Abstract
Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern varieties collected worldwide was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters over 2 years with three replications each year. The association panel was sorted into two subpopulations. Linkage disequilibrium ranged from 3.0 to 47.2 Mb across 12 chromosomes. A set of 102 markers significantly (p < 1.19–1.30 × 10−4) associated with SSC, FW, fruit shape, and fruit color was identified on 11 of the 12 chromosomes using a mixed linear model. The associations were compared with the known gene/QTLs for the same traits. Genetic analysis using F2 populations detected 14 and 4 markers significantly (p < 0.05) associated with SSC and FW, respectively. Some loci were commonly detected by both association and linkage analysis. Particularly, one novel locus for FW on chromosome 4 detected by association analysis was also identified in F2 populations. The results demonstrated that association mapping using limited number of InDel markers and a relatively small population could not only complement and enhance previous QTL information, but also identify novel loci for marker-assisted selection of fruit traits in tomato.
Highlights
Tomato (Solanum lycopersicum) is one of the most consumed vegetables and ranks second in production among the solanaceous crops worldwide
Polymorphisms within species was decreased from wild species S. pimpinellifolium to S. lycopersicum var. cerasiforme and to S. lycopersicum, the cultivated tomato
Re-sequencing genomes of 360 accessions reveals that the linkage disequilibrium (LD) decay with physical distance between SNPs occurred at 8.8 kb in S. pimpinellifolium, 256.8 kb in S. lycopersicum var. cerasiforme, and 865.7 kb in S. lycopersicum accessions (Lin et al, 2014)
Summary
Tomato (Solanum lycopersicum) is one of the most consumed vegetables and ranks second in production among the solanaceous crops worldwide (http://www.fao.org/statistics/en/). It is an excellent plant genetic analysis system, for investigating the mechanisms of fruit development, color formation, and nutrient accumulation. The combination of the economic importance and the potential health benefits make tomato fruits an important target for increasing the nutritional properties It has been well-known that wild tomato species bear small, round, red, or green fruits (Alpert et al, 1995). Only two loci for fruit weight (fw2.2 and fw3.2), four loci for fruit shape or size (ovate, sun, lc, and fas), three loci for SSC (LIN5, sucr, and Agp-L1), and several loci for color (e.g., r, gf, ogc, t, y, hp, hp2, hp, and del) have been wellcharacterized (Chetelat et al, 1995; Liu et al, 2003; Fridman et al, 2004; Petreikov et al, 2009; The Tomato Genome Consortium, 2012; van der Knaap et al, 2014)
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