Genetic loci regulating the concentrations of anthocyanins and proanthocyanidins in the pericarps of purple and red rice

Authors: CHEN, MING-HSUAN - Retired ARS Employee; Pinson, Shannon; Jackson, Aaron; Edwards, Jeremy

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2023
Publication Date: 5/13/2023
Citation: Chen, M., Pinson, S.R., Jackson, A.K., Edwards, J. 2023. Genetic loci regulating the concentrations of anthocyanins and proanthocyanidins in the pericarps of purple and red rice. The Plant Genome. https://doi.org/10.1002/tpg2.20338.
DOI: https://doi.org/10.1002/tpg2.20338

Interpretive Summary: Anthocyanins are the health-beneficial antioxidant compounds that make blueberries blue, while proanthocyanidins are the antioxidants in red foods, such as in cranberries or red wine. Rice can also provide these desirable compounds. While rice is traditionally eaten as white milled rice, consumption of unmilled whole-grain (brown) rice is a growing trend, particularly among consumers interested in increased fiber, protein, and nutrients, and reduced glycemic index. Increased consumption of whole-grain rice opens opportunity to further increase the health-benefits derived from eating rice in which the pericarp (the outer layer of the whole-grain brown rice) has been biofortified with pigmented antioxidants, resulting in rice that is red or purple instead of brown. At the initiation of this study, it was known that the purple bran (Pb) gene is a transcription factor that activates (turns on) or represses (turns off) the production of anthocyanins in rice pericarps resulting in purple or white grains, respectively. The red color (Rc) gene is a transcription factor that turns on or off the production of red-colored proanthocyanidins, resulting in red or white grain. The goal of the present study was to determine how rice regulates the concentrations of these compounds in their seed coats once their production is activated by Pb and Rc. To identify genes affecting the concentration of anthocyanin, we studied a subset of cross-progeny in which Pb was turned on, but the grains had light versus dark purple pericarp, which correlated also with lower versus higher concentrations of anthocyanin. These results identified two chromosomal regions containing genes that modulate anthocyanin concentrations, one on chromosome 3 which we call qPR3, and another on chromosome 7 named qPR7. Similarly, we used a different subset of progeny from the same white rice crossed with a red-and-purple rice parent and identified two genetic regions (qPR3 and qPR5) causing differences in proanthocyanidin content. Interestingly, the same qPR3 gene found to affect anthocyanin also affected proanthocyanidin. Anthocyanins and proanthocyanididins share a significant portion of the genes in the biosynthetic pathway, thus share common precursors prior to branching off near the end. The fact that qPR3 regulates concentrations of both compounds suggests this gene impacts the shared portion of the biosynthetic pathways. Therefore, we also tested whether there would be trade-off between these two pigmented antioxidants, with an increase of one compound lowering the other. Contrary to hypothesized detrimental trade-off, however, we found mutual enhancement between the Pb and Rc genes. Adding the active Rc gene to purple progeny lines having the active Pb-anthocyanin gene increased anthocyanins; while adding an active Pb gene to red progeny lines having the active Rc-proanthocyanin gene elevated proanthocyanin concentrations. This mutual enhancement indicates that these two genes (Pb and Rc), in addition to turning on the production of proanthocyanidins or anthocyanins, also increase enzyme activity and flow rates along one or more of the shared biosynthetic steps. This study informs rice breeders that molecular markers tagging five genes; namely Pb, Rc, and the three newly identified qPR3, qPR5 and qPR7, could be used to enhance the nutritional quality of rice varieties.

Technical Abstract: The pigmented flavonoids, anthocyanins and proanthocyanidins, have health promoting properties. Previous work determined that the purple bran (Pb) and red color (Rc) genes turn on and off the biosynthesis of anthocyanins and proanthocyanidins, respectively. Not yet known is how the concentrations of these pigmented flavonoids are regulated in grain pericarps. Quantitative trait locus (QTL) analysis in a population of rice F5 recombinant inbred lines (RILs) from a cross between ‘IR36ae’ (white pericarp) x ‘242’ (red and purple pericarp) revealed three QTLs associated with concentrations of anthocyanins (purple) or proanthocyanidins (red) in grain. Both anthocyanin and proanthocyanidin concentrations independently mapped to a 1.5 Mb QTL region on chromosome 3, named as qPR3, located between RM3400 (at 15.8 Mb) and RM15123 (17.3 Mb). Across two years, qPR3 explained 36.3 percent of variance in anthocyanin, and 35.8 percent of variance in proanthocyanidin concentrations. The qPR3 region encompassed a candidate gene encoding a MYB transcription factor previously known to regulate purple grain characteristics. Study of NIL progeny from plants homozygous for Pb but heterozygous for Rc (PbPbRcrc) showed that anthocyanin in RcRc progeny was 2.1 to 4.5 times higher than that in rcrc progeny. Similarly, study of PbPbRcRc versus PbPbrcrc NIL progeny showed that the activated Rc allele increased proanthocyanidin content by 70 percent. These increases in antioxidant concentrations revealed mutual enhancement, not a trade-off between these compounds that share precursors. This suggests that Pb and Rc upregulate shared pathway genes as they also serve as transcription factors that turn on and off anthocyanin and proanthocyanidin synthesis, respectively. This study provided molecular markers for facilitating marker-assisted selection of qPR3, qPR5, and qPR7 to enhance grain concentrations of pigmented flavonoids and documented that stacking Rc and Pb genes further increases both flavonoid compounds.