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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #312201

Research Project: Genomics and Bioinformatics Research in Agriculturally Important Organisms

Location: Genomics and Bioinformatics Research

Title: Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries

Author
item Saski, Christopher - Clemson University
item Bhattacharjee, Ranjana - International Institute Of Tropical Agriculture (IITA)
item Scheffler, Brian
item Asiedu, Robert - International Institute Of Tropical Agriculture (IITA)

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2015
Publication Date: 7/29/2015
Citation: Saski, C.A., Bhattacharjee, R., Scheffler, B.E., Asiedu, R. 2015. Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries. PLoS One. doi:10.1371/journal.pone.0134031.

Interpretive Summary: Yam (Dioscorea) is an important food source, especially in developing countries. However in the era of genomics and molecular tools for plant breeding, yam has not received the same attention as other crops. Yam also suffers from the fact that it is difficult to make crosses between individuals, but yam does have the advantage that it is vegetatively propagated. In order to make greater advances in developing improved yam cultivars, especially for disease traits, molecular breeding tools are needed that are especially developed for yam. In this work, an array of DNA markers were developed and validated. These include SSR markers (Simple Sequence Repeats) derived from expressed genes and genomic DNA and SNP markers (Single Nucleotide Polymorphisms). A new method was used to identify polymorphic SSR markers using bioinformatic tools based solely on genomic DNA sequences. In addition to identify SNP markers, a method for reduced sequence representation was tested on yam and it gave evidence that such a method could be used for economical application of SNPs in yam.

Technical Abstract: The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources such as SSRs, SNPs and InDels in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have not yet included the use of advanced technologies to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including EST-sequencing, de novo sequencing, and GBS profiles on two yam (Dioscorea alata L.) genotypes (used as parents to generate a mapping population for anthracnose disease) was performed to generate genomic resources for use in its improvement programs.