1. Doust, A.N., et al., Foxtail millet: a sequence-driven grass model system. Plant Physiol, 2009. 149(1): p. 137-41.
2. Diao, X. and G. Jia, Origin and domestication of foxtail millet, in genetics and genomics of setaria, A. Doust and X. Diao, Editors. 2017, Springer International Publishing: Cham. p. 61-72.
3. Zhang, G., et al., Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol, 2012. 30(6): p. 549-54.
4. Bennetzen, J.L., et al., Reference genome sequence of the model plant Setaria. Nat Biotechnol, 2012. 30(6): p. 555-61.
5. Yang, Z., et al., A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system. Nat Plants, 2020. 6(9): p. 1167-1178.
6. Wang, J., et al., De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance. BMC Plant Biol, 2021. 21(1): p. 271.
7. Peng, R. and B. Zhang, Foxtail millet: a new model for C4 plants. Trends Plant Sci, 2021. 26(3): p. 199-201.
8. Lata, C., S. Gupta, and M. Prasad, Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses. Crit Rev Biotechnol, 2013. 33(3): p. 328-43.
9. Okarter, N. and R.H. Liu, Health benefits of whole grain phytochemicals. Crit Rev Food Sci Nutr, 2010. 50(3): p. 193-208.
10. Shen, R., et al., Identification of carotenoids in foxtail millet (Setaria italica) and the effects of cooking methods on carotenoid content. Journal of Cereal Science, 2015. 61: p. 86-93.
11. Zhang, B., et al., Carotenoid composition and expression of biosynthetic genes in yellow and white foxtail millet [Setaria italica (L.) Beauv]. Journal of Cereal Science, 2019. 85: p. 84-90.
12. Fiedor, J. and K. Burda, Potential role of carotenoids as antioxidants in human health and disease. Nutrients, 2014. 6(2): p. 466-88.
13. Moreau, R.A., et al., A comparison of the levels of oil, carotenoids, and lipolytic enzyme activities in modern lines and hybrids of grain sorghum. Journal of the American Oil Chemists' Society, 2016. 93(4): p. 569-573.
14. Lamberts, L. and J.A. Delcour, Carotenoids in raw and parboiled brown and milled rice. Journal of Agricultural and Food Chemistry, 2008. 56(24): p. 11914-11919.
15. Qin, X., et al., Distinct expression and function of carotenoid metabolic genes and homoeologs in developing wheat grains. BMC plant biology, 2016. 16(1): p. 155-155.
16. Rodriguez-Concepcion, M., Supply of precursors for carotenoid biosynthesis in plants. Arch Biochem Biophys, 2010. 504(1): p. 118-22.
17. Vranova, E., D. Coman, and W. Gruissem, Network analysis of the MVA and MEP pathways for isoprenoid synthesis. Annu Rev Plant Biol, 2013. 64: p. 665-700.
18. Watkins, J.L. and B.J. Pogson, Prospects for carotenoid biofortification targeting retention and catabolism. Trends Plant Sci, 2020. 25(5): p. 501-512.
19. Paine, J.A., et al., Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nature Biotechnology, 2005. 23(4): p. 482-487.
20. Zunjare, R.U., et al., Influence of rare alleles of β-carotene hydroxylase and lycopene epsilon cyclase genes on accumulation of provitamin A carotenoids in maize kernels. Plant Breeding, 2017. 136(6): p. 872-880.
21. Cao, H., et al., A neighboring aromatic-aromatic amino acid combination governs activity divergence between tomato phytoene synthases. Plant Physiol, 2019. 180(4): p. 1988-2003.
22. Nogueira, M., et al., Subchromoplast sequestration of carotenoids affects regulatory mechanisms in tomato lines expressing different carotenoid gene combinations. Plant Cell, 2013. 25(11): p. 4560-79.
23. Chen, C., et al., TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 2020. 13(8): p. 1194-1202.
24. Nicolaides, N.C. and C.J. Stoeckert, Jr., A simple, efficient method for the separate isolation of RNA and DNA from the same cells. Biotechniques, 1990. 8(2): p. 154-6.
25. Pertea, M., et al., Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc, 2016. 11(9): p. 1650-67.
26. Wang, L., et al., DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 2010. 26(1): p. 136-8.
27. Kanehisa, M., et al., KEGG for linking genomes to life and the environment. Nucleic Acids Res, 2008. 36(Database issue): p. D480-4.
28. Livak, K.J. and T.D. Schmittgen, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 2001. 25(4): p. 402-8.
29. Brinkman, H.-J., et al., High food prices and the global financial crisis have reduced access to nutritious food and worsened nutritional status and health. The Journal of Nutrition, 2010. 140(1): p. 153S-161S.
30. Digesù, A.M., et al., Genetic variability in yellow pigment components in cultivated and wild tetraploid wheats. Journal of Cereal Science, 2009. 50(2): p. 210-218.
31. Leenhardt, F., et al., Genetic variability of carotenoid concentration, and lipoxygenase and peroxidase activities among cultivated wheat species and bread wheat varieties. European Journal of Agronomy, 2006. 25(2): p. 170-176.
32. Taylor, K.L., et al., High-performance liquid chromatography profiling of the major carotenoids in Arabidopsis thaliana leaf tissue. J Chromatogr A, 2006. 1121(1): p. 83-91.
33. Song, J., et al., Comparison of carotenoid composition in immature and mature grains of corn (Zea Mays L.) varieties. International Journal of Food Properties, 2016. 19(2): p. 351-358.
34. Owens, B.F., et al., A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels. Genetics, 2014. 198(4): p. 1699-1716.
35. Li, P., et al., Carotenoid biosynthetic genes in Brassica rapa: comparative genomic analysis, phylogenetic analysis, and expression profiling. BMC genomics, 2015. 16(1): p. 492-492.
36. Blanc, G. and K.H. Wolfe, Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution[W]. The Plant Cell, 2004. 16(7): p. 1679-1691.
37. Carretero-Paulet, L., et al., Enhanced flux through the methylerythritol 4-phosphate pathway in Arabidopsis plants overexpressing deoxyxylulose 5-phosphate reductoisomerase. Plant Molecular Biology, 2006. 62(4): p. 683-695.
38. Walter, M.H., J. Hans, and D. Strack, Two distantly related genes encoding 1-deoxy-d-xylulose 5-phosphate synthases: differential regulation in shoots and apocarotenoid-accumulating mycorrhizal roots. The Plant Journal, 2002. 31(3): p. 243-254.
39. Phillips, M.A., et al., Functional identification and differential expression of 1-deoxy-d-xylulose 5-phosphate synthase in induced terpenoid resin formation of Norway spruce (Picea abies). Plant Molecular Biology, 2007. 65(3): p. 243-257.
40. Cordoba, E., et al., Functional characterization of the three genes encoding 1-deoxy-D-xylulose 5-phosphate synthase in maize. Journal of Experimental Botany, 2011. 62(6): p. 2023-2038.
41. Berthelot, K., et al., Isopentenyl diphosphate isomerase: A checkpoint to isoprenoid biosynthesis. Biochimie, 2012. 94(8): p. 1621-1634.
42. Albrecht, M. and G. Sandmann, Light-stimulated carotenoid biosynthesis during transformation of maize etioplasts is regulated by increased activity of isopentenyl pyrophosphate isomerase. Plant physiology, 1994. 105(2): p. 529-534.
43. Sun, J., et al., A novel cytoplasmic isopentenyl diphosphate isomerase gene from tomato (Solanum lycopersicum): cloning, expression, and color complementation. Plant Molecular Biology Reporter, 2010. 28(3): p. 473-480.
44. Gallagher, C., M. Cervantes-Cervantes, and E. Wurtzel, Surrogate biochemistry: use of Escherichia coli to identify plant cDNAs that impact metabolic engineering of carotenoid accumulation. Applied Microbiology and Biotechnology, 2003. 60(6): p. 713-719.
45. Jin, H., Z. Song, and B.J. Nikolau, Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development. The Plant Journal, 2012. 70(6): p. 1015-1032.
46. Ye, X., et al., Engineering the provitamin a (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science, 2000. 287(5451): p. 303.
47. Fraser, P.D., et al., Manipulation of phytoene levels in tomato fruit: effects on isoprenoids, plastids, and intermediary metabolism. The Plant Cell, 2007. 19(10): p. 3194-3211.
48. Tomato Genome, C., The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-641.
49. Li, F., C. Murillo, and E.T. Wurtzel, Maize Y9 encodes a product essential for 15-cis-zeta-carotene isomerization. Plant Physiol, 2007. 144(2): p. 1181-9.
50. Xi, W., et al., The genes of CYP, ZEP, and CCD1/4 play an important role in controlling carotenoid and aroma volatile apocarotenoid accumulation of apricot fruit. Frontiers in Plant Science, 2020. 11: p. 2105.
51. Suematsu, K., et al., Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato. Scientific reports, 2020. 10(1): p. 20607-20607.
52. Gonzalez-Jorge, S., et al., ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing seed Plant Physiology, 2016. 171(3): p. 1837-1851.
53. Cruet-Burgos, C., et al., Advancing provitamin A biofortification in sorghum: Genome-wide association studies of grain carotenoids in global germplasm. The Plant Genome, 2020. 13(1): p. e20013.
54. Schaub, P., et al., Nonenzymatic β-carotene degradation in provitamin a-biofortified crop plants. Journal of Agricultural and Food Chemistry, 2017. 65(31): p. 6588-6598.
55. Bruno, M., et al., Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites. Journal of Experimental Botany, 2016. 67(21): p. 5993-6005.
56. Ohmiya, A., et al., Carotenoid cleavage dioxygenase (CmCCD4a) contributes to white color formation in chrysanthemum petals. Plant Physiology, 2006. 142(3): p. 1193-1201.
57. García-Limones, C., et al., Functional characterization of FaCCD1: a carotenoid cleavage dioxygenase from strawberry involved in lutein degradation during fruit ripening. Journal of Agricultural and Food Chemistry, 2008. 56(19): p. 9277-9285.
58. Campbell, R., et al., The metabolic and developmental roles of carotenoid cleavage dioxygenase4 from potato. Plant Physiology, 2010. 154(2): p. 656-664.
59. Shin, J., et al., Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors. Proceedings of the National Academy of Sciences, 2009. 106(18): p. 7660.
60. Bae, G. and G. Choi, Decoding of light signals by plant phytochromes and their interacting proteins. Annual Review of Plant Biology, 2008. 59(1): p. 281-311.
61. Shen, H., et al., Light-induced phosphorylation and degradation of the negative regulator PHYTOCHROME-INTERACTING FACTOR1 from Arabidopsis depend upon its direct physical interactions with photoactivated phytochromes. The Plant Cell, 2008. 20(6): p. 1586-1602.
62. Toledo-Ortiz, G., E. Huq, and M. Rodríguez-Concepción, Direct regulation of phytoene synthase gene expression and carotenoid biosynthesis by phytochrome-interacting factors. Proceedings of the National Academy of Sciences, 2010. 107(25): p. 11626.
63. Shi, H., et al., <em>Arabidopsis</em> DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination. Proceedings of the National Academy of Sciences, 2015. 112(12): p. 3817.
64. Zhu, L., et al., CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1. Nature Communications, 2015. 6(1): p. 7245.
65. Alvarez, J. and D.R. Smyth, CRABS CLAW and SPATULA, two Arabidopsis genes that control carpel development in parallel with AGAMOUS. Development, 1999. 126(11): p. 2377-2386.
66. Tsiantis, M., Plant development: multiple strategies for breaking seed dormancy. Current Biology, 2006. 16(1): p. R25-R27.
67. Josse, E.-M., et al., A DELLA in disguise: SPATULA restrains the growth of the developing arabidopsis seedling The Plant Cell, 2011. 23(4): p. 1337-1351.
68. Penfield, S., et al., Cold and light control seed germination through the bHLH transcription factor SPATULA. Current Biology, 2005. 15(22): p. 1998-2006.
69. Vaistij, F.E., et al., MOTHER-OF-FT-AND-TFL represses seed germination under far-red light by modulating phytohormone responses in <em>Arabidopsis thaliana</em>. Proceedings of the National Academy of Sciences, 2018. 115(33): p. 8442.
70. Eriksson, E.M., et al., Effect of the colorless non-ripening mutation on cell wall biochemistry and gene expression during tomato fruit development and ripening. Plant Physiology, 2004. 136(4): p. 4184-4197.
71. Wang, J.-W., B. Czech, and D. Weigel, miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana. Cell, 2009. 138(4): p. 738-749.
72. Gandikota, M., et al., The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. The Plant Journal, 2007. 49(4): p. 683-693.
73. Wei, S., et al., Enhanced seed carotenoid levels and branching in transgenic Brassica napus expressing the Arabidopsis miR156b gene. Journal of Agricultural and Food Chemistry, 2010. 58(17): p. 9572-9578.
74. Stanley, L. and Y.-W. Yuan, Transcriptional regulation of carotenoid biosynthesis in plants: so many regulators, so little consensus. Frontiers in Plant Science, 2019. 10: p. 1017.
75. Fujisawa, M., T. Nakano, and Y. Ito, Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation. BMC Plant Biology, 2011. 11(1): p. 26.
76. Fujisawa, M., et al., A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening. The Plant Cell, 2013. 25(2): p. 371-386.
77. Giménez, E., et al., Functional analysis of the Arlequin mutant corroborates the essential role of the Arlequin/TAGL1 gene during reproductive development of tomato. PloS one, 2010. 5(12): p. e14427-e14427.
78. Itkin, M., et al., TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network. The Plant Journal, 2009. 60(6): p. 1081-1095.
79. Martel, C., et al., The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent manner Plant Physiology, 2011. 157(3): p. 1568-1579.
80. Shima, Y., et al., Tomato FRUITFULL homologues act in fruit ripening via forming MADS-box transcription factor complexes with RIN. Plant Molecular Biology, 2013. 82(4): p. 427-438.