Efficiency of EUChip60K pipeline in fingerprinting clonal population of Eucalyptus globulus

Durán, Ricardo; Zapata-Valenzuela, Jaime; Balocchi, Claudio; Valenzuela, Sofía

doi:10.1007/s00468-017-1637-0

Cited by 4 publications

(8 citation statements)

References 28 publications

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“…Nevertheless, for the Eucalyptus genus, the use of RADseq-derived methods is scarce. To date, the easy access to the commercial SNP array (EUChip60K) has led researchers to use it in the analysis of the genus [41][42][43][44], rather than RADseq-derived methods. Some species are poorly or less frequently represented in this chip than E. grandis (which is represented for its economic importance), and for this reason, the population allele frequencies and genetic relationships between individuals can be affected [45][46][47].…”

Section: Discussionmentioning

confidence: 99%

“…RADseq and GBS-based methodologies have the potential to avoid this type of bias [30], but the experience in Eucalyptus reported to date is not encouraging. Indeed, Duran et al [41] applied GBS on 500 E. globulus individuals and only obtained 2597 polymorphic SNPs between them. The low number of markers suggests that the protocol should be improved for this genus in order to get enough whole genome coverage markers to perform population-level studies, such as genome-wide association mapping and genomic selection, among others.…”

Section: Discussionmentioning

confidence: 99%

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Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

et al. 2019

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Restriction site-associated DNA sequencing (RADseq) and its derived protocols, such as double digest RADseq (ddRADseq), offer a flexible and highly cost-effective strategy for efficient plant genome sampling. This has become one of the most popular genotyping approaches for breeding, conservation, and evolution studies in model and non-model plant species. However, universal protocols do not always adapt well to non-model species. Herein, this study reports the development of an optimized and detailed ddRADseq protocol in Eucalyptus dunnii, a non-model species, which combines different aspects of published methodologies. The initial protocol was established using only two samples by selecting the best combination of enzymes and through optimal size selection and simplifying lab procedures. Both single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were determined with high accuracy after applying stringent bioinformatics settings and quality filters, with and without a reference genome. To scale it up to 24 samples, we added barcoded adapters. We also applied automatic size selection, and therefore obtained an optimal number of loci, the expected SNP locus density, and genome-wide distribution. Reliability and cross-sequencing platform compatibility were verified through dissimilarity coefficients of 0.05 between replicates. To our knowledge, this optimized ddRADseq protocol will allow users to go from the DNA sample to genotyping data in a highly accessible and reproducible way.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

et al. 2019

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“…In particular, ddRADseq combined with reference genomic SNP calling yielded a higher number of reliable markers compared to other REbRRS methods such as GBS and RADseq in beech and oak Ulaszewski et al (2021) . In Eucalyptus , a few studies have used REbRRS methods, including GBS ( Grattapaglia et al, 2011 ; Durán et al, 2018 ; Klápště et al, 2021 ), DArT-seq ( Sansaloni et al, 2011 ; Marco de Lima et al, 2019 ), and ddRADseq ( Aguirre et al, 2019 ). Specifically, for E. dunnii ddRADseq has been optimized ( Aguirre et al, 2019 ), and there is a scale-up protocol ( Aguirre et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

Aguirre,

Villalba,

García

et al. 2024

Front. Genet.

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Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.

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“…It is imperative that farmers grow varieties that are true to type to maximize their economic value. However, as with several other clonally propagated crops (Akpertey et al, 2021; Bassil et al, 2020; de Wever et al, 2019; Dossett et al, 2012; Driskill et al, 2022; Durán et al, 2018; Montanari et al, 2020; Oraguzie et al, 2005; Zhang et al, 2006; Zurn et al, 2018), red raspberry suffers from clonal misidentification. Initially, red raspberry clonal identification was performed using morphological characteristics (Laurentin, 2009).…”

Section: Introductionmentioning

confidence: 99%

Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.)

Clare,

King,

Hardigan

et al. 2023

Plant Breeding

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Red raspberry is an economically important horticultural crop that is known for its fruit's sweet flavour and nutritional value. A reliable and economic genotyping platform is needed to facilitate clonal/variety identification. Previous attempts for clonal identification utilized morphological traits or low‐throughput, difficult to score dinucleotide‐containing simple sequence repeat molecular markers. Single nucleotide polymorphisms (SNPs), despite having lower allelic diversity, are numerous across the genome and more easily converted to high‐throughput assays restoring differential power. In this study, we use the kompetitive allele‐specific PCR (KASP™) chemistry, an affordable and high‐throughput platform, to develop a panel of SNPs to distinguish a diverse collection of red raspberry accessions for clonal identification. The panel consists of 48 KASP assays that show high concordance with whole genome sequencing, allelic balance, and recovery rate and a minimal set of 24 assays that distinguished the same accessions differentiated by the larger panel.

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Efficiency of EUChip60K pipeline in fingerprinting clonal population of Eucalyptus globulus

Cited by 4 publications

References 28 publications

Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.)

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