**3.2. Fusarium head blight**

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

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*

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

holds promise for future breeding of efficient and durable STB resistance.

**Resistance gene Marker type Marker name Location Reference** *Stb1* SSR Xbarc74, Xgwm335 5BL [8] *Stb2* SSR Xwmc406, Xbarc008 1BS [9] *Stb3* SSR Xwmc83 7AS [11] *Stb4* SSR Xgwm111, Xgwm44 7DS [16] *Stb5* SSR Xgwm44 7DS [17] *Stb6* SSR Xgwm369 3AS [12] *Stb7* SSR Xgwm160, Xwmc219, Xwmc319 4AL [18] *Stb8* SSR Xgwm146, Xgwm577 7BL [19] *Stb9* SSR Xfbb226, XksuF1b 2BL [20] *Stb10* SSR Xgwm848 1D [21] *Stb11* SSR Xbarc008 1BS [22] *Stb12* SSR Xwmc219, Xgw313 4AL [21]

*Stb13* SSR Xwmc396 7BL Wheat gene catalogue *Stb14* SSR Xwmc500, Xwmc632 3BS Wheat gene catalogue

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

*Stb16* SSR Xgwm494 3DL [23] *Stb17* SSR Xhbg247 5AL [23] *Stb18* SSR Xgpw5176, Xgpw3087 6DS [24] *StbWW* SSR Xbarc119b 1BS [25]

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

identified conferring STB resistance [7, 15].

6 Next Generation Plant Breeding

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 located during recent years [29]. The first QTL for type II resistance was identified in the spring wheat 'Sumai 3' on chromosome 3BS. This QTL was named *Fhb1* and characterised by molecular markers [35–37]. Recently, *Fhb1* was cloned from Sumai 3 and a pore-forming toxin-like (PFT) gene was found to confer FHB resistance [38]. *Fhb1* has been found to reduce FHB disease severity tremendously and MAS is employed to incorporate the resistance in breeding programs [29]. A QTL, named *Fhb2,* on chromosome 6BS was found to confer type II FHB resistance [39, 40]. Additionally, *Fhb4* was identified and located on chromosome 4B [41]. **Table 2** lists all FHB-resistant genes identified by molecular markers. Currently, breeders are pyramiding *Fhb1, Fhb2* and *Fhb4* in single breeding lines to obtain optimal FHB resistance [34]. Several additional QTL have been identified and located in numerous studies [29].


to YR even after having been cultivated for 60 years [51]. Additionally, several studies have mapped QTL to all wheat chromosomes except chromosome 1D and 3A [49]. Commonly used resistance genes employed in wheat breeding programs include *Yr*18, *Yr*29 and *Yr*36 [52–54]. *Yr36* is tightly linked to *Gpc-B*1, a high-protein gene, rendering varieties with *Yr36* and *Gpc-B*1 useful in breeding for YR resistance and improved quality. **Table 3** lists a selection of *Yr* genes

**Resistance gene Marker type Marker name Location Reference** *Yr5* SSR Xgwm501 2BL [55] *Yr7* SSR Xgwm526 2BL [56] *Yr15* SSR Xbarc8, Xgwm493 1BS [57] *Yr18* CAPS Cssfr6 7D [58] *Yr36* SSR Xgwm508, Xbarc136 6BS [54] *Yr60* SSR Xwmc776 4AL [59] *Yr76* SSR Xwmc11, Xwmc532 [60] *Yr78* SNP IWA7257 6BS [61]

Marker-Assisted Breeding in Wheat http://dx.doi.org/10.5772/intechopen.74724 9

Several incidences have been reported where *Yr* genes have been classified as ineffective. Some of the most widely used resistance genes including *Yr17* [62], *Yr27* [63] and *Yr31* [64]

Wheat is grown in large parts of the world and is used for animal feed or for a wide range of products such as pasta, biscuits, cakes and bread. The end-use quality differs greatly between wheat cultivars and is influenced by several traits, e.g., grain hardness, grain protein content, gluten content and composition and starch properties. Quality should therefore be an important focus in wheat breeding programs. However, wheat quality cannot be easily determined phenotypically, and different methods are preferred in different countries and industries. Methods for testing quality are typically time-consuming and costly and require relatively large amounts of grain, which is typically not available until late stages of breeding programs. Thus, markers for wheat quality traits can be very useful, as they enable screening of a high

Grain hardness influences milling, flour and end-use properties of wheat. Flour from grain with hard endosperm texture has higher water absorption than flour from soft grain and is therefore preferred for bread-making. A soft endosperm texture leads to less starch granule damage

that have been characterised and mapped with molecular markers suitable for MAS.

**Table 3.** A selection of the genes conferring YR resistance identified by molecular markers.

**4. Marker-assisted wheat breeding for improving quality traits**

number of lines and can be used early in breeding programs [65, 66].

have recently lost resistance towards YR.

**4.1. Grain hardness**

**Table 2.** Overview of the FHB-resistant genes identified in wheat using molecular markers.

## **3.3. Wheat stripe rust (yellow rust)**

Wheat stripe rust, mostly designated as 'yellow rust' (YR), causes major yield losses every year. The disease is caused by *Puccinia striiformis,* which belongs to the family *Pucciniaceae* of rust fungi. The most devastating epidemics occur in temperate areas with cool and humid summers or in warmer areas with cool nights. The fungus is heteroecious, i.e., it requires at least two hosts in order to proliferate. *P. striiformis* uses cereals as a primary host and *Berberis* spp. as a secondary host for sexual recombination. Typical, yellow stripes develop on the leaf in lesions. Spores continue to be produced as stripes spread longitudinally on the leaf. After the onset of senescence, *P. striiformis* will produce teliospores. Teliospores can infect the secondary host, *Berberis* spp., and initiate onset of pycnia infection of the *Berberis* leaf [46].

Breeding for YR resistance was initiated in 1905 by Biffen [47]. To date, more than 70 genes (*Yr* genes) conferring YR resistance have been identified [48]. Most of the catalogued genes confer seedling resistance, while relatively few confer adult plant resistance. In general, studies have shown that seedling resistance is conferred by single genes and the resistance is therefore easily overcome by the pathogen by mutations in virulence genes. Adult plant resistance is generally thought to be more durable [49]. High-temperature adult plant (HTAP) genes are expressed as the plants grow older and the weather becomes warmer [50]. HTAP genes confer a non-specific, quantitative resistance. Studies have proven that varieties with HTAP genes display resistance


**Table 3.** A selection of the genes conferring YR resistance identified by molecular markers.

to YR even after having been cultivated for 60 years [51]. Additionally, several studies have mapped QTL to all wheat chromosomes except chromosome 1D and 3A [49]. Commonly used resistance genes employed in wheat breeding programs include *Yr*18, *Yr*29 and *Yr*36 [52–54]. *Yr36* is tightly linked to *Gpc-B*1, a high-protein gene, rendering varieties with *Yr36* and *Gpc-B*1 useful in breeding for YR resistance and improved quality. **Table 3** lists a selection of *Yr* genes that have been characterised and mapped with molecular markers suitable for MAS.

Several incidences have been reported where *Yr* genes have been classified as ineffective. Some of the most widely used resistance genes including *Yr17* [62], *Yr27* [63] and *Yr31* [64] have recently lost resistance towards YR.
