# Pigment-Related Mutations Greatly Affect Berry Metabolome in San Marzano Tomatoes
## 1 Introduction  
Tomato (_Solanum lycopersicum_ L.) is among the most popular and highly consumed vegetables in the Mediterranean diet; its fruit contains many primary and secondary metabolites with remarkable nutritional and nutraceuticaltical values. Profiling of such metabolites in tomato has been performed in several studies by analysis of the carotenoid [1], phenolic [2], alkalioid [3, 4], and volatile [5, 6, 7] fraction. Many of these components show antioxidant activity and are thus responsible for beneficial effects on human health [8]. Others, including volatile compounds, play a fundamental role in defining the flavor and the palatability for consumers. Tomato ripening involves several physiological processes that include the visible breakdown of chlorophylls and the synthesis of carotenoids, with a massive accumulation of antioxidant phytonutrients such as lycopene and \(\alpha\)- and \(\beta\)-carotene. Besides carotenoids, the contents of other important antioxidants, such as ascorbic acid, \(\alpha\)-tocopherol, and phenolics, as well as of antinutrients such as glycoalkaloids (mostly \(\alpha\)-tomatine and dehydro-drotomatine), vary during ripening, thus influencing the nutritional value of the fruit [9; 10; 11]. On the other hand, fruits of the cultivated tomato do not normally produce high levels of anthocyanins, and flavonoid accumulation is limited to the peel. At the onset of ripening, there is also a dramatic shift in the profile of volatile compounds consisting of a marked increase in the production of a wide range of molecules which are attractive to seed dispersers and have an important effect on consumer preference [12; 13; 14]. For these reasons, secondary metabolism has become a target for tomato breeding, with the aim to improve the qualitative and quantitative composition of the berry and its organoleptic quality. Conventional and molecular breeding offer promising approaches to decrease or, more often, increase the occurrence of certain compounds or groups of compounds and to boost the production of metabolites not normally expressed in tomato fruits, such as flavonoids and anthocyanins [15]. For this purpose, photomorphogenic mutants have attracted considerable attention for their ability to induce pigment synthesis. Among them, the _high pigment-1_ (_hp-1_) and _hp-2_ mutations have been considered for their capacity to increase all classes of pigments, whereas the combination of the _Anthocyanin fruit (Aft)_ and _atroviolaceum (atv)_ variants were studied for their capacity to induce the production of anthocyanins. These mutations are involved in the light signaling machinery and have been shown to drive the overproduction of several flavonoid compounds in mature fruits, as well as carotenoid and other classes of metabolites [16; 17], depending on the type of the mutation. High pigment variants are controlled by monogenic recessive mutations. _hp-1_ was discovered as a spontaneous variant in 1917 at the Campbell Soup Company farms [18], and its phenotype was later attributed to a lesion in the _DNA Damage UV Binding protein 1_ (_SIDDB1_) [19]. _hp-2_ was induced by ethyl-methane sulphonate (EMS) in cv. Garim, a variety following the typology of the traditional Italian San Marzano landrace (SM) [20]. The _hp-2_ phenotype is caused by a mutation in the _Deetiolated1_ (_SIDET1_) gene [21]. Both _hp-1_ and _hp-2_ are characterized by an exaggerated light responsiveness; [PERSON] et al. [22] demonstrated their interaction in regulating the expression of hundreds of light-regulated genes, conferring unique the characteristics of higher anthocyanin levels in both roots and leaves, shorter hypocotyls, dwarfism, and more deeply pigmented fruits when compared with wild-type plants. These variants are currently used, in heterozygous condition, in processing and fresh market tomato hybrids [23]. With an opposite phenotype to high pigment variants, the _pigment diluter_ (_pd_) allele causes reduced levels of lycopene, carotenoids, and chlorophylls but enhanced content of polyphenols [24].