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

Bian, Yang; Ballington, James R.; Raja, Archana; Brouwer, Cory; Reid, Robert W.; Burke, Mark W.; Wang, Xinguo; Rowland, Lisa J.; Bassil, Nahla V.; Brown, Allan

doi:10.1007/s11032-014-0066-7

Cited by 67 publications

(87 citation statements)

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“…Genomic DNA was extracted and genotyped using sequence capture by Rapid Genomics (Gainesville, FL, USA). Polymorphisms were genotyped in genomic regions captured by 31,063 120-mer biotinylated probes, designed based on the 2013 blueberry draft genome sequence (Bian et al 2014; Gupta et al 2015). Sequencing was performed in the Illumina HiSeq2000 platform using 100 cycle paired-end sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…In order to compare the information captured by each genomic-based relationship matrix, we performed linkage disequilibrium (LD), and principal components (PC) analyses. Pearson correlation tests (r 2 ) were performed for pairwise LD estimation among SNPs within scaffolds, considering draft reference genomes (Bian et al 2014; Gupta et al, 2015). One SNP was randomly sampled per probe interval, and a total of 22,914 SNP were used in the analysis.…”

Section: Methodsmentioning

confidence: 99%

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Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in the phenotype prediction

Oliveira

Resende

Ferrao

et al. 2018

Preprint

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27Estimation of allele dosage in autopolyploids is challenging and current methods 28 often result in the misclassification of genotypes. Here we propose and compare the use of 29 next generation sequencing read depth as continuous parameterization for autotetraploid 30 genomic prediction of breeding values, using blueberry (Vaccinium corybosum spp.) as a 31 model. Additionally, we investigated the influence of different sources of information to 32 build relationship matrices in phenotype prediction; no relationship, pedigree, and genomic 33 information, considering either diploid or tetraploid parameterizations. A real breeding 34 population composed of 1,847 individuals was phenotyped for eight yield and fruit quality 35 traits over two years. Analyses were based on extensive pedigree (since 1908) and high-36 density marker data (86K markers). Our results show that marker-based matrices can yield 37 significantly better prediction than pedigree for most of the traits, based on model fitting and 38 expected genetic gain. Continuous genotypic based models performed as well as the current 39 best models and presented a significantly better goodness-of-fit for all traits analyzed. This 40 approach also reduces the computational time required for marker calling and avoids 41 problems associated with misclassification of genotypic classes when assigning dosage in 42 polyploid species. Accuracies are encouraging for application of genomic selection (GS) for 43 blueberry breeding. Conservatively, GS could reduce the time for cultivar release by three 44 years. GS could increase the genetic gain per cycle by 86% on average when compared to 45 phenotypic selection, and 32% when compared with pedigree-based selection.46 47 48 Polyploidy events are not an exception in plants, as about 70% of Angiosperms and 53 95% of Pteridophytes underwent at least one polyploidization event (Soltis and Soltis 1999). 54 Polyploids are normally grouped into two categories, autopolyploids and allopolyploids, but 55 intermediate forms are also possible, such as segmental allopolyploids (Spoelhof et al. 2017). 56 Thresholds for polyploid classification have been controversial, but following the general 57 taxonomic definition, autopolyploids arise from within-species whole genome duplication, 58 and allopolyploids arise from whole genome duplication prior to or after an inter-specific 59 hybridization event (Soltis et al. 2007). 60 Because speciation via ploidy increase can generate new phenotypic variability, this 61 phenomenon is considered a powerful evolutionary source (Hieter and Griffiths 1999; Soltis 62 et al. 2016). Despite the important role of polyploidization in plant evolution, its effects on 63 inheritance of many agronomic traits and population genetics are still poorly understood 64 when compared with diploid species (Dufresne et al. 2014). This especially holds true for 65 autopolyploids. The complex nature of autopolyploid genetics is due to the presence of 66 genotypes with higher allele dosage than diploids, larger number ...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in the phenotype prediction

Oliveira

Resende

Ferrao

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Genotyping was performed by RAPiD Genomics (Gainesville, FL, USA) using sequence capture. Briefly, 31,063 customdesigned biotinylated probes of 120-mer were developed based on the scaffolds of the blueberry draft genome sequence (2013 version) (Bian et al, 2014;Gupta et al, 2015). Sequencing was carried out in the Illumina HiSeq2000 platform using 100 cycle paired-end runs.…”

Section: Capture-seq Genotyping and Snp Callingmentioning

confidence: 99%

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

et al. 2018

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Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries and identify candidate genes affecting phenotypic variation. We performed a genome-wide association study (GWAS) assuming diploid and tetraploid inheritance, encompassing distinct models of gene action (additive, general, different orders of allelic interaction, and the corresponding diploidized models). A total of 1,575 southern highbush blueberry individuals from a breeding population of 117 full-sib families were genotyped using sequence capture and next-generation sequencing, and evaluated for eight fruit-related traits. For the diploid allele calling, 77,496 SNPs were detected; while 80,591 SNPs were obtained in tetraploid, with a high degree of overlap (95%) between them. A linear mixed model that accounted for population and family structure was used for the GWAS analyses. By modeling tetraploid genotypes, we detected 15 SNPs significantly associated with five fruit-related traits. Alternatively, seven significant SNPs were detected for only two traits using diploid genotypes, with two SNPs overlapping with the tetraploid scenario. Our results showed that the importance of tetraploid models varied by trait and that the use of diploid models has hindered the detection of SNP-trait associations and, consequently, the genetic architecture of some commercially important traits in autotetraploid species. Furthermore, 14 SNPs co-localized with candidate genes, five of which lead to non-synonymous amino acid changes. The potential functional significance of these SNPs is discussed.

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“…Vaccinium corymbosum (L.) (Southern Highbush blueberry) are native of the Southern United States and have been commercially produced for many years in different regions around the world, including Southern America and Europe (Dragovic‐Uzelac and others ; Bian and others ). Most recently, the cultivation of blueberries in Brazil have systematically increased with focus on adaptation of these varieties to Brazilian climate of the south and southeast, which has temperate climate with winter having very low temperatures.…”

Section: Introductionmentioning

confidence: 99%

Chemical Characterization and Cytotoxic Activity of Blueberry Extracts (cv. Misty) Cultivated in Brazil

Massarotto

Barcellos

Garcia

et al. 2016

Journal of Food Science

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Vaccinium corymbosum (L.) varieties cultivation is relatively recent in Brazil, but its production has been intensified given its good adaptability to the Southern Brazil climate. Blueberries are a rich source of phenolic compounds and contain significant levels of anthocyanins, flavonols, chlorogenic acids, and procyanidins, which lead to different biological activities. Chemical identification of skin and whole hydroalcoholic blueberry extracts (ExtSB and ExtWB) revealed the presence of anthocyanins concentrated in the skin and others chemicals compounds as quercetin glycosides, proanthocyanins dimers, citric, and chlorogenic acid in the pulp. Selectivity for tumor cell lines (Hep-2, HeLa, HT-29) using ExtSB and ExtWB extracts was observed through MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay after 24 h of treatment when compared to nontumor cells (MRC-5). Morphological changes and late stages of apoptotic and necrosis process were seen in HT-29 cell line after ExtWB treatment, compared to nontumor cell line MRC-5. These results are in agreement with other studies that indicate the activity of compounds such as anthocyanins and other molecules found in Southern Highbush blueberry variety, attributed to promote beneficial effects on health that may respond as cytotoxic natural agent and contribute to cancer treatment.

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

Cited by 67 publications

References 61 publications

Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in the phenotype prediction

Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in the phenotype prediction

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

Chemical Characterization and Cytotoxic Activity of Blueberry Extracts (cv. Misty) Cultivated in Brazil

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