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Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize

View ORCID ProfileJinliang Yang, View ORCID ProfileCheng-Ting “Eddy” Yeh, View ORCID ProfileRaghuprakash Kastoori Ramamurthy, Xinshuai Qi, View ORCID ProfileRohan L. Fernando, Jack C. M. Dekkers, Dorian J. Garrick, Dan Nettleton and View ORCID ProfilePatrick S. Schnable
G3: Genes, Genomes, Genetics November 1, 2018 vol. 8 no. 11 3567-3575; https://doi.org/10.1534/g3.118.200636
Jinliang Yang
Department of AgronomyDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583
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  • ORCID record for Jinliang Yang
Cheng-Ting “Eddy” Yeh
Department of Agronomy
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  • ORCID record for Cheng-Ting “Eddy” Yeh
Raghuprakash Kastoori Ramamurthy
Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583
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  • ORCID record for Raghuprakash Kastoori Ramamurthy
Xinshuai Qi
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
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Rohan L. Fernando
Department of Animal Science and Center for Integrated Animal Genomics
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  • ORCID record for Rohan L. Fernando
Jack C. M. Dekkers
Department of Animal Science and Center for Integrated Animal Genomics
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Dorian J. Garrick
Department of Animal Science and Center for Integrated Animal Genomics
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Dan Nettleton
Department of Statistics, Iowa State University, Ames, IA 50011
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Patrick S. Schnable
Department of Agronomy
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  • ORCID record for Patrick S. Schnable
  • For correspondence: schnable@iastate.edu
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    Figure 1

    Phenotypic distributions of the KRN trait in GWAS and validation populations. (A) Density plots of the four GWAS populations. Embedded picture shows the typical KRN counts for B73, B73xMo17 (BxM), Mo17xB73 (MxB) and Mo17 lines. (B) Density plots of two validation populations, elite inbred lines and extreme KRN accessions. Embedded pictures shows examples of an extreme low KRN accession and an extreme high KRN accession. (C) Density plots of cycle 30 long ear (C30 LE) and cycle 30 short ear (C30 SE) in the BSLE population. Embedded pictures indicate the ear length and KRN variation after 30 generations of selection. Blue and red dashed lines indicate the mean KRN values of B73 (KRN = 17.1) and Mo17 (KRN = 10.8).

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    Figure 2

    Stacked plots of GWAS and QTL results. From upper to lower panels are results from the Bayesian-based multi-variant (A) stepwise regression (B) and single variant(C) models for GWAS and the joint QTL mapping result (D). The red dashed line in the QTL plot indicates the 1,000 permutation threshold and black lines show the QTL confidence intervals. Red squares in panel (A), triangles in panel (B) and circles in panel (C) indicate the kernel row number associated variants selected for further genetic validation.

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    Figure 3

    Genetic validation results of selected kernel row number associated variants (KAVs). (A) Transformed P values using single variant (SV) model and posterior model frequencies using Bayesian-based multi-variant (BMV) model were extracted and plotted for the 77 informative KAVs identified by at least one of the three GWAS models. KAVs detected only by the SV model are plotted in the lower right quadrant, KAVs detected only by the stepwise regression model are plotted as non-gray dots in the lower left quadrant, the KAVs detected only by the BMV model are plotted in the upper left quadrant, KAVs detected by both the SV and BMV models are plotted in the upper right quadrant and control variants are plotted as gray dots in the lower left quadrant. Validated KAVs are marked in red. A control variant is a genomic variant that is randomly chosen from a set of SNPs that were not associated with KRN in the initial GWAS. (B) Venn diagram of the validation results.

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PUBLICATION INFORMATION

Volume 8 Issue 11, November 2018

G3: Genes|Genomes|Genetics: 8 (11)

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Multiparental Populations
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Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize

View ORCID ProfileJinliang Yang, View ORCID ProfileCheng-Ting “Eddy” Yeh, View ORCID ProfileRaghuprakash Kastoori Ramamurthy, Xinshuai Qi, View ORCID ProfileRohan L. Fernando, Jack C. M. Dekkers, Dorian J. Garrick, Dan Nettleton and View ORCID ProfilePatrick S. Schnable
G3: Genes, Genomes, Genetics November 1, 2018 vol. 8 no. 11 3567-3575; https://doi.org/10.1534/g3.118.200636
Jinliang Yang
Department of AgronomyDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jinliang Yang
Cheng-Ting “Eddy” Yeh
Department of Agronomy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Cheng-Ting “Eddy” Yeh
Raghuprakash Kastoori Ramamurthy
Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Raghuprakash Kastoori Ramamurthy
Xinshuai Qi
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
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  • Search for this author on this site
Rohan L. Fernando
Department of Animal Science and Center for Integrated Animal Genomics
  • Find this author on Google Scholar
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  • Search for this author on this site
  • ORCID record for Rohan L. Fernando
Jack C. M. Dekkers
Department of Animal Science and Center for Integrated Animal Genomics
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  • Find this author on PubMed
  • Search for this author on this site
Dorian J. Garrick
Department of Animal Science and Center for Integrated Animal Genomics
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  • Search for this author on this site
Dan Nettleton
Department of Statistics, Iowa State University, Ames, IA 50011
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Patrick S. Schnable
Department of Agronomy
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  • ORCID record for Patrick S. Schnable
  • For correspondence: schnable@iastate.edu
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Citation

Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize

View ORCID ProfileJinliang Yang, View ORCID ProfileCheng-Ting “Eddy” Yeh, View ORCID ProfileRaghuprakash Kastoori Ramamurthy, Xinshuai Qi, View ORCID ProfileRohan L. Fernando, Jack C. M. Dekkers, Dorian J. Garrick, Dan Nettleton and View ORCID ProfilePatrick S. Schnable
G3: Genes, Genomes, Genetics November 1, 2018 vol. 8 no. 11 3567-3575; https://doi.org/10.1534/g3.118.200636
Jinliang Yang
Department of AgronomyDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jinliang Yang
Cheng-Ting “Eddy” Yeh
Department of Agronomy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Cheng-Ting “Eddy” Yeh
Raghuprakash Kastoori Ramamurthy
Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Raghuprakash Kastoori Ramamurthy
Xinshuai Qi
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rohan L. Fernando
Department of Animal Science and Center for Integrated Animal Genomics
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Rohan L. Fernando
Jack C. M. Dekkers
Department of Animal Science and Center for Integrated Animal Genomics
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dorian J. Garrick
Department of Animal Science and Center for Integrated Animal Genomics
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dan Nettleton
Department of Statistics, Iowa State University, Ames, IA 50011
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patrick S. Schnable
Department of Agronomy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Patrick S. Schnable
  • For correspondence: schnable@iastate.edu

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