**8. Marker-assisted backcrossing approach in tomato breeding**

#### **8.1. Marker-assisted backcrossing**

The backcrossing method has been used extensively in plant breeding to incorporate one or a few genes from one plant possessing a unique trait (donor parent) into a desired adapted or elite variety (recurrent parent) that lacks few qualities such as disease resistance. In most cases, the parent used for backcrossing has a large number of desirable attributes but is deficient in only a few characteristics [62]. The application of molecular markers in backcrossing has increased the efficiency of selection. Marker-assisted backcrossing involves the use of molecular markers to track either the target locus or the background of the recurrent parent. The outcome of such a process is a cultivar that contains only the major gene that is obtained from the donor parent, while the genome of the recurrent parent remains intact.

#### **8.2. Marker-assisted backcrossing approaches**

Whereas [63] proposed two types of selections (foreground and background selection) under marker-assisted backcrossing, [64] identified three levels of marker-assisted backcrossing (foreground selection, recombinant selection and background selection).

#### **8.3. Foreground selection**

In the foreground selection, target locus of the donor parent is tracked using the selected molecular marker of interest [65]. The objective is to maintain the target locus in a heterozygous state (one donor allele and one recurrent parent allele) until the final backcross is completed. This is done to ensure that the locus that is targeted for improvement remains in a state of heterozygosity in the progeny for both donor and recurrent parent. The progeny are then selfed to ensure segregation and recombination in the next generation. Individuals that are found to be homozygous for the allele of interest are identified and selected [66].

The foreground selection is an efficient method to introgress favorable alleles into farmerpreferred varieties and elite cultivars of crops including maize. This approach ensures that only the gene of interest is transferred, while the genetic background of the elite cultivar remains intact. The resulting variety is the same as the original recurrent parent except the 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 dwarf virus in the progeny population. They observed that BC<sup>2</sup> F2 -derived progenies containing 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 markers tightly linked to salt tolerance in rice to screen BC<sup>1</sup> F1 progenies for the presence 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 heterozygous individuals were then selected for further evaluation in the program.

#### **8.4. Background selection**

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

The backcrossing method has been used extensively in plant breeding to incorporate one or a few genes from one plant possessing a unique trait (donor parent) into a desired adapted or elite variety (recurrent parent) that lacks few qualities such as disease resistance. In most cases, the parent used for backcrossing has a large number of desirable attributes but is deficient in only a few characteristics [62]. The application of molecular markers in backcrossing has increased the efficiency of selection. Marker-assisted backcrossing involves the use of molecular markers to track either the target locus or the background of the recurrent parent. The outcome of such a process is a cultivar that contains only the major gene that is obtained

Whereas [63] proposed two types of selections (foreground and background selection) under marker-assisted backcrossing, [64] identified three levels of marker-assisted backcrossing

In the foreground selection, target locus of the donor parent is tracked using the selected molecular marker of interest [65]. The objective is to maintain the target locus in a heterozygous state (one donor allele and one recurrent parent allele) until the final backcross is completed. This is done to ensure that the locus that is targeted for improvement remains in a state of heterozygosity in the progeny for both donor and recurrent parent. The progeny are then selfed to ensure segregation and recombination in the next generation. Individuals that

The foreground selection is an efficient method to introgress favorable alleles into farmerpreferred varieties and elite cultivars of crops including maize. This approach ensures that only the gene of interest is transferred, while the genetic background of the elite cultivar remains intact. The resulting variety is the same as the original recurrent parent except the

are found to be homozygous for the allele of interest are identified and selected [66].

is employed in our breeding programs to enable us ripe the benefits.

**8.1. Marker-assisted backcrossing**

100 Recent Advances in Tomato Breeding and Production

**8.2. Marker-assisted backcrossing approaches**

**8.3. Foreground selection**

**8. Marker-assisted backcrossing approach in tomato breeding**

from the donor parent, while the genome of the recurrent parent remains intact.

(foreground selection, recombinant selection and background selection).

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 of the recurrent parent genome [71, 72].

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 parent can be achieved at the BC<sup>2</sup> , BC<sup>3</sup> or BC<sup>4</sup> , thus shortening the process by two of the four backcross generations when markers are involved [69, 70, 72–74] (**Figure 1**).

#### **8.5. Recombinant selection**

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

approaches that may carry large segments of the donor parent even after several generations [79, 80]. Compared with conventional backcrossing approaches, marker-assisted backcrossing enables faster recovery of the recurrent parent genome especially when foreground and background selection are combined. In practice, both foreground and background selections

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

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

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In most developing countries such as Ghana, the development of new cultivars, for example tomato, maize, groundnut, cowpeas, has been achieved through conventional plant breeding method rather than transgenic breeding. It generally comprises of sequences of imbrications

• Assembling germplasm like landrace, wild types, improved and/or exotic types of tomatoes as sources of genetic diversity for the major breeding activities to create different

• Identification of superior recombinants through selection and testing. This comprise of the selection environment (e.g., promising against biotic and abiotic stresses), selection time (e.g., early against late generation), and the number of years and locations of testing.

This breeding method can take over five generations leading to increase in the number of years to develop an elite variety of a particular plant. Backcrossing is the breeding method, which involves transfer of alleles at one or more loci from a donor to an adapted variety or a desirable line [83, 84]. Recurrent backcrossing is the traditional backcrossing program based on the assumption proposed by [85] that the quantity of the recurrent parent genome is recovered at a rate of [1–(1/2)<sup>t</sup> + 1] where t is the number of generations of backcrossing. Thus, the expected recovery of the recurrent parent genome after six generations of backcrossing would be 99.2%, a situation called near-isogenic. An imperative objective of recurrent backcrossing is to reduce the effect of the donor genome, as the aim is to move just a few of its genes responsible for the target trait into the recurrent parent's genetic background. It is generally used to improve qualitatively inherited traits such as pests and diseases resistance, since the existence of target trait genes must be confirmed by individual phenotype in the successive cross-generations. Thus, individual phenotypic performance is a key indicator of the genotype, provided genes have a major effect on phenotypic performance and the phenotypic uncertainty is insignificant [86]. However, due to linkage between a target gene and nearby genes (which could code for economically undesirable traits) from the donor parent [87] and/or chance (stochastic or nonrandom positions of chiasmata), any specific backcross progeny will digress from this expectation. This digression has been experienced in couple of plants, for instance, where one tomato cultivar developed after 11 backcrosses still had the complete chromosome arm carrying the gene from the donor parent and introgressed fragments as large as 4 centimorgan (cM) found in tomato cultivars developed after 20 backcrosses, [88]. This was also found in a study conducted by [89] where the fragments around the introgressed genes in barleys diverse from about 1–14 cM in seven (7) generation backcrossed lines. Consequently, two main

are conducted simultaneously in the same backcross program.

of three corresponding stages:

recombinants.

**9. Progress and prospects of MAS in tomato breeding**

• Releasing, distribution, and utilization of new cultivars [81–83].

limitations of recurrent backcrossing approach have been identified:

**Figure 1.** Flowchart of foreground and background selection scheme. Source: http://passel.unl.edu/Image/siteImages/ MASFigure7Lg.jpg.

segment is slower than the unlinked regions [76]. After identification of individuals using foreground markers, single and double recombinant individuals carrying the donor alleles as well as the recurrent parents are selected [77, 78]. The use of flanking markers are able to greatly reduce the undesirable segment of the donor parent compared to the conventional approaches that may carry large segments of the donor parent even after several generations [79, 80]. Compared with conventional backcrossing approaches, marker-assisted backcrossing enables faster recovery of the recurrent parent genome especially when foreground and background selection are combined. In practice, both foreground and background selections are conducted simultaneously in the same backcross program.
