Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution

Salih Kafkas*, Xiaokai Ma, Xingtan Zhang, Hayat Topçu, Rafael Navajas-Pérez, Ching Man Wai, Haibao Tang, Xuming Xu, Mortaza Khodaeiaminjan, Murat Güney, Aibibula Paizila, Harun Karcı, Xiaodan Zhang, Jing Lin, Han Lin, Roberto de la Herrán, Carmelo Ruiz Rejón, Jerson Alexander García-Zea, Francisca Robles, Coral del Val MuñozAgnes Hotz-Wagenblatt, Xiangjia Jack Min, Hakan Özkan, Elmira Ziya Motalebipour, Hatice Gozel, Nergiz Çoban, Nesibe Ebru Kafkas, Andrej Kilian, Hua Xing Huang, Xuanrui Lv, Kunpeng Liu, Qilin Hu, Ewelina Jacygrad, William Palmer, Richard Michelmore, Ray Ming*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.

Original languageEnglish (US)
Article number100497
JournalPlant Communications
Issue number3
StatePublished - May 8 2023


  • Pistacia vera
  • domestication
  • pistachio
  • reference genome
  • sequencing
  • sex chromosome

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry
  • Biotechnology
  • Plant Science
  • Cell Biology


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