University of Illinois Urbana-Champaign

Utilizing maize genomics for pre-breeding insights

Sorgini, Crystal A.

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SORGINI-DISSERTATION-2018.pdf

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https://hdl.handle.net/2142/101199

Description

Title
Utilizing maize genomics for pre-breeding insights
Author(s)
Sorgini, Crystal A.
Issue Date
2018-04-19
Director of Research (if dissertation) or Advisor (if thesis)
Moose, Stephen P.
Doctoral Committee Chair(s)
Moose, Stephen P.
Committee Member(s)
  • Ainsworth, Elizabeth A.
  • Brown, Patrick J.
  • Rayburn, A. Lane
  • Sachs, Martin M.
Department of Study
Crop Sciences
Discipline
Crop Sciences
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Date of Ingest
2018-09-04T20:36:49Z
Keyword(s)
  • Maize
  • Genomics
  • Genetics
Abstract
Tropospheric ozone (O3) is estimated to cause billions of dollars in global crop losses, but few studies have investigated the effects of elevated O3 on growth and development of C4 crop plants. Free Air Concentration Enrichment (FACE) field experiments were used to evaluate the response of diverse maize inbred and hybrid lines under elevated O3 concentrations ([O3]). Lines were scored for flowering phenology and ear architecture traits. A multi-year analysis showed inconsistent effects of O3 on development. Hybrid ear length and diameter and inbred ear length were all significantly reduced under elevated [O3] compared to ambient conditions. Knowledge about the identity and location of agriculturally important quantitative trait loci (QTL) provides the basis for marker assisted selection in breeding programs. B73 and Mo17 Nearly Isogenic Lines (NILs) were evaluated at the FACE facility for leaf damage and QTL were mapped. In Mo17 NILs, a significant leaf damage QTL was identified on chromosome 2 at ~161 Mb (AGPv3). Results show that B73 introgressions into Mo17 in this region made NILs more susceptible. Leaf damage scores from the field in 2016 and 2017 had a strongly significant correlation (r = 0.93). Field and growth chamber results best fit is non-linear. It appears chambers can identify damage versus no-damage, but not a continuous degree of damage as seen in the field. This indicates the potential for higher-throughput phenotyping and fine mapping of early season O3 damage QTL in a controlled environment. Sensitive and tolerant NILs were identified. Co-dominant insertion/deletion markers flanking the QTL interval were designed and validated in parents and hybrids. This research supplies the resources for future experiments that combine growth chamber phenotyping and genetic fine-mapping to determine the gene(s) underlying this QTL for O3 tolerance. Current doubled haploid (DH) inducer markers are inefficient and have a higher probability of misclassification when used for classification of tropical germplasm. Yg3-N1582, a rare dominant mutant obtained from ethyl methanesulfonate (EMS) mutagenesis, has not been previously mapped. Phenotypically, Yg3-N1582 has yellow color expression at coleoptile emergence that does not persist beyond the seedling stage, is homozygous-viable, and is non-lethal with no apparent deleterious effects. The Yg3 mutation has potential as a haploid inducer marker in exotic germplasm and small breeding programs where the use of R1-Navajo and high oil inducers is not feasible. The yg3 gene maps to 173-175Mb (AGPv3) on chromosome 5, which does not coincide with any previously characterized yg mutant. Transcriptome profiling identified GRMZM2G165521 as a candidate gene that could underlie the mutant phenotype. GRMZM2G165521 is a predicted PPR protein involved in RNA editing and is orthologous to some mutants in rice that also condition ‘yg’ phenotypes. Sequencing of GRMZM2G165521 in the Yg3 background reveals a seven base pair insertion in the first intron relative to the wild-type reference line. This insertion results in an alternate transcription start site and open reading frame that eliminates the first exon of the PPR protein. The alignment of heterozygous yg3 RNAseq reads confirm transcription at the site of the insertion.
Graduation Semester
2018-05
Type of Resource
text
Permalink
http://hdl.handle.net/2142/101199
Copyright and License Information
Copyright 2018 Crystal Sorgini

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