A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in<i>Phoenix dactylifera</i>

Mathew, Lisa S.; Seidel, Michael; George, Binu; Mathew, Sweety; Spannagl, Manuel; Haberer, Georg; Torres, María Fernanda; Al-Dous, Eman K.; Al-Azwani, Eman K.; Diboun, Ilhem; Krueger, Robert R.; Mayer, Klaus; Mohamoud, Yasmin Ali; Suhre, Karsten; Malek, Joel A.

doi:10.1534/g3.115.018341

Cited by 63 publications

(61 citation statements)

References 44 publications

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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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“…For example, there has been a 100-fold decrease in diversity in chickpea compared to C. reticulatum, even though the distribution of the crop is far wider than its wild progenitor [7,27]. Nevertheless, if these population expansions are accompanied by introgression events, they may introduce additional alleles into a defined population, as may occur if a compatible wild relative co-occurs in a new area [106,107]. In crops with significant introgression or hybridization (such as North African dates or citrus) and in outcrossing perennials like most tree crops [108], genetic diversity may remain high or increase in cultivated populations compared to wild relatives.…”

Section: Reduced Genetic Diversity Of Cropsmentioning

confidence: 99%

The Impact of Genetic Changes during Crop Domestication

et al. 2018

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Abstract:Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These "selective sweeps" can allow mildly deleterious...

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“…Cultivar specific SNPs have been identified for eight date palm varieties by sequencing of mitochondrial and plastid genomes but the sequences of plastid and mitochondrial genomes were found to have low level of variation thus suggesting the use of nuclear SNPs for molecular characterization of date palm (Sabir et al, 2014). Recently genomic regions having geographically segregating SNPs were also identified by genotyping 65000 SNPs data from leaves and fruits of seventy female date palm cultivars from all the growing regions (Mathew et al, 2015).…”

Section: Date Palm Diversity Evaluation Based On Single Nucleotide Pomentioning

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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A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations inPhoenix dactylifera

Cited by 63 publications

References 44 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

The Impact of Genetic Changes during Crop Domestication

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

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