Accessing and Dissecting Useful Genetic Variations for Iron and Zinc Content in Pearl Millet (Pennisetum glaucum) Using Genome Wide Association Studies

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Student thesis: Doctoral ThesisDoctor of Philosophy

Original languageEnglish
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Award date2018
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Abstract

Iron/zinc deficiencies cause extensive health problems in developing countries and contribute to a loss of human potential. Many who suffer from micronutrient
deficiencies are dependent on staple crops to meet their dietary requirements. Thus, the biofortification of crop cultivars with elevated levels of grain micronutrients is becoming increasingly attractive and is largely facilitated by genetics/genomic platforms. Pearl millet is an excellent candidate for biofortification as it is accessible to many populations suffering with micronutrient malnutrition. It contains naturally high levels of micronutrients and thrives in dry, semi-arid regions where farming conditions are often unfavourable; therefore it is considered climate change ready.

The aim of this project was to utilise natural genetic variations, present in a
germplasm diversity panel of pearl millet to identify genes associated with iron/zinc uptake, with potential to contribute to the development of micronutrient-rich varieties. Iron/zinc levels were quantified in 230 lines by Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES) and ranged between 29.18–135.27mg/kg and 22.07–93.28mg/kg, respectively. Anti-nutritional factors affecting mineral bioavailability were also considered, including phytate and metal-chelating soluble phenolics. STRUCTURE analysis using Single Nucleotide Polymorphisms (SNPs), generated by Genotyping by Sequencing (GBS) revealed insignificant population structure, further supported by principal component analysis. The extent of Linkage Disequilibrium (LD) was also assessed among all pairs of loci and was found to be prominent on chromosomes 3 and 5. Genome Wide Association Studies (GWAS) resulted in hundreds of significant marker-trait-associations for grain iron/zinc content with p-values ranging from 3.99 E-06–7.54 E-07. Using the 4kb region surrounding the 35 most significant SNPs, a BLAST search of the NCBI
database revealed 6 candidate genes associated with iron/zinc uptake. The most
significant was YUCCA11, which drives zinc efficiency via auxin biosynthesis.
Additionally, haplotypes covering the YUCCA11 gene were identified and their
association with trait data was assessed

Keywords

  • plant genetics, micronutrients, GWAS, genomics, plant breeding, micronutrient malnutrition