Date of Award
Open Access Dissertation
To address the challenge of global mineral malnutrition, current biofortification research in crop plants aims to improve mineral concentration and micronutrient bioavailablity via genetic and traditional breeding methods. Many staple food crops are also used as biofuels, and the chemical and mineral composition of these energy crops directly affect biomass quality and subsequent energy output. Identification of genes and QTL that impact mineral and compositional traits in the grain and biomass of major cereals, including sorghum, is fundamental to developing breeding and selection methods aimed at increasing bioavailable minerals and improving biofuel suitability and seed nutritional quality. A combinatorial strategy using multiple “omics” methods is an effective approach to understand the molecular genetic systems integral to improving mineral profiles. We can utilize genomics to identify genes, markers and QTL for mineral traits of interest, integrate transcriptomics to evaluate the expression of candidate genes identified in target tissues and genotypes, and carry out ionomic studies to identify and characterize relationships and correlations among and between minerals and to identify common genetic or transcriptomic patterns underlying one or more mineral traits. Bioinformatics platforms and their associated databases are essential for the integration of these three “omics” approaches. With the goal of advancing sorghum functional genomics, we developed an Affymetrix microarray to quantify global gene expression and demonstrated its ability to measure gene expression from a series of sorghum lines. The array and the associated gene expression data were developed as a new resource for sorghum crop breeding and genomic discovery. Our expression atlas reports the transcript profiles of 78 sorghum tissues representing shoot, root, leaf, and stem from 6 sorghum lines including grain, sweet, and biomass sorghums. In addition to our sorghum transcriptomics study, we also integrated genomics and ionomics to identify and characterize the molecular genetic component of mineral compositional traits of interest. Here we describe the successful mineral profiling of a diverse panel of sorghum grain utilized to locate QTL for mineral traits. We ascertained genotypic correlations, between-trait correlations and QTL colocation. We observed QTL colocation in addition to strong phenotypic correlation of elements vital to plant and human nutrition, such as iron and manganese, which suggest that common molecular mechanisms may underlie the uptake and metabolism of these important mineral traits. Combined with high reported heritabilities, these analyses are also promising for the development of breeding strategies aimed at simultaneous improvement of multiple mineral traits in sorghum via marker-assisted selection. The integration of ionomics and genome-wide association allowed us to identify several germplasm sources, genomic loci and candidate genes as potential biofortification targets for marker-assisted breeding and genomic selection.
Shakoor, N.(2014). Compositional Traits in Sorghum Bicolor Characterized by Transcriptome, Ionome and Genome-wide Association Analysis. (Doctoral dissertation). Retrieved from http://scholarcommons.sc.edu/etd/3009