High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

Abstract

The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.

The use of historical datasets to develop multi-trait selection models in processing tomato

“…With the recent development of high-throughput genotyping tools (Sim et al 2012a), their use on a large number of accessions (Blanca et al 2015;Sim et al 2012b), and the release of sequence data for nearly 440 tomato genomes (Lin et al 2014; The 100 Tomato Genome Sequencing Consortium et al 2014), there is an abundance of information to facilitate selection. These resources have generated interest in developing models predicting breeding values for tomato improvement (Duangjit et al 2016;Hernán-dez-Bautista et al 2016;Yamamoto et al 2016a, b).…”

DNA Markers for Food Products Authentication

“…In tomato, it has been recently shown that population structure analysis based on SNP markers allowed the characterization and discrimination of landraces and varieties [36][37][38]. In addition, in cacao seeds, SNP fingerprints allowed the identification of an adulterant variety [39].…”

Structural analyses of the tomato genome

“…The 62,576 nonredundant putative SNPs reported by Hamilton et al (2012) will be a source of SNPs for cultivated tomato lines of S. lycopersicum (Sim et al 2012b). In addition, 171,792 SNP, insertion, and deletion candidates were also identified from the mapping analysis of 'Micro-Tom' BAC-end sequences compared with the reference genome of S. lycopersicum 'Heinz 1706' (Asamizu et al 2012).…”