Evaluating a Collection of Agronomic Traits to Better Understand the Importance of Epistasis and Epistasis by Environment Interaction in Maize.
by Baris Alaca
Date of Examination:2024-03-08
Date of issue:2024-04-05
Advisor:Prof. Dr. Stefan Scholten
Referee:Prof. Dr. Stefan Scholten
Referee:Prof. Dr. Timothy M. Beissinger
Referee:Prof. Dr. Reimund P. Rötter
Sponsor:General Directorate of Education Abroad (Yurt Dışı Eğitim Genel Müdürlüğü) Ministry of Education, Republic of Türkiye.
Persistent Address:
http://dx.doi.org/10.53846/goediss-10418
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Abstract
English
Maize, a key cereal crop, stands alongside wheat and rice in global importance. Its domestication from teosinte in southern Mexico 10,000 years ago marked a turning point in human agriculture. Over the centuries, maize has spread globally, becoming a staple crop vital for food, feed, and biofuel. Modern plant breeding techniques and improved genetic backgrounds have propelled maize production, making it adaptable to diverse environments and significantly contributing to global food security. The increase in agronomic traits owes to multiple factors, including advancements in plant genetics, agronomic practices, and technological innovations. Agronomic practices, precision agriculture, and remote sensing contribute to higher yields, underscoring the multidimensional approach to crop improvement. Molecular markers and genomic selection enable breeders to identify genes controlling crucial agronomic traits like yield, flowering time, and plant height. Genetic markers, especially single nucleotide polymorphisms (SNPs), have been pivotal in developing improved maize varieties. The integration of sequencing technology has revolutionized plant breeding, making genetic information more accessible. The decreasing cost of sequencing has facilitated genome exploration, enabling the identification of genes controlling agronomic traits. Furthermore, researchers have identified that additive genetic variation predominantly contributes to the variation within a population. However, it is acknowledged that additive variation does not fully account for heritability, leaving a portion known as missing heritability. Consequently, an increasing number of studies are directing their focus toward understanding and incorporating this missing heritability to enhance the prediction of quantitative agronomic traits. Epistasis, representing complex interactions between genes, is one approach employed to calculate this missing heritability. However, detecting epistatic interactions poses challenges, notably the multiple testing problem. Additionally, environmental factors can modify gene effects, complicating their detection. To address these complexities and identify epistatic interactions while considering the impact of the environment on genotypes, a unique population must be tested across various environments. The initial study aimed to identify epistasis by environment interactions using genomes-to-field (G2F) data tested in multiple environments. In the second study, we aimed to investigate origin-of-seed effects utilizing an Epistasis Mapping Population (EMP). Epistasis by environment (EEI) study delves into the complicated relationships between various agronomic traits in maize, exploring correlations, heritability, and quantitative trait loci (QTL) mapping across multiple environments to find the interactions between QTLs, QTLs by environment, and epistasis by environment interactions. The research investigated the following quantitative traits: pollination and silking days, plant and ear height, stand percentage, and yield. The initial analysis reveals strong correlations between pollen and silk days after pollination (DAP), as well as between plant height (PH) and ear height (EH). Moderate correlations exist among PH, EH, pollen DAP, and silk DAP, indicative of the intricate network of influences among these quantitative traits. Interestingly, the stand percentage exhibits a low correlation with other traits across locations, suggesting its sensitivity to external factors during the growing period. The subsequent QTL mapping analysis uncovers significant loci associated with the studied traits across environments. These findings align with previous research, emphasizing the genetic complexity of traits. Notably, the study identifies specific QTLs for each trait in different locations, underlining the substantial impact of environmental factors on trait expression. Our analysis extends to QTL-environment interactions, revealing location-specific markers and significant interactions for pollen DAP, silk DAP, PH, EH, and yield. This underscores the importance of considering the environment when interpreting genetic influences on these traits. Moreover, we identified significant epistatic interactions for each phenotypic trait. The following analysis introduces the concept of epistasis by environment interactions (EEI), illustrating pollen and silk DAP, PH, EH, and yield. EEI study comprehensively illustrates the genetic and environmental factors influencing agronomic traits in maize. Our research contributes valuable insights that can inform future breeding strategies and enhance our understanding of maize phenotypic traits' complex genetic and environmental interactions. In the second study, we utilized two diverse seed sources of Epistasis Mapping Populations (EMPs), which aim to identify epistatic interactions between genomic regions, to investigate origin-of-seed effects on mRNA levels. By comparing phenotypic performances, EMP helps identify regions of the genome where epistasis occurs, contributing valuable insights into gene regulation and species evolution. EMPs reduce the multiple-testing and provide a nuanced understanding of gene interactions. The study focused on the influence of origin-of-seed on maize seedlings at the V2 growth stage with EMPs. While complete sets of EMPs are traditionally required for studying epistatic interactions, the study uses a subset of genotypes in this part of the research question. Our study found no differentially expressed genes (DEGs) between two seed sources at the V2 growing stage. Despite limitations, such as a small sample size and focusing solely on mRNA expression, the study suggests that greenhouse and field environmental conditions do not significantly impact the progeny's gene expression at the V2 growing stage. In addition, robust comparisons between different genotypes validate the reliability of the analysis, reinforcing the conclusion that origin-of-seed effects do not lead to significant expression. Overall, this research contributes valuable insights into the origin-of-seed effect on maize seedlings, pointing out a direction for further investigations.
Keywords: Maize; Epistasis; Epistasis by environment interactions
