Chapter 14 - Molecular markers and genomics assisted breeding for improving crop plants

Abstract

Plant breeding, is an antediluvian activity that, began with inactive agriculture, which is figured to date back about 9000 to 11,000years. From the very beginning with the knowledge of domestication of the crops, humans started selection for the identifying the best and desirable plants over time. With the pioneering work of Gregor Johann Mendel, the new science of genetics evolved, and plant breeders applied hereditary laws in the selection procedure, but still, the selection was affected by the environment in any given season and the phenotypes were the output of genotype (G), the environment (E), and/or genotype × environment (G×E). Hence, genotype had always been a product of biased phenotypic selection. In 1953, with the discovery of the magical structure of DNA, it could be possible to get information on heredity, its code, and replication. This discovery led to most modern plant breeding, the science of genomics and molecular breeding. In this context, molecular markers such as RFLP, RAPD, IISR, STS, SSR, SNPs, InDels, and micro-Array played a very important role in DNA fingerprinting, characterization, diversity analyses, mapping, identification of genes/QTLs, validation, and assistance in selection. Molecular breeding includes Marker-assisted selection (MAS) for introgression of major single gene/QTL, Pyramiding for and major/minor QTLs in the single background, and genomic selection (GS) for selection of many effective minor QTLs in an individual. This chapter aims to cover the topics about general principles and methodologies of marker-assisted breeding with recent updates and a short introduction of molecular markers in plant breeding.