MutMap: a versatile tool for identification of mutant loci and mapping of genes
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With the advancement of sequencing technologies and improvement in data analysis tools, draft genomes of many organisms are readily available. Accessibility to such draft genome sequences assists researchers, especially, plant breeders, to rapidly identify genomic regions contributing to the observed phenotypic variation leading to identification of candidate genes for a particular trait. Traditionally gene mapping is a complex, time-consuming and costly affair requiring large mapping populations and abundant molecular markers spread across the entire linkage groups. With the emergence of re-sequencing techniques, quick mapping of genes has become possible with reduced time and cost by using approaches like SHOREmap, NGM and MutMap methodologies. Among these, MutMap is widely used because it is more focused on causal SNPs. This is made possible by generating a backcross population of the mutant genotype with the parent (wild type), thereby removing the false SNPs and retaining only the SNPs linked to the mutant phenotype. Improved and specialized methods of MutMap like MutMap+, MutMap-Gap, and QTL-Seq have also emerged to expand the horizon of application of MutMap approach. The Mutmap+ methodology is specially designed for capturing those traits where the homozygous mutant leads to either lethality or sterility. MutMap-Gap methodology identifies the mutation site present in the gap regions of the reference genome, whereas QTL-Seq is an improved version of MutMap, specially designed for mapping of quantitative trait loci (QTLs). All these methods are akin to bulked segregant analysis popularly employed for mapping simply inherited traits. These methods escape the requirement of genotyping all the individuals of the mapping population and generation of high-density linkage maps for mapping of the gene for the trait of interest. This article reviews various Next Generation Sequencing-based gene mapping technologies with more emphasis on MutMap and its modifications, and discusses their advantages and proven applications for gene mapping for subsequent crop improvement.
KeywordsMutMap EMS Bulked segregant analysis QTL-Seq NGS techniques
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Conflict of interest
The author declares that they have no conflict of interest.
- Chen, Z., Yan, W., Wang, N., et al. (2014). Cloning of a rice male sterility gene by a modified MutMap method. Chinese, 36(1), 85–93.Google Scholar
- GenBank, and WGS Statistics. (2018). https://www.ncbi.nlm.nih.gov/genbank/statistics/. Accessed 18 Jul 2018.
- Imamura, T., Takagi, H., Miyazato, A., et al. (2018). Isolation and characterization of the betalain biosynthesis gene involved in hypocotyl pigmentation of the allotetraploid Chenopodium quinoa. Biochemical and Biophysical Research Communications, 496, 280–286. https://doi.org/10.1016/j.bbrc.2018.01.041.CrossRefPubMedGoogle Scholar
- Michelmore, R. W., Paran, I., & Kesseli, R. V. (1991). Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Sciences, 88, 9828–9832.CrossRefGoogle Scholar
- Pandey, M. K., Khan, A. W., Singh, V. K., et al. (2017). QTL-Seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnology Journal, 15, 927–941. https://doi.org/10.1111/pbi.12686.CrossRefPubMedPubMedCentralGoogle Scholar
- Sevanthi, A. M. V., Kandwal, P., Kale, P. B., Prakash, C., Ramkumar, M. K., Yadav, N., et al. (2018). Whole genome characterization of a few EMS-induced mutants of upland rice variety Nagina 22 reveals a staggeringly high frequency of SNPs which show high phenotypic plasticity towards the wild-type. Front Plant Sci., 9, 1179. https://doi.org/10.3389/fpls.2018.01179.CrossRefPubMedPubMedCentralGoogle Scholar
- Takagi, H., Uemura, A., Yaegashi, H., et al. (2013b). MutMap-Gap: Whole-genome re-sequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. New Phytologist, 200, 276–283. https://doi.org/10.1111/nph.12369.CrossRefPubMedGoogle Scholar