Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense

Abstract

Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize–A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.

A low-cost greenhouse-based high-throughput phenotyping platform for genetic studies: a case study in maize under inoculation with plant growth-promoting bacteria

“…No significant interaction between genotype and management for both HTP and manually measured phenotypes may also indicate the absence of phenotypic plasticity for PGPB responses in our population. Our findings agree with those of Vidotti et al (2019a) and Vidotti et al (2019b), who did not find significant genotype and management interactions in hybrid maize using different genotypes and PGPB from this study. This might be because both managements were tested under nitrogen-limited conditions or the experiment only covered the early developmental stages.…”

Corn Responsiveness to Azospirillum: Accessing the Effect of Root Exudates on the Bacterial Growth and Its Ability to Fix Nitrogen

“…Therefore, further researches on the role of root exudates as mediators of the corn- Azospirillum symbiosis need to be carried out, including regarding the amino acids classes, as despite their null chemotaxis, they seemed to be determinant in the degree of the benefits provided by A. brasilense. Additionally, rather than being the cause of the responsiveness, root exudates are more likely to reflect the specificity of transcriptional signaling involved in the mutual recognitions between Azospirillum and its host plant [ 12 , 13 ].…”

“…Despite the consistent benefits obtained with the corn inoculation with Azospirillum , different degrees of positive outcomes have been reported in the literature [ 4 ]. Part of it has been attributed to genotypic variation of the host genetic background, including the composition of the metabolites it releases toward the rhizosphere [ 12 ]. Crops genotypes, including corn, may differ in the amount and the composition of their exudates, but the implications of this for the rhizosphere colonization by Azospirillum , or for the benefits it provides to plants, remain a poorly-understood subject [ 13 ].…”

Validation of functional polymorphisms affecting maize plant height by unoccupied aerial systems discovers novel temporal phenotypes

“…Outside of Farfan et al (2015) , hybrid maize populations have been used in relatively few other GWASs to discover SNPs. GWAS can comprise both additive and nonadditive SNP effects for the traits controlled by both overdominance and dominance conditions ( Warburton et al 2015 ; Wang et al 2017 ; Vidotti et al 2019 ; Galli et al 2020 ). So that validation of SNPs discovered in maize hybrid GWAS populations over multiple genetic backgrounds is important to find pure additive effects of candidate genes.…”