Randolph G. Gardner

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

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.

Formation of parthenocarpic fruit, undeveloped flowers and aborted flowers in tomato under moderately elevated temperatures

Abstract Incidence of parthenocarpic fruit, undeveloped flowers and flower abortion in tomato plants ( Lycopersicon esculentum Mill.) were compared under optimal temperature (OT, 28/22°C day/night) and chronic, mild high temperature conditions (HT, 32/26°C). Seeded fruits were found only under OT conditions, where 37±9% of all flowers developed into seeded fruit. However, flower aborted was also higher under OT, with an additional 24±7% of flowers aborted under optimal temperature conditions, compared to only 4±1% of flowers aborted under HT conditions. Under HT, most flowers (53±8%) developed into parthenocarpic fruit, and the remainder (43±7%) stayed on the plant as undeveloped flowers. A slow transition of undeveloped flowers to parthenocarpic fruit was also observed under HT. Factors determining whether flowers abort, develop parthenocarpically, remain on the plant without developing further, or develop into seeded fruit were discussed in relation to carbohydrate availability and the presence of seeded fruit on the vine.