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.
Highlights
Pistachio (Pistacia vera L.) is one of the most important nut crops in the world
The 17mer frequency distribution derived from the sequencing reads was plotted in Fig. 1; the peak of the 17-mer distribution was about 28, and the total K-mer count was 16,684,162,450; the genome size of pistachio was estimated as 596 Mb
The estimated genome size of pistachio was found to be smaller than that of apple [35], and larger than that of peach [36], sweet orange [37], and Simple sequence repeat (SSR) polymorphisms in Pistacia From the 59,280 SSRs detected in the genome survey of pistachio in this study, primer design was performed for 950 loci
Summary
Pistachio (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. The pistachio is native to the arid zones of Central Asia; it has been cultivated for 3000– 4000 years in Iran and was introduced into Mediterranean. 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 [4, 5]. Iran, the United States, Turkey, and Syria are the main pistachio producers in the world [6]. Wild trees of Pistacia species such as P. atlantica Desf., P
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
