Gene Sequence Variations of Carotenoid Biosynthesis Pathway in Thai Rice Varieties (Oryza sativa L.) from Transcriptome and Whole Genome Sequencing Analysis
Abstract
Lutein is a product from carotenoid biosynthetic pathway which is highly found in black rice pericarp. The purpose of this study was to identify sequence variations of genes in carotenoid biosynthetic pathway from Thai rice varieties with white (no lutein) and black (high lutein) pericarp by transcriptome and genome analyses. The sequences of 12 genes in the carotenoid synthesis showing variations between white and black rice were detected. The variations in gene regions were found in 5 genes which were phytoene desaturase (PDS), zeta-carotene isomerase (ZISO), lycopene epsilon-cyclase (LCYe), cytochrome P450 carotene beta-hydroxylase (Lut5, CYP97A) and cytochrome P450 type B (CYP97B). High levels of sequence variations in upstream region, gene region and downstream region were found in ZISO, CYP97A and CYP97B genes. Therefore, these three genes were probably key candidate genes related to lutein biosynthesis. The sequence variations of these genes in the carotenoid biosynthesis pathway will be used to develop DNA markers for selection of high lutein accumulation in rice breeding program. Keywords : Rice ; Sequence variation ; Carotenoid biosynthesis pathway ; Transcriptome sequencing ; Whole genome sequencingReferences
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Ashokkumar, K., Govindaraj, M., Adhimoolam Karthikeyan, V., & Warkentin, T. D. (2020). Genomics-integrated breeding for carotenoids and folates in staple cereal grains to reduce malnutrition. Frontiers in genetics, 11.
Badro, H., Ndjiondjop, M.-N., Furtado, A., & Henry, R. (2020). Sequence Variants Linked to Key Traits in Interspecific Crosses between African and Asian Rice. Plants, 9(12), 1653.
Bai, C., Capell, T., Berman, J., Medina, V., Sandmann, G., Christou, P., & Zhu, C. (2016). Bottlenecks in carotenoid biosynthesis and accumulation in rice endosperm are influenced by the precursor–product balance. Plant Biotechnology Journal, 14(1), 195-205.
Chen, Y., Li, F., & Wurtzel, E. T. (2010). Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiology, 153(1), 66-79.
Chettry, U., & Chrungoo, N. K. (2020). A multifocal approach towards understanding the complexities of carotenoid biosynthesis and accumulation in rice grains. Briefings in functional genomics, 19(4), 324-335.
Chettry, U., Chrungoo, N. K., & Kulkarni, K. (2019). Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.). Scientific reports, 9(1), 1-12.
Dibari, B., Murat, F., Chosson, A., Gautier, V., Poncet, C., Lecomte, P., . . . Blanco, A. (2012). Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. Bmc Genomics, 13(1), 1-14.
Kim, J. K., Lee, S. Y., Chu, S. M., Lim, S. H., Suh, S.-C., Lee, Y.-T., . . . Ha, S.-H. (2010). Variation and correlation analysis of flavonoids and carotenoids in Korean pigmented rice (Oryza sativa L.) cultivars. Journal of agricultural and food chemistry, 58(24), 12804-12809.
Li, J., Wang, S., Yu, J., Wang, L., & Zhou, S. (2013). A modified CTAB protocol for plant DNA extraction. Chinese Bulletin of Botany, 48(1), 72.
Lu, S., Zhang, Y., Zhu, K., Yang, W., Ye, J., Chai, L., . . . Deng, X. (2018). The citrus transcription factor CsMADS6 modulates carotenoid metabolism by directly regulating carotenogenic genes. Plant Physiology, 176(4), 2657-2676.
Lv, M.-Z., Chao, D.-Y., Shan, J.-X., Zhu, M.-Z., Shi, M., Gao, J.-P., & Lin, H.-X. (2012). Rice carotenoid β-ring hydroxylase CYP97A4 is involved in lutein biosynthesis. Plant and Cell Physiology, 53(6), 987-1002.
Niu, G., Guo, Q., Wang, J., Zhao, S., He, Y., & Liu, L. (2020). Structural basis for plant lutein biosynthesis from α-carotene. Proceedings of the National Academy of Sciences, 117(25), 14150-14157.
Pranathi, K., Viraktamath, B., Neeraja, C., Balachandran, S., Rao, P. K., Revathi, P., . . . Naik, S. B. (2016). Development and validation of candidate gene-specific markers for the major fertility restorer genes, Rf4 and Rf3 in rice. Molecular Breeding, 36(10), 1-14.
Ren, J., Zhang, F., Gao, F., Zeng, L., Lu, X., Zhao, X., . . . Dai, M. (2020). Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203. Scientific reports, 10(1), 1-15.
Stanley, L., & Yuan, Y.-W. (2019). Transcriptional regulation of carotenoid biosynthesis in plants: so many regulators, so little consensus. Frontiers in plant science, 10, 1017.
Villa-Rivera, M. G., & Ochoa-Alejo, N. (2020). Chili Pepper Carotenoids: Nutraceutical Properties and Mechanisms of Action. Molecules, 25(23), 5573.
Watkins, J. L., & Pogson, B. J. (2020). Prospects for carotenoid biofortification targeting retention and catabolism. Trends in plant science, 25(5), 501-512.
Welsch, R., Wüst, F., Bär, C., Al-Babili, S., & Beyer, P. (2008). A third phytoene synthase is devoted to abiotic stress-induced abscisic acid formation in rice and defines functional diversification of phytoene synthase genes. Plant Physiology, 147(1), 367-380.
Wurtzel, E. T. (2019). Changing form and function through carotenoids and synthetic biology. Plant Physiology, 179(3), 830-843.
Ashokkumar, K., Govindaraj, M., Adhimoolam Karthikeyan, V., & Warkentin, T. D. (2020). Genomics-integrated breeding for carotenoids and folates in staple cereal grains to reduce malnutrition. Frontiers in genetics, 11.
Badro, H., Ndjiondjop, M.-N., Furtado, A., & Henry, R. (2020). Sequence Variants Linked to Key Traits in Interspecific Crosses between African and Asian Rice. Plants, 9(12), 1653.
Bai, C., Capell, T., Berman, J., Medina, V., Sandmann, G., Christou, P., & Zhu, C. (2016). Bottlenecks in carotenoid biosynthesis and accumulation in rice endosperm are influenced by the precursor–product balance. Plant Biotechnology Journal, 14(1), 195-205.
Chen, Y., Li, F., & Wurtzel, E. T. (2010). Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiology, 153(1), 66-79.
Chettry, U., & Chrungoo, N. K. (2020). A multifocal approach towards understanding the complexities of carotenoid biosynthesis and accumulation in rice grains. Briefings in functional genomics, 19(4), 324-335.
Chettry, U., Chrungoo, N. K., & Kulkarni, K. (2019). Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.). Scientific reports, 9(1), 1-12.
Dibari, B., Murat, F., Chosson, A., Gautier, V., Poncet, C., Lecomte, P., . . . Blanco, A. (2012). Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. Bmc Genomics, 13(1), 1-14.
Kim, J. K., Lee, S. Y., Chu, S. M., Lim, S. H., Suh, S.-C., Lee, Y.-T., . . . Ha, S.-H. (2010). Variation and correlation analysis of flavonoids and carotenoids in Korean pigmented rice (Oryza sativa L.) cultivars. Journal of agricultural and food chemistry, 58(24), 12804-12809.
Li, J., Wang, S., Yu, J., Wang, L., & Zhou, S. (2013). A modified CTAB protocol for plant DNA extraction. Chinese Bulletin of Botany, 48(1), 72.
Lu, S., Zhang, Y., Zhu, K., Yang, W., Ye, J., Chai, L., . . . Deng, X. (2018). The citrus transcription factor CsMADS6 modulates carotenoid metabolism by directly regulating carotenogenic genes. Plant Physiology, 176(4), 2657-2676.
Lv, M.-Z., Chao, D.-Y., Shan, J.-X., Zhu, M.-Z., Shi, M., Gao, J.-P., & Lin, H.-X. (2012). Rice carotenoid β-ring hydroxylase CYP97A4 is involved in lutein biosynthesis. Plant and Cell Physiology, 53(6), 987-1002.
Niu, G., Guo, Q., Wang, J., Zhao, S., He, Y., & Liu, L. (2020). Structural basis for plant lutein biosynthesis from α-carotene. Proceedings of the National Academy of Sciences, 117(25), 14150-14157.
Pranathi, K., Viraktamath, B., Neeraja, C., Balachandran, S., Rao, P. K., Revathi, P., . . . Naik, S. B. (2016). Development and validation of candidate gene-specific markers for the major fertility restorer genes, Rf4 and Rf3 in rice. Molecular Breeding, 36(10), 1-14.
Ren, J., Zhang, F., Gao, F., Zeng, L., Lu, X., Zhao, X., . . . Dai, M. (2020). Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203. Scientific reports, 10(1), 1-15.
Stanley, L., & Yuan, Y.-W. (2019). Transcriptional regulation of carotenoid biosynthesis in plants: so many regulators, so little consensus. Frontiers in plant science, 10, 1017.
Villa-Rivera, M. G., & Ochoa-Alejo, N. (2020). Chili Pepper Carotenoids: Nutraceutical Properties and Mechanisms of Action. Molecules, 25(23), 5573.
Watkins, J. L., & Pogson, B. J. (2020). Prospects for carotenoid biofortification targeting retention and catabolism. Trends in plant science, 25(5), 501-512.
Welsch, R., Wüst, F., Bär, C., Al-Babili, S., & Beyer, P. (2008). A third phytoene synthase is devoted to abiotic stress-induced abscisic acid formation in rice and defines functional diversification of phytoene synthase genes. Plant Physiology, 147(1), 367-380.
Wurtzel, E. T. (2019). Changing form and function through carotenoids and synthetic biology. Plant Physiology, 179(3), 830-843.
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Published
2022-05-18
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