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United States Department of Agriculture

Agricultural Research Service

Research Project: MOLECULAR CHARACTERIZATION AND DIVERSITY ASSESSMENT OF COCOA GERMPLASM IN THE AMERICAS

Location: Sustainable Perennial Crops

Title: Ultra-barcoding in cacao (Theobroma spp.; malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

Authors
item Kane, Nolan -
item Sveinsson, Saemundur -
item Dempewolf, Hannes -
item Yang, Ji Yong -
item ZHANG, DAPENG
item Engels, Johannes -
item Cronk, Quentinue -

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 19, 2011
Publication Date: February 1, 2012
Citation: Kane, N., Sveinsson, S., Dempewolf, H., Yang, J., Zhang, D., Engels, J., Cronk, Q. 2012. Ultra-barcoding in cacao (Theobroma spp.; malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. American Journal of Botany. 99:320-329.

Interpretive Summary: DNA variation has been widely used to show evolutionary relationships of plant species. Plant scientists often need to know more about varieties and evolution within a species. We used genetic DNA sequencing to assemble large portions of genomes of nine cacao varieties (same species) and one related species. The variation in the DNA sequences allowed us to uniquely distinguish all varieties and the result successfully illuminated the evolutionary relationships among these varieties. This approach shows great promise for applications where very closely related plants must be distinguished, which makes this approach useful to plant breeders, germplasm curators and cacao farmers and will benefit chocolate consumers.

Technical Abstract: High-throughput next-generation sequencing was used to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao. All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA. Our data demonstrate that UBC is a viable, increasingly cost-effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished.

Last Modified: 9/29/2014