Germplasm Characterisation: Utilising the Underexploited Resources

Farmers, in the given geographical region, cultivate only a small set of crop varieties for a long period of time. Modern plant breeding programs also resulted in severe genetic bottleneck. As a consequence, reduction in genetic diversity is widespread among crop plants, and it is considered as a detrimental feature to the future farming process. This is because continuous use of same cultivars usually leads to at least (1) extensive existence of (as well as emergence of new) pest and diseases to the given crop species and (2) loss of landraces and wild species of the given crop plants (which is otherwise referred to as genetic erosion). Due to ever increasing population growth and continuous shrinking of farming lands, farmers are forced to cultivate crop plants under a wide range of latitudes and longitudes. This requires crop plants which can tolerate variations in light, temperature, water and nutrients besides occurrence of peculiar pest and diseases that challenge crop production in these environments. Conventional breeding approaches such as desirable phenotypic selection among the breeding materials have considerably contributed in genetic improvement of crops. However, only a few genetically improved lines are available to meet such challenges. The main limitations that prevent the further progress through conventional breeding methods are lack of adequate genetic/biochemical/molecular knowledge on expression of traits that are beneficial to the crop cultivation and production. Most of the agronomically and economically important traits are quantitative in nature and having complex inheritance. Thanks to the developments in nucleic acid characterisation and manipulation, it is now possible to genetically analyse and manipulate such quantitative traits using quantitative trait loci (QTL) mapping and marker-assisted selection (MAS). Thus, advances in molecular marker technologies have opened the door to new techniques for construction and screening of breeding populations, increase the efficiency of selection and accelerate the rates of genetic gain. By employing genetic and QTL mapping, a marker can either be located within the gene of interest or be linked to a gene determining a trait of interest. Consequently, MAS can be executed as a selection for a trait based on genotype using associated markers rather than the phenotype of the trait. This book is designed to describe the basics of genetic and QTL mapping using molecular markers and practicing MAS in crop plants with step-by-step procedures. In general, MAS scheme in genetic improvement of crop plants for the given trait involves (1) characterisation of germplasm for the trait of interest, (2) selection of extremely diverse parents, (3) development of mapping population, (4) selection of appropriate combinations of molecular markers and genotyping of parents and mapping population, (5) construction of genetic or linkage map, (6) phenotyping of mapping population for the selected trait, (7) QTL analysis by combining the data obtained from step 5 and 6, (8) fine mapping and validation of QTLs and (9) executing MAS for the target trait. Therefore, this first chapter of this book is keen to describe the leading vital step in MAS: characterisation of germplasm.