81, p < 0.01) with FrI long and FrII intermediate/short debranched amylopectin linear chains, respectively, and positively correlated (r = 0.79; p < 0.01) with FrIII very short linear chains. Slowly digestible (SDS) starch was positively correlated (r = 0.80, p < 0.01; 0.76, p < 0.01) with FrI and FrII, respectively, and negatively correlated (r = -0.76, p < 0.01) with FrIII. RVA breakdown viscosity was positively correlated (r = 0.88, p < 0.01) with RDS and negatively correlated (r = -0.89, p < 0.01) with SDS. Thus, the RVA method potentially could be used as a screening tool for starch digestion properties. This study reveals a molecular basis in amylopectin fine structure variability for starch digestion properties in rice cultivars and could have value in identifying slowly digesting cultivars as well as developing a breeding strategy to produce low glycemic rice cultivars. KEYWORDS: Rice; starch; RVA; amylopectin; digestibility.

Rice Pi-ta gene Confers Resistance to the Major Pathotypes of the Rice Blast Fungus in the United States.

ABSTRACT The Pi-ta gene in rice prevents the infection by Magnaporthe grisea strains containing the AVR-Pita avirulence gene. The presence of Pi-ta in rice cultivars was correlated completely with resistance to two major pathotypes, IB-49 and IC-17, common in the U.S. blast pathogen population. The inheritance of resistance to IC-17 was investigated further using a marker for the resistant Pi-ta allele in an F(2) population of 1,345 progeny from a cross of cv. Katy with experimental line RU9101001 possessing and lacking, respectively, the Pi-ta resistance gene. Resistance to IC-17 was conferred by a single dominant gene and Pi-ta was not detected in susceptible individuals. A second F(2) population of 377 individuals from a reciprocal cross between Katy and RU9101001 was used to verify the conclusion that resistance to IC-17 was conferred by a single dominant gene. In this cross, individuals resistant to IC-17 also were resistant to IB-49. The presence of Pi-ta and resistance to IB-49 also was correlated with additional crosses between 'Kaybonnet' and 'M-204', which also possess and lack Pi-ta, respectively. A pair of primers that specifically amplified a susceptible pi-ta allele was developed to verify the absence of Pi-ta. We suggest that Pi-ta is responsible for resistance to IB-49 and IC-17 and that both races contain AVR-Pita genes.