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

doi:10.1016/j.pld.2018.11.005

Plant Diversity ›› 2019, Vol. 41 ›› Issue (05): 330-339.DOI: 10.1016/j.pld.2018.11.005

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

Srinivasa R. Chaluvadi^a, Porter Young^a, Kentrez Thompson^a, Bochra Amina Bahri^b,c, Bhavesh Gajera^d, Subhash Narayanan^d, Robert Krueger^e, Jeffrey L. Bennetzen^a

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

收稿日期:2018-08-21 修回日期:2018-11-12 出版日期:2019-10-25 发布日期:2019-11-21
通讯作者: Jeffrey L.Bennetzen,E-mail addresses:maize@uga.edu.
作者简介: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
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.

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

Srinivasa R. Chaluvadi^a, Porter Young^a, Kentrez Thompson^a, Bochra Amina Bahri^b,c, Bhavesh Gajera^d, Subhash Narayanan^d, Robert Krueger^e, Jeffrey L. Bennetzen^a

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:2018-08-21 Revised:2018-11-12 Online:2019-10-25 Published:2019-11-21
Contact: Jeffrey L.Bennetzen,E-mail addresses:maize@uga.edu.
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.

摘要/Abstract

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 (F_ST=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

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 (F_ST=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

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.

图/表 4

表1 长期遮阴后全光照5天对比利时杜鹃和杜鹃叶片PSII最大光化学效率(Fv/Fm)、初始斜率(α)、最大光合电子传递速率(Jmax)和饱和光强(PARsat)的影响(平均值±标准误差, n = 5)

Table 1 Effects of natural sunlight exposure after long-term shading on the maximal quantum efficiency of PSII (Fv/Fm), initial slope (α), maximum photosynthetic electron flow (Jmax) and maximum irradiance (PARsat) in Rhododendron hybrida and R. simsii leaves (mean ± SE, n = 5)

参数 Parameter	比利时杜鹃 R. hybrida		杜鹃 R. simsii
参数 Parameter	遮阴 Shade	全光照 Sun	遮阴 Shade	全光照 Sun
F_v/F_m	0.793 ± 0.004^a	0.494 ± 0.029^b	0.817 ± 0.002^a	0.780 ± 0.002^b
α	0.392 ± 0.013^a	0.238 ± 0.018^b	0.333 ± 0.003^a	0.327 ± 0.007^a
J_max (μmol·m^-2·s^-1)	64.9 ± 6.8^a	37.8 ± 5.3^b	63.1 ± 8.3^a	74.9 ± 4.4^a
PAR_sat (μmol·m^-2·s^-1)	808.8 ± 37.0^a	818.4 ± 21.2^a	849.4 ± 24.3^b	943.2 ± 17.2^a

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

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

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