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Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution.
Kafkas, Salih; Ma, Xiaokai; Zhang, Xingtan; Topçu, Hayat; Navajas-Pérez, Rafael; Wai, Ching Man; Tang, Haibao; Xu, Xuming; Khodaeiaminjan, Mortaza; Güney, Murat; Paizila, Aibibula; Karci, Harun; Zhang, Xiaodan; Lin, Jing; Lin, Han; Herrán, Roberto de la; Rejón, Carmelo Ruiz; García-Zea, Jerson Alexander; Robles, Francisca; Muñoz, Coral Del Val; Hotz-Wagenblatt, Agnes; Min, Xiangjia Jack; Özkan, Hakan; Motalebipour, Elmira Ziya; Gozel, Hatice; Çoban, Nergiz; Kafkas, Nesibe Ebru; Kilian, Andrej; Huang, HuaXing; Lv, Xuanrui; Liu, Kunpeng; Hu, Qilin; Jacygrad, Ewelina; Palmer, William; Michelmore, Richard; Ming, Ray.
Affiliation
  • Kafkas S; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey. Electronic address: skafkas@cu.edu.tr.
  • Ma X; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, Fujian Agriculture and F
  • Zhang X; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Topçu H; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Navajas-Pérez R; Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
  • Wai CM; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  • Tang H; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Xu X; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen Un
  • Khodaeiaminjan M; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Güney M; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Paizila A; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Karci H; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Zhang X; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  • Lin J; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Lin H; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Herrán R; Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
  • Rejón CR; Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
  • García-Zea JA; Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
  • Robles F; Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
  • Muñoz CDV; Department of Computer Science, University of Granada, Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain.
  • Hotz-Wagenblatt A; German Cancer Research Center, Omics IT and Data Management Core Facility, Heidelberg, Germany.
  • Min XJ; Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA.
  • Özkan H; Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Motalebipour EZ; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Gozel H; Pistachio Research Institute, Sahinbey, Gaziantep 27060, Turkey.
  • Çoban N; Pistachio Research Institute, Sahinbey, Gaziantep 27060, Turkey.
  • Kafkas NE; Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
  • Kilian A; Diversity Arrays Technology, University of Canberra, Canberra, ACT, Australia.
  • Huang H; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Lv X; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Liu K; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Hu Q; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
  • Jacygrad E; Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
  • Palmer W; Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
  • Michelmore R; Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
  • Ming R; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: rayming@illinois.edu.
Plant Commun ; 4(3): 100497, 2023 05 08.
Article in En | MEDLINE | ID: mdl-36435969
ABSTRACT
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Pistacia Type of study: Prognostic_studies Language: En Journal: Plant Commun Year: 2023 Document type: Article
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Pistacia Type of study: Prognostic_studies Language: En Journal: Plant Commun Year: 2023 Document type: Article