Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

Abstract

BackgroundPistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species.ResultsTo explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species.ConclusionsThe results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3359-x) contains supplementary material, which is available to authorized users.

First microsatellite markers forScaligeria lazicaBoiss. (Apiaceae) by next-generation sequencing: population structure and genetic diversity analysis

“…The most probable number of clusters was identified by calculating the Delta K (DK), which is based on the rate of change in the log probability of data between successive K values (K = 1 to K = 5). The peak of the DK graph corresponds to the most probable number of populations in the data set, as previously discussed in Motalebipour et al [38]. The highest value of DK was found at K = 2 ( Figure 6), where all 44 genotypes were divided into two main groups: the RCH accessions and the other (RCE, TSM, TAD) accessions, which is similar to the UPGMA dendrogram ( Figure 4).…”

Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

“…Genetic markers can be used in plant breeding programs for germplasm evaluation and assessment of genetic diversity (Yang et al 2015). In recent years, studies have been conducted using molecular markers to investigate the diversity and genetic relationships of pistachios, including simple sequence repeat -SSR (Arabnezhad et al 2011;Ziya Motalebipour et al 2016), randomly amplified polymorphic DNA -RAPD (Hormaza et al 1998), start codon targeted -SCoT and inter-retrotransposon amplified polymorphism -IRAP (Sorkheh et al 2017), and amplified fragment length polymorphism -AFLP (Shanjani et al 2009). Inter-simple sequence repeats (ISSRs) technique is one of the polymerase chain reaction (PCR) based method, which involves the amplification of DNA segment present at an amplifiable distance between two identical microsatellite repeat regions oriented in opposite direction (Reddy et al 2002).…”

SSR Markers in the Genus Pistacia

“…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].…”

“…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][28][29] and from wild Pistacia species was performed in several studies [30][31][32][33].…”