Cultivated Tomato (Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes

Abstract

In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication.

The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

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Morphological Diversity, Genetic Characterization, and Phytochemical Assessment of the Cypriot Tomato Germplasm

“…Such alterations resulted in a general downgrade of nutritional properties, which are presently somewhat inferior in modern cultivars and hybrids mostly due to the increase of tomato fruit size and intensive cultivation crop schemes [ 16 ]. Moreover, the selection of a restricted number of genotypes has caused a genetic bottleneck in terms of variability, and currently less than 10% of the total genetic diversity is present in the S. lycopersicum gene pool [ 15 , 17 , 18 ]. As a result, there is a vivid debate among consumers on the usage of recently established commercial varieties at the expense of heirloom cultivars, since the latter are considered superior in several qualitative aspects regarding flavor, aroma and phytochemicals [ 4 ].…”

Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species

“… 2008 ; Abewoy Fentik 2017 ; Tamburino et al. 2020 ), indicated by only 5% of the genetic and chemical diversity of wild relatives remaining in the cultivated tomato (Miller and Tanksley 1990 ; Blanca et al. 2015 ; Fernie and Aharoni 2019 ; Mata-Nicolás et al.…”