Genomic approaches to impart extended shelf-life in tomato.
Authors: Arvind K Yadav, Rohini Sreevathsa, Rhitu Rai and Prasanta K Dash
National Research Centre on Plant Biotechnology, LBS Building, PUSA, New Delhi-110012.

Tomato is one of the most popular and versatile vegetables of the world, because of its taste, color, high nutritive value, and its diversified culinary and salad use. It is the world’s most consumed vegetable crop after potato and sweet potato and tops the list of canned vegetables. According to National Horticulture Board database, 18735.9 million tonnes tomatoes are produced annually on 882 million hectares of land in India (NHB Database, 2015).

Tomatoes are eaten directly as raw vegetable or consumed in a variety of processed products like ketch-up, sauce, chutney, juice, soup, paste, and puree etc. It is well known for its nutritional importance as it is a rich source of nutrients Na, K, Fe, vitamin A, vitamin C and antioxidants like lycopene and salicylate (Afzal et al. 2013). The red pigment of tomatoes is due to lycopene. Lycopene is an antioxidant which protects the cells from oxidative damage, so it decreases the risk of chronic diseases such as coronary heart diseases and cancer diseases (Taber et al. 2008). Bright red shade of tomato indicates high level of beta-carotene and lycopene. Lycopene, which is located in the cell wall of tomato is efficiently released on heating with oil. Additionally nutritional value of tomatoes is not lost during high-heat processing such as being canned or in ketchup processing (Debjit et al. 2012).

Tomato (Lycopersicon esculentum) belongs to the family Solanaceae that includes many species of economic importance such as tomato, potato, tobacco, pepper and eggplant. In recent years, interest of scientists in tomato as a model plant has significantly increased due to the fact that its genome has been sequenced (The Tomato Genome Consortium 2012). Tomato is an excellent model crop both for basic and applied research programs due to its useful features such as relatively short life cycle, abundant seed production, relatively small genome (950 Mb), lack of gene duplication, high self-fertility and homozygosity, easy way of controlling pollination and hybridization, and possibility to regenerate whole plants by tissue culture from different explants (Bai and Lindhout, 2007).

In November 2003, the International solanaceae project (http://, a consortium involving researchers from many countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States) launched the tomato genome-sequencing project with an objective to sequence gene-rich regions of the 12 chromosomes. In this endeavor, more than 1,200 bacterial artificial chromosomes (BACs) were sequenced (Mueller et al. 2005). In 2008, a whole-genome-sequencing strategy was also adopted with an aim to saturate the entire genome. Ultimately, a multi-national team of scientists from 14 countries contributed to the project and the tomato genome was successfully decoded (The Tomato Genome Consortium 2012).

Using an integrated approach based on EuGene and RNA-seq data it was predicted that tomato genome contained 34,727 protein-coding genes. Among all the predicted genes, 78 % of the genes were allocated a functional description i.e. the protein they code for, while remaining 22 % were categorised as "unknown Protein". In addition to the structural genes, it was found that tomato genome also codes for 96 known micro-RNAs. Comparative genomics involving tomato, potato, arabidopsis, rice and grape demonstrated that the protein coding genes were clustered into 23,208 gene groups and 5,165 gene groups as solanaceae specific, while 562 were tomato specific. Discovery of such genes/groups need to be investigated to delineate their roles in species specific traits, including fruit and tuber biogenesis.

Shelf-life is a major problem for any agricultural produce, especially in countries such as in Southeast Asia and Africa where farmers cannot afford controlled-environment storage. Taking tomato as an example, people prefer unshrivelled fruits for home consumption. Therefore, if wrinkling can be delayed, marketing time of tomato can be extended. Over the last two decades, genetic engineering has been used to extend tomato shelf-life by reducing the activity of cell-wall degrading enzymes and enhancing the levels of specific metabolites (Zhang et al. 2013). The FlavrSavr tomato (also known as CGN-89564) was the first genetically engineered food that was commercially grown and granted a license for human consumption by Food and Drug Administration in 1994. Unfortunately, the tomatoes had a bland taste and due to early ripening it was difficult to transport and thus were out of choice in the market by 1997. In China, Huzahong Agricultural University developed the GM tomato Huafan No 1 with long shelf-life and was the first GM plant to be approved for commercialization in 1996.

Controlling the rate of softening to extend shelf-life in tomato has been a key target since 1990s but with modest accomplishments. Hybrids grown nowadays contain ‘non-ripening mutations’ that slow ripening and improve shelf life, but adversely affect flavor and color. Kitagawa, M. et al., 2005, described that hybrids harboring ripening inhibitor (rin) produce firm fruits that ripen slowly but they often have poor flavor, meagerly develop color and possess reduced nutritional value. Genomic information (Wang et al. 2012) has been used for crop improvement in many crops (Dash et al. 2014) and was used to target ripening in tomato to impart natural texture changes and deliver the benefits of long shelf-life, improved transportability and disease resistance, without negative consequences of deterioration of color, aroma and taste. In this regard, it has been demonstrated that pectate lyase (pl) gene is crucial for fruit softening in strawberry. It was conclusively proved by silencing pl gene that reduced strawberry softening (Jiménez-Bermúdez, et al. 2002). However, role of pl gene in tomato softening was recently proved by Dr. Selman Uluisik group at UK. They targeted pl gene in tomato and found out five pl genes are expressed in Ailsa Craig variety of tomato. Out of five, only one allele (Solyc03g111690) was found to be expressed at a high level during ripening. This led to the conclusion that silencing pl gene will result in changes in fruit firmness and extended shelf-life with no obvious effects either on yield or weight, ethylene biosynthesis, color or total soluble solids compared to the controls (Uluisik et al. 2016). Thus, the transgenic tomato generated by plant genetic engineering is expected to cater to the market demand.


Fig 1. Silencing pectate lyase pl gene by RNAi technology inhibits tomato fruit softening and increases shelf-life of tomato stored in room temperature till 14 days after harvest. WT= wild type non-transgenic tomato, PL= Transgenic tomato with reduced pectate lyase gene activity. (Figure source Nature Biotechnology. Uluisik et al., (2016) doi:10.1038/nbt.3602, Permission Number- 3924260231173, Date-Aug 8, 2016).

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About Author / Additional Info:
Senior Scientist, Plant Biotechnology.