Abstract
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.
Highlights
Date palm (Phoenix dactylifera L., Arecaceae) is the primary crop in many countries in western Asia and northern Africa [1]
The four questions of our investigation are: (1) Is there heteroplasmy in the mitochondrial and plastid genomes?; (2) What is the effect of plastid DNA transfer to the mitochondrion on organellar single nucleotide polymorphisms (SNPs) analyses? (3) Are organellar SNPs useful for identification of date palm cultivars?; and (4) What are the phylogenetic relationships among cultivars?
The number of reads mapped to the mitochondrial genome varied from 854,270–1,495,892 depending on the cultivar, which included 1.41–2.07% of the total reads (Table 2)
Summary
Date palm (Phoenix dactylifera L., Arecaceae) is the primary crop in many countries in western Asia and northern Africa [1]. There have been numerous attempts to use molecular markers to characterize date palm biodiversity but most of these studies have relied on fragment data, such as RAPD, ISSR, SSR, and AFLP approaches, e.g., [10,11,12,13,14,15,16,17,18]. These methods have some merit, they are not as reliable in characterizing genetic diversity and identifying cultivars as more recent genomic approaches [19]. The four questions of our investigation are: (1) Is there heteroplasmy in the mitochondrial and plastid genomes?; (2) What is the effect of plastid DNA transfer to the mitochondrion on organellar SNP analyses? (3) Are organellar SNPs useful for identification of date palm cultivars?; and (4) What are the phylogenetic relationships among cultivars?
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