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Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping

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Title Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping
 
Creator Sahu, Kamlesh Kumar
Chattopadhyay, Debasis
 
Subject Domestication
Genome
SNP
Solanum lycopersicum
Wild tomato
 
Description Accepted date: 25 May 2017
BACKGROUND:
Cultivated tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potato and a member of thirteen interfertile species of Solanum genus. Domestication and continuous selection for desirable traits made cultivated tomato species susceptible to many stresses as compared to the wild species. In this study, we analyzed and compared the genomes of wild and cultivated tomato accessions to identify the genomic regions that encountered changes during domestication.
RESULTS:
Analysis was based on SNP and InDel mining of twentynine accessions of twelve wild tomato species and forty accessions of cultivated tomato. Percentage of common SNPs among the accessions within a species corresponded with the reproductive behavior of the species. SNP profiles of the wild tomato species within a phylogenetic subsection varied with their geographical distribution. Interestingly, the ratio of genic SNP to total SNPs increased with phylogenetic distance of the wild tomato species from the domesticated species, suggesting that variations in gene-coding region play a major role in speciation. We retrieved 2439 physical positions in 1594 genes including 32 resistance related genes where all the wild accessions possessed a common wild variant allele different from all the cultivated accessions studied. Tajima's D analysis predicted a very strong purifying selection associated with domestication in nearly 1% of its genome, half of which is contributed by chromosome 11. This genomic region with a low Tajima's D value hosts a variety of genes associated with important agronomic trait such as, fruit size, tiller number and wax deposition.
CONCLUSION:
Our analysis revealed a broad-spectrum genetic base in wild tomato species and erosion of that in cultivated tomato due to recurrent selection for agronomically important traits. Identification of the common wild variant alleles and the genomic regions undergoing purifying selection during cultivation would facilitate future breeding program by introgression from wild species.
KKS acknowledges fellowship from University Grants Commission, India.The project was funded by the National Institute of Plant Genome Research, Delhi, India.
 
Date 2017-06-05T06:51:54Z
2017-06-05T06:51:54Z
2017
 
Type Article
 
Identifier BMC Genomics, 18(1): 430
1471-2164
http://59.163.192.83:8080/jspui/handle/123456789/752
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3822-3
10.1186/s12864-017-3822-3
 
Language en_US
 
Publisher BioMed Central Ltd