TY - JOUR
T1 - Cross-species hybridization and the origin of North African date palms
AU - Flowers, Jonathan M.
AU - Hazzouri, Khaled M.
AU - Gros-Balthazard, Muriel
AU - Mo, Ziyi
AU - Koutroumpa, Konstantina
AU - Perrakis, Andreas
AU - Ferrand, Sylvie
AU - Khierallah, Hussam S.M.
AU - Fuller, Dorian Q.
AU - Aberlenc, Frederique
AU - Fournaraki, Christini
AU - Purugganan, Michael D.
N1 - Funding Information:
ACKNOWLEDGMENTS. We thank Marc Arnoux and Nizar Drou in the New York University Abu Dhabi (NYUAD) Center for Genomics and Systems Biology for technical assistance. We thank Robert R. Krueger (US Department of Agriculture), Claudio Littardi [Centro Studi e Ricerche per le Palme - Sanremo (CSRP), Italy], José Plumed (Botanical Garden of Valencia, Spain), Emmanuel Spick (Jardin des Plantes de Montpellier, France), William J. Baker (Kew Gardens, United Kingdom), Syed Summar Abbas Naqvi (Institute of Horticultural Sciences, Pakistan), Joel A. Malek (Weill Cornell Medical College in Qatar), Hendrik J. Visser [Date Palm Research and Development Unit (DPRU), United Arab Emirates University (UAEU)], Abdelouahhab Zaid (DPRU, UAEU) Khaled Masmoudi (International Center for Biosaline Agriculture), Nadia Haider (Atomic Energy Commission of Syria), Nabila El Kadri (Technical Center of Dates, Ministry of Agriculture, Kebili, Tunisia), Youssef Idaghdour (NYUAD), Deborah Thirkhill (Arizona State University Date Palm Collection), and Ghulam S. Markhand (Date Palm Research Institute, Abdul Latif University, Pakistan) for providing samples. We also thank Jeffrey Ross-Ibarra and two anonymous reviewers who helped improve the manuscript. We thank members of the M.D.P. laboratory and Jessica Molina Abdala for helpful discussions. This work was made possible by Jean-Christophe Pin-taud. This research was funded in part by an NYUAD Institute grant, as well as by grants from the US National Science Foundation Plant Genome Research Program and the Zegar Family Foundation (to M.D.P.).
Funding Information:
We thank Marc Arnoux and Nizar Drou in the New York University Abu Dhabi (NYUAD) Center for Genomics and Systems Biology for technical assistance. We thank Robert R. Krueger (US Department of Agriculture), Claudio Littardi [Centro Studi e Ricerche per le Palme - Sanremo (CSRP), Italy], José Plumed (Botanical Garden of Valencia, Spain), Emmanuel Spick (Jardin des Plantes de Montpellier, France), William J. Baker (Kew Gardens, United Kingdom), Syed Summar Abbas Naqvi (Institute of Horticultural Sciences, Pakistan), Joel A. Malek (Weill Cornell Medical College in Qatar), Hendrik J. Visser [Date Palm Research and Development Unit (DPRU), United Arab Emirates University (UAEU)], Abdelouahhab Zaid (DPRU, UAEU) Khaled Masmoudi (International Center for Biosaline Agriculture), Nadia Haider (Atomic Energy Commission of Syria), Nabila El Kadri (Technical Center of Dates, Ministry of Agriculture, Kebili, Tunisia), Youssef Idaghdour (NYUAD), Deborah Thirkhill (Arizona State University Date Palm Collection), and Ghulam S. Markhand (Date Palm Research Institute, Abdul Latif University, Pakistan) for providing samples. We also thank Jeffrey Ross-Ibarra and two anonymous reviewers who helped improve the manuscript. We thank members of the M.D.P. laboratory and Jessica Molina Abdala for helpful discussions. This work was made possible by Jean-Christophe Pintaud. This research was funded in part by an NYUAD Institute grant, as well as by grants from the US National Science Foundation Plant Genome Research Program and the Zegar Family Foundation (to M.D.P.).
Publisher Copyright:
© 2019 National Academy of Sciences. All Right Reserved.
PY - 2019/1/29
Y1 - 2019/1/29
N2 - Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions that were domesticated ∼7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of P. dactylifera and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives. Our results indicate that the North African population has mixed ancestry with components from Middle Eastern P. dactylifera and Phoenix theophrasti, a wild relative endemic to the Eastern Mediterranean. Introgressive hybridization is supported by tests of admixture, reduced subdivision between North African date palm and P. theophrasti, sharing of haplotypes in introgressed regions, and a population model that incorporates gene flow between these populations. Analysis of ancestry proportions indicates that as much as 18% of the genome of North African varieties can be traced to P. theophrasti and a large percentage of loci in this population are segregating for single-nucleotide polymorphisms (SNPs) that are fixed in P. theophrasti and absent from date palm in the Middle East. We present a survey of Phoenix remains in the archaeobotanical record which supports a late arrival of date palm to North Africa. Our results suggest that hybridization with P. theophrasti was of central importance in the diversification history of the cultivated date palm.
AB - Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions that were domesticated ∼7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of P. dactylifera and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives. Our results indicate that the North African population has mixed ancestry with components from Middle Eastern P. dactylifera and Phoenix theophrasti, a wild relative endemic to the Eastern Mediterranean. Introgressive hybridization is supported by tests of admixture, reduced subdivision between North African date palm and P. theophrasti, sharing of haplotypes in introgressed regions, and a population model that incorporates gene flow between these populations. Analysis of ancestry proportions indicates that as much as 18% of the genome of North African varieties can be traced to P. theophrasti and a large percentage of loci in this population are segregating for single-nucleotide polymorphisms (SNPs) that are fixed in P. theophrasti and absent from date palm in the Middle East. We present a survey of Phoenix remains in the archaeobotanical record which supports a late arrival of date palm to North Africa. Our results suggest that hybridization with P. theophrasti was of central importance in the diversification history of the cultivated date palm.
KW - Archaeobotany
KW - Crop wild relative
KW - Domestication
KW - Introgression
KW - Range expansion
UR - http://www.scopus.com/inward/record.url?scp=85060793076&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85060793076&partnerID=8YFLogxK
U2 - 10.1073/pnas.1817453116
DO - 10.1073/pnas.1817453116
M3 - Article
C2 - 30642962
AN - SCOPUS:85060793076
SN - 0027-8424
VL - 116
SP - 1651
EP - 1658
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 5
ER -