Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape.

Liang Sun,Jinshan Lin,Joshua J Blakeslee,Zhangjun Fei,Eudald Illa-Berenguer,Asela Wijeratne,Josh P Clevenger,Wenli Liu,Esther Van Der Knaap,Tea Meulia,Gustavo R Rodriguez

doi:10.1093/jxb/erv361

Abstract

fs8.1 is a major quantitative trait locus (QTL) that controls the elongated shape of tomato (Solanum lycopersicum) fruit. In this study, we fine-mapped the locus from a 47Mb to a 3.03Mb interval on the long arm of chromosome 8. Of the 122 annotated genes found in the fs8.1 region, 51 were expressed during floral development and six were differentially expressed in anthesis-stage ovaries in fs8.1 and wild-type (WT) lines. To identify possible nucleotide polymorphisms that may underlie the fruit shape phenotype, genome sequence analyses between tomato cultivars carrying the mutant and WT allele were conducted. This led to the identification of 158 single-nucleotide polymorphisms (SNPs) and five small indels in the fs8.1 interval, including 31 that could be associated with changes in gene expression or function. Morphological and histological analyses showed that the effects of fs8.1 were mainly on reproductive organ elongation by increasing cell number in the proximal-distal direction. Fruit weight was also increased in fs8.1 compared with WT, which was predominantly attributed to the increased fruit length. By combining the findings from the different analyses, we consider 12 likely candidate genes to underlie fs8.1, including Solyc08g062580 encoding a pentatricopeptide repeat protein, Solyc08g061560 encoding a putative orthologue of ERECTA, which is known to control fruit morphology and inflorescence architecture in Arabidopsis, Solyc08g061910 encoding a GTL2-like trihelix transcription factor, Solyc08g061930 encoding a protein that regulates cytokinin degradation, and two genes, Solyc08g062340 and Solyc08g062450, encoding 17.6kDa class II small heat-shock proteins.

Highlights

Fruit shape is an important horticultural trait for fruit and preferred for mechanically harvested processing tomatoes, vegetable crops
Genes underlying tomato fruit shape quantitative trait locus (QTL) were cloned via fine-mapping: LC probably encodes an orthologue of WUSCHEL, a homeodomain transcription factor that is required for maintaining the stem-cell identity in the shoot apical meristem (Mayer et al, 1998; Clark, 2001; Muños et al, 2011); FAS encodes CLV3, a small secreted protein that acts in the WUS–CLV3 signalling pathway (Schoof et al, 2000; Xu et al, 2015); and SUN encodes a member of the IQD family of calmodulinbinding proteins (Xiao et al, 2008)
One member of this family, AtIQD1, interacts with both kinesin light-chain-related protein-1 (KLCR1) and calmodulin/calmodulin-like proteins (CaM/CMLs), recruiting them to microtubules (Abel et al, 2005; Bürstenbinder et al, 2013); OVATE is the founding member of the OVATE family proteins (OFPs) and its members are often characterized as transcriptional repressors (Liu et al, 2002; Hackbusch et al, 2005; Wang et al, 2007, 2011)

Summary

Introduction

Fruit shape is an important horticultural trait for fruit and preferred for mechanically harvested processing tomatoes, vegetable crops. Genes underlying tomato fruit shape QTLs were cloned via fine-mapping: LC probably encodes an orthologue of WUSCHEL, a homeodomain transcription factor that is required for maintaining the stem-cell identity in the shoot apical meristem (Mayer et al, 1998; Clark, 2001; Muños et al, 2011); FAS encodes CLV3, a small secreted protein that acts in the WUS–CLV3 signalling pathway (Schoof et al, 2000; Xu et al, 2015); and SUN encodes a member of the IQD family of calmodulinbinding proteins (Xiao et al, 2008) One member of this family, AtIQD1, interacts with both kinesin light-chain-related protein-1 (KLCR1) and calmodulin/calmodulin-like proteins (CaM/CMLs), recruiting them to microtubules (Abel et al, 2005; Bürstenbinder et al, 2013); OVATE is the founding member of the OVATE family proteins (OFPs) and its members are often characterized as transcriptional repressors (Liu et al, 2002; Hackbusch et al, 2005; Wang et al, 2007, 2011). This has left a gap in our further understanding of the molecular basis of genes controlling of fruit shape and their putative interactions with each other

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Conclusion