Digital Theses Archive


Tesi etd-02012024-222653

Type of thesis
Identification of genetic determinants of maize (Zea mays L.) yield components in a multiparent population using genomics high-throughput phenotyping
Scientific disciplinary sector
Istituto di Scienze della Vita - PH.D. IN AGROBIODIVERSITY
relatore Prof. DELL'ACQUA, MATTEO
  • automated phenotyping
  • MAGIC population
  • Maize
  • photosynthesis
  • QTL mapping
  • seed traits
  • SPET genotyping
  • yield components
Exam session start date
Maize is an ideal C4 monoecious cereal crop with complex genomic and high heterogeneity. It can grow well in a very wide range of environments with different climates and geographical areas. Photosynthesis is one of the important physiological processes in plants to provide food for plant growth and development in each stage. Yield and yield components rely on the full support from photosynthesis during their development. Especially seed development counts on this process during the grain-filling period to mature embryo and endosperm which can determine the seed weight and size. In our study, looking for the QTL and potential candidate genes regulating the seed weight, and size, and relating to the photosynthetic process were focused by using MAGIC maize population genotyped by single primer enrichment technology (SPET). <br>We developed a large set of high-quality 79k SPET genotyping data of the MAGIC maize population to use for genetic studies. Using the genotyping data, the MAGIC population used in the present study was proved that as an unbiased population in one genetic structure for studying on genetic architecture of quantitative complex traits for QTL mapping and GWAS analysis. <br>According to the results from phenotyping analysis, seed weight, size, shape, and color have a high variation in the present population. Moreover, seed weight and size show a highly significant positive correlation with each other in both PC plots for two locations used by PC1 and PC2 and a significant association at a 95% confidence interval of the same traits in the same population between the two environments. We obtained a dataset accounting more than 130K raw datapoints, describing the diversity in terms of seed size, shape, color, and weight. We associate this diversity with the genetic constitution of the panel of maize lines via QTL mapping, which results in the identification of 54 significant signals highlighting the existence of pleiotropic QTLs controlling seed color size, shape on chromosome 1. Via differential expression of founders’ haplotypes we are able to identify differentially expressed genes which match the founders’ coefficients at the region. This way we identified two genes, orthologs of Arabidopsis’ cytochrome D and High chlorophyll fluorescence 243. Appling the same procedure we also detect two potential candidates for the variation of Hundred Seed Weight, which encode for KANADI protein and a subunit of light-harvesting chlorophyll-protein complex (A4). Interestingly, in the same region we also that the ortholog of SIP3, CBL-interacting protein kinase 6 (CIPK6), is also potentially contributing to seed size. These findings may provide the maize breeding community with preliminary evidence to further the knowledge of yield components and seed colour in maize. For photosynthesis, the two genes with known functional proteins were predicted as priority genes related to phenotypic variation in the kinetics of NPQ induction and relaxation and ΦPSII traits that have consistent correlations with each other. One of them VTE4 gene located within the QTL for NPQ induction on chromosome 5, and minor PSII antenna CP24 (lhcb6) gene resided within QTL in the distal portion of chromosome 10 which related to ΦPSII and NPQ parameters. In future, our findings will support to advanced molecular breeding programs to improve maize variety in a short period of time.