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2019 , Vol. 41 >Issue 05: 330 - 339

DOI: https://doi.org/10.1016/j.pld.2018.11.005

Articles

Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species

  • 胡文海 ,
  • 张斯斯 ,
  • 肖宜安 ,
  • 闫小红 ,
  • Srinivasa R. Chaluvadi ,
  • Porter Young ,
  • Kentrez Thompson ,
  • Bochra Amina Bahri ,
  • Bhavesh Gajera ,
  • Subhash Narayanan ,
  • Robert Krueger ,
  • Jeffrey L. Bennetzen
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  • a Department of Genetics, University of Georgia, Athens, GA, USA;
    b Institute of Plant Breeding, Genetics and Genomics(Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA;
    c Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 43 Avenue Charles-Nicolle, Tunis 1082, Tunisia;
    d Anand Agricultural University, Anand, India;
    e USDA-ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, USA
Srinivasa R.Chaluvadi,E-mail addresses:src@uga.edu;Porter Young,E-mail addresses:pfyoung52@gmail.com;Kentrez Thompson,E-mail addresses:kgt526@gmail.com;Bochra Amina Bahri,E-mail addresses:bbahri@uga.edu;Bhavesh Gajera,E-mail addresses:bhavesh.gajera7@gmail.com;Subhash Narayanan,E-mail addresses:subhu53@gmail.com;Robert Krueger,E-mail addresses:robert.krueger@ars.usda.gov

收稿日期: 2018-08-21

  修回日期: 2018-11-12

  网络出版日期: 2019-11-21

基金资助

This research was funded by endowment funds from the University of Georgia Giles Professorship and the Georgia Research Alliance. The authors also thank Jeff Wagner at the Georgia Genomics and Bioinformatics Core for assistance with SSR genotyping.

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Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species

  • Wen-Hai HU ,
  • Si-Si ZHANG ,
  • Yi-An XIAO ,
  • Xiao-Hong YAN ,
  • Srinivasa R. Chaluvadi ,
  • Porter Young ,
  • Kentrez Thompson ,
  • Bochra Amina Bahri ,
  • Bhavesh Gajera ,
  • Subhash Narayanan ,
  • Robert Krueger ,
  • Jeffrey L. Bennetzen
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  • a Department of Genetics, University of Georgia, Athens, GA, USA;
    b Institute of Plant Breeding, Genetics and Genomics(Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA;
    c Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 43 Avenue Charles-Nicolle, Tunis 1082, Tunisia;
    d Anand Agricultural University, Anand, India;
    e USDA-ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, USA

Received date: 2018-08-21

  Revised date: 2018-11-12

  Online published: 2019-11-21

Supported by

This research was funded by endowment funds from the University of Georgia Giles Professorship and the Georgia Research Alliance. The authors also thank Jeff Wagner at the Georgia Genomics and Bioinformatics Core for assistance with SSR genotyping.

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摘要

Date palm (Phoenix dactylifera), one of the most ancient crops, is grown commercially in>30 countries. Using whole plastome assemblies, phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris, Phoenix pusilla and Phoenix acaulis, which are native to the Indian subcontinent, and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia. Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci. Extensive genetic diversity was observed, with many accessions heterozygous for most markers in this clonally propagated crop. The average number of alleles per locus (42.1), expected heterozygosity (0.8), observed heterozygosity (0.47) and fixation indices (FST=0.42) demonstrated substantial genetic diversity and population structure. Iraqi accessions were found to have the richest allelic diversity, and the most private alleles. The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups, one group with predominantly African accessions and another predominantly Asian. Some germplasm, especially from Tunisia and Iraq, deviated from this generalization. Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures, with gene flow between Asian and African groups. Indian and Pakistani date palms were found to be most closely related to North African germplasm.

关键词： Date palm improvement; Germplasm dissemination; Plastome; Simple sequence repeats

本文引用格式

胡文海 , 张斯斯 , 肖宜安 , 闫小红 , Srinivasa R. Chaluvadi , Porter Young , Kentrez Thompson , Bochra Amina Bahri , Bhavesh Gajera , Subhash Narayanan , Robert Krueger , Jeffrey L. Bennetzen . Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species[J]. Plant Diversity, 2019 , 41(05) : 330 -339 . DOI: 10.1016/j.pld.2018.11.005

Abstract

Date palm (Phoenix dactylifera), one of the most ancient crops, is grown commercially in>30 countries. Using whole plastome assemblies, phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris, Phoenix pusilla and Phoenix acaulis, which are native to the Indian subcontinent, and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia. Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci. Extensive genetic diversity was observed, with many accessions heterozygous for most markers in this clonally propagated crop. The average number of alleles per locus (42.1), expected heterozygosity (0.8), observed heterozygosity (0.47) and fixation indices (FST=0.42) demonstrated substantial genetic diversity and population structure. Iraqi accessions were found to have the richest allelic diversity, and the most private alleles. The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups, one group with predominantly African accessions and another predominantly Asian. Some germplasm, especially from Tunisia and Iraq, deviated from this generalization. Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures, with gene flow between Asian and African groups. Indian and Pakistani date palms were found to be most closely related to North African germplasm.

Key words： Date palm improvement; Germplasm dissemination; Plastome; Simple sequence repeats

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