Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

Abstract

Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

Exploring genetic variation among Jordanian Solanum lycopersicon L. landraces and their performance under salt stress using SSR markers

“…SSRs are powerful molecular markers, simple, easy to use, and highly reproducible of polymorphism, and they are used for the study of genetic diversity [25]. SSR markers had been widely used to discover the genetic variation of many crop plants, for example, date palms, citrus, asparagus, mung bean, and Medicago [26][27][28][29][30]. Alvarez et al [22] used 17 microsatellite loci to evaluate genetic diversity in the Lycopersicon genus and found a high level of polymorphism, as well as many alleles, and the cross-pollinating species have higher gene diversity compared to self-pollinating species.…”

Evaluation of diversity in selected populations of Iranian date palm (Phoenix dactylifera L.) using ISSR markers

“…The most differentiated genotypes were observed in the Kerman region, which showed fewer admixtures than the other regions. Generally, the structure showed a shared ancestry between date palm genotypes and early adopted cultivars (Ahmed et al 2021). Elshibli and Korpelainen (2011) observed a high genetic diversity within the Sudan date palm resource groups.…”

“…Date palm or date (Phoenix dactylifera L.) is a diploid perennial species (2n = 2x = 36) of the Arecaceae family. Due to its economic importance (Ahmed et al 2021;Flowers et al 2019), this tree species has signi cant value regarding industrial, commercial, medicinal, and ornamental aspects (El-Far et al 2016; Kurup et al 2014). Date palms are sometimes cultivated through methods of sustainable agriculture in many arid and semiarid regions, such as the Middle East, North Africa, areas of East and South Africa, and some parts of Europe and the USA (Amom and Nongdam 2017; Flowers et al 2019).…”

“…Ampli ed fragment length polymorphic (AFLP) markers were applied to study the genetic diversity of date palm cultivars in Egypt and USA (California) (Adawy et al 2005;Battesti et al 2018;Chao and Krueger 2007). Simple Sequence Repeat markers or microsatellites (SSRs) have evaluated genetic diversity and population structures of date palms in Ethiopia (Ahmed et al 2021). Among the range of molecular markers, Inter Simple Sequence Repeat (ISSR) consists of the ampli cation of DNA fragments located in the gaps between the two microsatellite repeat regions on either side of the fragment (Ghasemi et al 2010).…”

Genetic diversity of sugar palm (Arenga pinnata) derived from nine regions in Indonesia based on SSR markers

“…The reproducibility of SSR markings is also relatively high (Nadeem et al 2018). Genetic diversity studies of several species of palm plants have been successfully conducted using SSR markers, including in oil palm (Arias et al 2015;Bakoume et al 2015;Ithnin et al 2017), Nypa fruticans (Jian et al 2010), date palm (Elmeer et al 2011;Al-Faifi et al 2016;Ahmed et al 2021), and coconut (Mahayu and Taryono 2019).…”