Genetic analysis of tocochromanol variation in maize using high-density linkage mapping

Megan E Fenton, Purdue University

Abstract

Vitamin E is an essential nutrient in the human diet and refers to eight distinct compounds that are collectively known as tocochromanols. Tocochromanols are grouped into two classes: tocotrienols and tocopherols. Tocochromanols are the major lipid-soluble antioxidants in maize (Zea mays L.) grain. Enhancing the tocochromanol content of maize derived foods through plant breeding has important nutritional and health implications. Chapter one is a literature review that provides a foundational understanding of the biosynthesis, function and genetic control of tocochromanols in plants, with specific attention to maize (Zea mays L.). Upon this foundation two research objectives were developed that work towards a better understanding of the genetic architecture of tocochromanols in plants. The two research objectives are (1) to investigate the genetic architecture of tocochromanol variation in maize (2) to explore the differences in genetic information explained by the data produced by two tocochromanol phenotyping methods. The first research objective is addressed in chapter two, in which high-density linkage mapping was used to explore the genetic architecture of tocochromanol content variation in two biparental maize populations. The second research objective is addressed in chapter three in which two biparental maize populations were phenotyped with two phenotyping systems to determine the ability of these two systems to effectively provide useful phenotypic information for the study of genetic architecture of tocochromanol variation in maize. Variation for tocochromanol content was previously assessed in a maize inbred association panel. The research presented in chapter two and three utilized four inbred lines exhibiting unique tocochromanol variation that were chosen from the maize inbred association panel, because the maize nested association mapping (NAM) founders did not exhibit unique variation for the tocochromanol compounds of interest. The NAM population is under study for tocochromanols. These four inbred lines were chosen to construct two biparental mapping populations, N6xNC296 and E2558WxCo125, which were developed to further dissect the genetic architecture of tocochromanol variation in maize grain. The N6xNC296 population exhibits variation for &agr;-tocopherol and &agr;-tocotrienol content. The E2558WxCo125 population exhibits variation in the ratio of total tocotrienol to total tocopherol. The populations were genotyped using genotyping-by-sequencing (GBS) and high-density linkage maps were constructed. Each of the two high-density genetic maps contain over 1,200 single nucleotide polymorphism (SNP) markers. The tocopherol and tocotrienol variation in two replicates of each population was quantified using high performance liquid chromatography (HPLC). Composite interval mapping identified a novel QTL associated with tocopherol ratio traits that contains homogentisate phytyl transferase (ZmVTE2) in the support interval. Overall this work illustrates the complementary nature of biparental mapping populations to genome wide association studies in order to further dissect genetic variation and potentially detect rare alleles. The genetic architecture of tocochromanols was further dissected by comparing the relative ability of two phenotyping methods to produce similar and accurate data to be used in genetic analysis. Recent advances in next-generation sequencing have drastically reduced the cost of genotyping. With such a vast reduction in resource use for genotyping, scientists can now examine phenotyping methods used to explore the genetic architecture of a given trait across the genome of the target plant species. Biochemical phenotyping is the determination of the steady state concentrations of a spectrum of biological compounds. The research presented in chapter three examines the efficacy of two biochemical phenotyping systems at determining the genetic architecture of tocochromanol variation in maize. The two phenotyping systems under comparison are well-tested robust methods that provide an accurate representation of tocochromanol phenotyping systems. There were moderate to strong correlations between the tocochromanol content data provided by the phenotyping systems. The two systems produced relatively similar QTL results, with some slight differences. The higher throughput biochemical phenotyping system detected a QTL with the ZmVTE2 gene in the support interval, which had not been previously reported in maize. The differences in these genetic results are likely due to differences in the extraction and chromatography methodologies. Overall the research presented in chapter three suggests that genetic mapping precision is not lost by implementing a system that utilizes microtitre plate technology over the standard methods. Furthermore, this research reinforces that time and attention is needed to develop precise and accurate high-throughput phenotyping systems that allow the genetic architecture of quantitative traits to be explored with greater precision.

Degree

M.S.

Advisors

Rocheford, Purdue University.

Subject Area

Botany|Genetics|Plant sciences

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