Fingerprinting and Gene Cloning

Abstract

In the past two decades, molecular markers have revolutionized plant breeding activities. The DNA markers are being used for fingerprinting of crop genotypes to enable their highly precise and reliable identification. Molecular marker profiles are useful in the assessment of genetic purity seed lots of varieties and hybrids and for the determination of the crop produce purity. Molecular markers based on chloroplast/mitochondrial genome allow reliable identification of cytoplasmic male sterile lines from their maintainer lines. Furthermore, close linkage of DNA markers with genes can be exploited for positional cloning of these genes. The positional cloning procedure does not require any more information about the target gene than the distinct and readily identifiable phenotype it produces; this property is used to carry out fine mapping to identify a pair of flanking markers closely linked to this gene. The genomic region carrying the target gene is further reduced through strategies of chromosome walking, chromosome jumping, and chromosome landing. The short candidate genomic region is analyzed to identify the candidate genes and then to confirm the findings using a strategy like genetic transformation. This approach has been used for cloning of several agronomically important genes/QTLs (quantitative trait loci) in species like rice, maize, wheat, Arabidopsis, etc. The present chapter is devoted to the discussion of various aspects relevant for DNA fingerprinting of crop genotypes and those for positional cloning of genes and QTLs.