The transition of muscadine grapes ( Vitis rotundifolia Michx.) from a wild fruiting plant to a domesticated crop has taken place in the last 150 years. Muscadine grapes are one of only two species in the Muscadinia subgenera of the Vitis genus. The Muscadinia differ substantially genetically and morphologically from the other Vitis species (subgenus Vitis ). Chromosomal differences between Muscadinia (2 x = 2 n = 40) and Vitis (2 x = 2 n = 38) have generally, although not completely, prevented the movement of genes between the subgenera. Partly due to this genetic isolation, muscadine grapes have been domesticated into a unique fruit crop with many differences from other grape cultivars. Muscadine grapes are grown throughout the southeastern United States and are one of the few fruit crops well suited to this hot and humid growing environment. Muscadines are prized in this region for their unique flavor and aroma and are grown as juice and wine grapes as well as for fresh consumption. Muscadine grapes are also gaining recognition for their high levels of beneficial phytochemicals. Despite these advantages, muscadines are not well known outside of the southeast United States. This is due in part to difficulties in long-term storage of the crop and also to the inherent difficulties in marketing an unfamiliar product. Several long-term breeding programs have transformed this crop from a functionally dioecious species bearing small berries with a tough skin and soft pulp to a hermaphroditic vine with large berries having a firm flesh and crisp skin. Recent success in intersubgeneric hybridization has resulted in the successful incorporation of stenospermocarpic seedlessness into muscadine. These breeding advances have opened exciting possibilities and positioned muscadine to transform from a niche to a mainstream crop.
After decades of prohibition of the cultivation and breeding of hemp ( Cannabis sativa < 0.3% ∆9-tetrahydrocannabinol [THC]), there is untapped potential for genetic improvement of this crop to provide food, feed, fiber, and medicinal compounds. Successful breeding efforts will require the development and characterization of germplasm resources, optimization of crossing methods, better understanding of sex determination, high-throughput phenotyping platforms, and deployment of genomic tools for rapid selection. This review provides a brief overview of these topics and some key opportunities for genetic improvement of hemp to support an emerging industry utilizing this newly legalized crop.
Genetic vulnerability refers to (sometimes catastrophic) actual or potential losses in the production of a crop (in quantity and/or quality), attributable to spatial or temporal reduction in the crop's biodiversity. Conversely, genetic resilience refers to the natural and anthropic capabilities of this biodiversity to mitigate these reductions in crop production. Here, an assessment is provided of genetic vulnerability and resilience of Phaseolus beans, which provide an abundant and sustainable source of protein and micronutrients for populations around the world. We provide an overview of the economic, nutritional, and cultural role of Phaseolus beans and phylogenetic and diversity analyses of the genus, its five domesticated species, and seven domestications, which provide key foundational information for this appraisal. We then assess the uniformity of the crop in the United States and the main drivers of genetic erosion in the centers of origin of the genus in the Americas. Next, the current and emerging breeding constraints are discussed for biotic and abiotic stresses, morphological and phenological traits, and dietary and cooking needs. To address these vulnerabilities, several resources have been developed and, which have been applied to increase the genetic resilience of Phaseolus beans. The resilience resources include genetic resources collections such as the global collection at the Centro Internacional de Agricultura Tropical (CIAT, Colombia), national collections in the United States, Brazil, the European Union, and elsewhere, which include wild and domesticated types across the genus but focus primarily on domesticated species. Resilience resources also include genome-wide reference DNA sequences for three of the five domesticated species, multiple diversity panels and recombinant inbred populations, and large sets of whole-genome diversity data based on single-nucleotide polymorphism (SNP) arrays, genotyping by sequencing, and whole-genome sequencing of germplasm sets. Numerous marker–trait associations and genes affecting agronomic traits have also been characterized in the genus. In turn, these resources have been successfully utilized to make Phaseolus beans more resistant against biotic and abiotic stresses (including those incurred by climate change) and to improve dietary and culinary quality through significant breeding efforts in the United States, at CIAT (mainly Latin America and Africa) and in national programs in Latin America and Eastern Africa. Future challenges remain, however, which include (1) a continued need for ex situ and in situ conservation of diversity, with agroecologically informed germplasm explorations and integration of farmers into conservation and breeding activities; (2) increased pre-breeding efforts involving gene bank curators and bean improvement scientists; (3) expansion of breeding of domesticated species other than common bean, where appropriate based on their potential adaptation to global climate change and consumer preferences; (4) an increased focus on culinary and dietary improvement; and (5) inclusion of microorganisms (both pathogenic and beneficial) in genetic conservation. We conclude that in the short term (~5 years), Phaseolus beans have limited genetic vulnerability. However, over the longer term, vulnerability due to several factors will increase, which can be addressed by a wide range of the resilience resources presented here.
Plant breeding primarily focuses on improving agronomy traits, e.g. yield, quality, host plant resistance to pathogens and pests, and abiotic stress tolerance; however, the methods for their genetic improvement are being rapidly enhanced through genomics and phenomics. In the Genomics–Phenomics–Agronomy (G-P-A) paradigm, diverse research approaches have been conducted to bridge any two of these elements, and recently, all of them together. This review first highlights the progress to link (1) genomics to agronomy, (2) genomics to phenomics, and (3) phenomics to agronomy. Secondly, the G-P-A domain is dissected into different layers, each addressing the three elements simultaneously. These layers include genetic dissection through gene mapping using genome-wide association studies and genomic selection using best linear unbiased prediction, Bayesian approaches, and machine learning. The objective of the review is to help readers to grasp the core developments among the exponentially growing literature in each of these fields. Through this review, the connections among the three elements of the G-P-A paradigm are coherently integrated toward the prospect of sustainable development of agronomy traits through both genomics and phenomics.
Issues surrounding soil fertility are fundamental to the productivity and sustainability of diverse agricultural production systems around the world. In developed economies, intensive fertilization is a chief economic, energetic, and environmental cost to crop production, depleting finite resources and causing massive pollution through leaching and runoff. In developing economies where access to, and utilization of soil amendments are rare, degraded soils with low nutrient availability are a primary constraint to yields. The most common challenges surrounding soil fertility in most production systems primarily involve nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), iron (Fe), and zinc (Zn). A chief component of a robust and pragmatic solution to these soil fertility issues lies in the development of more nutrient-efficient crops. In pursuit of this objective, root phenotypes that improve the efficiency of soil exploration and acquisition of resources offer exceptional opportunities as breeding targets. Natural variation for root phenotypes can have significant effects on soil resource extraction by modifying the placement of roots in soil domains where limiting resources are most available, improving the metabolic efficiency of soil exploration, as well as altering the radial and axial transport of resources. In this chapter, we review root anatomical and architectural phenes that have demonstrated benefit for enhancing acquisition of the most commonly limiting nutrients, and advocate for the consideration of root phenotypes in breeding programs focused on developing crops with greater nutrient efficiency.
Through plant agriculture, humans have modified their natural environment to produce food, fiber, fuel, and medicine. These products are the result of artificial selection that favors the accumulation of desirable phenotypes over time. This conscious, or subconscious, selection is initiated by the phenomenon of domestication, which is a well-described process with distinct stages on a continuum. While desirable phenotypes are seemingly constant across wide phylogenetic distances, the molecular basis of the phenotypic changes is often not. As the amount of genomic information has increased, the knowledge regarding the genetic basis of domestication in multiple plant species has become more accessible. The development of better phenotypic measurement tools, more sophisticated crossing schemes, and new statistical methods has helped to link genes to domestication traits. New molecular technologies such
While private sector support for graduate education can take many forms, student-led symposia represent one of the most effective ways to impact students and train our future workforce across the scientific community. The Plant Sciences Symposia Series (PSSS), initiated and sponsored by Corteva Agriscience (originally as its heritage company, DuPont-Pioneer), has been sponsoring student-led symposia since 2008 and has grown into a global network with broad impact on the support and empowerment of graduate students. These scientific conferences not only promote key scientific and technical learning but also provide experience in soft skills development, including teamwork, leadership, problem-solving, and communication. They also provide significant opportunities for networking and career exploration in an environment that fosters public–private interaction and communication. Data from 11 years of growth in the PSSS shows the impact of this program across the globe and the ways in which student leadership has allowed it to respond to the challenges of the COVID-19 pandemic.
Inter-connectivity amongst breeding program is a required part of funding agencies’ projects these days but has not been well characterized by plant breeders themselves. Here we discuss the regional and global scales of inter-connectivity for common bean breeding programs as this is useful case study for administrators and government decision makers setting the agendas for limited research and development moneys. Why beans? Common bean is arguably the second or third most important legume in the developing world based on total volume of production and within nation or regional and cross-regional trade. The species is challenging to breed for several reasons: it is (1) made up of two genepools; (2) has a range of seed types and colors; (3) is consumed directly and therefore quality is mainly determined by the consumer; (4) it is susceptible to many biotic and abiotic stresses; and (5) it is highly influenced by the wide range of environments in which it grows. Unlike some other legumes, common bean has some closely related species that are cultivated and can be used in inter-specific crosses. The strategies, germplasm availability and useful genes for breeding such a complex suite of sub-crops have been well studied and often reviewed. However, the literature does not contain much on the institutional context or networking of bean improvement programs, which in today's inter-connected world can be even more important than the biological constraints for achieving breeding goals. Therefore, the focus of this review is on who makes bean varieties, where they perform breeding operations and how the institutions and networks involved interact. Our chapter focuses on the institutional contacts of bean breeding that have led to successes or failures, accelerations or decelerations of varietal improvement in beans over the last half century. To explain our approach, one must consider a basic biological model of genotype (G) × environment (E) × institution (I) interaction rather than just G × E typically studied by most plant breeders. This review emphasizes the importance of bean research within national agricultural research systems (NARS) in developing countries, contextualized across networks of breeding programs, programs in academia in developing and developed countries and multiple international frameworks. We also discuss the ways that agenda setting occurs and how these are influenced by project funding and prioritization across the different nodes of plant breeding networks in national, network and international contexts.
Tomatoes are attacked by many pests, causing severe losses in fruit quality and marketable yield both directly through feeding on leaves, flowers, and fruit, and indirectly through pathogen transmission. Insect pests are largely controlled by application of insecticides. Even if insecticides are used within the framework of an IPM program, heavy reliance on insecticides for insect control is costly and can result in the rise of pesticide-resistant insects, adversely affect pollinators, and disrupt naturally occurring biocontrol insects. Reliance on insecticides is also of concern for the environment, and the heath of field workers and consumers. An alternate means of insect control is strongly needed for tomato production. The potential of plant secondary metabolites of wild relatives of crop species to provide insect resistance is an option to obtain sustainable insect resistance and reduce the dependance on insecticides for insect control. In tomato, one class of secondary metabolite with considerable potential for control of insects and insect-transmitted virus are acylsugars, which are compounds in the exudate of simple glandular trichomes in some wild Solanaceous species. In wild tomato species, acylsugars are composed of a sugar molecule, either glucose or sucrose, to which three or four, short to moderate length straight or branched chain fatty acids are attached by ester bonds. This chapter reviews a tomato breeding program that transferred acylsugar-mediated insect resistance from Solanum pennellii to tomato, spanning the time from the initial interspecific crosses through the development of the first tomato acylsugar benchmark line, CU97FL, development of subsequent benchmark lines, with fewer and smaller introgressions (CU071026 and CU17NBL), as well as the development of sister lines derived from CU071026 or CU17NBL. The sister lines differ in acylsugar levels or acylsugar chemistries due to the addition of one or more quantitative trait locus (QTL) impacting those traits. It also reviews the control provided by the best of these tomato acylsugar lines for insects and the virus they transmit, including western flower thrips and tomato-spotted wilt virus, Bemisia whitefly and tomato yellow leaf curl virus. The span of this program is synchronous with the years of rapid development by molecular biologists and geneticists of genetic, genomic, and molecular tools without which the success of this breeding program would not have been possible. Therefore, the review is structured to demonstrate the contribution that the development of these new tools and methodologies made to the stepwise advances in the acylsugar breeding program. The breeding program was also paralleled by supporting laboratory research, such as QTL analysis and testing of the impacts of purified acylsugars in vitro, and work done by cooperating biochemists on the chemistry of the acylsugars in the lines bred, and work done by collaborating entomologists, plant pathologists, and virologists who used the acylsugar lines bred to determine their impacts on insect species and the transmission of virus.
As genetic and archaeological evidence has developed over the past few years, it has become apparent that our most basic assumptions about how crops became incorporated into human culture may be in need of fundamental revision. Conventionally, crop origins have been understood through a local founding model in which one or multiple centers of small localized populations are formed through cultivation leading to domesticated forms as plants adapt to local human environments either over short, or more recently, longer time frames. However, the genetic expectations of such models are not being met by archaeogenomic and archaeological data. A key concept to the local founder model, the domestication bottleneck, is not supported by several lines of evidence including direct estimates of genetic diversity in the past, mutation load, strength of selection, and the theoretical balance between selection strength and population size. Key to this is the incorporation of models of evolution that are coherent with the development of archaeological thought in terms of conscious and unconscious modes of selection. Together, the data currently point away from a localized origin model and toward a diffuse landscape scale process which occurred over a very long period of time with sustained networks of contact. The domesticated forms that emerged from this process were diverse and consequently more adaptively robust with higher plasticity than would be expected from a local founder model.
Estimation of breeding values through Best Linear Unbiased Prediction (BLUP) using pedigree-based kinship and Marker-Assisted Selection (MAS) are the two fundamental breeding methods used before and after the introduction of genetic markers, respectively. The emergence of high-density genome-wide markers has led to the development of two parallel series of approaches inspired by BLUP and MAS, which are collectively referred to as Genomic Selection (GS). The first series of GS methods alters pedigree-based BLUP by replacing pedigree-based kinship with marker-based kinship in a variety of ways, including weighting markers by their effects in genome-wide association study (GWAS), joining both pedigree and marker-based kinship together in a single-step BLUP, and substituting individuals with groups in a compressed BLUP. The second series of GS methods estimates the effects for all genetic markers simultaneously. For the second series methods, the marker effects are summed together regardless of their individual significance. Instead of fitting individuals as random effects like in the BLUP series, the second series fits markers as random effects. Differing assumptions regarding the underlying distribution of these marker effects have resulted in the development of many Bayesian-based GS methods. This review highlights critical concept developments for both of these series and explores ongoing GS developments in machine learning, multiple trait selection, and adaptation for hybrid breeding. Furthermore, considering the increasing use and variety of GS methods in plant breeding programs, this review addresses important concerns for future GS development and application, such as the use of GWAS-assisted GS, the long-term effectiveness of GS methods, and the valid assessment of prediction accuracy.
Plant systems show dynamic responses, such as changes in architecture and physiology, to adjust their growth in changing environments. The reconfiguration of network modules underlies these responses. There is multi-scale regulation acting on these networks that can be measured as changes in mRNA synthesis, stability, and decay; and in protein translation, activity, affinity, and decay, among others. The regulatory linkages across biological scales can be constitutive, tunable, or switchable under changing environments. The ultimate goal of breeding efforts is to create novel ideotypes with desired traits, which maintain high yield despite challenging environments. Gain of beneficial or adaptive phenotypic traits in commercial crops is often due to ideal coupling/uncoupling of the network modules with tunable linkages from parental lines. Regulatory genomic variation of influential nodes in network modules perturbs network properties, such as hubs, topology, and clustering, and serves as a source of variation for novel traits. These critical variants that perturb network modules to create novel phenotypes can be discovered using natural diversity in wild relatives of cultivated crops, thereby aiding breeding programs for target discovery. Predictive modeling and quantitatively characterized synthetic modules provide detailed understanding on predictable and heritable behavior of complex regulatory and signaling networks, but implementation of these models in crop plants lags behind. Future efforts to incorporate multi-scale layers of information to predict systems level behavior of crop plant networks and their dynamics in changing environments are an exciting area.
Starch produced in the endosperm of cereals is the largest source of calories in the human diet. We know a great deal about the endosperm starch synthesis pathway and much of our understanding is due to the unique biology of maize or corn. The large naked kernels of corn held together as a family by the ear allow easy identification of the frequent endosperm mutations and their Mendelian inheritance. In addition, the large chromosomes of corn allowed mapping of the genes. Many of the mutations used to understand the pathway are lesions in genes that code for enzymes in the pathway. These same mutations have been used to improve eating quality and shelf life of sweet corn, allowing what was once a crop important only in North America to become a crop of worldwide importance. Some of these genes also allowed the introgression of non-sweet germplasm from the tropics, to increase adaptation to subtropical and tropical environments and improve resistance to insects and diseases. The high sugar alleles negatively affected germination and seedling vigor, but breeders and seed technologists have worked to reduce these negative effects.
Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Among the ~66 species in the genus Cucumis, cucumber is the only one with 2n = 2x = 14 chromosomes. The rest, including its sister species, C. hystrix, have 2n = 2x = 24 chromosomes or multiples of 12 chromosomes. Cucumber evolved from its extinct 2n = 24 ancestor through dysploid chromosome reduction, in which many chromosome rearrangement events (inversions, fusions, and translocations) were involved with the exception of cucumber Chromosome 7, which remained largely intact during the entire evolution of Cucumis. There are four cross-compatible botanical varieties in C. sativus, including the wild cucumber (C. s. var. hardwickii), the semi-wild Xishuangbanna cucumber (C. s. var. xishuangbannesis), the Sikkim cucumber (C.s. var. sikkimensis), and the cultivated cucumber (C.s. var. sativus). The wild cucumber is the progenitor of cultivated cucumber, but differentiated from the other three taxa in the amount and distribution of heterochromatin, as well as several large inversions. Cucumber has been cultivated in India for at least 3,000 years. It spread eastward to China and westward to Europe around 2,000, and 700–1500 years ago, respectively. Long-term selection and breeding practices have resulted in different ecotypes and market classes of cucumber, adapting the crop to local environments, production systems, processing requirements, and consumer needs. Recent molecular marker studies have provided more insights into the population structure and genetic diversity of the worldwide cucumber collection. The knowledge of cucumber evolution, domestication and genetic diversity will greatly help the conservation of genetic diversity, and efficient use of cucumber germplasm resources for cucumber improvement.
