Genetic Diversity and Population Structure of Native and Introduced Date Palm (Phoenix dactylifera) Germplasm in the United Arab Emirates

Chaluvadi, Srinivasa R.; Khanam, Sakina; Aly, Mohammed A. M.; Bennetzen, Jeffrey L.

doi:10.1007/s12042-014-9135-7

Cited by 35 publications

(21 citation statements)

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“…8 8 occurred once and spread among the cultivars as opposed to a convergent event between East and West subpopulations. With this in mind, the fact that we observe the allele in samples from both eastern and western subpopulations suggests that enough generations have passed for the allele with invertase deleted to spread in the population and to allow for sufficient genomic mixture such that the Sukkary and Naboot Ali are genetically more eastern cultivars while the Deglet Nour is genetically more western (Chaluvadi et al 2014;Mathew et al 2015;Thareja et al 2018). Where exactly the allele arose is difficult to determine.…”

Section: Discussionmentioning

confidence: 94%

“…In light of recent findings of a strong population division between eastern and western date palm cultivars (Chaluvadi et al 2014;Mathew et al 2015;Zehdi-Azouzi et al 2015;Flowers et al 2019) it is important to consider which geographical regions this allele is found in. All dates with high sucrose shared the same allele that contained the same structure of deletion and this suggests that this Date palm invertase deletion Page nr.…”

Section: Discussionmentioning

confidence: 99%

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Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Malek

Mathew

et al. 2019

Preprint

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The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content we analyzed date fruit metabolomics for association with genotype data from 121 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the betafructofuranosidase (invertase) gene in the reference Khalas genome, a low sucrose fruit. High sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains the all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end-point sucrose content in date fruit may be used in selective breeding in the future. Date palm, sucrose, invertaseDate palm invertase deletion

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Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Malek

Mathew

et al. 2019

Preprint

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“…The program's default settings for the admixture model and allele frequencies correlated were implemented. Detection of optimal K was done with STRUCTURE HARVESTER [64] using the delta K (ΔK) statistic, which is the second-order rate of change (InP(D)) across successive K values [63,65]. In this context, STRUCTURE HARVESTER uses ΔK to identify the highest value and henceforth the best K. Results from multiple replicates were summarized using the online pipeline Clumpak program [66] available at http://clumpak.tau.ac.il/.…”

Section: Genetic Structurementioning

confidence: 99%

Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

et al. 2020

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Background: The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations.Results: All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (F st = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R 2 = 0.67 and Uganda, R 2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities. Conclusions: The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.

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“…Genetic diversity in date palm may be the result of dissemination of the germplasm with human migration, human selection and clonal propagation (Chaludvadi et al, 2014). Commercial cultivars of date palm have been disseminated by offshoots from oasis situated in the center of origin and diversity of date palm in lower Mesopotamia and eastern Arabia.…”

Section: Introductionmentioning

confidence: 99%

Diversity Assessment and Cultivar Identification in Date Palm through Molecular Markers- A Review

Faqir

Muhammad²

2017

Turkish JAF Sci.Tech.

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Date palm has a long history of cultivation and a valuable germplasm with little knowledge about its genetic makeup and variation among the most cultivated cultivars. Diversity is the variability of a species. Plants show variation in yield, vegetative traits and morphological properties of fruits and seeds in response to environmental changes. Molecular markers or DNA markers have been in use since past three decades. The DNA profiles give information about the genotype, screen the whole genome and show variation in both the coding and noncoding region and hence give information about polymorphism. Since plastid genes are transferred mostly from the mother line, the identification of maternal lines is possible by the sequencing of plastid genes. Simple sequence repeats (SSRs) can detect length variation with the help of Polymerase Chain Reaction (PCR) and may be used as highly informative genetic markers. Single Nucleotide Polymorphism (SNPs) are the third generation of molecular markers. SNPs are more stable and have high fidelity of inheritance as compared to other marker systems. Molecular markers have been developed but they are not enough for sufficient diversity assessment. Therefore there is a need to increase the number of DNA markers in date palm. Previously, there are several studies to type various commercially important germplasm based on morphological or yield parameters. Morphological and biochemical markers are limited in number and are affected by environmental factors and growth stage of the plant which reduce their reliability in the assessment of diversity and characterization of the germplasm. This necessitates the use of genetic characterization, utilizing DNA markers, gene sequencing or SNP genotyping which can work independent of the plant growth stage and are not affected by environmental factors. A combination of morphological, biochemical and molecular characterization of the date palm cultivars can better assess the level of diversity and relationship among the cultivars.

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Genetic Diversity and Population Structure of Native and Introduced Date Palm (Phoenix dactylifera) Germplasm in the United Arab Emirates

Cited by 35 publications

References 35 publications

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

Diversity Assessment and Cultivar Identification in Date Palm through Molecular Markers- A Review

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