Jérémy Clotault; Didier Peltier; Vanessa Soufflet-Freslon; Mathilde Briard; Emmanuel Geoffriau

“ Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogenetics. ”

“ Balancing selection generally leads to an increase of diversity. HKA test was used to test for specific nucleotide diversity levels in these three genes. A model that assumes selection at these genes significantly improved the likelihood in comparison with the neutral model (ML-HKA test; χ2 = 12.39, df = 3, P<0.01) . The maximum likelihood estimate of the selection parameter k for CRTISO (k = 2.62) , LCYB1 (k = 2.38) and LCYE (k = 2.88) suggests a twofold increase in diversity over neutral expectations at these loci, in comparison with the other carotenoid biosynthesis genes analyzed. ”

“ One major drawback of signatures of selection is the confounding effect of demographic events and selection. For example, an excess of intermediate frequency variation is consistent with balancing selection but may also be driven by population scale events like population subdivision [43] . Therefore, the genetic differentiation between Western and Eastern cultivated carrots must be taken into account when testing carotenoid biosynthesis genes for selection [35] . ”

“ Selection was thus found to be directed to genes encoding enzymes located at metabolic nodes in central metabolism in Drosophila [3] and starch pathway in maize [4] .
Genes encoding upstream enzymes are expected to face stronger selective constraints and therefore to evolve more slowly than genes encoding downstream enzymes, maybe owing to differential pleiotropic effects [1] . Modeling showed that beneficial mutations are preferentially driven to upstream genes, and have a greater impact on flux control than downstream genes during adaptive evolution [2] . ”

“ Besides gene position in the pathway, the signal of balancing selection detected in carrot for CRTISO, LCYB1 and above all for LCYE confirms that reticulation of the pathway is a further factor influencing differential selection in the pathway. ”

“ Carrot domestication has led to a change between an uncolored root in wild carrots to a root with sometimes high carotenoid levels in cultivated carrots. This change should have been obtained by positive selection and should be linked to a reduction of diversity for targeted genes. In order to detect nucleotide diversity variations in carotenoid biosynthesis genes, we used HKA neutrality tests. ”

“ The models differed for parameter ω = dN/dS. Codons with ω = 1 are assumed to evolve neutrally, while codons with 0<ω<1 are assumed to evolve under purifying selection and codons with ω>1 are assumed to evolve under positive selection. The null model M0 assumes ω to be constant for all codons of the sequences analyzed and for all the branches concerned. We compared the likelihood of the null model M0 with two ‘branch models’ M1 and M2. M1 is the free ratios model which assumes an independent ω ratio for each branch. ”

“ Beyond coloring fruits, petals and some roots [30] , carotenoids act as accessory pigments in photosynthesis and are involved in dissipating excess excitation energy of chlorophyll molecules as heat by non-photochemical quenching (NPQ) , a fundamental process to preserve photosynthetic activity [31] . ”

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