Abstract
The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F2 populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.
Highlights
Tomato (Solanum lycopersicum L.) has been a model species for basic studies in plant biology
Mapping studies have focused on polymerase chain reaction (PCR)-based markers with genetic maps of cultivated tomato developed using 344 Simple Sequence Repeat (SSR) and 793 Singe Nucleotide Polymorphism (SNP) markers [9] and integrated S. lycopersicum x S. pimpinellifolium maps based on 434 PCR-based markers [10]
Among 7,720 scorable SNPs on the array, 3,640 were polymorphic between the parental lines and were analyzed in the mapping population. 3,503 SNP markers could be placed as codominant markers on the linkage map representing 1,076 unique map positions with an average marker bin interval of 1.6 Coverage Maker Interval (cM) and the largest gap of 9.7 cM on chromosome 12 (Table 1 and Table S2)
Summary
Tomato (Solanum lycopersicum L.) has been a model species for basic studies in plant biology. The strength of genetic resources anchored to high-density maps has permitted the map-based cloning of genes involved in disease resistance [1,2,3,4], plant and fruit development [5,6], and regulation of biochemical processes [7]. Mapping studies have focused on polymerase chain reaction (PCR)-based markers with genetic maps of cultivated tomato developed using 344 Simple Sequence Repeat (SSR) and 793 Singe Nucleotide Polymorphism (SNP) markers [9] and integrated S. lycopersicum x S. pimpinellifolium maps based on 434 PCR-based markers [10]. NGS has permitted genome-wide SNP discovery in many crop species including rice
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