**7. Applications of marker-assisted selection (MAS) in tomato breeding**

Marker-assisted selection (MAS) is a tool for crop improvement where an associated marker is used for indirect selection of a trait. In this case, you are selecting for a trait based on the genotype of an associated marker rather than the trait itself. It is a technique that has been extensively explored for a wide range of plant traits and can reduce the cost as well as increase the precision and efficiency of selection in breeding. With recent development of molecular tools and genetic maps, MAS has become more attractive and practical than before. Molecular markers are not affected by either genetic or environmental factors, making MAS a useful tool in crop improvement. Markers developed to be used for MAS must be tightly linked to the genes or QTLs. In recent years, it is widely accepted that QTL effects, QTL validation or fine mapping with high resolution is a requirement for MAS [37]. The most important issue in the application of molecular markers in plant breeding is that major effect QTLs or genes should be mapped with high accuracy. In addition, these genes should not have any negative effect on other traits. The use of MAS in tomato breeding started in the 1930s [35] much earlier than in many other crop species. It was employed for the improvement of many morphological, physiological, and disease resistant traits.

Although resistant genes or QTLs have been identified for many fungal diseases in tomato, only few of these are been used for MAS, while with the others, markers associated with resistant genes/loci have been identified, but there are no reports on PCR-based markers developed for resistance breeding. Typical examples are with Alternaria stem canker [38] and gray leaf spot [39] where RFLP markers have been reported, but no PCR-based markers developed; with anthracnose ripe rot, few RADP markers associated with QTLs [40] have been reported but not validated for MAS; with black mold, QTLs [39] have been identified, but there is no report for MAS; with corky root rot, RFLP markers have also been identified and converted to CAPS and additional RAPD markers identified [41], but there is no report of using these markers for MAS; with Fusarium crown root rot, a RAPD marker has been identified, which may be useful for MAS in tomato breeding [42]; with early blight, QTLs have been identified [43], but there is no PCR-based markers reported; with powdery mildew, several QTLs [44] have been identified, but there are no PCR-based markers closely linked to these QTLs identified; and with Septoria leaf spot, there has been no report of genetic mapping studies for resistance breeding. MAS has, however, been successful for resistance breeding in tomato for Fusarium wilt, late blight, leaf mold and Verticillium wilt. Molecular markers associated with Fusarium wilt resistance *I*, *I-1*, *I-2* and *I-3* [45] conferring resistance to four different races of the pathogen were identified, and PCR-based markers developed for all with the exception of *I-1* and used effectively for MAS; markers associated for late blight resistance *Ph*-*1*, *Ph*-*2* and *Ph*-*3* [46] has also been developed and used for tomato breeding; several PCR-based markers linked to the *Cf* gene for leaf mold [47] and Verticillium wilt [48] has also been reported and widely used for MAS.

and was assigned to the 12 linkage groups in tomato [35]. This facilitated the development of other maps including the tomato isozyme linkage map that was published in 1980. Then in 1986, another map consisting of RFLP and isozyme loci was also generated. Since then, several interspecific genetic linkage maps have been generated with RFLPs incorporating cleaved amplified polymorphic sequences (CAPS), SSR and SNP markers. Varying number of markers ranging from 93 to 4491 have been used for constructing linkage maps with a coverage of about 50% of the genome. Other intraspecific maps were later constructed using SSR and SNP markers. Identification and construction of these markers and maps, respectively, will be helpful in identifying useful genes or QTLs that can be introgressed into desirable genetic backgrounds for marker-assisted breeding [36]. This may not only hasten the breeding process, but will also allow pyramiding of desirable genes and QTLs from different genetic backgrounds, which will serve as an effective complementary approach to substantial

**7. Applications of marker-assisted selection (MAS) in tomato** 

Marker-assisted selection (MAS) is a tool for crop improvement where an associated marker is used for indirect selection of a trait. In this case, you are selecting for a trait based on the genotype of an associated marker rather than the trait itself. It is a technique that has been extensively explored for a wide range of plant traits and can reduce the cost as well as increase the precision and efficiency of selection in breeding. With recent development of molecular tools and genetic maps, MAS has become more attractive and practical than before. Molecular markers are not affected by either genetic or environmental factors, making MAS a useful tool in crop improvement. Markers developed to be used for MAS must be tightly linked to the genes or QTLs. In recent years, it is widely accepted that QTL effects, QTL validation or fine mapping with high resolution is a requirement for MAS [37]. The most important issue in the application of molecular markers in plant breeding is that major effect QTLs or genes should be mapped with high accuracy. In addition, these genes should not have any negative effect on other traits. The use of MAS in tomato breeding started in the 1930s [35] much earlier than in many other crop species. It was employed for the improvement of many morphological, physiological, and disease resistant traits. Although resistant genes or QTLs have been identified for many fungal diseases in tomato, only few of these are been used for MAS, while with the others, markers associated with resistant genes/loci have been identified, but there are no reports on PCR-based markers developed for resistance breeding. Typical examples are with Alternaria stem canker [38] and gray leaf spot [39] where RFLP markers have been reported, but no PCR-based markers developed; with anthracnose ripe rot, few RADP markers associated with QTLs [40] have been reported but not validated for MAS; with black mold, QTLs [39] have been identified, but there is no report for MAS; with corky root rot, RFLP markers have also been identified and converted to CAPS and additional RAPD markers identified [41], but there is no report of using these markers for MAS; with Fusarium crown root rot, a RAPD marker has been identified, which may be useful for MAS in tomato breeding [42]; with early blight, QTLs have been identified [43], but there is no

crop improvement.

98 Recent Advances in Tomato Breeding and Production

**breeding**

QTLs and molecular markers associated with resistance have also been identified in tomato for the various bacterial diseases; however, it is only markers that are tightly linked to RFLPs and PCR-based markers for gene *Pto* in bacterial speck [49] that have been used for resistance breeding via MAS. With the other bacterial diseases including the bacteria canker, bacterial spot and bacterial wilt, QTLs or RFLP markers have been identified and reported but are not commercially used for MAS. With bacterial canker, two QTLs [50] have been developed and could be useful for MAS. RFLP markers associated with *Rx*-*1* and *Rx*-*2* and Rx-*3* for bacterial spot have been reported [51], but *Rx*-*1, Rx*-*2* and Rx-*3* are independently associated with hypersensitive response in the greenhouse and are not polymorphic in most breeding populations and hence not useful for MAS breeding, while *Rx*-*3* is associated with both hypersensitive response and field resistance. CAPs markers have been developed for the gene *Rx*-*3* and used for MAS breeding. Several QTLs have also been identified for breeding for bacteria wilt resistance in tomato; however, two dominant markers associated with the gene *TRST*-*1* [52] have been suggested to be useful.

Although there has been reports on the identification of the resistant gene *Cmr* for the cucumber mosaic virus [53], *pot*-*1* gene for Potyviruses [54] and two QTLs associated with the tomato mottle virus, there are no reports of use of these markers in tomato breeding. With the tomato mosaic virus, PCR-based markers for *Tm*-*1*, *Tm*-*2*, and *Tm*-*22* -resistant gene have been reported to be used for MAS [55]. Several genes have also been reported to be resistant to the tomato spotted wilt virus; however, PCR-based markers for only resistant gene *Sw*-*5* have been reported to be developed and utilized by most tomato breeding programs [56]. With the tomato yellow leaf curl virus, PCR-based markers have been identified for and developed for *Ty*-*1*, *Ty*-*2*, *Ty*-*3* and *Ty*-*4*-resistant loci [57]; hence, these markers are not very consistent and hence the challenge in using them for MAS. In the early 1980s, linkage association between the gene *Mi* [58] controlling nematode (*Meloidogyne incognita*) resistance and *Aps-11* locus was reported [59]. RFLP markers associated with the *Aps-11* locus and PCR-based markers associated with the *Mi* gene [60] have been routinely used for the selection of root knot nematode resistance in tomato. The *Mi* gene has also been reported to be resistant to two biotypes of the whitefly *Bemisia tabaci*. Several studies have tried to identify genes or QTLs for insect resistance in tomato; however, there are fewer reports on the identification of these genes/QTLs [61]. This may be attributed to difficulties in phenotypic screening for insect resistance, linkage drag and ease of using pesticides for insect control. However, with the increasing crusade on integrated pest management and restrictions on the use of pesticides, new discoveries in marker development, it is expected that more efforts will be devoted to the identification, development and use of markers for insect resistance improvement in tomato. In tomato, molecular markers have been used to map genes or QTLs for abiotic environmental stresses (such as salinity, drought and heat) and many flower and fruit-related characteristics including exerted stigma, petal and sepal characters, fruit size, shape, color, soluble solids content, pH, lycopene, acidity, flavor, ripening, and many others. However, there is very little indication of the use of MAS for manipulating QTLs for these complex traits, although attempts are being made to improve some quantitative traits. Although MAS is as an effective tool for crop improvement, most breeding programs especially in Africa are not using it routinely. It is imperative that MAS is employed in our breeding programs to enable us ripe the benefits.

new gene. This prevents the need to promote the new variety [67]. This method is useful for traits that have laborious or time-consuming phenotypic screening procedures. It is also very effective for selecting reproductive traits at the seedling stage, so that only best plants are identified and tagged for backcrossing. Application of marker-assisted backcrossing enables the successful transfer of recessive alleles, which is difficult to do when using conventional approaches. Visscher et al. [68] reported that resistance in barley was improved following a successful tracking of a marker linked (0.7 cM) to the *Yd2* gene for resistance to barley yellow

ing the linked marker showed fewer leaf symptoms and gave much higher grain yield though they were together with progenies that lacked the marker (**Figure 1**). The method has also been successfully used to improve salinity tolerance in rice. This selection involved the use

of salt tolerance QTL. They were able to successfully identify individuals that carried homozygous loci from the heterozygous ones though they were phenotypically the same. These

The approach involves the use of flanking markers that are tightly linked to the genomic regions for recombinant selection and unlinked markers to select for the genomic background of the recurrent parent [69, 70]. Background markers are markers that are unlinked to the target gene. Therefore, these markers can be used to select against the donor genome. Individuals that are homozygous for as many alleles of the recurrent parent are selected for full recovery

The breeder selects the genome of the recurrent parent using marker alleles for all the genomic regions of the recurrent parent except the target locus. The target locus is then selected based on the phenotype. Sometimes, elite genes are colocated in the same genomic regions and may affect the final product if transferred together. Elimination of such regions is very difficult in conventional approaches. The application of marker-assisted backcrossing approaches using background selection enables the introgression of just the target locus. The background method of selection is important in eliminating such deleterious genomic regions of the donor parents that may negatively affect the final product. This is extremely useful because the recurrent parent recovery can be greatly accelerated. Conventional backcrossing takes a minimum of six backcross generations to recover the genome of the recurrent parent, with some fragments of the donor genome still remaining intact. However, the genome of the recurrent

, BC<sup>3</sup>

backcross generations when markers are involved [69, 70, 72–74] (**Figure 1**).

or BC<sup>4</sup>

This method of MABC approach is used to reduce the number of deleterious genes (linkage drag) that are transferred from the donor parent. It involves the simultaneous tracking of the genetic background of the recurrent parent and the allele of the donor parent in a heterozygous state [75]. Many undesirable genes that negatively affect crop performance may be linked to the target gene of the donor parent, and the rate of decrease of this undesirable

heterozygous individuals were then selected for further evaluation in the program.

F2

Marker-Assisted Selection (MAS): A Fast-Track Tool in Tomato Breeding

F1

, thus shortening the process by two of the four


http://dx.doi.org/10.5772/intechopen.76007

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progenies for the presence

dwarf virus in the progeny population. They observed that BC<sup>2</sup>

of markers tightly linked to salt tolerance in rice to screen BC<sup>1</sup>

**8.4. Background selection**

of the recurrent parent genome [71, 72].

parent can be achieved at the BC<sup>2</sup>

**8.5. Recombinant selection**
