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, 17 (1), 998

Genome Survey of Pistachio (Pistacia Vera L.) by Next Generation Sequencing: Development of Novel SSR Markers and Genetic Diversity in Pistacia Species

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Genome Survey of Pistachio (Pistacia Vera L.) by Next Generation Sequencing: Development of Novel SSR Markers and Genetic Diversity in Pistacia Species

Elmira Ziya Motalebipour et al. BMC Genomics.

Abstract

Background: 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. 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.

Results: To 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.

Conclusions: The 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.

Keywords: Genetic diversity; Genome size; Genome survey; Pistachio; SSR.

Figures

Fig. 1
Fig. 1
17 K-mer analysis for estimating the genome size of Pistacia vera cv. Siirt. The X-axis is depth (X) and the Y-axis is the proportion that represents the frequency at that depth. The H_0.01 means that the heterozygous rate is 1%
Fig. 2
Fig. 2
GC content and average sequencing depth. The X-axis represents GC content and the Y-axis represents the average depth. Red region whose average depth is around the half of main average depth, which may be caused by the high heterozygous rate
Fig. 3
Fig. 3
Distribution of 59,280 SSRs in the pistachio genome based on repeat type
Fig. 4
Fig. 4
Distribution of SSR motifs in pistachio at 40x coverage sequencing data. The X-axis represents motif types and the Y-axis represents the count of motifs in whole genome of pistachio
Fig. 5
Fig. 5
UPGMA dendrogram of 24 P. vera cultivars and 20 genotypes belongs to P. atlantica, P. integerrima, P. terebinthus, P. chinensis and P. lentiscus. The colors refers to population structure when K = 6, which all six Pistacia species were clearly separated
Fig. 6
Fig. 6
Population structure of 24 P. vera cultivars and twenty wild genotypes belong to P. atlantica, P. integerrima, P. terebinthus, P. chinensis and P. lentiscus. K = 2 to K = 10 represent the sub-populations
Fig. 7
Fig. 7
Values of DK. The modal value of this distribution is the true K(*) or the uppermost level of structure, here two (K = 2) clusters with 7 sub-clusters (K = 7)

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References

    1. Kafkas S. Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Syst Evol. 2006a;262(1–2):113–24.
    1. Parfitt DA, Badenes ML. Phylogeny of the genus Pistacia as determined from analysis of the chloroplast genome. P Natl Acad Sci USA. 1997;94:7987–92. doi: 10.1073/pnas.94.15.7987. - DOI - PMC - PubMed
    1. Crane JC. Pistachio tree nuts. Westport: Avipublishing Company; 1978.
    1. Hormaza JI, Dollo L, Polito VS. Determination of relatedness and geographic movements of Pistacia vera (Pistachio; Anacardiaceae) germplasm by RAPD analysis. Econ Bot. 1994;48(4):349–58. doi: 10.1007/BF02862231. - DOI
    1. Hormaza JI, Pinney K, Polito VS. Genetic diversity of pistachio (Pistacia vera, Anacardiaceae) germplasm based on randomly amplified polymorphic DNA (RAPD) markers. Econ Bot. 1998;52:78–87. doi: 10.1007/BF02861298. - DOI

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