**1. Introduction**

Wheat is one of the most important sources of food worldwide. Data from FAOSTAT indicate that the need is still growing, indicated by the steadily increasing yield since 1961 (**Figure 1**). The need for an enhanced wheat production combined with stagnation in the area cultivated (**Figure 1**) leads to a demand for a more effective and higher yielding wheat production.

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**3. Application of MAS in breeding for disease resistance in wheat** 

Plant diseases are a major constraint in wheat production and significant resources are allocated to control various diseases. The relatively long growing season of winter wheat renders it vulnerable to a range of diseases and breeding for disease resistance is generally thought to be the first line of defence [2]. Disease resistance is generally separated into quantitative and qualitative resistance. Qualitative resistance is most often controlled by a single gene and follows the genefor-gene hypothesis. Thus, an R gene in the host can specifically interact with an *Avr* gene in the pathogen to induce a defence reaction in the host. Qualitative resistance often mediates a complete resistance response, whereas quantitative resistance is regarded as an incomplete or partial resistance. This type of resistance is usually mediated by several minor genes, which are designated as a quantitative trait locus (QTL) [3]. Following the development of MAS, targeted pyramiding of several resistance genes in single lines is now possible. In the following sections, three severe diseases of wheat and correlated resistance genes are described. Common to these diseases is that fungicides are becoming less efficient. Hence, more effective approaches are desired.

Marker-Assisted Breeding in Wheat http://dx.doi.org/10.5772/intechopen.74724 5

One of the most important foliar diseases in wheat is Septoria tritici blotch (STB), caused by the fungus *Zymoseptoria tritici* formally known as *Septoria tritici* (anamorph) and *Mycosphaerella graminicola* L (teleomorph) [4]. STB is a devastating disease causing massive yield losses worldwide every year in wheat. Severe epidemics can reduce wheat yield by 35–50% [5]. Symptoms of the disease are chlorotic lesions on the leaf with black fruiting bodies containing fungal spores. Breeding strategies over the years have primarily focused on breeding for higher yield, in turn increasing the susceptibility towards STB [6]. Disease control can be performed by delaying sowing time, probably due to less time in the autumn for *Z. tritici* to infect seedlings and produce inoculum. Furthermore, the application of fungicides and implementation of resistant cultivars in breeding programs are widely used [5]. In previous years, several studies have identified STB resistance genes using molecular techniques.

*Stb1*, *Stb2* and *Stb3* were the first qualitative genes for STB resistance to be named [7]. Prior to that, STB resistance was thought of as a quantitative, polygenic trait. *Stb1* was mapped to the long arm of chromosome 5B in the cultivar Bulgaria88 [8]. *Stb2* was mapped to the short arm of chromosome 1B in the cultivar Veranopolis [9]. Additionally, *Stb11* was mapped to the short arm of 1B [10]. However, no studies have included an allelism test of *Stb2* and *Stb11*. *Stb3* was mapped to the short arm of 7A in Israel493 [11]. *Stb6* was mapped to the short arm of chromosome 3A in the cultivar Flame [12]. This gene is the only STB-resistant gene found to possess a gene-for-gene relationship, in which a specific R gene in the host interacts with an *Avr* gene in the pathogen. This was demonstrated in a study where Flame was found to confer specific resistance towards the *Z. tritici* isolate IPO323 [12]. This study conforms to the original gene-for-gene model proposed by Flor [13]. *Stb6* was subsequently found to be one of the most abundant STB-resistant genes in European wheat [14]. In total, 18 *Stb* genes have been

**diseases**

**3.1. Septoria tritici blotch**

**Figure 1.** Development in wheat cultivation in the years 1961–2016. The primary y-axis displays the area harvested in Mha (red line) and the secondary y-axis displays the yield in tones pr. ha (blue line). Data from FAOSTAT.

Marker-assisted selection (MAS) or molecular breeding offers an opportunity to accelerate the traditional breeding. Traditional breeding is based on phenotypic selection of genotypes obtained from crosses. Genotype × environment (G×E) interaction is a common problem including time-consuming and costly procedures of phenotyping. By employing molecular markers, desirable genes can be fixated in early generations of the breeding program. In addition, molecular markers are unaffected by environmental conditions and are detectable in all stages of the plant growth. Scientists and breeders across the world implement MAS in breeding programs [1].
