**3.1. Septoria tritici blotch**

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

**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.

MAS is based on the concept of genetic linkage between loci. This describes the tendency of loci located closely together on the same chromosome being more likely to be inherited together in a recombination event during meiosis. Thus, two alleles located very close on the

Molecular markers are used in MAS to highlight a place on the chromosome close to or in a specific gene of interest. The technique is based on detecting different alleles (polymorphisms) between several individuals. Due to genetic linkage, the molecular marker will reveal if the linked allele is present or not in a line. Several types of molecular markers exist, depending on the type of polymorphism. In today's MAS, markers detecting single nucleotide differences

breeding programs [1].

4 Next Generation Plant Breeding

are usually employed.

**2. Linkage and molecular markers**

chromosome will almost always be inherited together.

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 identified and mapped using various molecular markers. Additionally, several QTL have been identified conferring STB resistance [7, 15]. **Table 1** summarises major STB-resistance genes together with linked markers suitable for MAS. Additionally, several QTL have been identified conferring STB resistance [7, 15].

selection pressure placed on the pathogens by one major resistance gene promotes the rise of new adapted races in the pathogen population [27]. An earlier study has proved that commercial cultivation of a highly resistant cultivar can result in loss of resistance towards STB. The intensive cultivation of the variety Gene in the 1990s in Oregon, US, resulted in resistance breakdown. Gene was found to be resistant to two specific isolates, which were avirulent to *Stb6* and *Stb10* [28]. Gradually, an adaptation of *Z. tritici* to one of the resistance genes occurred and the resistance was lost [26]. In general, it appears that most *Z. tritici* isolates used in earlier studies are virulent to almost all *Stb* genes [7]. This may indicate that *Z. tritici* easily can overcome single qualitative resistance genes. In contrast, the quantitative resistance is regarded as more durable. This is due to a lower selection pressure on the pathogen as a result of smaller resistance effects of individual QTL [3]. Furthermore, since quantitative resistance is often polygenic, the mutation of one gene does not necessarily break down disease resistance completely.

Marker-Assisted Breeding in Wheat http://dx.doi.org/10.5772/intechopen.74724 7

Fusarium head blight (FHB) is an important disease in all wheat growing countries. Epidemics occur frequently, especially under seasons with regular rainfall [29]. The United States Department of Agriculture (USDA) has stated that FHB is the most devastating plant disease since the rust epidemics in the 1950s. FHB contaminates the grain with mycotoxins, in turn restricting its use for both animal and human consumption [30]. The disease is caused by several species of *Fusarium*; however, the predominant causal agent is the fungus *Fusarium graminearum* (teleomorph *Gibberella zeae*). The first symptoms of FHB on wheat plants occur shortly after flowering as diseased spikelets display premature bleaching. The bleaching usually spreads to the whole spike as the pathogen grows. When conditions are optimal for the pathogen, i.e., in a warm and moist environment, light pink coloured spores, called sporodochia, appear on individual spikelets. Later during the season, black fruiting bodies will appear. These are the sexual structures of the fungus, called perithecia. Disease progression results in shrinking and wrinkling of the grain inside the spike. As with the pathogen causing STB, *F. graminearum* produces both sexual and asexual spores: ascospores and macroconidia, respectively [30]. The major toxin produced by FHB in wheat is deoxynivalenol (DON). DON is a protein synthesis inhibitor also known as vomitoxin due to its negative impact on the digestive system of pigs. Several recommendations and restrictions have been made in order to keep DON levels sufficiently low in wheat for both animal and human consumption [31]. Chemical control and crop management are not sufficient to control FHB; thus, breeding resistant varieties plays a key role. Conventional breeding involves repeated testing of breeding lines under natural or artificial inoculations. This process is time-consuming, costly, and prone to influence by environment. Thus, it is relevant to supplement phenotypic selection with MAS for FHB resistance. [32]. FHB resistance is generally divided into three types: resistance to initial infection (type I), resistance to spreading of the pathogen in infected tissue (type II) and resistance to DON accumulation (type III) [33]. Several studies have demonstrated that FHB resistance is of quantitative nature [29]. Furthermore, the expression of resistance is highly dependent on the pathogen, the environment and the host [34], in turn complicating phenotypic selection. Several QTL for FHB resistance have been identified and

**3.2. Fusarium head blight**

One of the more promising resistance genes identified in recent years is *Stb16*. This gene was identified in synthetic hexaploid wheat lines, which represent a rich source of variation [23]. *Stb16* explained a high proportion of STB disease resistance and conferred resistance at the seedling stage to all tested *Z. tritici* isolates. Moreover, 20 tested isolates were all avirulent to this gene, indicating that *Stb16* confers broad-spectrum resistance. If this is the case, *Stb16* holds promise for future breeding of efficient and durable STB resistance.

In order to obtain the most resistant wheat variety, breeders should take a number of things into account. Since qualitative resistance genes often conform to the gene-for-gene hypothesis, they are readily overcome by the pathogen. Due to the high frequency of genetic recombination of *Z. tritici,* the specific recognition of R proteins by the host is lost [26]. Furthermore, the strong


The name of the resistance gene, marker type, marker name, the location on the genome and the reference are indicated.

**Table 1.** An overview of the named and mapped genes for STB resistance.

selection pressure placed on the pathogens by one major resistance gene promotes the rise of new adapted races in the pathogen population [27]. An earlier study has proved that commercial cultivation of a highly resistant cultivar can result in loss of resistance towards STB. The intensive cultivation of the variety Gene in the 1990s in Oregon, US, resulted in resistance breakdown. Gene was found to be resistant to two specific isolates, which were avirulent to *Stb6* and *Stb10* [28]. Gradually, an adaptation of *Z. tritici* to one of the resistance genes occurred and the resistance was lost [26]. In general, it appears that most *Z. tritici* isolates used in earlier studies are virulent to almost all *Stb* genes [7]. This may indicate that *Z. tritici* easily can overcome single qualitative resistance genes. In contrast, the quantitative resistance is regarded as more durable. This is due to a lower selection pressure on the pathogen as a result of smaller resistance effects of individual QTL [3]. Furthermore, since quantitative resistance is often polygenic, the mutation of one gene does not necessarily break down disease resistance completely.
