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.
Highlights
Selection of favorable alleles through domestication and breeding has led to dramatic changes in seed and fruit attributes, plant habit, and productivity
In order to establish an accurate and automatic genotype calling procedure for the GenomeStudio software that is usable across the entire genepool of cultivated tomato, clustering based on the Solanaceae Coordinated Agricultural Project (SolCAP) germplasm was cross-validated with a cluster file based on 92 hybrids developed independently by TraitGenetics [19]
The duplicate samples of Principe Borghese differed by 5.9%, but showed similar rates for no call (0.8% vs. 1.0%) and heterozygote call (0.2% vs. 0.2%). These results suggest that overall reproducibility is high, and that differential calls may result from DNA quality that affects the percentage of ‘‘no call’’, residual heterozygosity, and variation within accessions
Summary
Selection of favorable alleles through domestication and breeding has led to dramatic changes in seed and fruit attributes, plant habit, and productivity. For tomato (Solanum lycopersicum L), breeding has involved the competing forces of narrowed genetic variation due to best by best crosses followed by selection [1,2], and the expansion of genetic variation due to the introgression of genes for biotic stress resistance from wild species [3,4,5]. SNPs are distributed throughout a genome, they provide stable markers for genetic analysis, and their detection is amenable to automation It is increasingly cost and time efficient to genotype large populations in a high-throughput manner. Because of these advantages, SNPs have become a marker system of choice for genetic analysis in plant species. 62,576 non-redundant SNPs were identified based on transcritpome sequences for six tomato accessions [10]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
