Identification and Characterization of Intermediate Phenotypes to Decipher Genetic Architecture of Stalk Lodging Resistance in Maize (Zea Mays L.)

Maize is a key contributor to global food security and incurs severe yield losses due to stalk lodging, the permanent displacement of plants from an upright growth habit due to mechanical damage to the stem (stalk). Stalk lodging resistance, an indicator of the stalk ability to resist lodging, is a complex trait and determined by several structural, geometric, and material properties of stalks, collectively referred to as intermediate phenotypes, whose identity and genetic framework are poorly understood. Therefore, progress in resolving the genetic architecture of stalk lodging resistance was impeded by a lack of standardized phenotyping methodologies and a poor understanding of the intermediate phenotypes associated with stalk lodging resistance. To this end, my thesis work was focused on increasing the genetic resolution of stalk lodging resistance by unpacking the phenotypes underlying stalk lodging resistance, developing a high-density phenotype resource of the intermediate phenotypes identified, and uncovering the genetic basis of candidate intermediate phenotypes. Firstly, we assessed different phenotypes underlying stalk lodging resistance in a small yet genetically diverse set of maize hybrids and identified flexural stiffness, bending strength, diameter, and moment of inertia of stalks as important phenotypes associated with lodging resistance. Secondly, we generated a high-resolution phenotype dataset consisting of about 1.2 million data points recorded on 11 intermediate phenotypes measured on 31,260 stalks representing a panel of 566 maize inbred lines evaluated in four environments and captured substantial natural variation for these phenotypes. In the last objective, I characterized the phenotype variation of intermediate phenotypes and employed association mapping techniques to integrate the phenotype and whole genome resequencing data to identify several novel candidate loci underlying the intermediate phenotypes associated with stalk lodging resistance.