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

Mumm, Roland; Hageman, Jos A.; Calingacion, Mariafe; Vos, Ric C. H. de; Jonker, Harry; Erban, Alexander; Kopka, Joachim; Hansen, Thomas H.; Laursen, Kristian Holst; Schjøerring, Jan K.; Ward, Jane L.; Beale, Michael H.; Jongee, S.; Rauf, Ahamed Lebbe Abdul; Habibi, Fatemeh; Indrasari, Siti Dewi; Sakhan, Sophany; Ramli, Asfaliza; Romero, Marissa V.; Reinke, Russell; Ohtsubo, Ken’ichi; Boualaphanh, Chanthakhone; Fitzgerald, Melissa; Hall, Robert D.

doi:10.1007/s11306-015-0925-1

Cited by 35 publications

(25 citation statements)

References 47 publications

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“…Basmati 370 was chosen to be crossed with a local rice cultivar Hua Jing Xian 74, because of the uniquely long grains, soft and fluffy texture, and pleasant aroma during and after cooking. Basmati 370 is an indica rice variety (Mumm et al, 2016); Hua Jing Xian 74 is also an indica variety (Xi et al, 2006). All rice grains were cultivated in Hainan, China in November, 2013 and were harvested and stored under the same condition in April, 2014.…”

Section: Rice Grainsmentioning

confidence: 99%

Identification of putative metabolic biomarker underlying cooked rice elongation

Okpala¹,

Duan²,

Shen³

et al. 2017

Plant Omics

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Rice (Oryza sativa L.) is a staple food for over half of the world's population. However, rice grain quality is one of the major problems facing rice breeders across the world. Cooked rice elongation, cooked rice expansion, and water absorption have been identified as some of the parameters used in gauging rice grain quality. Biomarkers such as proteins or metabolites can be used to differentiate among a pattern of variations among various samples (e.g., various locations within a plant, various germplasm accessions); consequently, they present a type of internal validation for a given biological state. In the present study, we investigated the putative metabolite biomarkers associated with the variation of cooked rice elongation for Hua Jing Xian 74 (receptor), Basmati 370 (donor), and five hybrid lines resulting from a cross of these parent lines. We also investigated their cooked rice expansion and water absorption properties. After carrying out cooked rice elongation studies, metabolomics studies, correlation analyses, V-plot analyses, and thorough searches in public metabolite databases (Metlin, Massbank and KEGG), and in-house secondary metabolite database, we identified a metabolite with molecular weight of 280.25 and retention time of 6.4 min as a putative biomarker associated with cooked rice elongation in the varieties investigated. We also discovered that changes in cooked rice elongation and changes in cooked rice expansion follow a similar pattern; however, it appears that cooked rice elongation and cooked rice expansion do not affect water absorption in these rice lines. Our findings may facilitate the improvement of the cooked rice elongation of hybrids resulting from the crosses of Basmati 370 and Hua Jing Xian 74. Our results also offer interesting insight into cooked rice elongation, cooked rice expansion, and water absorption.

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Section: Rice Grainsmentioning

confidence: 99%

Identification of putative metabolic biomarker underlying cooked rice elongation

Okpala¹,

Duan²,

Shen³

et al. 2017

Plant Omics

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“…Hua Jing Xian 74 is an indica cultivar [7] and Basmati 385 is also an indica cultivar [8]. Studies have suggested that cooked rice grains with extensive elongation are often more desirable rice varieties [6].…”

Section: Cooked Rice Elongationmentioning

confidence: 99%

Comparisons of Cooking and Eating Qualities of Two Indica Rice Cultivars

Okpala¹,

Duan²,

Shen³

et al. 2017

J Rice Res

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The cooking and eating qualities of rice are some of the problems facing by rice producers and consumers around the world. In this study we investigated the cooking and eating qualities of Basmati 385 and Hua Jing Xian 74. Both are rice cultivars with different phenotypic traits.The results show that Basmati 385 increased by an average of 102.14% after cooking while Hua Jing Xian 74 increased by an average of 69.91% after cooking. Basmati 385 had a pasting temperature of 78°C, while Hua Jing Xian 74 had a pasting temperature of 84°C. However, Hua Jing Xian 74 had a final viscosity of 4,686 cP while Basmati 385 had a final viscosity of 3,514 cP. The amylose contents of the two cultivars were also different; Hua Jing Xian 74 had an amylose content of 19.4%, while that of Basmati 385 was 18%. We also discovered that the starch granule morphology of the two cultivars were remarkably different.The lower pasting temperature of Basmati 385 positively correlated with good cooking qualities of rice. However, Hua Jing Xian 74 appears to have relatively better eating qualities due to its higher viscosity and higher amylose content. It would be pertinent to do more research about hybrid lines resulting from a cross of Hua Jing Xian 74 and Basmati 385, to see if they possess the good cooking qualities of Basmati 385 and the good eating qualities of Hua Jing Xian 74.

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“…Gong et al (2013) found several large effect mQTLs for rice traits and attributed this successful experiment to their use of high density of SNP markers and robust metabolomics method. (Mumm et al, 2016)…”

Section: Metabolomics: a Phenotyping Platform For Breedingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Volatile compounds can be identified with gas chromatography and mass spectrometry (GC-MS) (Buttery et al, 1988, Concepcion et al, 2015, Mumm et al, 2016, Daygon et al, 2016. The analysis of rice by GC-MS has revealed several odour-active volatile compounds that may provide the characteristic aroma of different rice varieties (Calingacion et al, 2012, Mumm et al, 2016. The presence of these volatile compounds may relate to the degradation of lipids, particularly the oxidation of fatty acids that are found on the surface of starch granules (Lam and Proctor, 2003), or inside the granules themselves (Zhou et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

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Understanding the genetics and chemistry of important quality traits in rice (Oryza sativa L.)

Concepcion¹

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Rice grain quality is a determinant of rice breeding success. Although several studies have independently looked at the different traits of quality to infer the phenotype of the grain, few studies have identified the various metabolites that are produced in high quality rice. In recent years, genetic markers have proven to be effective in increasing the efficiency of breeding line selection and therefore shortening the breeding cycle. In complex traits such as rice grain quality, the availability of more specific phenotypes will increase the value of these genetic markers. Many traits of quality in rice are associated with starch; however, lipids interact with starch and have been shown to influence many of the traits of eating quality and aroma. To identify these new phenotypes and understand their genetic basis, using relevant tools that can discriminate between the phenotypes of varieties at the metabolite and genetic levels is necessary. To identify these new phenotypes, in Chapter 3, a set of 40 Cambodian rice varieties were screened for physical and texture-associated traits including apparent amylose content (AAC), gelatinisation temperature (GT), gel consistency (GelCon) and pasting properties and then a subset from this set was screened for volatile compounds using a two-dimensional gas chromatography-time-of-flightmass spectrometer (GC×GC-TOF-MS) and fatty acids (FA) using gas chromatography-mass spectrometry (GC-MS). The FA analysis showed that unsaturated FA (UFA) oleic (C18:1n-9) and linoleic acid (C18:2n-6) were the most abundant in milled rice grains, followed by palmitic acid (C16:0). These results infer about the lipid origin of odour-active volatile compounds, which were found to be characterising the group of known fragrant, low amylose and soft-textured rice varieties, including the Jasmine-style indica variety Phka Rumduol (PRD). To identify the genetic determinants of these important traits of quality, in Chapters 4 and 5, quantitative trait loci (QTL) mapping was carried out for the texture and aroma traits in PRD using a population of about 300 F6 recombinant-inbred lines (RIL) derived from an intraspecific cross between PRD and Thmar Krem (TMK), both of which were identified as the most discriminating varieties in Chapter 3. This RIL population was genotyped for single nucleotide polymorphisms (SNPs). QTL analysis revealed large-effect QTLs for AAC, GT and all of the pasting properties. Candidate genes for these QTLs relate back to the starch biosynthesis pathways. Major QTLs were colocalised to the Waxy (Wx) gene and starch synthase IIa (SSIIa) on chromosome 6. Minor QTLs on chromosomes 3 and 8 were identified for AAC, SB, PV and HPC, and at chromosomes 4 and 7 for GT and pasting temperature (PTemp). This chapter has shown that the rice texture is regulated by multiple genes and that although correlations do exist among the routinely measured textural traits, these correlations may not necessarily translate into the already existing molecular markers. Publications included in this thesis...

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

Cited by 35 publications

References 47 publications

Identification of putative metabolic biomarker underlying cooked rice elongation

Identification of putative metabolic biomarker underlying cooked rice elongation

Comparisons of Cooking and Eating Qualities of Two Indica Rice Cultivars

Understanding the genetics and chemistry of important quality traits in rice (Oryza sativa L.)

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