Quality control genotyping for assessment of genetic identity and purity in diverse tropical maize inbred lines
- 838 Downloads
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.
KeywordsInbred Line Simple Sequence Repeat Marker Double Haploid Seed Source Cetyl Trimethyl Ammonium Bromide
We thank Veronica Ogugo for sample preparation and DNA extraction. This work was carried out under the Drought Tolerant Maize for Africa (DTMA) and Water Efficient Maize for Africa (WEMA) projects undertaken by CIMMYT and national partners in Africa, and funded by the Bill and Melinda Gates Foundation.
- Gupta K, Balyan S, Edwards J, Isaac P, Korzun V, Rodër M, Gautier MF, Joudrier P, Schlatter R, Dubcovsky J, De La Pena C, Khairallah M, Penner G, Hayden J, Sharp P, Keller B, Wang C, Hardouin P, Jack P, Leroy P (2002) Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet 105:413–422PubMedCrossRefGoogle Scholar
- Heckenberger M, Bohn M, Ziegle JS, Joe LK, Hauser JD, Hutton M, Melchinger AE (2002) Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties. I. Genetic and technical sources of variation in SSR data. Mol Breed 10:181–191CrossRefGoogle Scholar
- Heckenberger M, Voort JR, Melchinger AE, Peleman J, Bohn M (2003) Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties. II. Genetic and technical sources of variation in AFLP data and comparison with SSR data. Mol Breed 12:97–106CrossRefGoogle Scholar
- Jones DF (1945) Heterosis resulting from degenerative changes. Genetics 30:527–542Google Scholar
- Rholf FJ (1993) NTSYS-pc, numerical taxonomy and multivariate analysis system. Exeter software, New YorkGoogle Scholar
- Rogers JS (1972) Measures of genetic similarity and genetic distance. Stud Genet VII Univ Texas Publ 7213:145–153Google Scholar
- Semagn K, Magorokosho C, Vivek BS, Makumbi D, Beyene Y, Mugo S, Prasanna BM, Warburton ML (2012) Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers. BMC Genomics 13:113. doi: 10.1186/1471-2164-13-113 PubMedCrossRefGoogle Scholar