This indicates that despite the drastic reduction in defense, some mechanisms have remained in domesticated types or have been recently introgressed by geneflow from wild populations. Identifying and amplifying these anti-herbivore defense mechanisms in modern cultivars, as well as introducing new mechanisms from wild relatives and landraces, could greatly improve productivity and profitability, while limiting the use of toxic agrochemicals. Like other crops, Lima bean has lost many of its mechanisms of defense against insect herbivores during the bottlenecks of domestication and modern breeding programs. This is illustrated by the finding that wild P. lunatus seedlings have greater chemical diversity than their domesticated relatives . Lima beans have been used as an experimental model in numerous studies of herbivoreinduced direct and indirect defenses . Previous studies have examined the role of cyanogenesis, volatile organic compounds, blueberry package and extrafloral nectaries as plant defense mechanisms against herbivores . Due to the high metabolic cost to the plant of producing these defensive compounds, P. lunatus makes tradeoffs between direct and indirect defense mechanisms .
The goal of the research presented In this dissertation Is to understand the domestication history, current variability, and breeding potential of the antiherbivore defense traits in Lima bean with a special emphasis on cultivars adapted to the Central Valley of California and cyanogenesis as a mechanism of defense against Lygus hesperus. Lima Beans as the Predominant Grain Legume in California Lima beans are one of five domesticated species in the genus Phaseolus. They were independently domesticated first in Central Mexico and again on the western slope of the Andes Mountains of Ecuador and northern Peru . Dating of starch grains on human dental remains, indicates that beans were domesticated in Northern Peru approximately 8000 years ago . Estimates for the date of domestication of Lima beans in Mexico are less certain but range from 2300-3400 years ago . The domesticated Andean gene pool is characterized by large flat seeds while the Mesoamerican gene pool has smaller round or flat seeds . Lima beans are multi-annual or semi-perennial, with crops typically needing 115- 135 days to reach maturity . They are adapted to a range of climates but are especially suited to warm and humid environments . Lima beans are grown in many regions of the world, including Africa, Asia, and Central and South America . In the United States, California is the primary growing region for mature dry Lima beans, where they are an important crop for the agricultural systems of the Central Valley.
As a nitrogen-fixing, highly vigorous rotation crop for tomatoes and other high-value crops, Lima beans provide an essential service of sustaining soil fertility and breaking pest and weed lifecycles . Additionally, Lima beans are very drought tolerant, making them ideal for the perennial water shortages experienced by California in recent decades . Two market classes – small white and large white – are grown in the state. Baby Limas are grown mostly in the region around Sutter and Colusa Counties. Large Limas, which need cooler nighttime temperatures, are grown mostly in Stanislaus County . Approximately 20,200 acres of Lima beans were grown in 2018, representing nearly half of the dry bean production in the state . Improved cultivars of Lima bean yield approximately 2,500-3,500 pounds per acre . Production of Lima bean in California is limited by its vulnerability to L. hesperus. Regular treatment in the field with pesticides, specifically pyrethroids, is the only known effective method of control . This practice is costly for a low-value crop like Lima beans and is unsuitable for organic production.Herbivory by the polyphagous, native Californian insect Lygus hesperus Knight , negatively affects the yields of several important crops, including alfalfa, strawberries, safflower, peaches, almonds, and dry beans . Current methods of controlling L. hesperus are costly, environmentally toxic, and only moderately effective . In sensitive crops like alfalfa and Lima bean, L. hesperuscan cause up to 70% yield loss as measured in sprayed versus unsprayed plots . There are typically four or five generations of L. hesperus each summer, with variability due to climate . The rate of development is dependent on temperature, but it takes on average 27 days from egg to reproductive adult at 20°C . Each generation develops from egg to adult with five nymphal instars going through incomplete metamorphosis .
All nymphs are flightless, but adults are highly mobile . L. hesperus are omnivorous but feed mostly on plant tissue . Their style of feeding is known as rupture feeding or “lacerate and flush.” Feeding starts with the insect probing the food tissue with its straw-like stylet, causing cells to rupture. Saliva secreted from the stylet has enzymes like polygalacturonase and -amylase, which further break down the tissue, creating a slurry that the insect can ingest through their stylet tube . L. hesperus feeding on Lima beans results in the abscission of flowers or young pods and consequently, yield loss. When feeding occurs on mature pods seed viability may be reduced and scarring can occur on seeds, thereby lowering market value . Adults spend about 20% of their time, and nymphs about 30% of their time, probing plants with their stylets. Actual ingestion represents only 3% of the probing time . The mechanical and chemical damage caused by this frequent probing and feeding behavior contributes to the heavy impact that L. hesperus have on crop yields.Understanding the mechanisms and inheritance patterns of L. hesperus tolerance or resistance in Lima bean will aid efforts to breed new varieties that require fewer pesticides and are suitable for organic production. To start, chapter 1 presents a comprehensive review of the literature on how domestication has affected the genetics of insect defense traits. Chapter 2 details the results of a genome-wide association study of cyanogenesis in Lima bean. The goal of this study was to explain how cyanogenesis has been affected by domestication in the Mesoamerican gene pool of Lima beans, with special consideration of the cyanogenic capacity of California cultivars. Chapter 3 will explore the variation and heritability of the tolerance or resistance to L. hesperus in cultivars of Lima bean adapted to the Central Valley of California. This will include a study of how cyanogenesis in Lima bean is affected by the presence of L. hesperus, specifically to determine the extent to which this trait is constitutive or induced. Analysis of the survival and reproduction of L. hesperus on varieties of Lima bean with variable expression of cyanogenesis will also be presented.The processes of cultivation and domestication have transformed wild species into crop plants that are an invaluable food source for the human population. These same processes have also made crop plants more vulnerable to damage by insect pests than their wild relatives . Globally, blueberry packaging insect herbivory accounts for an estimated 18-20% of yield loss during crop production . It is expected that these losses will increase if current trends in climate change continue . Recovering the defensive abilities of crop wild relatives in domesticated plants would result in reduced need for pesticides – which are harmful to human and environmental health – as well as an increase in global food security. Plant defenses against insect herbivores typically consist of complex suites of traits . These may include resistance traits like chemical deterrents, physical barriers, and reduced palatability, or tolerance traits like increased vigor and delayed phenology . Defensive traits can also involve attraction or resource benefits for beneficial organisms such as parasitoids and predators of insect herbivores .
Defense traits may be constitutively expressed and may also be induced to a higher level of expression by factors such as the presence of the target herbivore or volatile signals from a neighboring plant . Induction of a defense trait may occur immediately or slowly over time . The response can also be localized tothe area immediately surrounding the site of damage or be widespread throughout the plant . Several environmental factors can affect the expression of these traits including light intensity , the interspecific and intraspecific diversity of neighboring plants , photoperiod, temperature, and climate . Control of these traits typically involve the expression of multiple loci, which may be linked to other useful or unfavorable agronomic traits . The process of domestication involves selecting wild plants with desirable agronomic traits. The resulting crop plants typically exhibited some or all a suite of traits known as the domestication syndrome. This can include increased palatability, loss of dormancy, seed retention, increased seed size, and seed number . Selection intensity varied across crops and domestication events and there is serious academic debate about the duration and intentionality of this process . Identifying the genes that control agronomically important traits and understanding the way in which they have been affected by domestication is foundational to conserving, amplifying, and increasing their utility. This review will focus on the ways in which the process of domestication has altered the genes underlying plant defenses against insect herbivores. Prior reviews have focused on the mechanisms and physiology of plant defense against insect pests as well as the ways in which domestication has affected the interactions between crop plants, insect herbivores, and higher trophic levels . To my knowledge this is the first review on the subject of how domestication has affected plant and insect herbivore interactions with a specific focus on crop genetics.Domesticated gene pools have significantly less genetic diversity than wild gene pools . During the transition from wild plant to domesticated crop, diversity is lost during the actual domestication process as well as during cultivation, dispersal outside the center of origin, and later improvement through modern breeding . This loss of diversity within crop species has contributed to a loss of insect herbivore resistance traits . This is illustrated in maize through a comparison of teosinte, maize landraces from within the center of origin, maize landraces from outside the center of origin, and modern maize cultivars. Each stage of transition resulted in changes to the anti-herbivore defense strategies as well as changes in gene expression . A similar pattern can be seen in an analysis of the GsRbohA1 locus in soybean of which the A haplotype confers resistance against common cutworm . This allele was only present in 2.2% of modern cultivars compared with 23.5% of landraces and 95.6% of wild accessions . In the case of some anti-herbivore defense mechanisms, the selection against certain phenotypes had clear benefit to human consumers. For example, selections against genotypes which produce toxic compounds like cyanogenic glycosides, or distasteful physical defenses like trichomes, improved the safety and palatability of food . However, several important defense traits such as herbivore-induced volatile organic compounds cannot be perceived by casual observation and have only recently been revealed by careful scientific study . Despite the impossibility of direct selection for or against these traits prior to their discovery, several studies have identified differences in the expression between wild and domesticated crop plants. For example, in several studies of phytophagous insects and their parasitoids, parasitism was higher for hosts on domesticated rather than cultivated plants . In other studies, reduced predation or parasitism was attributed to the loss of chemical diversity or volatile signals . The loss or amplification of indirect anti-herbivore defense traits may be due to genetic drift, linkage, pleiotropic effects, or selection for alternate resource allocation. However, these were not intentionally selected against as their function has only recently been discovered . Breeding programs with little or no insecticide protection may help maintain insect defense traits compared to programs in which insecticides protect plants and mask susceptibility . Two early steps in the process of domestication were cultivation and storage, the intentional planting of future crop species and the saving of seeds between planting seasons . Both cultivation and storage created novel selection pressures on crop plants and their insect herbivores. Traits changed in frequency from the wild population when under the selection pressures of cultivation and storage . For example, in common bean, Phaseolus vulgaris, resistance to Mexican bean weevil Zabrotes subfasciatus is most likely due to a protein ofthe APA family, arcelin . Arcelin is only found in some accessions of wild Phaseolus vulgaris from Mesoamerica and is controlled by a single mendelian gene for which arcelin production alleles are dominant over alleles for its absence .