Genetic dissection of carotenoid concentration and compositional traits in maize grain

Carotenoid compounds are derivatives of a well described secondary metabolic pathway in plants, participating in a diverse array of physiological functions, and are nutritionally valued vitamin precursors in the human diet. With the goal of enhancing the quantity (concentration) and quality (composition) of carotenoids in consumable plant tissues such as grain, breeding approaches have sampled from the extensive phenotypic variation that exists for these traits among maize inbreds. The predominant carotenoids in maize grain include lutein and zeaxanthin, which are collectively called di-hydroxy xanthophyll carotenoids, as well as alpha-carotene, beta-carotene and beta-cryptoxanthin, which are proVitamin A carotenoids. While phenotypic sampling and recombination across diverse maize germplasm has been successful, response to phenotypic selection has not been large enough to satisfy target nutritional levels. Greater phenotypic gain may be more predictably achieved if: 1) the genetic network regulating biological functions which contribute to carotenoid accumulation was better understood; and 2) the relative effect of the genetic loci controlling this quantitative trait was known, especially in varying genetic backgrounds. To this end, an investigation of the genetic basis for variation in carotenoid concentration and composition was performed in the studies presented here. Two QTL analyses revealed gene networks likely involved in carotenoid biosynthesis, conversion, and degradation as the primary drivers of variation in carotenoid concentration and composition. Investigation of one QTL hotspot on maize chromosome 9, observed to account for significant phenotypic variation in almost all carotenoid intermediates, revealed an allelic series associated with a large reduction in the major carotenoid intermediates of maize grain. This QTL, encoding carotenoid cleavage dioxygenase 1 (ccd1), showed a substrate preference for all measured carotenoids except beta-carotene. We further evaluated allelic variation affecting carotenoid composition focusing on two genes within the carotenoid biosynthesis pathway at lycopene epsilon cyclase (lcye) and beta-carotene hydroxylase (crtRB1). Variation at each of these genes was found to significantly affect carotenoid ratios or intermediates hypothesized to change through predicted substrate-enzyme interactions. Several other traits including total carotenoid concentration, were unexpectedly affected. Using allele-specific marker assisted selection at lcye and crtRB1 in synthetic populations developed for high total carotenoid content lead to a 3.95-11.33-fold improvement in beta-carotene and 1.45-3.22-fold improvement in proVitamin A for the favorable genotypes. The combined information from these studies highlights new genetic targets for further improvement of carotenoid concentration and composition, and provides guidelines for the selection and recombination of desirable genetic variation in breeding germplasm