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Open Access Publications from the University of California

Scholarly Works (67 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2014)
The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail.
    Cover page: The contribution of genetic and genomic approaches to plant domestication studies
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2023)
    Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earths resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
      Cover page: Biocultural diversity and crop improvement.
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2009)
      Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F ST, and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F ST value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.
        Cover page: Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae)
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2019)
        Landscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris , the progenitor of common bean ( P. vulgaris ), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and that the species colonized areas with different temperature and rainfall compared to its core area of origin. Thus, this species provides an opportunity to examine to what extent adaptation of a species can be broadened or, conversely, ecological or geographical distribution can be limited by inherent adaptedness. In the current study, we applied a landscape genomics approach to a collection of 246 wild common bean accessions representative of its broad geographical and climatic distribution and genotyped for ∼20K SNPs. We applied two different but complementary approaches for identifying loci putatively involved in environmental adaptation: i) an outlier-detection method that identifies loci showing strong differentiation between sub-populations; ii) an association method based on the identification of loci associated with bio-climatic variables. This integrated approach allowed the identification of several genes showing signature of selection across the different natural sub-populations of this species, as well as genes associated with specific bio-climatic variables related to temperature and precipitation. The current study demonstrates the feasibility of landscape genomics approach for a preliminary identification of specific populations and novel candidate genes involved in environmental adaptation in P. vulgaris . As a resource for broadening the genetic diversity of the domesticated gene pool of this species, the genes identified constitute potential molecular markers and introgression targets for the breeding improvement of domesticated common bean.

        Author Summary

        The ancestral form of common bean has an unusually large distribution in the Americas, extending over 10,000 km from ∼35° N. Lat. to ∼35° S. Lat. This wide distribution results from discrete long-range dissemination events to the Andes region from the original environments in Mesoamerica. It also suggests adaptation to new environments that are distinct from those encountered in Mesoamerica. In this research, we identified genes that may be involved in adaptation to climate variables in these new environments using two methods. A first method – outlier detection – was used to identify genome regions that differentiated the wild bean groups in the Andes resulting from discrete dissemination events among themselves and the different groups in Mesoamerica. The second method – genome-wide association – was used to identify candidate genome regions correlated with these same variables across the entire distribution from Mesoamerica to the southern Andes. The two methods identified two sets of candidate genes, several of which were related to the water status of plants, and illustrate how the genetic architecture of adaptation following long-range dissemination. This study provides sets of candidate genes as well as candidate wild bean populations that need to be corroborated for their use in increasing the water use efficiency of domesticated beans.
          Cover page: Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)
          • Thesis
          • Peer Reviewed
          UC Davis Electronic Theses and Dissertations (2022)

          Terminal drought is an increasing issue for chickpea production. Chickpea (Cicer arietinum L.) is a pulse crop consumed worldwide, providing important food resources across the globe. To reduce or eliminate the major crop losses caused by terminal drought at the end of the chickpeas production period, efforts to breed for various agronomic traits, foremost being under drought conditions, are required. A recombinant inbred population consisting of 149 progeny lines resulting from the cross ILC 588 (drought tolerance) x ILC 3279 (drought susceptible) and generously provided by ICARDA (Hamwieh et al. 2013), was analyzed for yield, 100-seed weight, and days to 50% flowering under irrigated and non-irrigated conditions in Davis, California over three years (2019-2021) to identify QTL related to these agronomic traits. Phenotypic evaluation identified differences between treatments and RILs. A linkage map was created and utilized to identify QTL for the three agronomic traits for possible inclusion into breeding programs or future research.

            Cover page: Analysis of the Inheritance of Field Drought Tolerance in ILC 588 x ILC 3279 Recombinant Inbred Population of Chickpea
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2015)
            Plant aquaporins are a large and diverse family of water channel proteins that are essential for several physiological processes in living organisms. Numerous studies have linked plant aquaporins with a plethora of processes, such as nutrient acquisition, CO2 transport, plant growth and development, and response to abiotic stresses. However, little is known about this protein family in common bean. Here, we present a genome-wide identification of the aquaporin gene family in common bean (Phaseolus vulgaris L.), a legume crop essential for human nutrition. We identified 41 full-length coding aquaporin sequences in the common bean genome, divided by phylogenetic analysis into five sub-families (PIPs, TIPs, NIPs, SIPs and XIPs). Residues determining substrate specificity of aquaporins (i.e., NPA motifs and ar/R selectivity filter) seem conserved between common bean and other plant species, allowing inference of substrate specificity for these proteins. Thanks to the availability of RNA-sequencing datasets, expression levels in different organs and in leaves of wild and domesticated bean accessions were evaluated. Three aquaporins (PvTIP1;1, PvPIP2;4 and PvPIP1;2) have the overall highest mean expressions, with PvTIP1;1 having the highest expression among all aquaporins. We performed an EST database mining to identify drought-responsive aquaporins in common bean. This analysis showed a significant increase in expression for PvTIP1;1 in drought stress conditions compared to well-watered environments. The pivotal role suggested for PvTIP1;1 in regulating water homeostasis and drought stress response in the common bean should be verified by further field experimentation under drought stress.
              Cover page: Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)
              • Thesis
              • Peer Reviewed
              UC Davis Electronic Theses and Dissertations (2022)

              Lima beans (Phaseolus lunatus) are a globally important crop with great potential to contribute to future food security through their high nutritional value, vigor, drought tolerance, and ability to fix nitrogen. A major limiting factor for the contribution of Lima beans to the global food supply is their susceptibility to herbivory by insects like Lygus hesperus. The goal of the research presented in this dissertation is to understand the domestication history, current variability, and breeding potential of the anti-herbivore defense traits in Lima bean with a special emphasis on cultivars adapted to the Central Valley of California, and on cyanogenesis as a mechanism of defense against L. hesperus. Chapter 1 is a comprehensive review of the existing research on the effect of domestication on anti-herbivore defense traits. In chapter 2, a genome-wide association study is used to explore the inheritance of cyanogenesis in Lima beans within the Mesoamerican gene pool. This study identified highly significant SNPs for the release of cyanide immediately following tissue disruption that could contribute to a deterrence defense strategy. Significant SNPs were also identified for a more sustained release of cyanide that could contribute to a defense strategy of herbivore intoxication. In chapter 3, the trait of cyanogenesis is characterized and studied for its plasticity in the presence of L. hesperus and its effect on the survival and growth of L. hesperus populations. This study found that cyanogenesis was not induced by the presence of L. hesperus and the survival and reproduction of L. hesperus was negatively correlated with the cyanogenic capacity of their Lima bean host. These results advance the study of anti-herbivore defense mechanisms and the complex relationships between crop plants and their insect pests. They will contribute to efforts of crop improvement for reduced pesticide use and increased food security.

                Cover page: Lima beans on defense: studies of cyanogenesis and the complex relationship of crop plants and insect herbivores
                • Thesis
                • Peer Reviewed
                UC Davis Electronic Theses and Dissertations (2022)

                Monitoring and sampling insects provide critical data for decision making in integrated pest management strategies and plant breeding. Manual sampling and monitoring methods may be biased by interactions between the method, the cropping system, and the size and behavior of the target insects, as well as circadian and seasonal dynamics. These methods may also be limited by the quantity of time and labor required for collection and processing. Novel autonomous insect sensors resolve some of these limitations but may present new challenges. Understanding the limitations and biases of established and novel methods will improve the quality of available data. This study examines the biases of circadian flight activity and seasonal dynamics on water trap, vacuum, and autonomous sensor data with a focus on the crop pest, the Western Tarnished Plant Bug, Lygus hesperus (Hemiptera: Miridae Knight) in fields of Lima beans, Phaseolus lunatus. The study also includes sensor measurements of L. hesperus in a controlled laboratory environment. A strong multimodal circadian effect was observed in sensed and vacuumed L. hesperus. The laboratory results also revealed a similar pattern of daytime and crepuscular activity but lacked a midday activity peak observed in the field. Correlations were strong between total sensed insects and water trap data from over the course of the entire season, indicating that the novel autonomous insect sensor could be a good substitute for conventional monitoring methods. More research will be needed to determine the thresholds of sensed insect data that correspond with established measures for integrated pest management and breeding. Consideration of these biases will result in higher quality data that will be useful for advancing the development of insect resistant crop varieties and improving pest management.

                  Cover page: Insect sampling biases of automated and manual methods informed by circadian flight activity
                  • Thesis
                  • Peer Reviewed
                  UC Davis Electronic Theses and Dissertations (2021)

                  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.

                    Cover page: 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.)
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2021)
                    A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.
                      Cover page: Pod Shattering in Grain Legumes: Emerging Genetic and Environment-Related Patterns
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