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Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies.

ABSTRACT: Germination of 2000-year-old seeds of Phoenix dactylifera from Judean desert archaeological sites provides a unique opportunity to study the Judean date palm, described in antiquity for the quality, size, and medicinal properties of its fruit, but lost for centuries. Microsatellite genotyping of germinated seeds indicates that exchanges of genetic material occurred between the Middle East (eastern) and North Africa (western) date palm gene pools, with older seeds exhibiting a more eastern nuclear genome on a gradient from east to west of genetic contributions. Ancient seeds were significantly longer and wider than modern varieties, supporting historical records of the large size of the Judean date. These findings, in accord with the region's location between east and west date palm gene pools, suggest that sophisticated agricultural practices may have contributed to the Judean date's historical reputation. Given its exceptional storage potentialities, the date palm is a remarkable model for seed longevity research.

SUBMITTER: Sallon S

PROVIDER: S-EPMC7002127 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies.

Sallon Sarah S Cherif Emira E Chabrillange Nathalie N Solowey Elaine E Gros-Balthazard Muriel M Ivorra Sarah S Terral Jean-Frédéric JF Egli Markus M Aberlenc Frédérique F

Science advances 20200205 6

Germination of 2000-year-old seeds of <i>Phoenix dactylifera</i> from Judean desert archaeological sites provides a unique opportunity to study the Judean date palm, described in antiquity for the quality, size, and medicinal properties of its fruit, but lost for centuries. Microsatellite genotyping of germinated seeds indicates that exchanges of genetic material occurred between the Middle East (eastern) and North Africa (western) date palm gene pools, with older seeds exhibiting a more eastern ...[more]

PMID: 32076636

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Project description:Investigating crop origins is a priority to understand the evolution of plants under domestication, develop strategies for conservation and valorization of agrobiodiversity and acquire fundamental knowledge for cultivar improvement. The date palm (Phoenix dactylifera L.) belongs to the genus Phoenix, which comprises 14 species morphologically very close, sometimes hardly distinguishable. It has been cultivated for millennia in the Middle East and in North Africa and constitutes the keystone of oasis agriculture. Yet, its origins remain poorly understood as no wild populations are identified. Uncultivated populations have been described but they might represent feral, i.e. formerly cultivated, abandoned forms rather than truly wild populations. In this context, this study based on morphometrics applied to 1625 Phoenix seeds aims to (1) differentiate Phoenix species and (2) depict the domestication syndrome observed in cultivated date palm seeds using other Phoenix species as a "wild" reference. This will help discriminate truly wild from feral forms, thus providing new insights into the evolutionary history of this species. Seed size was evaluated using four parameters: length, width, thickness and dorsal view surface. Seed shape was quantified using outline analyses based on the Elliptic Fourier Transform method. The size and shape of seeds allowed an accurate differentiation of Phoenix species. The cultivated date palm shows distinctive size and shape features, compared to other Phoenix species: seeds are longer and elongated. This morphological shift may be interpreted as a domestication syndrome, resulting from the long-term history of cultivation, selection and human-mediated dispersion. Based on seed attributes, some uncultivated date palms from Oman may be identified as wild. This opens new prospects regarding the possible existence and characterization of relict wild populations and consequently for the understanding of the date palm origins. Finally, we here describe a pipeline for the identification of the domestication syndrome in seeds that could be used in other crops.

Project description:Objective:Heavy metals are major elements polluting our universe. The inhalation, ingestion or even contacting human body with these elements results in huge health problems. The most common pollutant in our surrounding is mercury. Therefore, the present study aimed to elucidating the protective ability of hot water extracts of dandelion (DA), coriander (CO), date palm seeds (DS), probiotic supernatant (PS) and their combined mixture against mercury-induced neurotoxicity and altered testosterone levels in male rats. Methods:Fifty six male rats were randomly allotted into seven groups (n?=?8?rats/group). Group1 (negative control; NC) animals were fed on the basal diet only, group2 (positive controls; PC) animals were fed on the basal diet and given an aqueous solution of mercuric chloride (25?ppm mercuric) in drinking water. Animals of the antioxidant-treated groups (3-7) were fed on the basal diet and given an aqueous solution of mercuric chloride (25?ppm mercuric) in drinking water together with the herbal antioxidant extracts and probiotics (25?ml/rat/day) throughout the experimental period. Where, group3 (Hg/CO) given coriander extract, group4 (Hg/DA) given dandelion extract, group5 (Hg/DS) given date palm seeds extract, group6 (Hg/PS) given probiotic supernatant, and group7 (Hg/Mix) given mixture of equal quantities of probiotic supernatant together with the three herbal extracts. The treatment lasted for 6 weeks, animals were sacrificed and blood samples were collected. Blood testosterone, enzyme activity and histopathological sections were performed. Results:The obtained data exhibited that mercury intoxication revealed increases of lactic dehydrogenase and decreases of glutathione-s-transferase and testosterone. Light microscopic investigations of the brain cortex and cerebellum were suggestive of multiple foci of inflammation, cellular infiltration, gliosis and degeneration. Moreover, decreased glial fibrillary acidic protein (GFAP)-immunoreactivity and potential astrocyte toxicity both reflected impaired neuro-protective function of astrocytes necessary for maintaining the brain structure and function. Conclusion:Administration of the herbal extracts and their mixture with probiotics enhance the body defense and contain protective factor against mercury neurotoxicity and for maintaining normal testosterone levels in male rats. Also, treatment restored the normal control levels of biochemical attributes and histological architecture.

Project description:Background: Date palm (Phoenix dactylifera L.) is a cultivated woody plant with agricultural and economic importance in many countries around the world. With the advantages of next generation sequencing technologies, genome sequences for many date palm cultivars have been released recently. Short sequence repeat (SSR) and single nucleotide polymorphism (SNP) can be identified from these genomic data, and have been proven to be very useful biomarkers in plant genome analysis and breeding. Results: Here, we first improved the date palm genome assembly using 130X of HiSeq data generated in our lab. Then 246,445 SSRs (214,901 SSRs and 31,544 compound SSRs) were annotated in this genome assembly; among the SSRs, mononucleotide SSRs (58.92%) were the most abundant, followed by di- (29.92%), tri- (8.14%), tetra- (2.47%), penta- (0.36%), and hexa-nucleotide SSRs (0.19%). The high-quality PCR primer pairs were designed for most (174,497; 70.81% out of total) SSRs. We also annotated 6,375,806 SNPs with raw read depth≥3 in 90% cultivars. To further reduce false positive SNPs, we only kept 5,572,650 (87.40% out of total) SNPs with at least 20% cultivars support for downstream analyses. The high-quality PCR primer pairs were also obtained for 4,177,778 (65.53%) SNPs. We reconstructed the phylogenetic relationships among the 62 cultivars using these variants and found that they can be divided into three clusters, namely North Africa, Egypt - Sudan, and Middle East - South Asian, with Egypt - Sudan being the admixture of North Africa and Middle East - South Asian cultivars; we further confirmed these clusters using principal component analysis. Moreover, 34,346 SSRs and 4,177,778 SNPs with PCR primers were assigned to shared cultivars for cultivar classification and diversity analysis. All these SSRs, SNPs and their classification are available in our database, and can be used for cultivar identification, comparison, and molecular breeding. Conclusion:DRDB is a comprehensive genomic resource database of date palm. It can serve as a bioinformatics platform for date palm genomics, genetics, and molecular breeding. DRDB is freely available at http://drdb.big.ac.cn/home.

Project description:BackgroundPlants are considered the primary source of many principal bioactive compounds that have been utilized in a wide range of applications including the pharmaceutical and biotechnological industries. Therefore, there is an imperative need to modulate the production of natural bioactive components. The present study aimed to determine the importance of dried and pulverized date palm seeds (DPS) as a natural elicitor for the synthesis of secondary metabolites in Lotus arabicus L.ResultsThe presence of various antioxidant compounds, simple sugars, amino acids, fatty acids and reasonable mineral contents was distinct in the phytochemical characterization of DPS. The major components detected in DPS analysis were the 5-(hydroxymethyl) furfural and 2,3-dihydro-3,5-dihydroxy-6-methyl-4H-pyranone. The induced callus of L. arabicus (seven weeks old) was supplemented with DPS at different concentrations (0, 2, 4, 8 and 10 g/l) in culture media. Treatment with 8 g/l DPS induced the highest antioxidant capacity, ascorbic acid content and secondary metabolites (total phenolics and flavonoids) in the produced callus. Stress biomarkers (hydrogen peroxide and malondialdehyde) were found in the control ranges except at 10 g/l DPS. The expression patterns of key genes involoved in secondary metabolism modulation, such as phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS) and deoxyxylulose phosphate reductoisomerase (DXR), were triggered after DPS treatments. Moreover, the quantitative profiling of phenolic and flavonoid compounds showed that supplementation with DPS, especially at 8 g/l, led to pronounced increases in most of the measured compounds.ConclusionThe marked upregulation of eliciting-responsive genes and overproduction of secondary metabolites provide molecular-based evidence for intensifying the principal pathways of phenylpropanoid, flavonoid and terpenoid biosynthesis. Overall, the present in vitro study highlights the stimulating capacity of DPS utilization to improve the bioactive components of L. arabicus at the physiological and molecular levels, enhancing its potential as a medicinal herb.

Dataset Information

Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies.

Publications

Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies.

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