ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2012
Quality control genotyping for assessment of genetic identity and purity in diverse tropical maize inbred lines.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Genetic diversity and population structure of early-maturing yellow and orange maize inbred lines for improved breeding applications.PloS one · 2026Article
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- Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.).The plant genome · 2024Article
- Genetic diversity and population structure of maize inbred lines using phenotypic traits and single nucleotide polymorphism (SNP) markers.Scientific reports · 2023Article
- Article
- Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses.Plants (Basel, Switzerland) · 2022Article
- Genetic Diversity, Population Structure and Linkage Disequilibrium Analyses in Tropical Maize Using Genotyping by Sequencing.Plants (Basel, Switzerland) · 2022Article
- Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries.Gates open research · 2022Article
- Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array.Scientific reports · 2021Article
- Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species.Scientific reports · 2021Article
- Article
- Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses.BMC plant biology · 2020Article
- Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the GenusFrontiers in plant science · 2020Article
- Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs.PloS one · 2020Article
- Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands.Scientific reports · 2019Article
- Development of a cost-effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections.Ecology and evolution · 2019Article
- An Integrated Molecular and Conventional Breeding Scheme for Enhancing Genetic Gain in Maize in Africa.Frontiers in plant science · 2019Review
- Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing ofMolecular breeding : new strategies in plant improvement · 2018Article
- Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs.Frontiers in plant science · 2018Article
- Development of species diagnostic SNP markers for quality control genotyping in four rice (Molecular breeding : new strategies in plant improvement · 2018Article
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Authors and funding
7 authors.
Funding
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Abstract
Quality control (QC) genotyping is an important component in breeding, but to our knowledge there are not well established protocols for its implementation in practical breeding programs. The objectives of our study were to (a) ascertain genetic identity among 2-4 seed sources of the same inbred line, (b) evaluate the extent of genetic homogeneity within inbred lines, and (c) identify a subset of highly informative single-nucleotide polymorphism (SNP) markers for routine and low-cost QC genotyping and suggest guidelines for data interpretation. We used a total of 28 maize inbred lines to study genetic identity among different seed sources by genotyping them with 532 and 1,065 SNPs using the KASPar and GoldenGate platforms, respectively. An additional set of 544 inbred lines was used for studying genetic homogeneity. The proportion of alleles that differed between seed sources of the same inbred line varied from 0.1 to 42.3 %. Seed sources exhibiting high levels of genetic distance are mis-labeled, while those with lower levels of difference are contaminated or still segregating. Genetic homogeneity varied from 68.7 to 100 % with 71.3 % of the inbred lines considered to be homogenous. Based on the data sets obtained for a wide range of sample sizes and diverse genetic backgrounds, we recommended a subset of 50-100 SNPs for routine and low-cost QC genotyping, verified them in a different set of double haploid and inbred lines, and outlined a protocol that could be used to minimize errors in genetic analyses and breeding.
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