In Silico Identification and Experimental Validation of Insertion-Deletion Polymorphisms in Tomato Genome

Abstract

Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion–deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.

Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis

“…InDel markers have been deployed in forensic and genetic studies in humans as well as in several plants/crops like wheat, rice, barley, mustard, citrus, tomato, and Arabidopsis (Yang et al, 2014; Lu et al, 2015; Zhou et al, 2015). The availability of draft genome assemblies of groundnut progenitors (Bertioli et al, 2016; Chen et al, 2016) have provided an excellent opportunity for initiating several genomic and genetic studies such as SNP discovery, gene prediction, gene expression, comparative genomics, genetic diversity, genetic mapping, and molecular breeding (Pandey et al, 2016).…”

“…Accuracy in InDels identification basically depends on the quality of sequencing data, scheme, and parameters used for data extraction. One and two base pairs InDels were not included between A and B subgenomes in order to avoid over reckoning of small InDels due to sequencing errors as earlier experienced in tomato crop by Yang et al (2014). In groundnut, identification of InDels have been reported from expressed sequence tags (ESTs) data and was used for studying genetic diversity in cultivated groundnuts (Liu et al, 2015).…”

“…Considering the similarities between two diploid subgenomes of tetraploid groundnut (Bertioli et al, 2016), the genome sequences of A. duranensis (accession V14167 for A subgenome,) and A. ipaënsis (accession K30076 for B subgenome,) were used for mining the InDels using the methodology depicted by Yang et al (2014). Briefly, the fasta files for A and B subgenomes were downloaded from PeanutBase site (https://www.peanutbase.org/) and InDels were identified using MUGSY software (Angiuoli and Salzberg, 2011).…”

“…Insertions-deletions (InDels) are the second most prevalent and frequent structural variations detected across the plant genomes (Yang et al, 2014; Lu et al, 2015). InDels originate as a consequence of some cellular events like replication slippage, transposable elements, and crossing-over (Moghaddam et al, 2014).…”

Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers

“…For this reason, the polymorphism level of molecular markers in the cultivated tomato gene pool is lower than that in other autogamous species (Archak et al, 2002). In recent years, researchers have started to develop molecular markers for cultivated tomato and to construct intraspecific genetic linkage maps (Shirasawa et al, 2010;Hamilton et al, 2012;Yang et al, 2014). Therefore, increased numbers of molecular markers with a higher level of polymorphism can be applied for QTL mapping and genetic analysis in the cultivated tomato.…”