Genetic diversity and phylogenetic relationships among citrus germplasm in the Western Caucasus assessed with SSR and organelle DNA markers

Самарина, Л. С.; Kulyan, R. V.; Koninskaya, N. G.; Gorshkov, V. M.; Ryndin, Alexey; Hanke, Magda-Viola; Flachowsky, Henryk; Reim, Stefanie

doi:10.1016/j.scienta.2021.110355

Cited by 10 publications

(6 citation statements)

References 47 publications

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“…We suggested that InDel markers would be efficient to reveal the detailed genetic structure of the satsuma collection and identify hybrids because these markers were designed for satsuma species [10]. However, a low level of genetic admixtures was observed in satsuma clusters in particular, which is consistent with our previous study conducted with SSR markers [34]. Another study reported that InDel markers showed a low intraspecific diversity in several citrus species [35].…”

Section: Genetic Structure Of the Citrus Germplasm Collection Based O...supporting

confidence: 85%

“…Another study reported that InDel markers showed a low intraspecific diversity in several citrus species [35]. In general, a discrepancy between the morphological diversity and genetic homogeneity of cultivars within a species is common [34][35][36][37] since most varieties of secondary species originated from a clonal breeding and the fixation of somatic mutations [19,38,39]. Apomixis in mandarins, oranges, and lemons is also a possible reason for the low intraspecific genetic diversity.…”

Section: Genetic Structure Of the Citrus Germplasm Collection Based O...mentioning

confidence: 99%

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InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

Kulyan

Самарина

Shkhalakhova

et al. 2023

IJMS

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Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification of valuable accessions. In this study, the efficiency of 36 SCoT markers and 60 InDel markers were evaluated as part of the broad citrus collection of the Western Caucasus. The interspecific and intraspecific genetic diversity and genetic structures were analyzed for 172 accessions, including 31 species and sets of the locally derived cultivars. Single markers, such as SCoT18 (0.84), SCoT20 (0.93), SCoT23 (0.87), SCoT31 (0.88), SCoT36 (0.87) и LG 1-4 (0.94), LG 4-3 (0.86), LG 7-11 (0.98), and LG 8-10 (0.83), showed a high discriminating power, indicating the good applicability of these markers to assess intraspecific diversity of the genus Citrus. Overall, SCoT markers showed a higher level of polymorphism than InDel markers. According to analysis of population structure, SCoT and InDel markers showed K = 9 and K = 5 genetic clusters, respectively. The lowest levels of genetic admixtures and diversity were observed among the locally derived satsumas and lemons. The highest level of genetic admixtures was observed in the lime group. Phylogenetic relationships indicated a high level of interspecific genetic diversity but a low level of intraspecific diversity in locally derived satsumas and lemons. The results provide new insight into the origin of citrus germplasms and their distribution in colder regions. Furthermore, they are important for implementing conservation measures, controlling genetic erosion, developing breeding strategies, and improving breeding efficiency.

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Section: Genetic Structure Of the Citrus Germplasm Collection Based O...supporting

confidence: 85%

Section: Genetic Structure Of the Citrus Germplasm Collection Based O...mentioning

confidence: 99%

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

Kulyan

Самарина

Shkhalakhova

et al. 2023

IJMS

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“…Whole genome sequencing has been performed to assess genetic relationships and evolutionary history in citrus [ 4 , 56 ]. Phylogenetic analyses have also been performed using chloroplast sequence information [ 57 , 58 ].…”

Section: Resultsmentioning

confidence: 99%

Conserving Citrus Diversity: From Vavilov’s Early Explorations to Genebanks around the World

Volk¹,

Gmitter

Krueger

2023

Plants

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Citrus is among the most economically important fruit crops. Its vast species diversity and global production was observed by N.I. Vavilov during his international plant explorations from the early to mid-1900s. Currently, ex situ citrus collections located around the world conserve and protect citrus genetic resources, as revealed in a survey conducted in 2021. Responses were received from 43 collections in 27 countries, of which 35 provided data regarding collection composition, management practices, and security, as well as other information. The six largest citrus collections have between 1000 and 1735 accessions. The largest accession holdings are mandarins and sweet oranges, although all citrus fruit types are maintained: mandarin, sweet orange, lemon, pummelo, grapefruit, hybrids, lime, sour orange, citron, kumquat, papeda, finger lime, and crop wild relatives. Diseases pose significant threats to collections, though some collections are maintained in a clean-plant state as a result of intensive sanitation efforts. National and regional quarantine regulations often limit the export and import of citrus plants or propagative materials, thus limiting the availability of materials at an international level. Resources, both financial and human, are necessary to ensure the long-term safety and security of citrus collections on a global scale. Future efforts to develop citrus genebanking communities will provide opportunities for improved conservation, as well as collaborations and training.

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“…The length of the burn-in period was set at 10,000, and the number of Markov chain Monte Carlo (MCMC) repeats after burn-in was set at 100,000 to estimate individual admixture proportions ( Q ). Evanno’s method [ 49 ] and the online software Structure Harvester [ 50 ] were used to determine the optimal grouping K values [ 51 , 52 , 53 ]. Principal coordinate analysis (PCoA) was performed using GenAlex 6.41 software [ 54 , 55 ].…”

Section: Methodsmentioning

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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Genetic diversity and phylogenetic relationships among citrus germplasm in the Western Caucasus assessed with SSR and organelle DNA markers

Cited by 10 publications

References 47 publications

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus

Conserving Citrus Diversity: From Vavilov’s Early Explorations to Genebanks around the World

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

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