Molecular phylogeny of date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia by DNA fingerprinting

Abstract

Genetic diversity among 13 different cultivars of date palm (Phoenix dactylifera L.) of Saudi Arabia was studied using random amplified polymorphic DNA (RAPD) markers. The screening of 140 RAPD primers allowed selection of 37 primers which revealed polymorphism, and the results were reproducible. All 13 genotypes were distinguishable by their unique banding patterns produced by 37 selected primers. Cluster analysis by the unweighted paired group method of arithmetic mean (UPGMA) showed two main clusters. Cluster A consisted of five cultivars (Shehel, Om-Kobar, Ajwa, Om-Hammam and Bareem) with 0.59-0.89 Nei and Li's coefficient in the similarity matrix. Cluster B consisted of seven cultivars (Rabeeha, Shishi, Nabtet Saif, Sugai, Sukkary Asfar, Sukkary Hamra and Nabtet Sultan) with a 0.66-0.85 Nei and Li's similarity range. Om-Hammam and Bareem were the two most closely related cultivars among the 13 cultivars with the highest value in the similarity matrix for Nei and Li's coefficient (0.89). Ajwa was closely related with Om-Hammam and Bareem with the second highest value in the similarity matrix (0.86). Sukkary Hamra and Nabtet Sultan were also closely related, with the third highest value in the similarity matrix (0.85). The cultivar Barny did not belong to any of the cluster groups. It was 34% genetically similar to the rest of the 12 cultivars. The average similarity among the 13 cultivars was more than 50%. As expected, most of the cultivars have a narrow genetic base. The results of the analysis can be used for the selection of possible parents to generate a mapping population. The variation detected among the closely related genotypes indicates the efficiency of RAPD markers over the morphological and isozyme markers for the identification and construction of genetic linkage maps.

Molecular variability and population structure of a core collection of date palm (Phoenix dactylifera L.) cultivars from Australia and the Middle East

“…There are reported to be 650 cultivars in Iraq (Ibrahim, 2008), 340 in Saudi Arabia (Al-Mssallem, 1996) and 135 in the United Arab Emirates (Ghaleb, 2008). Morphological characterization has identified more than 220 clonally propagated cultivars in Morocco (Toutain, 1972), 140 in Tunisia, 450 in Saudi Arabia, 400 in Sudan, 1,000 in Algeria (Al-Khalifah and Askari 2003), over 300 in Pakistan and more than 200 in the Sultanate of Oman (Al-Yahyai and AlKhanjari, 2008). The introduction of date palms in Australia commenced in the 1890s by cameleers and well-established populations commonly exist around isolated springs and waterholes on outback transportation routes (McColl, 1992;Petherbridge, 1980).…”

“…Restriction fragment length polymorphisms (RFLP) were used for date palm cultivar identification (Corniquel and Mercier, 1994), however the technique was considered laborious and unsuitable for studying large numbers of samples. Other molecular markers including random amplified polymorphic DNA (RAPD) (Sedra et al, 1998;Soliman et al, 2003;Williams et al, 1990), inter simple sequence repeats (ISSR) (Hamza et al, 2013;Hamza et al, 2012), amplified fragment length polymorphism (AFLP) (Al-Khalifah and Askari, 2003;Cao and Chao, 2002;El-assar et al, 2005;Elassar et al, 2003); simple sequence repeat (SSR) (Ahmed and AlQaradawi, 2009;Al-Ruqaishi et al, 2008;Elsafi, 2012;Elshibli and Korpelainen, 2008;Pintaud et al, 2010;Zehdi et al, 2004;Zehdi et al, 2012;Zehdi-Azouzi et al, 2015;Zehdi-Azouzi et al, 2016), chloroplast DNA analysis (Sakka et al, 2013;Rhouma-Chatti et al, 2014) and inter-primer binding site (iPBS) (Al-Najm et al, 2016) were used to assess the genetic diversity of date palm germplasm collected from a variety of countries. Other researchers used a combination of these marker systems to study the genetic diversity of date palm germplasm (Abdulla and Gamal, 2010;Adawy et al, 2005;Hussein et al, 2005;Saker et al, 2006;Saker et al, 2000).…”

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

“…In the KSA there are around 450 cultivars of date palm [25], it is large country and features wide variations in geographical and environmental conditions, there are distinctive types of dates in each region. Previously, Al-Bakr et al and Hussein et al [26,27] divided the local cultivars in the KSA into three main divisions based on the geographic regions in which they were observed.…”

Molecular and morphological analyses of date palm (Phoenix dactylifera L.) subpopulations in southern Tunisia

“…Several markers have been used in date palm studies, random amplification polymorphism DNA (RAPD) (Sedra et al, 1998;Ben Abdallah et al, 2000;Trifi et al, 2000;Al-Khalifa and Askari, 2003), inter simple sequence repeats (ISSR) (Zehdi et al, 2002), random amplified microsatellites polymorphism (RAMPO) (Rhouma, 2008) and amplified fragment length polymorphism (AFLP) (Snoussi et al, 2001;Rhouma et al, 2007). Restriction fragment length polymorphisms (RFLPs) have been evaluated for date palm clone identif ication (Corniquel and Mercier, 1994;Sakka et al, 2003), but the technique is laborious and so not well suited to studies involving a large number of samples.…”