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RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73
Zhikai Liang1, James C Schnable1
1Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States of America.
Plos One
|June 28, 2016
Summary
Genetic research stocks, like maize inbred B73, show significant variation due to contamination and mutations. This highlights the need for genetic purity in research to ensure reliable genomic and phenotypic studies.
Area of Science:
- Genetics and Genomics
- Plant Science
- Molecular Biology
Background:
- Identically named genetic research lines frequently harbor uncharacterized genetic variation.
- This variation arises from cross-contamination, unintentional crossing, residual heterozygosity, or de novo mutation.
- The maize (Zea mays ssp. mays) inbred line B73 is a widely used reference genotype in genetic and genomic research.
Purpose of the Study:
- To assess genetic variation within the widely used maize inbred B73.
- To identify distinct genetic clades within samples purported to be B73.
- To quantify the proportion of genetic variation across different research groups using B73.
Main Methods:
- Analysis of 27 large-scale RNA-seq datasets from 20 independent global research groups.
- Comparative genomic analysis to identify distinct haplotypes within B73 samples.
- Assessment of genetic relatedness between B73 samples from different sources.
Main Results:
- Several distinct genetic clades were identified among putatively B73 maize samples.
- Some clades were characterized by genomic blocks with haplotypes not matching the reference B73 genome.
- Approximately 2.3% of the analyzed maize genotype exhibited multiple distinct haplotypes across different research groups.
Conclusions:
- Significant genetic variation exists within commonly used maize B73 research stocks.
- The observed variation can lead to distinct genetic clades, impacting research reproducibility.
- Ensuring genetic integrity of research stocks is crucial for accurate genetic, genomic, and phenotypic studies.
