Developing a molecular linkage map for and understanding the biochemical mechanisms and underlying genetic architecture of biotic stress resistance in lima bean (Phaseolus lunatus L.)

Lima bean (Phaseolus lunatus L.) is a leguminous crop grown in the Americas, Europe, Africa, and Asia by subsistence farmers and commercial farmers alike. Lima beans are the most significant dry bean crop grown in California, and due to heavy biotic stress, there is a demand for the breeding of more productive and resilient cultivars. Lima bean has lagged in the development of genetic resources to advance the understanding of the population structure, domestication, and divergence from other legume species, hindering the development of improved lima bean cultivars. This dissertation establishes a high-quality molecular linkage map for lima bean and evaluates the role of two putative biochemical mechanisms of biotic stress resistance to gain information on the underlying genetics of and enhance breeding efforts for biotic stress resistance in lima bean. The first chapter of this dissertation focuses on the development of a genetic map based on a biparental recombinant inbred line population of lima beans, aligned to both the lima bean and common bean reference genomes. Alignment of the genetic map to the new lima bean reference genome enabled the characterization of chromosome morphology, calculation of recombination rates within and across chromosomes, and definitions of the euchromatic and pericentromeric regions across chromosomes for lima bean. Alignment of the genetic map to the common bean reference genome highlighted the variations in chromosome morphology between lima bean and common bean and identified previously unknown and confirmed suspected genomic rearrangements, while confirming the strong synteny between the two closely related species. The second chapter of this dissertation focuses on the identification of significant QTL for key agronomic and domestication traits in the UC 92 – UC Haskell biparental recombinant inbred line population of lima beans. QTLs of domestication traits in lima bean are identified in this population and their putative orthologs in common bean. A major QTL underlying determinacy was identified on chromosome 1 and collocates with major QTLs for flowering time and inflorescence position. The genetic interactions and transgressive segregation and directionality of desirable traits for breeding are reviewed and their correlations with other traits and potential impacts towards breeding advancements are analyzed. The third chapter analyzed the variation in volatile cyanide production in different reproductive tissues of lima beans across environments subject to different levels of biotic stress as a putative biochemical mechanism of stress resistance in lima beans. Using a panel of 12 cultivars adapted to California, the variation in volatile cyanide production was evaluated across different time intervals and following repeated injury in the floral bud, immature pod, mature pod, and fresh seed tissue. There was a significant decline in volatile cyanide production from the immature (floral bud and immature pod) to the mature (mature pod and fresh seed) tissues. Studying the volatile cyanide production in the biparental recombinant inbred line population across environments subject to a range of biotic stress levels due to insecticide applications, demonstrated an increase in volatile cyanide production in plots that were subject to biotic stress. Using this biparental RIL population, a major QTL underlying volatile cyanide production in the floral bud and immature pod tissue was identified on chromosome 5, and with two and three other minor QTLs, respectively, explain over 97.5% of the phenotypic variation for these traits and maintained high heritability across environments. The fourth chapter analyzed the variation in polygalacturonase inhibition in the floral bud tissue of lima beans across environments subject to different levels of biotic stress as a putative biochemical mechanism of stress resistance in lima beans. The variation in crude plant extract protein concentration and the inhibition of polygalacturonase sourced from Lygus hesperus and Aspergillus niger was evaluated across environments subject to different biotic stress due to insecticide applications; these biochemical traits were evaluated in a panel of 12 California-adapted cultivars and a biparental recombinant inbred line population. There was a significant (p < 0.05) and consistent difference between the insecticide applications on all three biochemical traits studied, with higher levels observed in the treatments that controlled for biotic stress with insecticide applications. Major QTLs were identified for both crude plant extract protein concentration and polygalacturonase inhibition of A. niger on chromosome 1. While all three biochemical traits had low levels of heritability, they had positive correlations with yield across the different environments subject to biotic stress. Collectively this dissertation provides a high-quality genetic map as a key genetic and genomic resource for lima bean research, and insight into the synteny and rearrangements between lima bean and its closest relative, common bean. This genetic map combined with analysis of two putative mechanisms for biotic stress resistance allows QTL mapping of biotic stress resistance traits, which can aid in the development and advancement of lima bean cultivars with improved biotic stress resistance in the California region