A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms

Abstract

BackgroundThe date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified.ResultsHere we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome.ConclusionsBased on a modified gentoyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.

Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes

“…As expected, such comparisons have revealed larger differences in species with heteromorphic sex chromosomes (see Supplementary Table S1, and [7]). However, to determine the actual size of the non-recombining SDR of the chromosome of the heterogametic sex (Y or W), it is necessary to identify markers on the sex chromosome, and to use them to build genetic maps that estimate the region that does not recombine in one sex, e.g., [18,19] (Supplementary Table S1). Alternatively, sex-linked markers may be used to identify, and then to sequence, bacterial artificial chromosomes (BACs) that contain long sections of the SDR [20], with subsequent assembly and potential chromosome-walking [21,22].…”

Genetic Diversity and the Impact of Geographical Location on the Relationships Between Phoenix dactylifera L. Germplasms Grown in Saudi Arabia

“…Another draft included the date palm chloroplast genome [23]; the project was a joint venture between the Beijing Genomic Centre in China and the King AbdulAziz City for Science and Technology in Riyadh, Saudi Arabia. More recently, the first complete date palm genomic map [24] was constructed based on sequences taken from three males and three females from both Asia and Africa. This genetic map was combined with the genomic data from three commercially important palms-date, oil and coconut-and the application of this genomic information is expected to improved production and save these commercial cultivars.…”

Pedigree-based linkage map in two genetic groups of oil palm

“…To overcome these limitations, consensus genetic maps are obtained by integrating multiple unrelated genetic maps sharing common markers. Such consensus genetic maps have been constructed using JoinMap (Millan et al 2010), CarthaGène (Billotte et al 2010;Duarte et al 2014;Mathew et al 2014), or MergeMap (Wu et al 2011. Recently, the R package LPmerge has been also used to produce a genetic consensus map .…”