**1. Introduction**

*Pistacia* is a genus in the Anacardiaceae family which also contains cashew, mango, poison ivy, poison oak, pepper tree, and sumac plants [1]. The genus is estimated to be about 80 million years old [2]. It contains at least 11 species, and *P. vera* L. (pistachio) is the only cultivated one for its edible nuts [3]. In addition, its nuts are considerably larger than all the other species in the genus. The other species grow in the wild, and several of them have been used for many years as rootstock seed sources for *P. vera*. Furthermore, most of them have also been used as forest trees [4]. According to the Food and Agriculture Organization of the United Nations, the world production of pistachios in 2017 was 1,115,066 MT, ranking fifth in world tree nut production behind cashews (*Anacardium occidentale* L.), walnuts (*Juglans regia* L.), chestnuts (*Castanea* spp.), and almonds [*Prunus dulcis* (Mill.) D.A. Webb], and currently, Iran, the United States, and Turkey are the main pistachio producers in the world [5].

*Pistacia* species are dioecious and wind pollinated; however monoecious individuals within *P. atlantica* were also reported [6]. *P. vera* is believed to be the most ancestral species in the genus, and the other species are probably its derivatives [7]. There are two centers of diversity of cultivated pistachio: one comprises the Mediterranean region of Europe, Northern Africa, and the Middle East countries. The second comprises the Eastern part of Zagros Mountains from Crimea to the Caspian Sea. Pistachio cultivation extended westward from its center of origin to

Italy, Spain, and other Mediterranean regions of Southern Europe, North Africa, and the Middle East, as well as to China and more recently to the United States and Australia [8–10].

The *Pistacia* genus is distributed mainly across subtropical regions of the northern hemisphere and consists of both evergreen and deciduous species with shrub and/or tree-like growth habits [7]. Although *P. vera* is a commercially grown species in a number of semi-arid regions worldwide, the species remains quite underexploited when its wide native range and inherent genetic diversity are considered [8, 11, 12]. For instance, commercial pistachio cultivation is done in only a few countries in the world. Besides, pistachio production is done with a very limited number of cultivars in those countries, and most of them are seedling selections from the nature [1, 13]. This narrow genetic base in the production presents a threat in pistachio against new diseases and pests as well as changing ecological conditions. Therefore, the germplasm collections have great potentials to increase the genetic diversity and to develop pistachio cultivars for current production areas and/or to expand the regions where reliable commercial production is possible.

Dioecy and a long juvenile period are the primary difficulties encountered in breeding and genetic studies of *Pistacia*. The long juvenile period in combination with dioecious character causes large investments of time and land for characterization and evaluation of progenies in a breeding program. Furthermore, the genetic control of the most economically significant traits is not clearly understood, including disease and pest resistance, yield, nut quality characteristics, and alternate bearing in pistachio. Therefore, current technologies such as molecular markers are good facilities to overcome such difficulties in the breeding programs. Pistachio is a diploid plant which has a haploid chromosome number of n = 15. It is also highly heterozygous species due to dioecy [1, 14].

DNA markers have played a major role in breeding programs for several decades in plants. Several molecular markers such as randomly amplified polymorphic DNA (RAPD) [15], simple sequence repeat (SSR) [16, 17], sequence-related amplified polymorphism (SRAP) [18], amplified fragment length polymorphism (AFLP) [4], inter-simple sequence repeat (ISSR) [19], selectively amplified microsatellite polymorphic loci (SAMPL) [20], and single-nucleotide polymorphisms (SNPs) [21] have been used to assess the genetic diversity, fingerprinting, phylogenetic relationships, germplasm characterization, sex determination, genetic linkage mapping, and QTL analysis in cultivated and wild *Pistacia* species.

In pistachio, most of the cultivars in the production are earlier selections either by growers or breeders. Pistachio cultivars from controlled crosses are in a limited number, and selected genotypes in the current breeding programs are under evaluations in different countries. Using molecular tools in conventional breeding programs can be a good advance in pistachio. Initial molecular studies in pistachio were mainly on germplasm characterization by using different molecular marker techniques. Identification of molecular markers linked to sex determination was also studied that allows early selections of females in a cultivar breeding program [21–23]. Recently, the markers linked to sex have been used in a cultivar breeding program in Turkey [24].

SSRs are useful as molecular markers and very polymorphic due to the high mutation rate affecting the number of repeat units [25]. They are very useful for assaying diversity in natural populations or germplasm collections and for fingerprinting and parental identification. They are also very valuable markers especially for genetic linkage mapping and evolutionary studies [26] and have a high level of transferability between closely related species. The development of SSR markers from *P. vera* [14, 16, 17, 27–29] and from wild *Pistacia* species was performed in several studies [30–33].

**95**

**Figure 1.**

*et al. [14].*

*SSR Markers in the Genus* Pistacia

specific F1 population.

genome size of pistachio as 600 Mb.

**2. SSR distribution in** *P. vera*

*DOI: http://dx.doi.org/10.5772/intechopen.89966*

The first complete genetic linkage map was constructed in pistachio by [34] who used SRAP, ISSR, and AFLP markers in an inter-specific F1 population derived from a cross between *P. vera* and *P. atlantica*. Recently, Khodaeiaminjan et al. [28] constructed the first complete SSR-based linkage map of pistachio using an intraspecific F1 population. More recently, Motalebipour et al. [35] constructed a genetic linkage map and performed the first QTL analysis in pistachio by using an inter-

Next-generation sequencing (NGS) has provided a new perspective for research,

In this chapter, SSR abundance, distribution of their use as useful markers in the characterization of germplasm resources, taxonomy and phylogenetic analysis in the genus, as well as their transferability among *Pistacia* species are discussed.

Motalebipour et al. [14] performed a genome survey study in pistachio and estimated genome size of pistachio as 600 Mb. The authors used 26.77 Gb Illumina PE (pair-end) reads of Siirt cultivar to estimate genome size and to reveal SSR distribution in pistachio genome. Motalebipour et al. [14] detected a total of 59,280 di-, tri-, tetra-, penta-, and hexa-nucleotide SSR motifs, and the dinucleotide motifs were the most abundant type of repeats (63.2%) in pistachio (**Figure 1**), followed by tri- (18.0%), tetra- (12.8%), penta- (3.8%), and hexanucleotide motifs (2.2%). Motalebipour et al. [14] searched repeat motifs in their genome survey study in pistachio, and AT/AT (23.0%) and TA/TA (21.6%) were the most abundant repeats, followed by AG/CT (7.6%) and GA/TC (6.2%), AAT/ATT (4.1%), CA/TG (2.6%), and TAA/ATT (2.6%) (**Figure 2**). The most abundant tetra- and penta-nucleotide

*Distribution of 59,280 SSRs in the pistachio genome based on repeat type. Obtained from Motalebipour* 

owing to its high throughout and speed of data generation. It made easy to perform whole genome and transcriptome sequencing in a short time and low cost. Motalebipour et al. [14] performed genome survey study in pistachio and estimated

#### *SSR Markers in the Genus* Pistacia *DOI: http://dx.doi.org/10.5772/intechopen.89966*

The first complete genetic linkage map was constructed in pistachio by [34] who used SRAP, ISSR, and AFLP markers in an inter-specific F1 population derived from a cross between *P. vera* and *P. atlantica*. Recently, Khodaeiaminjan et al. [28] constructed the first complete SSR-based linkage map of pistachio using an intraspecific F1 population. More recently, Motalebipour et al. [35] constructed a genetic linkage map and performed the first QTL analysis in pistachio by using an interspecific F1 population.

Next-generation sequencing (NGS) has provided a new perspective for research, owing to its high throughout and speed of data generation. It made easy to perform whole genome and transcriptome sequencing in a short time and low cost. Motalebipour et al. [14] performed genome survey study in pistachio and estimated genome size of pistachio as 600 Mb.

In this chapter, SSR abundance, distribution of their use as useful markers in the characterization of germplasm resources, taxonomy and phylogenetic analysis in the genus, as well as their transferability among *Pistacia* species are discussed.
