Chapter 1 10 1.1.3 Tomato genomic resources Recent advances in genomic research have significantly contributed to our understanding of the tomato species. The initial tomato genome was derived from the Heinz cultivar (Sato et al., 2012). Leveraging the existing S. lycopersicum cv. Heinz genome as a reference, and with extensive sequencing, and incorporating additional single-nucleotide polymorphisms (SNPs), this ultimately culminated in the final M82 genome (Bolger et al., 2014). Notably, the genome of Solanum lycopersicum cv. M82 was meticulously sequenced in conjunction with the Solanum pennellii genome, The 950-Mb tomato genome exhibits a distinct structure, comprising gene-rich euchromatin and gene-poor pericentromeric heterochromatin (Michaelson et al., 1991; Barone et al., 2008). Given the challenge of sequencing the heterochromatic fraction with its repetitive sequences, the initial strategy focused on sequencing the euchromatic portion, estimated to constitute one-quarter (220 Mb) of the tomato genomic sequence, encompassing over 90% of the genes. Various tools have been developed for the Tomato Genome Sequencing Project, (Sherman and Stack, 1995; Todesco et al., 2008; Mueller et al., 2009; Sato et al., 2012; Bolger et al., 2014). S. lycopersicum cv. M82’s genetic information has provided valuable insights into the molecular mechanisms underlying various traits in tomatoes. M82 tomatoes are widely used in comparison to S. pennellii in drought resistance study, fruit development, and genetic comparison in stress (Gong et al., 2010; Ikeda et al., 2017; Liu et al., 2018; Reynoso et al., 2019; Watanabe et al., 2021). For example, the wild tomato relative Solanum pennellii shows a strong response to shade and in contrast, the domestic tomato S. lycopersicum, which has been bred for production in field conditions, shows a milder response (Bush et al., 2015). However, the Shade Avoidance Syndrome (SAS) mechanisms within the different tomato species are not fully characterized, and we set out to explore the significant changes of commercial tomato plants in stem elongation. 1.1.4 Summary Tomato is an economically important crop, renowned as a well-established stress study model and offers distinctive genetic resources. Despite not having received the same level of attention as Arabidopsis, recent research has delved into the molecular and physiological aspects of SAS in tomato. The uniqueness of tomatoes, with their specific growth patterns, hormonal dynamics, and stem structures, using tomato as a model adds an intriguing layer to our understanding of adaptive strategies under varied light conditions.
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