Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries

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 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 been limited 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 expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches in generating genomic resources provides a non-biased glimpse into the publicly available EST-sequences, yam genome, and GBS profiles with affirmation that the genomic complexity can be methodically unraveled and constitute a critical foundation for future studies in linkage mapping, germplasm analysis, and predictive breeding.

An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)

“…The DNA samples collected from the mapping population and the two parents were shipped to GBRU, USDA-ARS, Stoneville for further analysis. A total of 1152 EST-SSRs were generated from >40,000 EST-sequences [23], which were tested for polymorphism on the two parents. A total of 435 SSRs were polymorphic, 329 did not produce any amplified products, and remaining 388 SSRs were monomorphic.…”

“…Subsequently, a total of 44,757 EST-sequences, with an average length of 500 bp, were generated from the cDNA libraries of two resistant (TDa 87-01091 and TDa 95/00328) and one susceptible (TDa 95-310) genotypes of D. alata for anthracnose disease [22]. These EST-sequences were further annotated to obtain 1,152 EST-SSRs [23] and a total of 380 polymorphic EST-SSRs were used in the present study to develop the genetic linkage map and identify QTL (s) for anthracnose disease.…”

Development of a cost‐effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections

“…However, these tools were not tailored for routine collection management. genomic resources (Saski, Bhattacharjee, Scheffler, & Asiedu, 2015;Tamiru et al, 2017), the design of such markers for D. alata collection management would be worthwhile. Besides the development of high-throughput methods for genome-wide variant detection, such as genotyping-by-sequencing (Davey et al, 2011) paired with cost-effective SNP assay (Broccanello et al, 2018) as KASPar can lead to the development of appropriate markers for collection management.…”

“…Regarding the recent release of yam (Dioscorea spp.) genomic resources (Saski, Bhattacharjee, Scheffler, & Asiedu, 2015;Tamiru et al, 2017), the design of such markers for D. alata collection management would be worthwhile. Indeed, once developed they do not require any specific bioinformatics or wet chemistry skills.…”

Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

“…Use of molecular markers has become significant for accurate identification of these yams to the species level and to harness the genetic diversity inherent in them. Different markers including Restriction fragment length polymorphism (RFLP) [31], Random amplified polymorphic DNA (RAPD) [32], Simple sequence repeat (SSR) [32], Inter-simple repeat (ISSR) [12] and Amplified fragment length polymorphism (AFLP) [32] and gene sequencing [33] [34] have been applied in the characterization of yam species. The use of molecular tools to support morphotaxonomy-based identification is important to clear ambiguous species classification.…”