Assessing genetic diversity of wild southeastern North American Vaccinium species using microsatellite markers

Bassil, Nahla V.; Bidani, Amira; Hummer, Kim E.; Rowland, Lisa J.; Olmstead, James W.; Lyrene, P. M.; Richards, Christopher M.

doi:10.1007/s10722-017-0585-2

Cited by 17 publications

(14 citation statements)

References 32 publications

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“…Discussion SSR MARKER. The SSR marker is a powerful, reliable, and useful tool for molecular breeding and for assessing the genetic diversity of plants because of its codominance and ability to reveal a high number of alleles per locus (Bassil et al, 2018;El-Esawi et al, 2016;Liang et al, 2015;Liu et al, 2015;Rodolfi et al, 2018). This is the first study to assess the genetic diversity and relationships among 23 wild Chinese Vitis species/cultivars using this powerful microsatellite technique.…”

Section: Resultsmentioning

confidence: 99%

“…The branchlets have arachnoid tomentum and fall off later; the shape of the mature leaf is oval and the number of mature leaf lobes is three; the lower side prostrate hairs between the veins of young leaves are sparse; and there are no glandular hairs on shoots. Bassil et al (2018) also used SSRs to identify four accessions of previously undescribed hybrid origin during an analysis of the genetic diversity of wild Vaccinium species. Cao et al (2020) reported that five previously unknown grape accessions were matched by SSRs.…”

Section: Resultsmentioning

confidence: 99%

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Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

Li¹,

Fan²,

Zhang³

et al. 2021

J. Amer. Soc. Hort. Sci.

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Chinese wild Vitis is a useful gene source for resistance to biotic and abiotic stresses, although there is little research on its genetic diversity and structure. In this study, nine simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure among 100 Vitis materials. These materials included 77 indigenous accessions representing 23 of 38 wild Vitis species/cultivars in China, 18 V. vinifera cultivars, and the five North American species V. aestivalis, V. girdiana, V. monticola, V. acerifolia, and V. riparia. The SSR loci used in this study for establishing an international database (Vitis International Variety Catalogue) revealed a total of 186 alleles in 100 Vitis accessions. The mean values for the gene diversity (GD) and polymorphism information content (PIC) per locus were 0.91 and 0.90, respectively, which indicates that the discriminatory power of the markers is high. Based on the genetic distance data, the 100 Vitis accessions were divided into five primary clusters by cluster analysis, and five populations by structure analysis; these results indicate these Chinese wild grapes were more genetically close to European grapes than to North American species. In addition, the clustering patterns of most accessions correlated with the geographic distribution. An analysis of molecular variance (AMOVA) revealed that 3.28%, 3.27%, and 93.46% of the variance occurred between populations, between individuals within populations, and between individuals within the entire population, respectively. In addition, we identified three previously undescribed accessions (Wuzhi-1, MZL-5, and MZL-6) by cluster analysis. Our results reveal a high level of genetic diversity and variability in Vitis from China, which will be helpful in the use of genetic resources in future breeding programs. In addition, our study demonstrates that SSR markers are highly suitable for further genetic diversity analyses of Chinese wild grapes.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

Li¹,

Fan²,

Zhang³

et al. 2021

J. Amer. Soc. Hort. Sci.

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“…It has been a regular practice to use molecular markers for diversity analyses in blueberries, including restriction fragment length polymorphism (RFLP) [ 12 ], random amplified polymorphic DNA (RAPD) [ 13 , 14 ], amplified fragment length polymorphism (AFLP) [ 13 ], inter simple sequence repeat (ISSR) [ 15 , 16 ], simple sequence repeat (SSR) [ 10 , 17 , 18 , 19 ], express sequence tag–polymerase chain reaction (EST–PCR) and cleaved amplified polymorphic sequences (CAPSs) derived from EST–PCR markers [ 10 , 19 ]. EST–PCR markers were initially used in highbush blueberries [ 20 ] and have also been found appropriate for genetic association studies on lowbush [ 10 , 21 , 22 ] and rabbiteye blueberries [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Blueberry Genotypes Estimated by Antioxidant Properties and Molecular Markers

Bhatt

Debnath

2021

Antioxidants

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Blueberries (Vaccinium spp.) have gained much attention worldwide because of their potential health benefits and economic importance. Genetic diversity was estimated in blueberry hybrids, wild clones and cultivars by their antioxidant efficacy, total phenolic and flavonoid contents, and express sequence tag–simple sequence repeat (SSR) (EST–SSR), genomic (G)–SSR and express sequence tag–polymerase chain reaction (EST–PCR) markers. Wide diversity existed among the genotypes for antioxidant properties, with the highest variation for DPPH radical scavenging activity (20-fold), followed by the contents of total flavonoids (16-fold) and phenolics (3.8-fold). Although a group of 11 hybrids generated the maximum diversity for antioxidant activity (15-fold), wild clones collected from Quebec, Canada, had the maximum variation for total phenolic (2.8-fold) and flavonoid contents (6.9-fold). Extensive genetic diversity was evident from Shannon’s index (0.34 for EST–SSRs, 0.29 for G–SSR, 0.26 for EST–PCR) and expected heterozygosity (0.23 for EST–SSR, 0.19 for G–SSR, 0.16 for EST–PCR). STRUCTURE analysis separated the genotypes into three groups, which were in agreement with principal coordinate and neighbour-joining analyses. Molecular variance suggested 19% variation among groups and 81% among genotypes within the groups. Clustering based on biochemical data and molecular analysis did not coincide, indicating a random distribution of loci in the blueberry genome, conferring antioxidant properties. However, the stepwise multiple regression analysis (SMRA) revealed that 17 EST–SSR, G–SSR and EST–PCR markers were associated with antioxidant properties. The study is valuable to breeding and germplasm conservation programs.

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“…The use of high-density SNPs for genetic analysis research in blueberry has been limited until recent advancements in next-generation sequencing (NGS) technologies. Several studies have used older generation types of molecular markers in highbush blueberry for population structure analysis: random amplification of polymorphic DNA (RAPD), simple sequence repeats [ 6 , 19 , 23 , 24 ], expressed sequence tag (EST)-PCR markers [ 19 , 25 , 26 ], and retrotransposon-based sequence-specific amplification polymorphism markers [ 27 ]. However, such marker systems have several limitations and are not amenable for high-throughput screening of larger populations.…”

Section: Introductionmentioning

confidence: 99%

Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives

Kulkarni

Vorsa

Natarajan

et al. 2020

IJMS

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Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily V. corymbosum) and southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the V. corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single-nucleotide polymorphisms, which were used for principal component, haplotype, and admixture analysis. Principal component analysis revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.

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Assessing genetic diversity of wild southeastern North American Vaccinium species using microsatellite markers

Cited by 17 publications

References 32 publications

Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

Genetic Diversity of Blueberry Genotypes Estimated by Antioxidant Properties and Molecular Markers

Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives

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