MutMap Technique: A Streamlined Approach for Identification of Candidate Genes

Current advances in next generation sequencingNext generation sequencing (NGS) have revolutionised different aspects of genomics. The availability of highly efficient de novo sequencing techniques has directed elucidation of the draft genome sequences of various species of crops. In order to utilise this sequence information for improvement of economically important crop, the genome must be annotated and the genetic architecture of loci affecting different economically important traits must be identified. Availability of large mapping population and ample molecular markers densely covering the whole genome are prerequisite for traditional gene mapping strategies which make them complex, costly and time demanding. The advent of resequencing techniques and evolution of novel approaches including next-generation mapping (NGM), SHOREmap, MutMap etc., have been instrumental in reducing the time and cost required for identification of candidate genes. Among these, MutMap technique which mainly focusses on causal SNPsSingle nucleotide polymorphism (SNPs) is widely used. MutMap is a highly efficient forward geneticsForward genetics technique used for detection of genomicGenomics region responsible for expression of a mutant phenotypeMutant phenotypes. As this mapping strategy is not based on the linkage information, it may do not necessitate mapping population genotyping or linkage map construction thereby accelerating the process of gene identification. The technique is particularly useful in identification of genomic regions having a minor effect on traitTraits phenotype. A number of different candidate gene identification approaches, namely MutMap-Gap, MutMap plusMutMap plus and QTL-Seq, have been extended from the basic MutMap technology. The Mutmap plusMutMap plus methodology is generally used for mapping loci wherein homozygosity leads to either sterility or lethality. MutMap-Gap identifies loci existing in the non-sequenced regions of the reference genome and QTL-Seq is a MutMap variant specifically used for mapping of loci controlling quantitative traits/ QTLs. This chapter provides a detailed account of gene mapping techniques based on Next Generation SequencingNext generation sequencing (NGS) namely MutMap and its modifications and also highlights their importance in crop improvement.