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United States Department of Agriculture

Agricultural Research Service


Location: Genetic Improvement for Fruits & Vegetables Laboratory

Title: Patterns of simple sequence repeats in cultivated blueberries (Vaccinium section Cyanococcus spp.) and their use in revealing genetic diversity and population structure

item Bian, Yang
item Ballington, James
item Raja, Archana
item Brouwer, Cory
item Reid, Robert
item Burke, Mark
item Wang, Xinguo
item Rowland, Lisa
item Bassil, Nahla
item Brown, Allan

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2014
Publication Date: 7/12/2014
Publication URL:
Citation: Bian, Y., Ballington, J., Raja, A., Brouwer, C., Reid, R., Burke, M., Wang, X., Rowland, L.J., Bassil, N.V., Brown, A. 2014. Patterns of simple sequence repeats in cultivated blueberries (Vaccinium section Cyanococcus spp.) and their use in revealing genetic diversity and population structure. Molecular Breeding. 34(2):675-689.

Interpretive Summary: Blueberry is an important fruit crop native to North America. The time required for plant breeders to develop new blueberry varieties can be reduced through the use of DNA markers associated with plant attributes. However, development of DNA-based markers in blueberry has been limited until recently by the scarcity of DNA sequence data available to scientists. The objectives of this study were to develop new DNA-based markers and use the markers to characterize a large collection of blueberry varieties. From this study, 136 new markers were developed and the markers were used to determine genetic relationships among the varieties. The information obtained can be used by blueberry breeders to better select plants to be used in breeding improved varieties. In addition, these markers will be a valuable resource for scientists carrying out genetic research on blueberry.

Technical Abstract: Blueberry (Vaccinium section Cyanococcus spp.) is an important small fruit crop native to North America that has not been effectively characterized for genetic diversity. Development of molecular markers in blueberry has been limited by the scarcity of genomic resources. The objectives of this study were to develop molecular markers from an emerging genomic draft sequence and characterize a representative collection of 150 blueberry accessions using genomic SSR markers and existing EST-SSRs. Genomic scaffolding was assembled using shotgun and paired end 454 libraries of 3, 8, and 20 Kb insert size from a diploid V. corymbosum ‘W8520’. Of the assembled 358 Mb sequence, a total number of 43,594 SSRs were identified (122 per Mb) with dinucleotide repeats found to be the most abundant repeat types in all genomic regions except in predicted gene coding sequences (CDS). SSRs were longest and occurred more frequently in the predicted 5’ untranslated region (5’ UTR), while SSRs were shorter and less common in the predicted CDS. AG/CT and AAG/CTT were the most frequent motifs while CG/CG and CCG/CGG motifs were the least common di- and trinucleotide motifs, respectively, in both genome and transcribed DNA. For this project, 136 SSR primer-pairs were designed and validated. A polymorphic rate of 94% was observed from a subset of 71 of these with screening panels representing multiple species and ploidy levels. Genetic diversity and population structure were evaluated with 150 blueberry accessions based on both new genomic SSR and previously available EST-SSR markers to efficiently characterize both neutral and adaptive molecular diversity. An average of 14.2 alleles and 56.0 allele phenotypes per locus were detected among 150 accessions with a combined 42 genomic SSR and EST-SSR markers. Neighbor joining cluster analysis grouped the 150 accessions by species, ploidy levels and known pedigree information. Rabbiteye blueberry (V. virgatum) was genetically distinct from other species shown by principal coordinate analysis and structure analysis. Three sub-populations were detected among highbush accessions largely attributable to the distinction between northern and southern highbush and founder effect of the cultivar ‘Weymouth’.

Last Modified: 10/15/2017
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