Diversity and comparative genomics studies in mung bean [Vigna radiata (L.) Wilczek]

Abstract

Mung bean (Vigna radiata (L) Wilczek), a drought-tolerant, short-duration pulse crop, is a source of high-quality protein, folates, fiber, carbohydrates, and vitamins. It is known to contribute to a balanced diet by complementing cereals in South Asia, Africa, and some parts of South America. Although domesticated and consumed by large populations in middle to low-income countries for centuries, mung bean has not been a significant crop in the western world until recently, with minimal breeding work in North America and Europe. However, extra effort in research is needed as climate change threatens food security, intensified campaigns about sustainable agriculture, and the shifting consumer preferences towards healthier plant-based protein products. This work is part of the ongoing breeding efforts to establish mung bean as a cash crop in the Midwestern United States. To develop a body of knowledge on mung bean in the Midwestern US we have conducted multiple studies collated in this dissertation. The study described in chapter two, was designed to (1) to study the root traits related to the phenotypic and genetic diversity of 375 genotypes of the Iowa Mung bean Diversity (IMD) panel and (2) to conduct genome-wide association studies of root-related traits using the Automated Root Image Analysis (ARIA) software. We collected, imaged, and analyzed over 9,000 digital images at three-time points (days 12, 15, and 18 after germination). Broad-sense heritability at days 15 (0.22–0.73) and 18 (0.23–0.87) was higher than that for day 12 (0.24–0.51). We also report genotypes with topsoil foraging and “steep, cheap, and deep” root ideotypes. We identified markers significantly associated with the lateral root angle (LRA) on chromosomes 2, 6, 7, and 11, length distribution on chromosome 8, and total root length-growth rate, volume, and total dry weight on chromosomes 3 and 5. We report beta-galactosidase 3 associated with the LRA, which has previously been implicated in the adventitious root development via transcriptomic studies in mung bean. Leaves are central to key processes in plants such as photosynthesis, light interception, biomass accumulation, and yield. In chapter three, we collected over 5000 leaf images from 484 genotypes of IMD panel over two years (2020 and 2021) with two replications per experiment. Leaf traits were extracted using image analysis, analyzed, and used for association mapping. Morphological diversity included leaflet type (oval or lobed), leaflet size (small, medium, large), lobed angle (shallow, deep), and vein coloration (green, purple). A regression model was developed to predict each ovate leaflet’s area (adjusted R2 = 0.97; residual standard errors of <= 1.10). Using association mapping, we identified candidate genes that would need further investigation to uncover their roles in leaf development, growth, and function. Association mapping and QTL (Quantitative Trait Analysis) methods have been useful in mapping candidate genes controlling traits of interest. However, there still exist a lag to transition from discovery of candidate genes and their use in breeding programs is due to several known reasons. In chapter four, we used functional and comparative genomics to investigate days to flowering with respect to four species: Glycine max (soybean), Phaseolus vulgaris (common bean), Vigna unguiculata (cowpea), and Vigna radiata (mung bean). This study will help to refine and validate candidate genes for days to flowering trait in mung bean, which is important as it determines optimal reproductive success. These analyses confirmed the tight linkage between plant height and days to flowering and identified several candidate genes underlying this agronomically important trait.