Application of genomics and molecular genetics in date palm (Phoenix dactylifera L.)

Date palm (Phoenix dactylifera L.) is a diploid with 18 pairs of chromosomes and an estimated genome size of 658 Mb. It is a dioecious perennial monocot, with a long generation time (a period of 4-5 years until first flowering). Date palm is one of the major fruit crops grown in the Gulf countries and particularly in the Sultanate of Oman. Approximately 250 varieties of date palm are recorded throughout the country with evaluation and characterization based on morphological and reproductive traits (e.g. fruit color, fruit shape and fruit weight). Limited molecular characterization work has been undertaken for date palm germplasm in general and Omani date palm germplasm, in particular. The principal focus of this study was to: investigate the genetic diversity of Omani date palm germplasm and compare it with 'exotic' germplasm, to differentiate between female and male plants at the molecular level and to construct an initial genetic map for date palm.\ud \ud Samples were taken from eight parents of the available Omani date palm controlled crosses (Khalas 4, Khalas 13 male, Um-Alsela, Khori male, Bami, Naghal, Bahlani male, and Khasab) with 90 date palms from the BC1 and F1 populations, from 194 Omani date palm accessions (151 female cultivars and 43 male trees), together with samples from Italy (Sanremo and Bordighera), USDA-ARS, France, Iraq, Libya, Sudan and Iran.\ud \ud The F-statistics analysis showed that the genetic variation between female and male accessions based on random markers was only 2.1 %, while within the broader group of Omani female and male accessions the molecular variation was 97%, suggesting that the Omani female and male accessions have little consistent divergence, compared to the large-scale divergence within Omani germplasm, so male palm have been derived from most genetic origins in Oman. Additionally, the Principal Coordinates Analysis (PCA) and bootstrap consensus phenetic tree showed that the Omani accessions were closely related to each other and there was no clear genetic differentiation between female and male cultivars.\ud \ud A high degree of genetic variation was observed between germplasm from Oman, Italy, USDA-ARS, France, Iraq, Libya, Sudan and Iran as measured by Fst (19.7 %). The PCA showed that the Europe-Africa (Italy, France, Libya and Sudan) accessions are distinguished from West-Asia (Oman, Iraq and Iran) accessions and have their own autochthonous origin, a finding which was strongly validated by bootstrap consensus tree test.\ud \ud A medium density genetic map in date palm was constructed using 53 individuals from BC1 and 30 individuals from F1 populations. The BC1 map consisted of 270 markers (28 SSR and 242 SNP) distributed into 29 linkage groups with total genetic length of 1.486.7 cM, while the F1 map consisted of 591 markers (21 SSR and 570 SNP) distributed into 30 linkage groups with total genetic length of 2,385.6 cM. A total of 25 combined linkage groups were possible by combining both BC1 and F1 maps through common markers.\ud \ud A sex-link marker locus was developed and found to predict a high level of discrimination between male and female date palms among multiple varieties distributed across the wide range of cultivation, with an accuracy of 100% in the Omani crosses, 96% in the broad Omani material and 86% in the broadest date palm germplasm. This marker was also mapped in both BC1 and F1 at 42.8 cM and 4.9 cM in linkage groups 18 and 29, respectively and on combined group 19 at 42.8cM