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, 20 (1), 79

Whole Genomes and Transcriptomes Reveal Adaptation and Domestication of Pistachio

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Whole Genomes and Transcriptomes Reveal Adaptation and Domestication of Pistachio

Lin Zeng et al. Genome Biol.

Abstract

Background: Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses.

Results: Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection.

Conclusions: Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.

Keywords: Artificial selection; Crop domestication; Genome; Pistacia vera.

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Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Pistachio genome evolution. a Tree, flower, immature seeds, and mature seeds of pistachio Ghazvini. b Example microsynteny analysis indicating that no lineage-specific whole genome duplication occurred in pistachio. Microcollinearity patterns between genomic regions from Amborella, pistachio and the populus. Rectangles represent predicted gene models, with blue and green showing relative gene orientations. Gray ribbons connect the matching gene pairs. c Expansion (red numbers) and contraction (blue numbers) of gene families in different plants
Fig. 2
Fig. 2
Transcriptome analysis of saline-treated pistachio. a Expression heatmap of genes in the “oxidation-reduction process”. C, control pistachio leaf; S, saline-treated pistachio leaf. ncontrol = 3, nsalinity = 3. Expression values were normalized by log2 (FPKM+1). b Expression values (FPKM) of CYP74A in the leaf (left) and root (right). c Relative expression levels of seven genes in the category “response to jasmonic acid”
Fig. 3
Fig. 3
Signal of introgression among different wild species detected by the TreeMix program. Hybridization likely occurs among the different close relatives in nature. However, no introgression was detected from other wild species to cultivated pistachio
Fig. 4
Fig. 4
Phylogenetic analysis of wild and domestic pistachio. a Phylogenetic tree. Cultivars of group I (red), cultivar group II (green), and wild pistachio (blue) are marked in different colors from top to bottom. b PCA analysis. From left to right, the three squares indicate cultivar group I, cultivar group II, and wild pistachio. c Admixture analysis. From left to right, the three groups, i.e., cultivar group I, cultivar group II, and wild pistachio are marked by different colors. d From left to right, representative dry seeds from cultivar group I, cultivar group II, and wild pistachio. e Correlation between the proportion of cultivar genetic component and dried pistachio fruit weight
Fig. 5
Fig. 5
Artificial selection on pistachio tree size. a From left to right are the photographs of trees of wild pistachio, Badami-zarand cultivar, and Ohadi cultivar; the trees are of the same age and grown under similar conditions at the Pistachio Research Center, Rafsanjan, Iran. The same marker post is located beside each of the trees. b FST, θπ, and Tajima’s D value of SAUR55 between cultivated and wild pistachio. c Relative expression levels of SAUR55 in the leaf and root, ncultivar = 3, nwild = 3

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