Clonal diversity and genetic differentiation revealed by SSR markers in wild<i>Vaccinium macrocarpon</i>and<i>Vaccinium oxycoccos</i>

Zalapa, Juan; Bougie, Tierney; Schlautman, Brandon; Wiesman, Eric; Guzman, Aidee; Fajardo, Diego; Steffan, Shawn A.; Smith, Tyler

doi:10.1111/aab.12173

Cited by 21 publications

(29 citation statements)

References 41 publications

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“…Specifically, alteration of anthocyanin glycosylation has been accomplished in cranberry through interspecific hybridization to increase glucose-conjugated anthocyanins (Vorsa and Polashock 2005). Additionally, a number of genetic diversity studies of V. oxycoccos and V. macrocarpon using SCARs, SSRs, and amplified fragment length polymorphisms (AFLPs) have been conducted in order to describe available wild germplasm and to increase understanding of the evolutionary relationships between the two species and their various ploidy levels (Polashock and Vorsa 2002;Fajardo et al 2012;Zalapa et al 2014;Schlautman et al 2015). Moreover, 12 SSRs developed for cranberry genetic diversity assessment were all positioned and evenly distributed among nine linkage groups of the current map, which confirms the validity of recent V. macrocarpon and V. oxycoccos genetic diversity studies (Fajardo et al 2012;Zalapa et al 2014) (Fig.…”

Section: Comparative Genomics In Vacciniummentioning

confidence: 99%

Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

et al. 2015

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Since its domestication 200 years ago, breeding of the American cranberry (Vaccinium macrocarpon) has relied on phenotypic selection because applicable resources for molecular improvement strategies such as marker-assisted selection (MAS) remain limited. To enable MAS in cranberry, the first high-density SSR linkage map with 541 markers representing all 12 cranberry chromosomes was constructed for the CNJ02-1 progeny from a cross of elite cultivars, CNJ97-105-4 and NJ98-23. The population was phenotyped for a 3-year period for total yield (TY), mean fruit weight (MFW), and biennial bearing index (BBI), and data were analyzed using mixed models and best linear unbiased predictors (BLUPs). Significant differences between genotypes were observed for all traits. Quantitative trait loci (QTL) analyses using BLUPs identified four MFW QTL on three linkage groups (LGs), three TY QTL on three LGs, and one BBI QTL which colocalized with a TY QTL. Local BLAST of a cranberry nuclear genome assembly identified homologous sequences for the mapped SSRs which were then anchored to 12 pseudo-chromosomes using the linkage map information. Analyses comparing coding regions (CDS) anchored in the cranberry linkage map with grape, kiwifruit, and tomato genomes were Electronic supplementary material The online version of this article (

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Section: Comparative Genomics In Vacciniummentioning

confidence: 99%

Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

et al. 2015

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“…Although there are some reports on diversity analysis in cranberry using RAPD (Novy et al 1994;Debnath 2005Debnath , 2007a, sequence-characterized amplified regions (Polashock and Vorsa 2002), AFLP (Polaschock and Vorsa 1996) and SSRs (Zhu et al 2012;Fajardo et al 2013;Zalapa et al 2014), relatively little is known about the genetic diversity of a wide range of wild cranberry populations. The only two studies to assess the genetic diversity of wild V. macrocarpon populations are by Debnath (2007a) in 43 Canadian clones using 14 RAPD markers and by Zalapa et al (2014) in five populations collected from Jackson County, Wisconsin, USA, who used 11 SSR markers.…”

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confidence: 99%

“…The only two studies to assess the genetic diversity of wild V. macrocarpon populations are by Debnath (2007a) in 43 Canadian clones using 14 RAPD markers and by Zalapa et al (2014) in five populations collected from Jackson County, Wisconsin, USA, who used 11 SSR markers.…”

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EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships

Bykova

Debnath

2015

Can. J. Plant Sci.

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An, D., Bykova, N. V. and Debnath, S. C. 2015. EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships. Can. J. Plant Sci. 95: 1155Á1165. The cranberry (Vaccinium marcrocarpon Ait.) is a woody, evergreen, perennial vine with great potential for economic and health benefits. Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. One hundred and two wild cranberry clones collected from four Canadian provinces and five cultivars were screened with inter simple sequence repeat (ISSR), expressed sequence tagÁ simple sequence repeat (EST-SSR) and ESTÁpolymerase chain reaction (PCR) markers to validate the genetic diversity and relationships among them. EST-PCRs (0.54) and EST-SSRs (0.35) generated higher frequency of major alleles than ISSRs (0.08), but ISSRs presented a higher level of polymorphism and greater polymorphic information content and expected heterozygosity than EST-SSRs and EST-PCRs. Combined cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) separated the wild clones and cultivars into four main clusters, which was in agreement with the principal coordinate (PCo) analysis. Analysis of molecular variation detected sufficient variations among genotypes within communities and among communities within provinces with ISSR (66 and 36%, respectively), EST-PCR (72 and 34%, respectively) and EST-SSR (72 and 34%, respectively) markers. These values were 71 and 35%, respectively, for combined analysis. Combined use of three types of molecular markers, for the first time in Vaccinium species, detected a sufficient degree of variation among cranberry genotypes, allowing for differentiation and rendering these technologies valuable for genotype identification in a diverse cranberry germplasm and for more efficient parental choice in the current cranberry breeding program. Abbreviations: AFLP, amplified fragment length polymorphism; AMOVA, analysis of molecular variance; CCC, cophenetic correlation coefficient; EST, expressed sequence tag; ISSR, inter simple sequence repeat; PCo, principal coordinate; PCR, polymerase chain reaction; PIC, polymorphism information content; RAPD, randomly amplified polymorphic DNA; SSR, simple (short) sequence repeat; UPGMA, unweighted pair group method with arithmetic means Can.

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“…Both plants were maintained clonally under greenhouse conditions at the University of Wisconsin-Madison (Wisconsin, USA). These accessions have been extensively used in different marker studies, providing a unique genetic fingerprint based on nuclear and organellar information as well as known genetic relationships based on relatively diverse samples of V. macrocarpon, V. microcarpum, and V. oxycoccos [19,[31][32][33]. In Figure 1, we show distinctive plant characteristics and attributes of each our V. microcarpum and V. macrocarpon accession.…”

Section: Plant Materialsmentioning

confidence: 99%

“…Zhu et al (2012) developed and tested a set of nuclear SSR markers and further validated them using diverse samples including wild and cultivated cranberries. Similarly, Zalapa et al (2015) studied genetic variability among wild V. macrocarpon populations, and found a rich clonal diversity within the species. In addition, the same authors were able to clearly differentiate, based on SSR markers, V. microcarpum and V. oxycoccos from V. macrocarpon, although some genotypes presented certain overlap between species.…”

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confidence: 99%

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

Diaz‐Garcia¹,

Rodríguez-Bonilla²,

Smith

et al. 2019

Preprint

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Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry and could be useful to improve fruit quality such as phytochemical content, and given their northern distribution, could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V.microcarpum. Finally, we provided important data regarding the polyploid origin of V.oxycoccos.

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Clonal diversity and genetic differentiation revealed by SSR markers in wildVaccinium macrocarponandVaccinium oxycoccos

Cited by 21 publications

References 41 publications

Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

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