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Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.).

ABSTRACT: Estimation of phytoene, lycopene, ?-carotene, lutein, and zeaxanthin in grains of white, brown and purple cultivars of rice revealed marked differences in the levels of these carotenoid intermediates amongst the cultivars. Grains of white rice did not show any significant accumulation of carotenoid intermediates at any stage of development. On the other hand, grains of the purple cultivar accumulated 49.16?±?5?µg of ?-carotene, 28.89?±?3.2?µg of lutein and 34.65?±?4.6?µg of zeaxanthin per gm of grain fresh weight. In addition to PSY1, higher expression of ?LCY than ?LCY appears to be an important factor in determining the flux of pathway towards synthesis of ?-? branch carotenoids in purple rice. This cultivar showed a higher fold change in carotenoid precursors during transition from milky to doughing stages and an enhanced flux of lycopene towards ?-carotene during grain maturation. Our results indicate that higher level of carotenoids in purple rice is a consequence of higher expression of genes involved in pyruvate metabolism as well as those involved in carotenoid biosynthesis such as PSY1, PDS and ?-LCY. Co-expression networking revealed a strong positive relationship between the expression profiles of genes involved in carotenoid biosynthesis and genes coding for geranylgeranyl transferase type II, glutathione S-transferase, DnaJ and SET domain containing proteins as well as MADS26 and R2R3MYB family of transcription factors.

SUBMITTER: Chettry U

PROVIDER: S-EPMC6367445 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.).

Chettry Upasna U Chrungoo Nikhil K NK Kulkarni Kirti K

Scientific reports 20190207 1

Estimation of phytoene, lycopene, β-carotene, lutein, and zeaxanthin in grains of white, brown and purple cultivars of rice revealed marked differences in the levels of these carotenoid intermediates amongst the cultivars. Grains of white rice did not show any significant accumulation of carotenoid intermediates at any stage of development. On the other hand, grains of the purple cultivar accumulated 49.16 ± 5 µg of β-carotene, 28.89 ± 3.2 µg of lutein and 34.65 ± 4.6 µg of zeaxanthin per gm of ...[more]

PMID: 30733556

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Project description:Grain minerals in rice, especially those in milled grains, are important sources of micro-nutrition elements, such as iron (Fe), zinc (Zn), manganese (Mn), copper (Cu), and selenium (Se), and of toxic heavy metal elements, especially cadmium (Cd), for populations consuming a rice diet. To date, the genetic mechanism underlying grain mineral concentrations (GMCs) in milled grain remains largely unknown. In this report, we adopted a set of 698 germplasms consisting of two subsets [indica/Xian (X-set) and japonica/Geng (G-set)], to detect quantitative trait loci (QTL) affecting GMC traits of Fe, Zn, Cd, Mn, Cu, and Se in milled grains. A total of 47 QTL regions, including 18 loci and 29 clusters (covering 62 Cd loci), responsible for the GMCs in milled grains were detected throughout the genome. A joint exploration of favorable haplotypes of candidate genes was carried out as follows: (1) By comparative mapping, 10 chromosome regions were found to be consistent with our previously detected QTL from linkage mapping. (2) Within eight of these regions on chromosomes 1, 4, 6, 7, and 8, candidate genes were identified in the genome annotation database. (3) A total of 192 candidate genes were then submitted to further haplotype analysis using million-scale single nucleotide polymorphisms (SNPs) from the X-set and the G-set. (4) Finally, 37 genes (19.3%) were found to be significant in the association between the QTL targeting traits and the haplotype variations by pair-wise comparison. (5) The phenotypic values for the haplotypes of each candidate were plotted. Three zinc finger (like) genes within two candidate QTL regions (qFe6-2 and qZn7), and three major GMC traits (Fe, Zn, and Cd) were picked as sample cases, in addition to non-exhausted cross validations, to elucidate this kind of association by trait value plotting. Taken together, our results, especially the 37 genes with favorable haplotype variations, will be useful for rice biofortification molecular breeding.

Dataset Information

Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.).

Publications

Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.).

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