Doctor of Philosophy / Department of Agronomy / Geoffrey Morris / Climate change has been anticipated to affect agriculture, with most the profound effect in regions where low input agriculture is being practiced. Understanding of how plants evolved in adaptation to diverse climatic conditions in the presence of local stressors (biotic and abiotic) can be beneficial for improved crop adaptation and yield to ensure food security. Great genetic diversity exists for agroclimatic adaptation in sorghum (Sorghum bicolor L. Moench) but much of it has not been characterized. Thus, limiting its utilization in crop improvement. The application of next-generation sequencing has opened the plant genome for analysis to identify patterns of genome-wide nucleotide variations underlying agroclimatic adaptation. To understand the genetic basis of adaptive traits in sorghum, the genetic architecture of sorghum inflorescence traits was characterized in the first study. Phenotypic data were obtained from multi-environment experiments and used to perform joint linkage and genome-wide association mapping. Mapping results identified previously mapped and novel genetic loci underlying inflorescence morphology in sorghum. Inflorescence traits were found to be under the control of a few large and many moderate and minor effect loci. To demonstrate how our understanding of the genetic basis of adaptive traits can facilitate genomic enabled breeding, genomic prediction analysis was performed with results showing high prediction accuracies for inflorescence traits. In the second study, the sorghum-nested association mapping (NAM) population was used to characterize the genetic architecture of leaf erectness, leaf width, and stem diameter. About 2200 recombinant inbred lines were phenotyped in multiple environments. The obtained phenotypic data was used to perform joint linkage mapping using ~93,000 markers. The proportion of phenotypic variation explained by QTL and their allele frequencies were estimated. Common and moderate effects QTL were found to underlie marker-trait associations. Furthermore, identified QTL co-localized with genes involved in both vegetative and inflorescence development. Our results provide insights into the genetic basis of leaf erectness and stem diameter in sorghum. The identified QTL will also facilitate the development of genomic-enable breeding tools for crop improvement and molecular characterization of the underlying genes Finally, in a third study, 607 Nigerian accessions were genotyped and the resulting genomic data [about 190,000 single nucleotide polymorphisms (SNPs)] was used for downstream analysis. Genome-wide scans of selection and genome-wide association studies (GWAS) were performed and alongside estimates of levels of genetic differentiation and genetic diversity. Results showed that phenotypic variation in the diverse germplasm had been shaped by local adaptation across climatic gradient and can provide plant genetic resources for crop improvement.

<p dir="ltr">Uncovering the mechanisms of senescence in maize will give us a deeper understanding needed to drive future yield increases. Previous work on senescence response to sink disruption has identified a set of genes and biochemical mechanisms. Still, little is understood about the impact of this phenotype on yield and other commercially relevant traits. Uncovering the genetic basis of senescence in maize and testing the effect of these alleles on yield will provide a mechanistic framework for considering this trait to drive future yield increases.</p><p dir="ltr">Ear removal experiments demonstrated that senescence timing is insensitive to the presence or absence of an ear outside a critical window from 10 to 45 days after pollination. Nitrogen fertilization did not impact the SSRS response measured in the upper canopy. In further characterizing the SSRS phenotype, we have provided a spatial and temporal map of the B73 senescence response to sink disruption from the top of the plant to the ear leaf and discovered that this phenomenon is dose dependent and proportional to the size of the sink across two genotypes and years. This relationship was successfully used to predict kernel numbers and grain weight from spectral leaf properties as early as 4 weeks after pollination using remote sensing under agronomic conditions.</p><p dir="ltr">A population of 343 exPVP inbred lines was evaluated for source-sink regulated senescence and hybrid testcrosses were made for a subset of 200 inbred lines to testers for measurement of yield and ear photometry phenotypes. Source-sink regulated senescence of inbred parents was correlated with the yield of intra-family hybrids but was not generally correlated with the yield of hybrids made from crosses between two heterotic groups. The presence of multiple significant SNP association at the Bonferroni-corrected threshold at loci that are associated both with kernel traits and SSRS suggests shared genetic regulation of two traits that is likely driving the observed trait correlations of SSRS with kernel size and yield.</p><p dir="ltr">The maize nested association mapping (NAM) parents reveal a previously unknown breadth of SSRS phenotypes in the global diversity of maize germplasm. Mapping genes for SSRS in the NAM populations supports previously reported loci with large, dominant effects as well as evidence for previously unreported modifiers that are capable of suppressing the dominant alleles and producing a quantitative distribution in SSRS phenotypes. There are distinct alleles within sub-populations worth further study such as sweetcorn populations with non-senescence responses to sink disruption. A multi-factor analysis for QTL mapping, GWAS, and mutant variant sequencing identified highly significant loci on chromosomes 1 from 30.4Mbp to 35.8Mbp, chromosome 2 from 183.2Mbp to 190.8Mbp, chromosome 4 from 38.2Mbp to 134.8Mbp (crosses a centromere), chromosome 5 from 140.8Mbp to 233.9Mbp, chromosome 8 from 112.5Mbp to 123.8Mbp, and chromosome 8 from 155.7Mbp to 163.9Mbp. Candidate genes co-located with Bonferroni SNP in these regions may contribute to SSRS phenotypes through regulation of autophagy, accumulation of flavonoids, and sequestration of sugar in cell walls as an alternative sink. It is possible that co-regulation of these genes could cause all of them to be involved in the stress response of B73 to sugar accumulation. To find the causal variants for these traits, fine mapping and comparisons of near-isogenic lines will be required to narrow the list of candidate genes. Uncovering the alleles responsible for SSRS in global maize diversity could provide the building blocks for a physiological approach to increasing yields through optimizing the senescence responses to elevated sugar levels during grain-fill.</p>