**2. Linkage mapping in strawberry**

The principle of genetic mapping is that genes segregate on chromosome recombination during meiosis [20]. If two genes do not segregate independently, that means they are closely linked to each other on the same chromosome. The genes that are very close to each other or tightly linked will be transferred together from the parent to the progenies. While the two genes are not close to each other on the same chromosome the chance of them segregating separately from each other is increased. Thus, the genetic distance between genes can be calculated accordingly.

The first step of genetic mapping is the selection of two genetically very distant parents that demonstrate obvious genetic differences in many traits of interest. The parents must be far apart genetically for the exhibition of sufficient polymorphism. However, if two parents are too distant genetically, some undesirable events can accrue, such as sterility in progenies and high segregation distortion during the linkage analysis.

The structure of populations consists of two ways; firstly, inbred lines derived from homozygous parents; the second one is the inbreeding lines or cultivars and individuals derived from the crossing of the allogamy species. Thus, two-way

pseudo-testcross, half-sib, and full-sib populations derived from crossings can be used for genetic mapping in outcrossing species. The progenies from the selfing of the F1 generation (F2), backcross (BC), recombinant inbred lines (RILs), double haploids (DHs), and near isogenic lines (NILs) can be preferred for mapping in alloploid species according to the breeding objectives [14, 21, 22]. The selection of population type plays an important role in successfully constructing the linkage maps. Although F2 progenies are obtained from selfing F1 hybrids, BC lines are generated by crossing F1 progenies back with one of the parents. RILs are produced by single-seed selections derived from individuals of the F2 population. The selections should be continued from six to eight generations. Double haploid lines (DHLs) are developed by doubling the gametes of individuals. DHLs regenerate in tissue culture studies after chromosome doubling from pollen grains or haploid embryos derived from crosses.

The first aim of molecular breeding is the construction of linkage groups. The linkage mapping detects genes or markers association with molecular markers and their chromosomal positions and they are valuable tools in order to perform positional cloning of desired/known genes or related regions and to consist of contigs and scaffolds of physical maps at the chromosomal level.

The first linkage mapping report in *Fragaria* was performed using an isozyme marker and a morphological (yellow fruit color) trait, using individuals of a cross between *F. vesca* cultivars Yellow Wonder and Baron Solemacher [23]. Another finding was reported that an isozyme locus (PGI-2) was used in the same population in non-runnering r locus-related morphological traits [24]. The first linkage map in *Fragaria* was constructed similarly in diploid *F. vesca* [25]. The difference between these maps was that they were constructed in the F2 population produced by crossing Baron Solemacher and W6, a non-runnering European cultivar belonging to *Fragaria vesca ssp. vesca*, and *Fragaria vesca ssp. americana* W6, a wild runnering genotype. A total of 75 random amplified polymorphic DNA (RAPD) markers, two isozymes, an STS marker associated with the alcohol dehydrogenase gene, and the runnering locus were used in linkage mapping, and the length of the map in seven linkage groups was calculated as 445 cM.

The genetic linkage map of octoploid strawberries was constructed by using amplified fragment length polymorphism (AFLP) markers [26]. A total of 515 markers and 119 F1 plants of a two-way pseudo-test cross of Capitola (CA75.121– 101 *×* Parker) and CF1116 (Pajaro *×* (Earliglow *×* Chandler)) were used in linkage map construction. A total of 28 and 30 linkage groups were constructed in the maternal and paternal linkage maps. The female map covered 1604 cM and the male map length was 1496 cM. The second map of the diploid *Fragaria* population was generated from the F2 population developed from an interspecific hybridization of *F. vesca* 815 and *F. bucharica* 601 [27]. A total of 78 markers were mapped, 68 of them were simple sequence repeats (SSRs), and the map length was computed as 448 cM. This mapping was important because it was the first SSR-based linkage map in strawberry. This map was enriched by different mapping studies using restriction fragment length polymorphism (RFLPs), AFLPs, SSRs, SNPs, expressed sequence tags (ESTs) and gene-specific markers located in seven linkage groups and the total map length was 528.1 cM. This map is considered the reference framework map in the genus *Fragaria* [27–32].

An AFLP-based genetic map was generated by Lerceteau-Köhler et al. [26], and this map was enriched by Rousseau-Gueutin et al. [33]. The researchers explained that a total of 213 genotypes and many AFLP markers, sequence-characterized

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

amplified regions (SCARs) and SSRs were located in linkage groups. In the female map, 367 loci were mapped into 28 linkage groups, and the map length was 2582 cM, while a total of 440 markers were placed into 26 linkage groups in the male map and the length was 2165 cM. The final map is considered as the first comprehensive reference map for octoploid strawberries. This map helps the construction of the homoeologous of the four *Fragaria* x *ananassa* linkage groups using the *F. vesca* reference map. Another linkage map was also constructed in *F. virginiana*. A total of 319 and 331 SSR-based markers were located in 33 and 32 linkage groups which belong to maternal and paternal maps, respectively [34, 35]. One of the most comprehensive linkage maps in octoploid strawberries was constructed with 490 transferrable SSR or gene-specific markers in individuals obtained from Redgauntlet *×* Hapil. The authors stated that the constructed linkage map can be used as a framework for future genetic studies and to facilitate the marker-assisted selection in octoploid strawberry breeding. This high-density map was constructed which represents 91% of the *Fragaria* x *ananassa* genome having a map length of 2140.3 cM and consisting of 549 markers [36].

A total of 186 SSR markers were mapped into 28 linkage groups in octoploid strawberry, derived from Holiday *×* Korona crossing, the estimated map length was 2050 cM [37]. Another linkage map in *Fragaria* x *ananassa* was generated using a total of 4474 SSRs (3746 EST-SSRs in *F. vesca*, 603 EST-derived in *Fragaria* x *ananassa,* and 125 transcriptomic-derived from *Fragaria* x *ananassa*) were used for mapping. All markers were first mapped onto a parent-specific linkage map using three different populations such as 02–19 *×* Sachinoka, Kaorino *×* Akihime, and 0212921 *×* 0212921 inbred lines which were assembled onto one linkage map. The constructed map length was calculated as 2364.1 cM [38]. The backcross progenies of a cross between *F. vesca* and *F. viridis* were utilized in linkage mapping and the map length was computed as 241.6 cM [39, 40]. The construction of linkage groups in octoploid strawberries can be used for comparative studies between the diploid and octoploid maps.

The development of NGS technology and a decrease in unit cost in sequencing increased the improvement of the different sequencing platforms such as ddRAD-seq, DarT-seq, and WGRS (whole genome re-sequencing). Construction of the well-saturated linkage maps is very important for the discrimination of the homoeologous belonging to each chromosome in strawberries. Tennessen et al. [41] used a novel approach called Phylogenetics of Linkage-MapAnchored Polyploid Sub-genomes (POLiMAPS) and understanding of the octoploid strawberry sub-genomes in *F. vesca* subsp. *bracteata*, *Fragaria chiloensis*, and *F. virginiana* populations. The researchers stated that one of these sub-genomes is close to diploid *F. vesca* and the diploid *F. iinumae*, others are close to an unknown ancestor of *F. iinumae*. Meanwhile, the IStraw 90 K Axiom® array was developed by the RosBREED project with international cooperation. The IStraw 90 K Axiom® array was mined from the first draft of the *F. vesca* genome (v1.0). This array contributed to the construction of the map for detection of the homoeologous sub-genomes [42]. It was constructed by using 26 *Fragaria* species, 16 *F.* x *ananassa* and 10 individuals belonging to wild strawberry species. Totally, mined 6594 SNP loci were located on the first SNP linkage map generated by Bassil et al. [42]. The digest restriction-associated DNA sequencing and diversity array technology were used for the construction of high-density linkage maps (ddRAD-Seq, [43]; DarT, [44]). In another study, the IStraw90 SNP array and genotyping by sequencing technology (GBS) were utilized by Mahoney et al. [45] in order to construct a highly saturated

linkage group in diploid strawberry, *F. iinumae*. Sargent et al. [36] consisted of the highly saturated linkage map using many polymorphic loci (8407 SNPs) and the IStraw 90 K Axiom® and this map contributed to the detection of the *F. ananassa* genome structure. The SNP alleles on the linkage map were compared with the corresponding *F. vesca* and *F. iinumae* alleles, and the haploSNPs were categorized in the current study. HaploSNPs, which are sub-genome specific markers that have saturated common markers, can be used to compare QTL regions in strawberries, revealing the ancestral-associated loci [36]. These linkage maps provided a better understanding of the genome structure of the octoploid strawberry and increased the interest in SNP-based linkage mapping studies for practical breeding applications.

In strawberry breeding, the development of linkage maps is very important in order to reveal the genetic structure of complex traits because this complexity can be only solved using the QTL mapping and/or association mapping approaches [46]. Although a few association mapping studies have been reported in strawberries, many genetic mapping studies have been performed using biparental populations that have been generated from different crosses [26, 32, 33, 47–50].
