Dataset Information

RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73.

ABSTRACT: Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several clearly distinct clades were identified among putatively B73 samples. A number of these clades were defined by the presence of clearly defined genomic blocks containing a haplotype which did not match the published B73 reference genome. The overall proportion of the maize genotype where multiple distinct haplotypes were observed across different research groups was approximately 2.3%. In some cases the relationship among B73 samples generated by different research groups recapitulated mentor/mentee relationships within the maize genetics community.

SUBMITTER: Liang Z

PROVIDER: S-EPMC4922647 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73.

Liang Zhikai Z Schnable James C JC

PloS one 20160627 6

Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old ...[more]

PMID: 27348435

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Project description:Genome-wide gene expression atlas of maize inbred line B73. Maize inbred B73 was used for constructing the gene atlas. Plants were grown in Plano silt loam soil at the West Madison Agricultural Research Station, Verona, WI during Summer 2008. During field preparation, 200 kg/acre of Urea (46-0-0) was applied. One day after planting, herbicides including Callisto (142 g/acre), Dual II (710 ml/acre), and Simazine (227 g/acre) were applied. For collection of seed tissues, shoots were covered before silk emergence avoiding any injury to the plants. Plants were self-pollinated on the same day to establish a common time initiation point for the harvest timeline. Greenhouse-grown plants were propagated by growing five plants per pot (30 cm top diameter, 28 cm height, 14.5 L volume) containing Metro-Mix 300 (Sun Gro Horticulture, Bellevue, WA, USA) with no additional fertilization. The growing conditions were 27 deg. C day and 24 deg. C night temperature with a 16h light (5:00am to 9:00pm) and 8h dark regime. Germinating seed tissue was generated by soaking seeds in distilled water in a Petri dish for 12h and then placing seeds between layers of moist paper towels for another 12h to allow germination. The field samples were collected between 8:00am and 10:00am, approximately 3 hours after sunrise. The greenhouse samples were collected between 8:00am and 9:00am, three hours after turning on the lights. Three biological replicates were collected for each tissue type. For all the tissues except germinating seeds, a biological replicate was constituted by collecting and pooling samples from three competitive randomly chosen plants. For germinating seed, ten randomly chosen seeds were pooled to form a biological replicate. The harvested tissues were immediately frozen in liquid nitrogen and stored at -80 deg. C. Total RNA was extracted using TRIZOL reagent (Invitrogen, http://www.invitrogen.com) following the manufacturer's protocol, and purified using RNeasy MinElute Cleanup Kit (Qiagen, http://www.qiagen.com) following the manufacturer's instructions. PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rajandeep S Sekhon. The equivalent experiment is ZM29 at PLEXdb.

Dataset Information

RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73.

Publications

RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73.

Similar Datasets

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