Mariafe Calingacion

The origin and evolution of fragrance in rice (Oryza sativa L.)

Fragrance in the grain is one of the most highly valued grain quality traits in rice, yet the origin and evolution of the betaine aldehyde dehydrogenase gene (BADH2) underlying this trait remains unclear. In this study, we identify eight putatively nonfunctional alleles of the BADH2 gene and show that these alleles have distinct geographic and genetic origins. Despite multiple origins of the fragrance trait, a single allele, badh2.1, is the predominant allele in virtually all fragrant rice varieties today, including the widely recognized Basmati and Jasmine types. Haplotype analysis allowed us to establish a single origin of the badh2.1 allele within the Japonica varietal group and demonstrate the introgression of this allele from Japonica to Indica. Basmati-like accessions were nearly identical to the ancestral Japonica haplotype across a 5.3-Mb region flanking BADH2 regardless of their fragrance phenotype, demonstrating a close evolutionary relationship between Basmati varieties and the Japonica gene pool. These results clarify the relationships among fragrant rice varieties and challenge the traditional assumption that the fragrance trait arose in the Indica varietal group.

Diversity of Global Rice Markets and the Science Required for Consumer-Targeted Rice Breeding

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a ‘one size fits all’ crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.

Is there a second fragrance gene in rice

Aromatic rice is highly prized by most rice consumers, and many countries cultivate traditional and improved aromatic varieties. 2-Acetyl-1-pyrroline (2AP) is the major aromatic compound in rice, and is believed to accumulate because of an eight-base-pair (8-bp) deletion in an allele at the fragrance locus. In this study, 2AP was quantified and the presence or absence of the fragrance allele (fgr) was determined in 464 samples of traditional varieties of rice from the T.T. Chang Genetic Resources Centre at the International Rice Research Institute. It was shown that a number of aromatic varieties, primarily from South and South-East Asia, do not carry the 8-bp deletion, but 2AP was identified in both raw and cooked rice of these varieties. We suggest that the 8-bp deletion in fgr is not the only cause of aroma, and at least one other mutation drives the accumulation of 2AP. The amount of 2AP in most uniform fgr genotypes was not significantly different from that in aromatic nfgr genotypes, but several fgr genotypes, primarily from South Asia, reproducibly accumulated exceptionally large amounts of 2AP. We suggest that the mutation leading to 2AP in aromatic nfgr varieties possibly originated several times and, through either domestication or evolution, the fgr gene and other alleles leading to 2AP have combined in South Asia, leading to several highly aromatic traditional varieties. The identification of multiple mutations for 2AP will enable rice breeding programmes to select actively for multiple genetic sources of 2AP, leading to the development of highly aromatic and, consequently, high-quality varieties of rice.

A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties

Using a novel approach combining four complementary metabolomic and mineral platforms with genome-wide genotyping at 1536 single nucleotide polymorphism (SNP) loci, we have investigated the extent of biochemical and genetic diversity in three commercially-relevant waxy rice cultivars important to food production in the Lao People’s Democratic Republic (PDR). Following cultivation with different nitrogen fertiliser regimes, multiple metabolomic data sets, including minerals, were produced and analysed using multivariate statistical methods to reveal the degree of similarity between the genotypes and to identify discriminatory compounds supported by multiple technology platforms. Results revealed little effect of nitrogen supply on metabolites related to quality, despite known yield differences. All platforms revealed unique metabolic signatures for each variety and many discriminatory compounds could be identified as being relevant to consumers in terms of nutritional value and taste or flavour. For each platform, metabolomic diversity was highly associated with genetic distance between the varieties. This study demonstrates that multiple metabolomic platforms have potential as phenotyping tools to assist breeders in their quest to combine key yield and quality characteristics. This better enables rice improvement programs to meet different consumer and farmer needs, and to address food security in rice-consuming countries.

Understanding the Jasmine phenotype of rice through metabolite profiling and sensory evaluation

IntroductionAromatic rices are culturally and economically important for many countries in Asia. Investigation of the volatile compounds emitted by rice during cooking is the key to understanding the flavour of elite aromatic rice varieties.ObjectivesThe objectives of this study were to compare Jasmine-type aromatic rices from the Greater Mekong Subregion and Australia in terms of their metabolomics and sensory profiles and to draw out associations between the volatile organic compounds and human sensory perception of rice aroma.MethodsA set of aromatic rice varieties from South East Asia and Australia, along with non-aromatic controls, was grown in tropical and temperate areas of Australia. Untargeted metabolite profiling of volatile compounds, from the heated rice flour, by static headspace extraction and separation by two dimensional gas chromatography time-of-flight mass spectrometry was performed. Volatile compounds were also assayed in the standard references used in the sensory evaluation and compared to the compounds detected in the headspace of rice.ResultsWhile 2-acetyl-1-pyrroline (2-AP) was a discriminating compound, we identified several of its structural homologues, and a number of other metabolites that were consistently detected in fragrant Jasmine rice. 2-AP producing rice varieties have different sensory properties and these variations were defined by the discriminating compounds identified in each rice type.ConclusionsThe results of this study are valuable in understanding the aspects of aromatic rice that are important to consumers, and in the identification of compounds that breeding programs can use to select for pleasant aromas, enabling breeding programs to target markets with greater accuracy.

Delving deeper into technological innovations to understand differences in rice quality

Increasing demand for better quality rice varieties, which are also more suited to growth under sub-optimal cultivation conditions, is driving innovation in rice research. Here we have used a multi-disciplinary approach, involving SNP-based genotyping together with phenotyping based on yield analysis, metabolomic analysis of grain volatiles, and sensory panel analysis to determine differences between two contrasting rice varieties, Apo and IR64. Plants were grown under standard and drought-induced conditions. Results revealed important differences between the volatile profiles of the two rice varieties and we relate these differences to those perceived by the sensory panel. Apo, which is the more drought tolerant variety, was less affected by the drought condition concerning both sensory profile and yield; IR64, which has higher quality but is drought sensitive, showed greater differences in these characteristics in response to the two growth conditions. Metabolomics analyses using GCxGC-MS, followed by multivariate statistical analyses of the data, revealed a number of discriminatory compounds between the varieties, but also effects of the difference in cultivation conditions. Results indicate the complexity of rice volatile profile, even of non-aromatic varieties, and how metabolomics can be used to help link changes in aroma profile with the sensory phenotype. Our outcomes also suggest valuable multi-disciplinary approaches which can be used to help define the aroma profile in rice, and its underlying genetic background, in order to support breeders in the generation of improved rice varieties combining high yield with high quality, and tolerance of both these traits to climate change.

Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics.

The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding where global targets are focused on both yield stability and grain quality. In the present paper we have exploited advanced, multi-platform metabolomics approaches to determine the biochemical differences in 31 rice varieties from a diverse range of genetic backgrounds and origin. All were grown under the specific local conditions for which they have been bred and all aspects of varietal identification and sample purity have been guaranteed by local experts from each country. Metabolomics analyses using 6 platforms have revealed the extent of biochemical differences (and similarities) between the chosen rice genotypes. Comparison of fragrant rice varieties showed a difference in the metabolic profiles of jasmine and basmati varieties. However with no consistent separation of the germplasm class. Storage of grains had a significant effect on the metabolome of both basmati and jasmine rice varieties but changes were different for the two rice types. This shows how metabolic changes may help prove a causal relationship with developing good quality in basmati rice or incurring quality loss in jasmine rice in aged grains. Such metabolomics approaches are leading to hypotheses on the potential links between grain quality attributes, biochemical composition and genotype in the context of breeding for improvement. With this knowledge we shall establish a stronger, evidence-based foundation upon which to build targeted strategies to support breeders in their quest for improved rice varieties.

Quality evaluation, fatty acid analysis and untargeted profiling of volatiles in Cambodian rice

This study provides the first investigation of the physical traits, pasting properties and volatile compounds of Cambodian rice cultivars, including traditional, improved, and improved traditional varieties, allowing for their differentiation as high and low quality rice. Analysis of the grain quality traits illustrates interesting features of traditional varieties and correlations between traits that assist with understanding texture. Untargeted profiling of volatile compounds shows that high quality fragrant varieties not only contain 2-acetyl-1-pyrroline but also several other compounds, including aldehydes, alcohols and 2-alkylfurans that contribute to overall aroma. Moreover, low odour threshold volatile compounds, which can be derived from the oxidation of unsaturated fatty acids, were more abundant in the fragrant varieties. The percentage area of both oleic and linoleic acid were found to be significantly different among the rice varieties tested. Such findings suggest that unsaturated fatty acids in milled rice contribute to rice fragrance, and thereby to overall quality.

Metabolomics and genomics combine to unravel the pathway for the presence of fragrance in rice

Since it was first characterised in 1983, 2-acetyl-1-pyrroline (2AP) has been considered to be the most important aroma compound in rice. In this study, we show four other amine heterocycles: 6-methyl, 5-oxo-2,3,4,5-tetrahydropyridine (6M5OTP), 2-acetylpyrrole, pyrrole and 1-pyrroline, that correlate strongly with the production of 2AP, and are present in consistent proportions in a set of elite aromatic rice varieties from South East Asia and Australia as well as in a collection of recombinant inbred lines (RILs) derived from indica Jasmine-type varieties, Australian long grain varieties (temperate japonica) and Basmati-type rice (Grp V). These compounds were detected through untargeted metabolite profiling by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOF-MS), and their identity were confirmed by comparison with authentic standards analysed using gas chromatography mass spectrometry (GC-MS) and High Resolution GC × GC-TOF-MS (GC × GC HRT-4D). Genome-wide association analysis indicates that all compounds co-localised with a single quantitative trait locus (QTL) that harbours the FGR gene responsible for the production of GABA. Together, these data provide new insights into the production of 2AP, and evidence for understanding the pathway leading to the accumulation of aroma in fragrant rice.

A Multidisciplinary Phenotyping and Genotyping Analysis of a Mapping Population Enables Quality to Be Combined with Yield in Rice

In this study a mapping population (F8) of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design. All grain was harvested to determine variation in yield across the population. The grains were then polished following standard procedures prior to performing the phenotyping analyses. A Gas Chromatography—Mass Spectrometry approach was used to determine the volatile biochemical profiles of each line and after data curation and processing, discriminatory metabolites were putatively identified based on in-house and commercial spectral libraries. These data were used to predict the potential role of these metabolites in determining differences in aroma between genotypes. A number of QTLs for yield and for individual metabolites have been identified. Following these combined multi-disciplinary analyses, it proved possible to identify a number of lines which appeared to combine the favourable aroma attributes of IR64 with the favourable (higher) yield potential of Apo. As such, these lines are excellent candidates to assess further as potential genotypes to work up into a new variety of rice which has both good yield and good quality, thus meeting the needs of both farmer and consumer alike.