**6. Marker-assisted selection (MAS) in strawberry**

Marker-assisted selection is one of the most important breeding techniques that shorten the breeding period in modern molecular breeding studies. To date, different marker technics such as SSRs and SNPs were used in octoploid strawberry breeding programs for MAS associated with many agronomical traits [44, 52, 92].

Simple sequence repeat markers are preferred in molecular studies due to their high level of polymorphism, abundance in the whole genome, co-dominant nature, and reliability. However, this system is not cost-effective for screening of large breeding populations. Another reason is that it produces more than a pair of alleles due to having sub-genomes of octoploid strawberries. Thus, SSRs are not practical because of their multi-allelic nature for large breeding populations and for cloning of associated genes. Although rapid DNA isolation protocols and next-generation genotyping platforms were recently developed by Noh et al. [93] for strawberry breeding, these applications are very expensive and laborious because of the need to obtain high-quality DNA in species with a high content of phenolic compounds, such as strawberry.

In the last two decades, high-resolution melting (HRM) and TaqMan-based markers have been utilized for MAS in strawberry breeding effectively. On the other hand, probe-based methods such as Kompetitive Allele-Specific PCR (KASP) markers can be designed for any species because they are flexible. However, these markers are not feasible for multiplex genotyping while HRM is a post-PCR analysis and does not require sequence validation of the target region. In this regard, SNP-based DNA markers such as endpoint genotyping and KASP should be continued for use in marker-assisted breeding in strawberries.

There is a desirable strategy in MAS is that detected QTL is governed by one or a few major loci or genes. Especially if loci on major QTLs were located in a single subgenome and this is a positive situation for effective MAS in the cultivated octoploid strawberry. The validated DNA loci associated with traits have been widely used in numerous breeding programs, and the detected linked DNA loci have recently been verified and will be used in breeding programs [61].

The c-decalactone is a volatile compound and is responsible for 'peach-like' aroma in strawberries. Chambers et al. [82] and Sánchez-Sevilla et al. [53] identified the fatty acid desaturase gene (FaFAD1), which is responsible for the c-decalactone biosynthesis process. Sánchez-Sevilla et al. [53] discovered a desaturase gene (FaFAD1) on LG III and they tested all cultivars. Although the gene responsible for this volatility was amplified in less than half of the cultivars, it did not amplify in the rest of the cultivars. The researchers developed a functional SCAR marker in the upstream region of the strawberry genome. The gene created a 500 bp PCR product if the strawberry cultivars have this gene, if not, it does not generate any PCR product. An SSR marker responsible for this volatile compound was developed on an 11 kb upstream genic region related to FaFAD1. It generated a PCR product with 205 bp.

One of the HRM primer pairs developed in the FaFAD1 genic region, GDHRM5 has been used in the UF breeding program. Developing a codominant marker is desired to distinguish individuals with homozygous and heterozygous loci. Recently, a candidate gene associated with mesifurane, the FaOMT gene, was replaced on LG VII [52]. The authors developed the marker based on agarose gel and they identified the functional PCR amplification in 248 bp and the non-functional locus in 217 bp (after 30 bp deletion). Thus, the scoring of the products was performed according to the absence or presence of amplification of the mesifurane gene.

Remontancy is defined as the unresponsiveness of the day-light and it is an important trait to provide throughout the whole season of production in strawberry cultivation. Gaston et al. [59] detected the QTL linked to the day-neutrality, transition from short-day to remontant blooming, governed by the FaPFRU locus identified in the UC Davis breeding program. Another genetic mapping discovery revealed that an SSR locus detected was mostly associated with FaPFRU [94]. This SSR marker was validated in RosBREED germplasm and about 90% of the accessions that were not producing any bands on 129 bp did not flower under the long day conditions.

The screening of populations using the DNA marker for disease resistance in strawberry become more popular, particularly in the last decades. The resistance to *C. acutatum* pathogenicity test is one of these tests, and the Rca2 locus was found to be associated with this trait [68]. It has a dominant allele that is responsible for resistance, and these AFLP markers were converted into two SCAR markers, which amplified a 240 bp PCR product. Thus, these SCAR markers have been used easily in separation by agarose gel-based electrophoresis. The resistance to root and crown rot caused by *P. cactorum* locus was found as the FaRPc2 on the linkage group VII [74]. The FaRPc2 is detected in the major QTL region, which is responsible for about 35–40% of the phenotypic variation [61]. Van de Weg [95] identified the gene resistance to red stele in strawberries. The Rpf1 gene has been used for MAS as resistance factor R1 to *P. fragariae* var. *fragariae*. Recently, one SSR marker associated with R1 was developed and amplification was performed in 99% of the strawberry samples [61]. The previous study took place using a total of 49 *F.* x *ananassa* individuals to verify the Rfp1 gene that is associated with disease resistance. The results demonstrated that 17 accessions created the PCR fragment while 32 individuals were evaluated as susceptible [96]. The angular leaf spot disease caused by *X. fragariae* is the main problem in strawberries. Recently, a single dominant locus located in linkage group VI was associated with this bacterial disease resistance in octoploid strawberries [73].

The reason for the high interest and appreciation for strawberries is their sweetness. And with the method developed by Schwieterman et al. [97], the sweetness can be predicted in strawberry individuals. The QTL region associated with the soluble solids content (SSC) is an indicator of sweetness in strawberries [98], EMFv006 was

#### *Quantitative Trait Loci Associated with Agronomical Traits in Strawberry DOI: http://dx.doi.org/10.5772/intechopen.108311*

located on LG VI using the 'Capitola' CF1116 population [51]. The QTL analysis was performed using the 609 strawberry accessions, which consisted of worldwide promising lines or selections and cultivars in 2011 and 2012 [96, 99] The detected QTL was determined very closely near to the EMFv006 SSR marker on LG VI [61]. Verma et al. [61] investigated the association of this marker with the SSC trait in different germplasm sets, but there was no association between the trait and marker EMFv006. That means using this marker in MAS studies may not be a good idea.

In this section, we summarized QTLs associated with important agronomical traits and different disease resistance traits, which are very important in strawberry breeding. And these QTLs can be converted into DNA markers that are closely linked to the desired traits. These markers can be used in MAS in strawberry breeding due to their easy scoring, not being complicated, and giving more accurate results. These markers were developed for MAS in many genetic resources as a common idea for solving the problems encountered in strawberry breeding.
