Dissecting regulatory eQTLs of the carotenoid biosynthetic pathway in tomato fruit using S.lycopersicum x S. pennellii introgression lines

Li, Jie (2018) Dissecting regulatory eQTLs of the carotenoid biosynthetic pathway in tomato fruit using S.lycopersicum x S. pennellii introgression lines. Doctoral thesis, University of East Anglia .

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Abstract

Tomato (Solanum lycopersicum) ripening involves a number of physiological processes that include the visible breakdown of chlorophyll and build-up of carotenoids, with massive accumulation of antioxidant compounds such as lycopene and β-carotene (provitamin A) within the chromoplasts. Although the catalytic steps of the carotenoid biosynthetic pathway have been well-characterised, the regulatory mechanisms that control carotenoid accumulation remain poorly understood.
In this study, I used expression quantitative trait loci (eQTL) analysis to obtain a comprehensive understanding of the genetic basis of regulation of carotenoid biosynthesis in tomato fruit using the S. lycopersicum x S. pennellii introgression population. In total, 31 cis-eQTLs related to 18 carotenoid biosynthetic genes were identified, and the isoforms of some structural genes functional during fruit ripening were identified in this analysis. Six trans-eQTL hotspots were identified for lycopene biosynthesis. Co-expression analysis of one of the trans-eQTL candidates, residing in IL2-1, revealed that a basic helix-loop-helix transcription factor, SlHONG likely acts as a positive regulator of lycopene accumulation in fruit, by activating the expression of the structural genes involved in lycopene biosynthesis. SlRIN, a master regulator of fruit ripening, binds directly to two adjacent CArG motifs in the promoter of SlHONG, to control the expression of SlHONG in an ethylene-independent manner. Genome-scale phylogenetic analysis of bHLH proteins in Arabidopsis and tomato found SlHONG was the most similar protein to BEE2 in Arabidopsis, which is involved in brassinosteroid signalling by forming the BEE complex together with another three bHLH transcription factors. bHLH transcription factors potentially involved in the BEE complex with SlHONG in tomato, were identified by phylogenetic analysis and interactions between the candidate proteins were detected. SlHONG was identified as a regulator of lycopene biosynthesis in tomato fruit, and may be under the control of multi-layered regulatory mechanisms.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Zoe White
Date Deposited:	22 May 2019 13:50
Last Modified:	22 May 2019 13:50
URI:	https://ueaeprints.uea.ac.uk/id/eprint/71098
DOI:

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