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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Whole mitochondrial and plastid genome SNP analysis of nine date palm cultivars reveals plastid heteroplasmy and close phylogenetic relationships among cultivars
PLoS ONE, Volume 9, No. 4, Article e94158, Year 2014
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Description
Date palm is a very important crop in western Asia and northern Africa, and it is the oldest domesticated fruit tree with archaeological records dating back 5000 years. The huge economic value of this crop has generated considerable interest in breeding programs to enhance production of dates. One of the major limitations of these efforts is the uncertainty regarding the number of date palm cultivars, which are currently based on fruit shape, size, color, and taste. Whole mitochondrial and plastid genome sequences were utilized to examine single nucleotide polymorphisms (SNPs) of date palms to evaluate the efficacy of this approach for molecular characterization of cultivars. Mitochondrial and plastid genomes of nine Saudi Arabian cultivars were sequenced. For each species about 60 million 100 bp paired-end reads were generated from total genomic DNA using the Illumina HiSeq 2000 platform. For each cultivar, sequences were aligned separately to the published date palm plastid and mitochondrial reference genomes, and SNPs were identified. The results identified cultivar-specific SNPs for eight of the nine cultivars. Two previous SNP analyses of mitochondrial and plastid genomes identified substantial intra-cultivar (= intra-varietal) polymorphisms in organellar genomes but these studies did not properly take into account the fact that nearly half of the plastid genome has been integrated into the mitochondrial genome. Filtering all sequencing reads that mapped to both organellar genomes nearly eliminated mitochondrial heteroplasmy but all plastid SNPs remained heteroplasmic. This investigation provides valuable insights into how to deal with interorganellar DNA transfer in performing SNP analyses from total genomic DNA. The results confirm recent suggestions that plastid heteroplasmy is much more common than previously thought. Finally, low levels of sequence variation in plastid and mitochondrial genomes argue for using nuclear SNPs for molecular characterization of date palm cultivars. © 2014 Sabir et al.
Authors & Co-Authors
Sabir, Jamal S.M.
Saudi Arabia, Jeddah
King Abdulaziz University
Arasappan, Dhivya
United States, Austin
The University of Texas at Austin
Bahieldin, Ahmed M.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Cairo
Ain Shams University
Abo-Aba, S. E.M.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Giza
National Research Centre
Bafeel, Sameera Omar
Saudi Arabia, Jeddah
King Abdulaziz University
Zari, Talal A.
Saudi Arabia, Jeddah
King Abdulaziz University
Edris, S. A.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Cairo
Ain Shams University
Shokry, Ahmed M.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Giza
Agricultural Genetic Engineering Research Institute Agerl
Gadalla, Nour O.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Giza
National Research Centre
Ramadan, Ahmed M.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Giza
Agricultural Genetic Engineering Research Institute Agerl
Atef, Ahmed
Saudi Arabia, Jeddah
King Abdulaziz University
Al-Kordy, Magdy A.A.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Giza
National Research Centre
El-Domyati, Fotouh M.
Saudi Arabia, Jeddah
King Abdulaziz University
Egypt, Cairo
Ain Shams University
Jansen, Robert K.
Saudi Arabia, Jeddah
King Abdulaziz University
United States, Austin
The University of Texas at Austin
Statistics
Citations: 14
Authors: 14
Affiliations: 5
Identifiers
Doi:
10.1371/journal.pone.0094158
e-ISSN:
19326203
Research Areas
Cancer
Genetics And Genomics