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

This study aimed to develop novel SSR markers in tomato. Several BAC clones along chromosome 3 in tomato were selected based on their content. The criteria was the availability of genes, either directly or indirectly related to stress response (drought, salinity, and heat) in tomato. A total of 20 novel in silico SSR markers were developed and 96 important nearby genes were identified. The identified nearby genes represent different tomato genes involved in plant growth and development and biotic and abiotic stress tolerance. The developed SSR markers were assessed using tomato landraces. A total of 29 determinate and semi-determinate local tomato landraces collected from diverse environments were utilized. A total of 33 alleles with mean of 1.65 alleles per locus were scored, showing 100% polymorphic patterns, with a mean of 0.18 polymorphism information content (PIC) values. The mean of observed and expected heterozygosity were 0.19 and 0.24, respectively. The mean value of the Jaccard similarity index was used for clustering the landraces. The developed microsatellite markers showed potential to assess genetic variability among tomato landraces. The genetic distance information reported in this study can be used by breeders in future genetic improvement of tomato for tolerance against diverse stresses.

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“…Ref. [ 45 ] obtained 100% of polymorphism for 4 SSR primers out of 5 for 39 Jordanian tomato landraces. Ref.…”

Section: Discussionmentioning

confidence: 99%

Development of SSR Markers Linked to Stress Responsive Genes along Tomato Chromosome 3 (Solanum lycopersicum L.)

Brake

Al-Qadumii

Hamasha

et al. 2022

BioTech

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“…Additionally, Yücel et al [49] observed that the fresh root weight, fresh shoot weight, dry root weight, and dry shoot weight decreased by screening nine chickpea genotypes under water limited conditions. Drought stress is significantly affected by the proline concentrations in the leaf tissue for tomato accessions [8]. A highly significant increment in proline content was detected at 40%FC compared to the control treatment (100% FC).…”

Section: Drought Tolerancementioning

confidence: 94%

“…It is known that tomato production is increased considerably worldwide [2][3][4][5]. In Jordan, a wide range of tomato cultivars and accessions were gathered from farmers and stored in the seed bank at the National Agricultural Research Center (NARC) [6][7][8]. In Jordan, the production of tomatoes increases year by year with high ability of export.…”

Section: Introductionmentioning

confidence: 99%

“…SSRs are sections of DNA consisting of (1)(2)(3)(4)(5)(6) or (2)(3)(4)(5)(6)(7) base pair units tandemly repeated throughout the genome [20,[22][23][24], to detect the variation degree [9,21,24] or phylogenetic [25][26][27]. The hypervariability character of SSR markers, based on microsatellite DNA loci, enables this method to be the main major in studying plant population genetics [8,20,[28][29][30][31]. SSRs can be used in gene mapping studies, for example, using 65 SSR primer pairs by Liu et al [32] in the cotton genome mapping [33].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Characterization of Tomato (Solanum lycopersicum L.) Accessions under Drought Stress

et al. 2022

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Exploring the genetic diversity among plant accessions is important for conserving and managing plant genetic resources. In the current study, a collection of forty-six tomato accessions from Jordan were evaluated based on their performance and their morpho-physiological, in addition to molecularly characterizing to detect genetic diversity. Tomato accessions seedlings were exposed to drought stress with 70% field capacity and 40% field capacity under field conditions in Jordan. Drought stress had significantly negatively influenced the dry root weight, fresh root weight, root growth rate, fresh shoot weight, dry shoot weight, and shoot growth rate. Moreover, proline content showed a highly significant increase of 304.2% in response to drought stress. The analysis of twenty morphological characters revealed a wide range of variations among tomato accessions. Accessions were screened with fourteen SSR primers; six primers were informative to explain the genetic diversity. Based on resolving power, primers LEct004 and LEat018 were most significant with all 46 accessions. Interestingly, polymorphic information content (PIC) values ranged from 0.00 (Asr2 marker) to 0.499 (LEct004), which confirms that the SSR markers are highly informative. Our findings provide new insights into using informative molecular markers to elucidate such wide genetic variation discovered in our collections from Afraa and Abeel (the southern part of Jordan). Interestingly, the SSR markers were associated with genes, e.g., LEat018 with ACTIN_RELATED PROTEIN gene, the LEct004 with the HOMEOBOX PROTEIN TRANSCRIPTION FACTORS gene, and Asr2 with ABA/WDS. Moreover, the AUXIN RESPONSE FACTOR8 gene was associated with the LEta014 SSR marker and the LEta020 with the THIOREDOXIN FAMILY TRP26 gene. Therefore, the genetic diversity analysis and functional annotations of the genes associated with SSR information obtained in this study provide valuable information about the most suitable genotype that can be implemented in plant breeding programs and future molecular analysis. Furthermore, evaluating the performance of the collection under different water regimes is essential to produce new tomato varieties coping with drought stress conditions.

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“…SSR molecular marker technology involves tandem repeat sequence consisting of 1–6 nucleotides as repeat units, which has excellent characteristics such as co-dominant inheritance, high polymorphism, good reproducibility, and stable and accurate results. It has emerged as a key molecular marker technology for plant genetic diversity analysis, population structure research, variety identification, and molecular ID construction [ 4 , 5 , 6 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

Bai

Zhang

et al. 2023

Plants

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To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.

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

Cited by 14 publications

References 71 publications

Development of SSR Markers Linked to Stress Responsive Genes along Tomato Chromosome 3 (Solanum lycopersicum L.)

Development of SSR Markers Linked to Stress Responsive Genes along Tomato Chromosome 3 (Solanum lycopersicum L.)

Molecular Characterization of Tomato (Solanum lycopersicum L.) Accessions under Drought Stress

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

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