TY - JOUR
T1 - Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution
AU - Kafkas, Salih
AU - Ma, Xiaokai
AU - Zhang, Xingtan
AU - Topçu, Hayat
AU - Navajas-Pérez, Rafael
AU - Wai, Ching Man
AU - Tang, Haibao
AU - Xu, Xuming
AU - Khodaeiaminjan, Mortaza
AU - Güney, Murat
AU - Paizila, Aibibula
AU - Karcı, Harun
AU - Zhang, Xiaodan
AU - Lin, Jing
AU - Lin, Han
AU - Herrán, Roberto de la
AU - Rejón, Carmelo Ruiz
AU - García-Zea, Jerson Alexander
AU - Robles, Francisca
AU - Muñoz, Coral del Val
AU - Hotz-Wagenblatt, Agnes
AU - Min, Xiangjia Jack
AU - Özkan, Hakan
AU - Motalebipour, Elmira Ziya
AU - Gozel, Hatice
AU - Çoban, Nergiz
AU - Kafkas, Nesibe Ebru
AU - Kilian, Andrej
AU - Huang, Hua Xing
AU - Lv, Xuanrui
AU - Liu, Kunpeng
AU - Hu, Qilin
AU - Jacygrad, Ewelina
AU - Palmer, William
AU - Michelmore, Richard
AU - Ming, Ray
N1 - The authors would like to thank the Scientific and Technological Research Council of Turkey (project nos. TUBITAK-TOVAG 100 O 113 and TUBITAK-TOVAG 113 O 962), the University of Çukurova Scientific Research Projects Unit (project nos. FDK-2015-3641, FDK-2015-3642, FBA-2015-4521, FBA-2015-4538, FBA-2016-5406, FBA-2016-5442, FBA-2016-5407, FDK-2017-9232, FBA-2017-8250, and FBA-2020-11957), the Ministerio de Ciencia e Innovación of Spain (project nos. AGL2009-09094 and RYC-2011-08653), the University of Granada (project no. PP2016-PIP13), and the Natural Science Foundation of Fujian Province, China (project nos. 2021J01142 and 2018J01606) for providing financial support for this research. The authors wish to thank the Gaziantep Pistachio Research Institute and University of Çukurova in Turkey for providing plant materials.
The authors would like to thank the Scientific and Technological Research Council of Turkey (project nos. TUBITAK-TOVAG 100 O 113 and TUBITAK-TOVAG 113 O 962 ), the University of Çukurova Scientific Research Projects Unit (project nos. FDK-2015-3641 , FDK-2015-3642 , FBA-2015-4521 , FBA-2015-4538 , FBA-2016-5406 , FBA-2016-5442 , FBA-2016-5407 , FDK-2017-9232 , FBA-2017-8250 , and FBA-2020-11957 ), the Ministerio de Ciencia e Innovación of Spain (project nos. AGL2009-09094 and RYC-2011-08653 ), the University of Granada (project no. PP2016-PIP13 ), and the Natural Science Foundation of Fujian Province , China (project nos. 2021J01142 and 2018J01606 ) for providing financial support for this research. The authors wish to thank the Gaziantep Pistachio Research Institute and University of Çukurova in Turkey for providing plant materials.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - domestication
KW - pistachio
KW - Pistacia vera
KW - reference genome
KW - sequencing
KW - sex chromosome
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U2 - 10.1016/j.xplc.2022.100497
DO - 10.1016/j.xplc.2022.100497
M3 - Article
C2 - 36435969
AN - SCOPUS:85147031095
SN - 2590-3462
VL - 4
JO - Plant Communications
JF - Plant Communications
IS - 3
M1 - 100497
ER -