A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels

Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A.     

Proximate mechanisms of colour variation in the frillneck lizard: geographical differences in pigment contents of an ornament

Animal coloration has evolved in contexts such as communication, camouflage, and thermoregulation. Most studies of animal coloration focus on its adaptive benefits, whereas its underlying mechanisms have received less attention despite their potential influence on adaptive benefits. In fish and reptiles, for example, colour variation from yellow to red can be produced by carotenoid and/or pteridine pigments, which differ dramatically in the way they are obtained (carotenoids through diet and pteridines synthesized de novo). Hence, potential adaptive benefits could differ greatly depending on the relative contribution to coloration of different pigments. In the present study, we investigate the mechanisms underlying colour variation in the frill of the Australian frillneck lizard (Sauropsida: Chlamydosaurus kingii). Frill colour varies between populations across the species' range (red, orange, yellow or white). We argue that this geographical variation results from different concentrations of carotenoids and pteridines in the frill. Frill carotenoid concentrations were lower in eastern populations (yellow and white forms), and pteridines were present only in the red and orange forms, thereby explaining their redder hues. The observed geographical variation in frill carotenoids suggests variation in carotenoid availability across the species' range, which is backed up by the finding that plasma carotenoid concentrations were higher in the red (western) compared to the yellow (eastern) form. Although no correlations were found between individual colour measurements, frill pigments and plasma carotenoids, our results suggest that selective pressures vary across the species' range and we speculate that predation pressures and/or intrasexual signalling context differ between forms.     

Carotenoid limitation of sexual coloration along an environmental gradient in guppies

Carotenoids produce most of the brilliant orange and yellow colours seen in animals, but animals cannot synthesize these pigments and must rely on dietary sources. The idea that carotenoids make good signals because they are a scarce limiting resource was proposed two decades ago and has become the leading hypothesis for the role of carotenoids in animal communication. To our knowledge, until now, however, there has been no direct evidence that carotenoids are a limiting resource in nature. We showed that carotenoid availability in the wild limits the expression of sexual coloration in guppies (Poecilia reticulata), a species in which females prefer males with brighter orange carotenoid-containing spots. Further, the degree of carotenoid limitation varies geographically along a replicated environmental gradient (rainforest canopy cover), which opens new avenues for testing signal evolution theory.     

An experimental test of mate choice for red carotenoid coloration in the marine copepod Tigriopus californicus

Colorful ornaments are hypothesized to have evolved in response to sexual selection for honest signals of individual quality that provide information about potential mates. Red carotenoid coloration is common in diverse groups, and in some vertebrate taxa, red coloration is a sexually selected trait whereby mates with the reddest ornaments are preferred . Despite being widespread among invertebrates, whether red carotenoid coloration is assessed during mate choice in these taxa is unclear. The marine copepod Tigriopus californicus displays red coloration from the accumulation of the carotenoid astaxanthin. Previous research on copepods has shown that astaxanthin provides protection from UV radiation and xenobiotic exposure and that carotenoid production is sensitive to external stressors. Because of the condition dependency of the red coloration, we hypothesized that Tigriopus would use it as a criterion during mate choice. To test this hypothesis, we conducted trials in which males chose between females that were wild-type red (carotenoid-rich algae diet) or white (carotenoid-deficient yeast diet). To control for dietary differences and to isolate the effect of carotenoid coloration, we also presented males with restored-red females fed a carotenoid-supplemented yeast diet. We found that wild-type red females were weakly preferred over white females. After controlling for diet, however, we found that restored-red females were avoided. Our observations do not support the hypothesis that male copepods prefer the carotenoid coloration of females during mate choice. We hypothesize that algal-derived compounds other than carotenoids play a role in mate choice. Red coloration in copepods appears to be a condition-dependent trait that is not assessed during mating.     

Novel methoxy-carotenoids from the burgundy-colored plumage of the Pompadour Cotinga Xipholena punicea

Recent advances in the fields of chromatography, mass spectrometry, and chemical analysis have greatly improved the efficiency with which carotenoids can be extracted and analyzed from avian plumage. Prior to these technological developments, Brush (1968) [1] concluded that the burgundy-colored plumage of the male pompadour Cotinga Xipholena punicea is produced by a combination of blue structural color and red carotenoids, including astaxanthin, canthaxanthin, isozeaxanthin, and a fourth unidentified, polar carotenoid. However, X. punicea does not in fact exhibit any structural coloration. This work aims to elucidate the carotenoid pigments of the burgundy color of X. punicea plumage using advanced analytical methodology. Feathers were collected from two burgundy male specimens and from a third aberrant orange-colored specimen. Pigments were extracted using a previously published technique (McGraw et al. (2005) [2]), separated by high-performance liquid chromatography (HPLC), and analyzed by UV/Vis absorption spectroscopy, chemical analysis, mass spectrometry, nuclear magnetic resonance (NMR), and comparison with direct synthetic products. Our investigation revealed the presence of eight ketocarotenoids, including astaxanthin and canthaxanthin as reported previously by Brush (1968) [1]. Six of the ketocarotenoids contained methoxyl groups, which is rare for naturally-occurring carotenoids and a novel finding in birds. Interestingly, the carotenoid composition was the same in both the burgundy and orange feathers, indicating that feather coloration in X. punicea is determined not only by the presence of carotenoids, but also by interactions between the bound carotenoid pigments and their protein environment in the barb rami and barbules. This paper presents the first evidence of metabolically-derived methoxy-carotenoids in birds.     

Dietary carotenoids change the colour of Southern corroboree frogs

Animal coloration can be the result of many interconnected elements, including the production of colour‐producing molecules de novo, as well as the acquisition of pigments from the diet. When acquired through the diet, carotenoids (a common class of pigments) can influence yellow, orange, and red coloration and enhanced levels of carotenoids can result in brighter coloration and/or changes in hue or saturation. We tested the hypothesis that dietary carotenoid supplementation changes the striking black and yellow coloration of the southern corroboree frog (Pseudophryne corroboree, Amphibia: Anura). Our dietary treatment showed no measurable difference in colour or brightness for black patches in frogs. However, the reflectance of yellow patches of frogs raised on a diet rich in carotenoids was more saturated (higher chroma) and long‐wave shifted in hue (more orange) compared to that of frogs raised without carotenoids. Interestingly, frogs with carotenoid‐poor diets still developed their characteristic yellow and black coloration, suggesting that their yellow colour patches are a product of pteridines manufactured de novo.     

Pteridine, not carotenoid, pigments underlie the female-specific orange ornament of striped plateau lizards (Sceloporus virgatus)

Indicator models of sexual selection suggest that signal honesty is maintained via costs of ornament expression. Carotenoid-based visual signals are a well-studied example, as carotenoids may be environmentally limited and impact signaler health. However, not all bright yellow, orange and red ornaments found in vertebrates are carotenoid-based; pteridine pigments may also produce these colors. We examine the contribution of carotenoid and pteridine pigments to the orange reproductive color of female striped plateau lizards (Sceloporus virgatus). This color ornament reliably indicates female mate quality, yet costs maintaining signal honesty are currently unknown. Dietary carotenoid manipulations did not affect orange color, and orange skin differed from surrounding white skin in drosopterin, not carotenoid, content. Further, orange color positively correlated with drosopterin, not carotenoid, concentration. Drosopterin-based female ornaments avoid the direct trade-offs of using carotenoids for ornament production vs egg production, thus may relax counter-selection against color ornament exaggeration in females. Direct experimentation is needed to determine the actual costs of pteridine-based ornaments. Like carotenoids, pteridines influence important biological processes, including immune and antioxidant function; predation and social costs may also be relevant.     

Genetic basis and fitness correlates of dynamic carotenoid‐based ornamental coloration in male and female common kestrels Falco tinnunculus

Knowledge of the genetic basis of sexual ornaments is essential to understand their evolution through sexual selection. Although carotenoid‐based ornaments have been instrumental in the study of sexual selection, given the inability of animals to synthesize carotenoids de novo, they are generally assumed to be influenced solely by environmental variation. However, very few studies have directly estimated the role of genes and the environment in shaping variation in carotenoid‐based traits. Using long‐term individual‐based data, we here explore the evolutionary potential of a dynamic, carotenoid‐based ornament (namely skin coloration), in male and female common kestrels. We first estimate the amount of genetic variation underlying variation in hue, chroma and brightness. After correcting for sex differences, the chroma of the orange‐yellow eye ring coloration was significantly heritable (h² ± SE = 0.40 ± 0.17), whereas neither hue (h² = 0) nor brightness (h² = 0.02) was heritable. Second, we estimate the strength and shape of selection acting upon chromatic (hue and chroma) and achromatic (brightness) variation and show positive and negative directional selection on female but not male chroma and hue, respectively, whereas brightness was unrelated to fitness in both sexes. This suggests that different components of carotenoid‐based signals traits may show different evolutionary dynamics. Overall, we show that carotenoid‐based coloration is a complex and multifaceted trait. If we are to gain a better understanding of the processes responsible for the generation and maintenance of variation in carotenoid‐based coloration, these complexities need to be taken into account.     

Carotenoid Crystal Formation in Arabidopsis and Carrot Roots Caused by Increased Phytoene Synthase Protein Levels

Background

As the first pathway-specific enzyme in carotenoid biosynthesis, phytoene synthase (PSY) is a prime regulatory target. This includes a number of biotechnological approaches that have successfully increased the carotenoid content in agronomically relevant non-green plant tissues through tissue-specific PSY overexpression. We investigated the differential effects of constitutive AtPSY overexpression in green and non-green cells of transgenic Arabidopsis lines. This revealed striking similarities to the situation found in orange carrot roots with respect to carotenoid amounts and sequestration mechanism.

Methology/Principal Findings

In Arabidopsis seedlings, carotenoid content remained unaffected by increased AtPSY levels although the protein was almost quantitatively imported into plastids, as shown by western blot analyses. In contrast, non-photosynthetic calli and roots overexpressing AtPSY accumulated carotenoids 10 and 100-fold above the corresponding wild-type tissues and contained 1800 and 500 µg carotenoids per g dry weight, respectively. This increase coincided with a change of the pattern of accumulated carotenoids, as xanthophylls decreased relative to β-carotene and carotene intermediates accumulated. As shown by polarization microscopy, carotenoids were found deposited in crystals, similar to crystalline-type chromoplasts of non-green tissues present in several other taxa. In fact, orange-colored carrots showed a similar situation with increased PSY protein as well as carotenoid levels and accumulation patterns whereas wild white-rooted carrots were similar to Arabidopsis wild type roots in this respect. Initiation of carotenoid crystal formation by increased PSY protein amounts was further confirmed by overexpressing crtB, a bacterial PSY gene, in white carrots, resulting in increased carotenoid amounts deposited in crystals.

Conclusions

The sequestration of carotenoids into crystals can be driven by the functional overexpression of one biosynthetic enzyme in non-green plastids not requiring a chromoplast developmental program as this does not exist in Arabidopsis. Thus, PSY expression plays a major, rate-limiting role in the transition from white to orange-colored carrots.     

A Genome-Wide Association Study Identifies the Genomic Region Associated with Shell Color in Yesso Scallop, <Emphasis Type="Italic">Patinopecten yessoensis</Emphasis>

The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform. A total of 322,332,684 high-quality reads were obtained, and the average sequencing depth was 18.4×. One genomic region on chromosome 11 that included 239 single-nucleotide polymorphisms (SNPs) was identified as significantly associated with shell color. After verification by high-resolution melting in another population, two SNPs were selected as specific loci for reddish-orange shell color. These two SNPs could be used to improve the selective breeding progress of true-breeding strains with complete reddish-orange scallops. In addition, within the significantly associated genomic region, candidate genes were identified using marker sequences to search the draft genome of Yesso scallop. Three genes (LDLR, FRIS, and FRIY) with known functions in carotenoid metabolism were identified. Further study using high-performance liquid chromatography proved that the relative level of carotenoids in the reddish-orange shells was 40 times higher than that in the brown shells. These results suggested that the accumulation of carotenoids contributes to the formation of reddish-orange shells.     

Endosymbiotic bacteria as a source of carotenoids in whiteflies

Although carotenoids serve important biological functions, animals are generally unable to synthesize these pigments and instead obtain them from food. However, many animals, such as sap-feeding insects, may have limited access to carotenoids in their diet, and it was recently shown that aphids have acquired the ability to produce carotenoids by lateral transfer of fungal genes. Whiteflies also contain carotenoids but show no evidence of the fungus-derived genes found in aphids. Because many sap-feeding insects harbour intracellular bacteria, it has long been hypothesized that these endosymbionts could serve as an alternative source of carotenoid biosynthesis. We sequenced the genome of the obligate bacterial endosymbiont Portiera from the whitefly Bemisia tabaci. The genome exhibits typical signatures of obligate endosymbionts in sap-feeding insects, including extensive size reduction (358.2 kb) and enrichment for genes involved in essential amino acid biosynthesis. Unlike other sequenced insect endosymbionts, however, Portiera has bacterial homologues of the fungal carotenoid biosynthesis genes in aphids. Therefore, related lineages of sap-feeding insects appear to have convergently acquired the same functional trait by distinct evolutionary mechanisms—bacterial endosymbiosis versus fungal lateral gene transfer.     

Red fish, blue fish: trade-offs between pigmentation and immunity in Betta splendens

Carotenoid pigments are responsible for many examples of sexuallyattractive red, orange, and yellow coloration in animals andplay an important role in antioxidant and immune defenses. Becausevertebrates cannot synthesize carotenoids, limited dietary availabilitymay impose a trade-off between maintaining ornamental colorationand health. We used an experimental approach to test the carotenoidtrade-off hypothesis in the fighting fish Betta splendens, byexamining whether carotenoid allocation strategies differ amongconspecifics that exhibit a gradient of body coloration fromblue to red. We found that male redness is underlain by carotenoidsand that females preferred to associate with red males overblue males, suggesting a sexually-selected advantage to beingred. Moreover, we found strong experimental support for thecarotenoid trade-off hypothesis, as individuals that variedin color did not appear to allocate carotenoids equally to bothimmune response and coloration. Redder fish given supplementalcarotenoids increased in both immune response (to a phytohemagglutinationchallenge) and redness compared with controls. In contrast,bluer fish given supplemental carotenoids did not become morered but instead benefited immunologically more so than eithercontrol or redder supplemented fish. These results enhance ourunderstanding of the evolution and plasticity of carotenoidmobilization and utilization pathways in animals.     

EVOLUTION OF CAROTENOID PIGMENTATION IN CACIQUES AND MEADOWLARKS (ICTERIDAE): REPEATED GAINS OF RED PLUMAGE COLORATION BY CAROTENOID C4‐OXYGENATION

Many animals use carotenoid pigments to produce yellow, orange, and red coloration. In birds, at least 10 carotenoid compounds have been documented in red feathers; most of these are produced through metabolic modification of dietary precursor compounds. However, it is poorly understood how lineages have evolved the biochemical mechanisms for producing red coloration. We used high‐performance liquid chromatography to identify the carotenoid compounds present in feathers from 15 species across two clades of blackbirds (the meadowlarks and allies, and the caciques and oropendolas; Icteridae), and mapped their presence or absence on a phylogeny. We found that the red plumage found in meadowlarks includes different carotenoid compounds than the red plumage found in caciques, indicating that these gains of red color are convergent. In contrast, we found that red coloration in two closely related lineages of caciques evolved twice by what appear to be similar biochemical mechanisms. The C4‐oxygenation of dietary carotenoids was responsible for each observed transition from yellow to red plumage coloration, and has been commonly reported by other researchers. This suggests that the C4‐oxygenation pathway may be a readily evolvable means to gain red coloration using carotenoids.     

Lipid-dissolved γ-carotene, β-carotene,and lycopene in globular chromoplasts of peach palm (Bactris gasipaes Kunth) fruits

Main conclusion

High levels of β-carotene, lycopene, and the rare γ-carotene occur predominantly lipid-dissolved in the chromoplasts of peach palm fruits. First proof of their absorption from these fruits is reported. The structural diversity, the physical deposition state in planta, and the human bioavailability of carotenoids from the edible fruits of diverse orange and yellow-colored peach palm (Bactris gasipaes Kunth) varieties were investigated. HPLC–PDA–MSⁿ revealed a broad range of carotenes, reaching total carotenoid levels from 0.7 to 13.9 mg/100 g FW. Besides the predominant (all-E)-β-carotene (0.4–5.4 mg/100 g FW), two (Z)-isomers of γ-carotene (0.1–3.9 mg/100 g FW), and one (Z)-lycopene isomer (0.04–0.83 mg/100 g FW) prevailed. Approximately 89–94 % of total carotenoid content pertained to provitamin A carotenoids with retinol activity equivalents ranging from 37 to 609 µg/100 g FW. The physical deposition state of these carotenoids in planta was investigated using light, transmission electron, and scanning electron microscopy. The plastids found in both orange and yellow-colored fruit mesocarps were amylo-chromoplasts of the globular type, containing carotenoids predominantly in a lipid-dissolved form. The hypothesis of lipid-dissolved carotenoids was supported by simple solubility estimations based on carotenoid and lipid contents of the fruit mesocarp. In our study, we report first results on the human bioavailability of γ-carotene, β-carotene, and lycopene from peach palm fruit, particularly proving the post-prandial absorption of the rarely occurring γ-carotene. Since the physical state of carotenoid deposition has been shown to be decisive for carotenoid bioavailability, lipid-dissolved carotenoids in peach palm fruits are expected to be highly bioavailable, however, further studies are required.     

Carotenoid‐based plumage coloration in golden‐crowned kinglets Regulus satrapa: pigment characterization and relationships with migratory timing and condition

Carotenoid‐based ornamental coloration has long been proposed to honestly signal quality due to its dependence on individual condition. Because migration can be one of the most stressful periods of an animal's annual cycle, developing colourful plumage may be particularly challenging for species in which migration and moult periods overlap or occur sequentially. The purpose of this study was to investigate pigmentary and condition‐dependent bases of carotenoid colour variation in a small migratory passerine, the golden‐crowned kinglet Regulus satrapa (Family Regulidae). We captured 186 male and female kinglets of various ages during fall migration in southwestern Ontario, Canada and recorded arrival date, body condition index, fat and pectoral muscle scores, wing mite infestation, and feather growth rate as measures of condition. We quantified crown coloration using reflectance spectrometry and analyzed feather carotenoids using high‐performance liquid chromatography. Yellow crown feathers of female kinglets contained only yellow hydroxycarotenoids, whereas orange feathers of males harboured a suite of eight carotenoid pigments. Males with longer wavelength orange crown hues deposited greater concentrations of ketocarotenoids, especially canthaxanthin. Female kinglets with longer wavelength crown hues and males with longer wavelength crown hues and more saturated crown coloration left for migration earlier in the year. Females with longer wavelength crown hues had fewer feather mites and tended to be in better condition. However, male kinglets with more saturated coloration possessed smaller pectoral muscles. This is the first study to identify plumage carotenoids in this North American bird family and to determine the pigmentary basis for both inter‐ and intrasexual colour variation. Our results provide further support for the condition‐dependence of carotenoid coloration and suggest that ornamental elaboration in both sexes may encode information about fall condition and migratory performance.     

Carotenoid scarcity, synthetic pteridine pigments and the evolution of sexual coloration in guppies (Poecilia reticulata).

Carotenoid-based sexual coloration is the classic example of an honest signal of mate quality. Animals cannot synthesize carotenoid pigments and ultimately depend on dietary sources. Thus, in carotenoid-poor environments, carotenoid coloration may be a direct indicator of foraging ability and an indirect indicator of health and vigour. Carotenoid coloration may also be affected, more directly, by parasites in some species. Carotenoids are not, however, the only conspicuous pigments available to animals. Pteridine pigments, with similar spectral properties, are displayed in the exoskeletons and wings of insects, the irides of birds and the skins of fishes, lizards and amphibians. Unlike carotenoids, pteridines are synthesized de novo by animals. We report that the orange spots that male guppies (Poecilia reticulata) display to females contain red pteridine pigments (drosopterins) in addition to carotenoids. We also examined the relationship between drosopterin production by males and carotenoid availability in the field. The results contrasted sharply with the hypothesis that males use drosopterins to compensate for carotenoid scarcity: males used more, not less, drosopterins in streams with higher carotenoid availability. The positive association between drosopterin use and carotenoid availability could reflect the costs of drosopterin synthesis or it could be a consequence of females preferring a particular pigment ratio or hue. Male guppies appear to use drosopterin pigments in a manner that dilutes, but does not eliminate, the indicator value of carotenoid coloration.     

Carotenoids bolster immunity during moult in a wild songbird with sexually selected plumage coloration

Carotenoid‐based colours in animals are valuable models for testing theories of sexual selection and life‐history trade‐offs because the pigments used in coloration are chemically tractable in the diet and in the body, where they serve multiple purposes (e.g. health enhancement, photoprotection). An important assumption underlying the hypothesized signalling value of carotenoid coloration is that there is a trade‐off in carotenoid pigment allocation, such that not all individuals can meet the physiological/morphological demands for carotenoids (i.e. carotenoids are limited) and that only those who have abundant supplies or fewer demands become the most colourful. Studies of carotenoid trade‐offs in colourful animals have been limited largely to domesticated species, which may have undergone artificial selection that changed the historical/natural immunomodulatory roles of carotenoids, to young animals lacking carotenoid‐based signals or to species displaying carotenoid‐based skin and bare parts. We studied the health benefits of carotenoids during moult in house finches (Carpodacus mexicanus), which display sexually selected, carotenoid‐based plumage coloration. We manipulated dietary carotenoid availability during both winter (nonmoult) and autumn (moult) in captive males and females and found that carotenoid‐supplemented birds mounted stronger immune responses (to phytohemagglutinin injection and to a bacterial inoculation in blood) than control birds only during moult. This study provides experimental, seasonal support for a fundamental tenet of Lozano's ‘carotenoid trade‐off’ hypothesis and adds to a growing list of animal species that benefit immunologically from ingesting higher dietary carotenoid levels. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 560–572.