Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

Ebrahimi, Aziz; Zarei, Abdolkarim; Lawson, Shaneka S.; Woeste, Keith; Smulders, M.J.M.

doi:10.1007/s11295-016-1075-y

Cited by 33 publications

(31 citation statements)

References 29 publications

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“…Our A E numbers were lower than N A in all loci, an indication that not all alleles contributed to diversity. Similar observations were made in previous SSR studies of walnut trees ( Pop et al, 2013 ; Pollegioni et al, 2014 ; Vahdati et al, 2015 ; Ebrahimi et al, 2016 ; Ebrahimi et al, 2017 ). Among the loci evaluated, only WGA9 had PIC values below 0.50, indicating the studied loci are informative and appropriate for genetic diversity studies.…”

Section: Discussionsupporting

confidence: 90%

“…Alleles showing frequencies below 0.05 were considered rare alleles thus, 65% of alleles had frequencies below 5%. Higher rare allele frequencies were also reported in a previous study of walnut trees ( Ebrahimi et al, 2016 ).…”

Section: Discussionsupporting

confidence: 81%

“…Relatively high levels of polymorphism were observed across J. regia accessions in the present study. Mean N A was 6.89 per locus, which was lower than our previous work with the same primer set and similar numbers of accessions (11.5 alleles) ( Ebrahimi et al, 2016 ). The lower allele numbers observed in our experiment could be attributed to the bias toward the specific walnut types used in our study.…”

Section: Discussioncontrasting

confidence: 78%

“…Outcrossing species usually have considerably higher levels of genetic diversity ( Nybom, 2004 ). The “Early Mature” samples in our study were propagated from seeds, as is standard for the vast majority of existing J. regia germplasm in Iran ( Ebrahimi et al, 2016 ). Thus, high levels of rare and private alleles can be attributed to seed propagation and the allogamous nature of J. regia .…”

Section: Discussionmentioning

confidence: 99%

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Evaluation of genetic variability among “Early Mature”Juglans regiausing microsatellite markers and morphological traits

Ebrahimi

Zarei

Fardadonbeh

et al. 2017

PeerJ

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Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. “Early mature” and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among “Early Mature” Persian walnut accessions and provide a comparison with “normal growth” accessions. Six maturation related characteristics were also measured in “Early Mature” samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in “Early Mature” seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of “Early Mature” accessions. The “Early Mature” type had higher number of alleles, number of effective allele, and Shannon index compared to the “Normal Growth” group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. “Early Mature” and “Normal Growth” walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated “Early Mature” and “Normal Growth” samples entirely. The presence of moderate to high genetic diversity in “Early Mature” walnuts and high genetic differentiation with “Normal Growth” walnuts, indicated that “Early Mature” walnuts were more diverse and distinct from “Normal Growth” samples. Moreover, our results showed SSR markers were useful for differentiating between “Early Mature” and “Normal Growth” walnuts. A number of identified loci have potential in breeding programs for identification of “Early Mature” walnuts at the germination phase.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 81%

Section: Discussioncontrasting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

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Evaluation of genetic variability among “Early Mature”Juglans regiausing microsatellite markers and morphological traits

Ebrahimi

Zarei

Fardadonbeh

et al. 2017

PeerJ

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“…Considerable phenotypic and genetic variability can be observed in this wide distribution area, especially in the Eastern countries, where walnuts can still be found in wild fruit forests. Many studies on genetic diversity in walnut have outlined a genetic differentiation between Eastern and Western genotypes (Ebrahimi et al 2016; Marrano et al 2018). Moreover, walnuts from Eastern Europe, Central Asia, and China exhibit higher genetic diversity and a higher number of rare alleles than the genotypes from Western countries (Bernard et al 2018a).…”

Section: Introductionmentioning

confidence: 99%

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Marrano

Britton

Zaini

et al. 2019

Preprint

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27The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements 28 in the characterization of walnut genetic and functional variation. However, it is highly 29 fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to 30 fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly 31 of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-32 read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the 33 previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the 34 full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences 35 at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 36 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of 37 the new protein-coding genes (90%) are full-length, which represents a significant improvement 38 compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new 39 chromosome-level genome on different areas of walnut research. By studying the proteome 40 changes occurring during catkin development, we observed that the virtual proteome obtained 41 from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the 42 identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale 43 genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously 44 undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic 45 regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler 46 v2.0 is a valuable resource to understand and explore walnut biology better.47 48Persian walnut (Juglans regia L.) is among the top three most-consumed nuts in the world, and 50 over the last ten years, its global production increased by 37% (International Nut and Dried Fruit 51

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Morphological to Molecular Markers: Plant Genetic Diversity Studies in Walnut (Juglans regia L.)—A Review

et al. 2023

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Persian walnut populations have tremendous morphological and allelic diversity in their germplasm due to heavy outcrossing and years of seed multiplication. These variations are assessed by morphological, cytological, biochemical and molecular markers. Various researchers have used different tree, foliage, flower, nut, and kernel traits to evaluate morphological/phenotypic diversity. In walnut, morphological indices are considered the first to describe and classify the germplasm, but the environment influences them. In comparison, DNA-based markers can detect genetic diversity at any stage of plant development and have been shown to be a potential tool for assessing variation at the DNA level and deciphering genetic relationships within and between species. Microsatellites are very powerful and informative among DNA-based markers in studying genetic relationships and genetic identity at different levels. They are neutral, highly frequent, uniformly distributed, hypervariable, codominant, highly reproducible, produce many alleles per locus, and require a small amount of DNA for analysis. Current breeding objectives can be achieved by selecting superior genotypes from the germplasm, supplemented by molecular characterization in the selection of parents for each breeding program. Therefore, the use of morphological and molecular markers is recommended for efficient exploration and utilization of germplasm resources and to improve diversity among genetic resources. The published literature on morphological and molecular markers, especially SSRs, is presented in this review to provide current insights into the level of genetic diversity in walnut.

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Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

Cited by 33 publications

References 29 publications

Evaluation of genetic variability among “Early Mature”Juglans regiausing microsatellite markers and morphological traits

Evaluation of genetic variability among “Early Mature”Juglans regiausing microsatellite markers and morphological traits

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Morphological to Molecular Markers: Plant Genetic Diversity Studies in Walnut (Juglans regia L.)—A Review

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