Comparison of Kompetitive Allele Specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize

BMC Genomics

Research Article

Maryke Labuschagne¹  Berhanu Tadesse Ertiro²  Mosisa Worku³  Biswanath Das³  Michael Olsen³  Kassa Semagn³  Veronica Ogugo³ 

[1] Department of Plant Sciences, University of Free State, Bloemfontein, South Africa;Ethiopian Institute of Agricultural Research (EIAR), Bako National Maize Research Center, Bako, West Shoa, Oromia, Ethiopia;International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, 00621, Nairobi, Kenya;

关键词: Genetic purity;    Genetic identity;    High marker density;    Low marker density;    Quality analysis;    Single nucleotide polymorphism;   

DOI  :  10.1186/s12864-015-2180-2

 received in 2015-09-02, accepted in 2015-10-31,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundQuality control (QC) analysis is an important component in maize breeding and seed systems. Genotyping by next-generation sequencing (GBS) is an emerging method of SNP genotyping, which is being increasingly adopted for discovery applications, but its suitability for QC analysis has not been explored. The objectives of our study were 1) to evaluate the level of genetic purity and identity among two to nine seed sources of 16 inbred lines using 191 Kompetitive Allele Specific PCR (KASP) and 257,268 GBS markers, and 2) compare the correlation between the KASP-based low and the GBS-based high marker density on QC analysis.ResultsGenetic purity within each seed source varied from 49 to 100 % for KASP and from 74 to 100 % for GBS. All except one of the inbred lines obtained from CIMMYT showed 98 to 100 % homogeneity irrespective of the marker type. On the contrary, only 16 and 21 % of the samples obtained from EIAR and partners showed ≥95 % purity for KASP and GBS, respectively. The genetic distance among multiple sources of the same line designation varied from 0.000 to 0.295 for KASP and from 0.004 to 0.230 for GBS. Five lines from CIMMYT showed ≤ 0.05 distance among multiple sources of the same line designation; the remaining eleven inbred lines, including two from CIMMYT and nine from Ethiopia showed higher than expected genetic distances for two or more seed sources. The correlation between the 191 KASP and 257,268 GBS markers was 0.88 for purity and 0.93 for identity. A reduction in the number of GBS markers to 1,343 decreased the correlation coefficient only by 0.03.ConclusionsOur results clearly showed high discrepancy both in genetic purity and identity by the origin of the seed sources (institutions) irrespective of the type of genotyping platform and number of markers used for analyses. Although there were some numerical differences between KASP and GBS, the overall conclusions reached from both methods was basically similar, which clearly suggests that smaller subset of preselected and high quality markers are sufficient for QC analysis that can easily be done using low marker density genotyping platforms, such as KASP. Results from this study would be highly relevant for plant breeders and seed system specialists.

【 授权许可】

CC BY   
© Ertiro et al. 2015