Genomic dissection of a tropical maize diversity panel: a study on molecular characterization and resistance to the corn stunt disease complex

• Autor(a) principal: Espolador, Fernando Garcia
• Data de Publicação: 2020
• Tipo de documento: Tese
• Idioma: eng
• Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
• Texto Completo: https://www.teses.usp.br/teses/disponiveis/11/11137/tde-15072020-142738/
• topic: Spiroplasma kunkelii; Spiroplasma kunkelii; Zea mays; Zea mays; Diversity panel; Maize bushy stunt phytoplasma; Maize bushy stunt phytoplasma; Painel de diversidade; Structure

The tropical maize is an important pool of genetic diversity to be explored in breeding programs to face new agricultural challenges, nevertheless it requires genetic characterization. For instance, the corn stunt disease complex (corn stunt disease and maize bushy stunt disease) caused significative losses in the last crop seasons, but its genetic control and resistant germplasm are poorly comprehended. In this study, we assembled and genetically characterized a tropical maize diversity panel in order to construct a representative pool of tropical germoplasm for genetic studies and to investigate the genes associated with the resistance of corn stunt disease complex, as well as the potential sources of resistance. For that, 360 inbred lines highly diverse were genotyped using a genotyping-by-sequencing approach with restriction enzymes PstI and MseI and aligned to the version 5 of the B73 reference genome. For genetic assessments, two datasets were considered: one with the raw data, and the second one with data imputed and filtered for quality control, retaining only biallelic markers with minor allelic frequency higher than 0.05, call rate higher than 0.95, and linkage disequilibrium (r2) lower than 0.99. Genome wide association study (GWAS) was performed incorporating the genomic relationship matrix and 3 main principal components to deal with panel structure. Using the filtered dataset, we analyzed the traits proportion of survivor plants (PSP), sanity score in survivor plants (SSSP), and whole sanity score (WSS) which were evaluated in two sites in the State of São Paulo, Brazil. The raw dataset contained 196,803 SNPs well distributed across the chromosomes. The proportion of missing data was 0.391 and the average observed heterozygosity was 0.036. The filtered dataset, containing 14,655 SNPs, showed similar estimates of populational genetic parameters compared to the first one. The structure analysis indicated that this panel comprises nine subpopulations. Through GWAS, 13 markers were significant to the traits and presented functions mainly related to cellulose metabolism, auxin pathway, genes of defense and response to phagocyte oxidase activity, and anthocyanin production. The candidate genes were associated, for example, with the response of glucose accumulation in leaves, the reduction of auxin content, and the direct defense-attack against the pathogens. For each of the traits, we found lines with the totality of favorable alleles in homozygosis, which would facilitate transfering resistance genes to other genotypes. Additionally, the lines from the ancestral PF-41X05-33-05B exhibited high content of favorable alleles to all the traits simultaneously. Our findings reveal underlying genetic mechanisms triggered by plants in response to the corn stunt disease complex and allowed the identification of potential resistant inbred lines. These results can substantially improve the genetic gains when incorporated in breeding programs and constitute an important contribution to the genetic comprehension of the tropical maize germplasm.