Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species
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...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2019-10-01
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| Series: | Plant Diversity |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468265918301355 |
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| author | Srinivasa R. Chaluvadi Porter Young Kentrez Thompson Bochra Amina Bahri Bhavesh Gajera Subhash Narayanan Robert Krueger Jeffrey L. Bennetzen |
| author_facet | Srinivasa R. Chaluvadi Porter Young Kentrez Thompson Bochra Amina Bahri Bhavesh Gajera Subhash Narayanan Robert Krueger Jeffrey L. Bennetzen |
| author_sort | Srinivasa R. Chaluvadi |
| collection | DOAJ |
| description | 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. Keywords: Date palm improvement, Germplasm dissemination, Plastome, Simple sequence repeats |
| first_indexed | 2024-12-13T23:10:07Z |
| format | Article |
| id | doaj.art-01882cffd1ff406a80549e4d525bfb67 |
| institution | Directory Open Access Journal |
| issn | 2468-2659 |
| language | English |
| last_indexed | 2024-12-13T23:10:07Z |
| publishDate | 2019-10-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Plant Diversity |
| spelling | doaj.art-01882cffd1ff406a80549e4d525bfb672022-12-21T23:28:08ZengKeAi Communications Co., Ltd.Plant Diversity2468-26592019-10-01415330339Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related speciesSrinivasa R. Chaluvadi0Porter Young1Kentrez Thompson2Bochra Amina Bahri3Bhavesh Gajera4Subhash Narayanan5Robert Krueger6Jeffrey L. Bennetzen7Department of Genetics, University of Georgia, Athens, GA, USADepartment of Genetics, University of Georgia, Athens, GA, USADepartment of Genetics, University of Georgia, Athens, GA, USAInstitute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 43 Avenue Charles-Nicolle, Tunis 1082, TunisiaAnand Agricultural University, Anand, IndiaAnand Agricultural University, Anand, IndiaUSDA-ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, USADepartment of Genetics, University of Georgia, Athens, GA, USA; Corresponding author.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. Keywords: Date palm improvement, Germplasm dissemination, Plastome, Simple sequence repeatshttp://www.sciencedirect.com/science/article/pii/S2468265918301355 |
| spellingShingle | 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 Plant Diversity |
| title | Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species |
| title_full | Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species |
| title_fullStr | Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species |
| title_full_unstemmed | Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species |
| title_short | Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species |
| title_sort | phoenix phylogeny and analysis of genetic variation in a diverse collection of date palm phoenix dactylifera and related species |
| url | http://www.sciencedirect.com/science/article/pii/S2468265918301355 |
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