A map of single nucleotide polymorphisms of the date palm (Phoenix dactylifera) based on whole genome sequencing of 62 varieties

Authors: HAZZOURI, K - New York University; FLOWERS, J - New York University; VISSER, J - United Arab Emirates; KHIERALLAH, H - United Arab Emirates; ROSAS, U - Universidad Nacional Autonoma De Mexico; PHAM, G - New York University; MEYER, R - New York University; JOHANSEN, C - New York University; MARKHAND, G - Shah Abdul Latif University; MASMOUDI, K - International Center For Biosaline Agriculture Of Dubai; HAIDER, N - Damascus University; KADRI, N - Damascus University; IDAHGDHOUR, Y - New York University; MALEK, J - Weill Medical College - Cornell; THIRKHILL, D - University Of Arizona; Krueger, Robert; ZAID, A - United Arab Emirates; PURUGGANAN, M - New York University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2015
Publication Date: 11/9/2015
Publication URL: http://handle.nal.usda.gov/10113/61691
Citation: Hazzouri, K.M., Flowers, J.M., Visser, J., Khierallah, H.M., Rosas, U., Pham, G.S., Meyer, R.S., Johansen, C.K., Markhand, G.S., Masmoudi, K., Haider, N., Kadri, N., Idahgdhour, Y., Malek, J., Thirkhill, D., Krueger, R., Zaid, A., Purugganan, M.D. 2015. A map of single nucleotide polymorphisms of the date palm (Phoenix dactylifera) based on whole genome sequencing of 62 varieties. Nature Communications. 6:8824.

Interpretive Summary: Characterization of genome diversity in date palm cultivars and discovery of genes controlling traits of interest will improve the prospect of breeding date palms for yield and other agronomic traits, while providing a means to answer long-standing questions about date palm diversity and the history of domestication. In this report, we present whole genome re-sequencing of 62 varieties of P. dactylifera. The sequenced cultivars originate from locations spanning the traditional range of date palm cultivation from North Africa to the Middle East, as well as newer production areas in Pakistan. We report a comprehensive catalog of ~ 12,000,000 genome-wide polymorphisms in date palms. This SNP dataset provides key information on the population structure and evolutionary history of P. dactylifera, offers new tools for mapping agriculturally important genes in date palms using GWAS mapping, provides markers for use in varietal identification and identifies potential mutations that could provide new opportunities for crop improvement. Our finding that North African and Middle Eastern/South Asian date palm varieties are genetically distinct, as well as the late appearance of date palms in the North African archaeological data, may indicate that date palms were domesticated in the Middle East with the rise of oasis agriculture and subsequently spread westward. This molecular map of date palm polymorphisms provides a foundational resource that will address challenges faced in date palm biotechnology and help develop hypotheses for genotype/phenotype relationships for traits of agronomic importance. We have identified possible selective sweeps within P. dactylifera, multiple candidate mutations that could affect, for example, disease resistance and fruit color (the VIR gene orthologue), leading to the possibility of marker assisted selection and targeted breeding of varieties for specific traits.

Technical Abstract: Date palm is one of the few crop species that thrive in arid environments and are the most significant fruit crop in the Middle East and North Africa, but lacks genomic resources that can accelerate breeding efforts. Here, we present the first comprehensive catalogue of ~12 million common single nucleotide polymorphisms (SNPs) based on whole genome re-sequencing in this fruit tree species. Linkage disequilibrium (LD) decays at ~40 Kb, and the SNP data, indicate a major genetic divide between date palms from North Africa and the Middle East/South Asia. The analyses reveal candidate mutations for trait variation, including a copia retrotransposon insertion in the R2R3 myb-like orthologue of the oil palm Virescens (VIR) gene that appears to underlie fruit color variation in date palms. This date palm SNP map expands the toolkit available to advance breeding for yield in the face of biotic and abiotic pressures.