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

Content Provider	Springer Nature : BioMed Central
Author	Ertiro, Berhanu Tadesse Ogugo, Veronica Worku, Mosisa Das, Biswanath Olsen, Michael Labuschagne, Maryke Semagn, Kassa
Abstract	Background Quality 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. Results Genetic 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. Conclusions Our 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.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-015-2180-2.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-015-2180-2
Journal	BMC Genomics
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-11-06
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetic purity Genetic identity High marker density Low marker density Quality analysis Single nucleotide polymorphism
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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