Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification

Abstract

Dietary vitamin A deficiency causes eye disease in 40 million children each year and places 140 to 250 million at risk for health disorders. Many children in sub-Saharan Africa subsist on maize-based diets. Maize displays considerable natural variation for carotenoid composition, including vitamin A precursors alpha-carotene, beta-carotene, and beta-cryptoxanthin. Through association analysis, linkage mapping, expression analysis, and mutagenesis, we show that variation at the lycopene epsilon cyclase (lcyE) locus alters flux down alpha-carotene versus beta-carotene branches of the carotenoid pathway. Four natural lcyE polymorphisms explained 58% of the variation in these two branches and a threefold difference in provitamin A compounds. Selection of favorable lcyE alleles with inexpensive molecular markers will now enable developing-country breeders to more effectively produce maize grain with higher provitamin A levels.

Fig. 1

Simplified carotenoid biosynthetic pathway in plants (29). Enzymatic reactions are represented by arrows, dashed lines represent multiple enzymatic steps. Substrates in red were evaluated in this study. Compounds: GGPP, geranylgeranyl diphosphate; ABA, abscisic acid. Enzymes: PSY, phytoene synthase; PDS, phytoene desaturase; Z-ISO, 15-cis zetacarotene isomerase; ZDS, zetacarotene desaturase; CRTISO, carotene isomerase; HYD, carotene hydroxylase enzymes, which include ε- and β-ring hydroxylases.

Fig. 2

Grain color and carotenoid content. The graphs depict the low correlation between visual grain color and total carotenoids, β-carotene, and β-cryptoxanthin in diverse inbreds. In these kernels, the shade of yellow ranges from white (score of 1) to dark orange (score of 6). White kernels were excluded from the analysis. The difficulty in visual selection for β-carotene content is further exemplified by the images on the left, where the yellow maize below has higher β-carotene than the orange variety above. These correlations are across the diverse panel of 228 maize inbreds; correlations for grain color and total carotenoids are higher when scored across segregating populations and narrow ranges of germ plasm, but correlations for β-carotene and β-cryptoxanthin remain low.

Fig. 3

Schematic diagram of the maize lcyE. Putative transcription start sites are depicted with orange arrow, translated exons as black squares, and the sampled regions as gray boxes. Polymorphisms that significantly associated with changes in flux between the lutein and zeaxanthin branches of the pathway are labeled with asterisks. The 5′ transposable element insertion(s) are represented by the white triangles. Positions relative to the sequence alignment are indicated numerically above the polymorphisms.