InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes

High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymorphism) are the new generation of molecular markers and can basically meet the need of fine mapping. InDel and SNP markers can be developed through bioinformatics. These markers are valuable markers with the characters of low cost, high specificity and stability. This article introduced the methods for designing InDel and SNP markers, taking the mapping of a rice rolled leaf gene as an example. In addition, some key factors in improving the design efficiency were also discussed.

Assessment of SNP and InDel Variations Among Rice Lines of Tulaipanji x Ranjit

Genotyping by sequencing(GBS) is the recent approach of next-generation sequencing technique for discovering and genotyping single nucleotide polymorphisms(SNPs) in crop species. Genotypic variation studies(SNPs and insertion-deletions/In Dels) were performed using four rice lines based on GBS data by aligning to the reference genome Nipponbare. Local aromatic rice landrace Tulaipanji was crossed with Ranjit, and two distinct lines were identified from the progenies: one line with awns and aroma traits and the other without awns and aroma. Total number of SNPs and In Dels identified were 52 810 and 4 327 at read depth 10, respectively. Out of the total polymorphic SNPs/In Dels, 16 490 were intergeneric, 7 812 were inside gene, and 4 435 were intronic. Phylogenetically, Tulaipanji was closer to the reference genome nipponbare. Based on recurrent parent genome analysis, out of 10 013 alleles, 92.52% was introgressed into progeny-awn from Tulaipanji and 7.48% from Ranjit, whereas progeny-awnless carried 89.19% alleles from Ranjit and only 10.81% alleles from Tulaipanji. In addition, progeny-awn was the highest heterozygous(83.88%) and progeny-awnless was the least(2.24%) at this fifth generation of recombinant inbred lines. These SNP variations may be linked to the phenotypic traits and can be utilized in crop improvement through linkage mapping. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.

Pharmacogenetics and cancer management

The science of one’s genetic background and its impact on disease susceptibility and drug response has come of age and firmly established its proper place in the clinic.Its impact is felt more in the treatment of cancer than any other disease area several reasons:critical time,narrow therapeutic index and overlapping toxicity window.We realize that the true potential of pharmacogenetics will be realized when we have been able to integrate other variants like insertion-deletion,copy number variation,etc.,in addition to single nucleotide polymorphism for their collective influence on drug response and toxicity.Technology has rapidly evolved and has become affordable to be used in the clinic once it gets standardized and validated not only in one population but in several major world population-particularly those which are under-represented in human variant database.