Introduction

Plant breeding and traits

Breeders want to improve their crops for many traits: yield, fruit taste, resistance to pathogens, processing quality (e.g. bread baking in wheat), tolerance to drought, etc. Many of these traits are quantitative, i.e. they are varying along a continuous distribution from low to high trait values. Only few characters are qualitative, i.e. they can be scored as discrete values or in clearly distinct classes such as white versus red flowers. Some of these, like for example monogenic resistances, may still require special phenotyping trials to score, for every individual in a population, the genotype.

Quantitative traits often are determined by several to many genes, each with a possibly small effect on the trait value. In addition to the genetic effects, the environment may add to the variation that we observe in the quantitative trait values. Consequently, phenotype does not directly reflect the genotype. A further difficulty is that many quantitative traits cannot be evaluated well on single plants, but should be measured on a larger number of plants of every genotype. For example, in wheat, yield and bread-baking quality cannot be measured on the basis of single plants. Also, bread-baking quality is a rather cumbersome trait to evaluate, requiring expensive analysis in the laboratory.

Marker-assisted selection

All these complications make it an attractive idea for the breeder to select directly for the presence of favorable genes and against unfavorable genes, instead of on the basis of test results for quantitative traits. What the breeder would really want is to be able to directly select the genotype, but for many traits they can only observe the phenotype and even then it may require considerable costs, time and effort. "Marker-assisted selection" (MAS) is the strategy that aims at replacing phenotypic selection or complementing phenotypic selection with selection based on genotype as established from the DNA sequence in the region of a gene of interest.

Molecular markers have additional advantages, as will be shown in more detail later: they can be used for early selection, off-season and off-location seleection, they can speed up the selection process, they can allow more seedlings to be evaluated, and they can even be used to select for phenotypic traits that are not or cannot be measured (e.g. a disease resistance in the absence of the disease itself) or to enable combining multiple genes that based on the phenotype could not be distinguished individually. They can also help in finding the exact location of functional genes in order to enable cloning of these genes and they help to understand the genetic basis of many traits.

Authors and credentials

Authors of this module are lecturers of the chair groups Plant Breeding and Nematology of Wageningen University, the Netherlands:
Dr. J.C. Goud, Dr. R.E. Niks, Dr. Chris Maliepaard, and Ir. H. Thiewes.

Part of the content of this module is roughly based on the following scientific article:
B.C.Y. Collard, M.Z.Z. Jahufer, J.B. Brouwer & E.C.K. Pang (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica (2005) 142: 169–196.

 

Arrangements have been made with Springer publishers and with the first author to use the text. However, the text in this module has been changed considerably from the original text in the article.