Comparison of Kompetitive Allele Specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize.
Comparison of Kompetitive Allele Specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize.
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DOI：
10.1186/s12864-015-2180-2
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发表时间：
2015-11-06
期刊：
影响因子：
4.4
通讯作者：
Semagn K
中科院分区：
文献类型：
--
作者：
Ertiro BT;Ogugo V;Worku M;Das B;Olsen M;Labuschagne M;Semagn K
质量控制（QC）分析是玉米育种和种子系统的重要组成部分。通过下一代测序（GBS）进行基因分型是SNP基因分型的新兴方法，其越来越多地被用于发现应用，但其用于QC分析的适用性尚未被探索。利用191个竞争等位基因特异性PCR（KASP）和257，268个GBS标记对16个自交系的2 ~ 9个种源进行遗传纯度和同一性评价，并比较KASP标记低密度和GBS标记高密度的相关性。每个种子来源内的遗传纯度对于KASP从49%至100%变化，对于GBS从74%至100%变化。从CIMMYT获得的所有自交系中，除了一个外，均显示98 - 100%的同源性，与标记类型无关。相反，从EIAR和合作伙伴获得的样品中，仅分别有16%和21%的KASP和GBS纯度≥ 95%。同一品系多个来源间的遗传距离KASP为0.000 ~ 0.295，GBS为0.004 ~ 0.230。来自CIMMYT的5个品系在同一品系名称的多个来源之间显示出≤ 0.05的距离;其余11个自交系，包括来自CIMMYT的2个和来自埃塞俄比亚的9个，在两个或更多种子来源之间显示出高于预期的遗传距离。191个KASP和257，268个GBS标记之间的相关性对于纯度为0.88，对于同一性为0.93。GBS标记数量减少到1，343，相关系数仅下降0.03。我们的结果清楚地表明，无论用于分析的基因分型平台的类型和标记的数量如何，种子来源（机构）的起源在遗传纯度和同一性方面都存在高度差异。虽然KASP和GBS之间存在一些数值差异，但从两种方法得出的总体结论基本相似，这清楚地表明预选和高质量标记物的较小子集足以用于QC分析，其可以使用低标记物密度基因分型平台（如KASP）轻松完成。这项研究的结果将是高度相关的植物育种和种子系统专家。本文的在线版本（doi：10.1186/s12864-015-2180-2）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi:10.1186/s12864-015-2180-2) contains supplementary material, which is available to authorized users.