Making a chocolate chip: development and evaluation of a 6K SNP array for<i>Theobroma cacao</i>

Livingstone, Donald; Royaert, Stefan; Stack, Conrad; Mockaitis, Keithanne; May, Greg; Farmer, Andrew; Saski, Christopher; Schnell, R. J.; Kuhn, David N.; Motamayor, Juan Carlos

doi:10.1093/dnares/dsv009

Cited by 37 publications

(47 citation statements)

References 43 publications

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“…The high concordance between genotyping and SNP calling data from Sanger sequencing and NGS genome sequencing revealed the robustness of our selection criteria. Our genotyping success rate (91%) exceeded those recorded for other plant species with the same Infinium technology and in the same genotyping throughput range (6-10k) (Chagn e et al 2012;Verde et al 2012;Bachlava et al 2012;Peace et al 2012;Sim et al 2012;Delourme et al 2013;Li et al 2014;Dalton-Morgan et al 2014;Lepoittevin et al 2015;Livingstone et al 2015). The success of the SNP array was due to the composition of the SNP discovery panel reflecting the genetic diversity of the populations under study.…”

Section: Discussionsupporting

confidence: 50%

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New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Faivre-Rampant

Zaina

Jorge

et al. 2016

Molecular Ecology Resources

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Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.

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Section: Discussionsupporting

confidence: 50%

“…; Livingstone et al . ). The success of the SNP array was due to the composition of the SNP discovery panel reflecting the genetic diversity of the populations under study.…”

Section: Discussionmentioning

confidence: 97%

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Faivre-Rampant

Zaina

Jorge

et al. 2016

Molecular Ecology Resources

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“…RNA-seq datasets (Schmitz, Schultz et al 2011, Brown, Kroon et al 2012, Chodavarapu, Feng et al 2012, Perazzolli, Moretto et al 2012, Tomato Genome 2012, Amborella Genome 2013, International Peach Genome, Verde et al 2013, Schmitz, He et al 2013, Seymour, Koenig et al 2014, Tang, Dong et al 2014, Livingstone, Royaert et al 2015, Wang, Yuan et al 2015, Bewick, Ji et al 2016 were downloaded from the Gene Expression Omnibus (GEO) and the NCBI Short Read Archive (SRA) for reanalysis. B. distachyon and C. sativus RNA-seq libraries were constructed using Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina Inc.) and sequenced on a NextSeq500 at the Georgia Genomics Facility.…”

Section: Rna-seq Mapping and Analysismentioning

confidence: 99%

“…RNA-seq datasets [11,14,47,49,54,89,91,[97][98][99][100][101][102] were downloaded from the Gene Expression Omnibus (GEO) and the NCBI Short Read Archive (SRA) for reanalysis. B. distachyon and C. sativus RNA-seq libraries were constructed using Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina Inc.) and sequenced on a NextSeq500 at the Georgia Genomics Facility.…”

Section: Rna-seq Mapping and Analysismentioning

confidence: 99%

Widespread natural variation of DNA methylation within angiosperms

Niederhuth¹,

Bewick²,

Ji³

et al. 2016

Preprint

115

226

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To understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time. These results show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

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“…Recently, a large number of SNPs have been detected by aligning RNA sequence (RNAseq) data of 16 cacao cultivars to the assembled Matina 1–6 transcriptome (Livingstone et al ., ). In this study, a saturated genetic linkage map with 2589 SNPs was constructed.…”

Section: Introductionmentioning

confidence: 97%

Cacao biotechnology: current status and future prospects

Wickramasuriya

Dunwell

2017

Plant Biotechnology Journal

108

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Summary Theobroma cacao—The Food of the Gods, provides the raw material for the multibillion dollar chocolate industry and is also the main source of income for about 6 million smallholders around the world. Additionally, cocoa beans have a number of other nonfood uses in the pharmaceutical and cosmetic industries. Specifically, the potential health benefits of cocoa have received increasing attention as it is rich in polyphenols, particularly flavonoids. At present, the demand for cocoa and cocoa‐based products in Asia is growing particularly rapidly and chocolate manufacturers are increasing investment in this region. However, in many Asian countries, cocoa production is hampered due to many reasons including technological, political and socio‐economic issues. This review provides an overview of the present status of global cocoa production and recent advances in biotechnological applications for cacao improvement, with special emphasis on genetics/genomics, in vitro embryogenesis and genetic transformation. In addition, in order to obtain an insight into the latest innovations in the commercial sector, a survey was conducted on granted patents relating to T. cacao biotechnology.

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Making a chocolate chip: development and evaluation of a 6K SNP array forTheobroma cacao

Cited by 37 publications

References 43 publications

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Widespread natural variation of DNA methylation within angiosperms

Cacao biotechnology: current status and future prospects

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