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

Upasna Chettry,Kirti Kulkarni,Nikhil K Chrungoo

doi:10.1038/s41598-018-38233-8

Abstract

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 grain fresh weight. In addition to PSY1, higher expression of βLCY than εLCY appears to be an important factor in determining the flux of pathway towards synthesis of β-β 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 β-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 β-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.

Highlights

As a staple food of bulk of the population of Southeast Asia, rice grains contribute significantly towards meeting nutritional requirements of the people of this region
We developed a nested network between the differentially expressed genes involved in phenyl propanoid biosynthesis, pyruvate metabolism, fatty acid metabolism, carotenoid biosynthesis and plant hormone signal transduction using “CytoScape tool”
Even though the basic biosynthetic pathways leading to synthesis of the core secondary metabolites have been well-characterized, the mechanisms underlying various regulatory controls in carotenoid biosynthesis continue to be a matter of debate

Summary

Introduction

As a staple food of bulk of the population of Southeast Asia, rice grains contribute significantly towards meeting nutritional requirements of the people of this region. With a limited knowledge of the regulatory controls involved in carotenoid biosynthesis in rice, availability of mutants with altered carotenoid biosynthetic pathway would have been an important milestone in understanding carotenoid biosynthesis in this crop. While such a collection of mapped and biochemically characterized mutants is available in other grain crops such as maize[4,5], not many mutants of this type have been identified in rice. While the mutations confirmed the role of PDS, ZDS CRITSO and βLCY in carotenoid biosynthesis, they did not provide any information on the regulatory controls involved in carotenoid biosynthesis in rice.

Methods

Results

Conclusion