Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing

Authors: MAHAMOUD, Y - Weill Medical College - Cornell; MATHEW, L - Weill Medical College - Cornell; TORRES, M - Weill Medical College - Cornell; YOUNUSKUNJU, S - Weill Medical College - Cornell; Krueger, Robert; SUHRE, K - University Of Cincinnati; MALEK, J - Weill Medical College - Cornell

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2019
Publication Date: 6/18/2019
Citation: Mahamoud, Y.A., Mathew, L.S., Torres, M.F., Younuskunju, S., Krueger, R., Suhre, K., Malek, J. 2019. Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing. BMC Genomics. 20:498. https://doi.org/10.1186/s12864-019-5834-7.
DOI: https://doi.org/10.1186/s12864-019-5834-7

Interpretive Summary: Date palms have been cultivated for millennia in the Middle East and North Africa. The area around Iraq and Iran is considered to be the center of origin and diversity for the date palm. Recent molecular studies have revealed two major subpopulations of cultivars centered around the Eastern range (the Arabian Peninsula, Iraq, and parts of South Asia) and the Western Range (North Africa), which were also thought to be two distinct centers of domestication. In the current study, 200 date palms from across the growing region were analyzed. Single nucleotide polymorphisms (SNPs) were called from the mitochondrial and chloroplastic genomes. A total of four haplotypes were found, including two new haplotypes, one in Iraq/Iran/Oman and the other in Tunisia/Algeria/Egypt. The data suggests that there were three very early centers of cultivation, followed by a fourth that probably derived from Arabia. North African cultivars were closer to P sylvestris than to other cultivars when looked at in the mitochondrial and choroplastic regions.

Technical Abstract: The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. To better understand the origins of date palm cultivation we sequenced and analyzed over 200 mitochondrial and chloroplast genomes from a geographically diverse set of date palms. Here we show that, based on mitochondrial and chloroplast genome-wide genotyping data, the most common cultivated date palms contain 4 haplotypes that appear associated with geographical region of cultivar origin. These data suggest at least 3 and possibly 4 original maternal contributions to the current date palm population and doubles the original number. One new haplotype was found mainly in Tunisia, Algeria and Egypt and the second in Iraq, Iran and Oman. This discovery will further inform understanding of the history and origins of cultivated date palm.