Perennializing crops such as sorghum (Sorghum bicolor) offer the potential to provide food security in regions with degrading soils and limited rainfall. Genomic prediction is a very useful tool for expediting the adaptation of perennial sorghum to such regions of the world. We assessed the performance of two genomic prediction models in two perennial sorghum populations derived from S. bicolor and Sorghum halepense crosses. The first model is a standard genomic best linear unbiased prediction (GBLUP) model, while the second model (called MultiBLUP) is a multi-kernel extension of GBLUP that partitions genome-wide single-nucleotide polymorphisms based on proximity to a priori genomic features. We used real and simulated data to better understand how models performed under the influence of different genetic architectures. The results from the real traits showed that incorporating genome-wide association study-derived information into the MultiBLUP model did not consistently improve genomic prediction accuracy over the standard GBLUP model. The results from the simulated traits provided further insights into the conditions under which GBLUP provides higher predictive abilities over the MultiBLUP approach. Mainly, as quantitative trait nucleotide size increases, so does GBLUP’s predictive ability over MultiBLUP. Our findings suggest that leveraging prior knowledge of trait-associated genomic regions does not yield more accurate predictions of traits critical for perennial sorghum breeding.

Perennial crops, compared to annual cereals, offer multiple advantages that enhance crop resilience and promote sustainable agricultural practices such as low economic input, better soil health, increased carbon sequestration, etc. Sorghum (Sorghum bicolor), one of the top five cereals grown in the world, is currently under threat from sugarcane aphid (SCA; Melanaphis sacchari). In this study, we explored the molecular and genetic mechanisms that mediate the interaction between SCA and perennial sorghum (Sorghum bicolor x Sorghum halepense). We employed the use of RNA-sequencing to investigate the transcriptomic responses of perennial sorghum genotypes with varying resistance levels to SCA infestation, aiming to identify key factors underlying resistance at early (6 and 24 h post-infestation) and late (7 d post infestation) time points. Temporal transcriptomic profiling revealed that SCA infestation triggered distinct changes in the expression levels of genes associated with various defense mechanisms in the sorghum genotypes. We identified 10,620 differentially expressed genes across early and late time points and highlighted key regulators of plant defense mechanisms. Weighted co-expression network analysis revealed that aphid infestation altered expression levels of genes corresponding to different biological and metabolic processes. Compared to the control and SCA-susceptible perennial sorghum plants, SCA feeding significantly induced the expression of genes related to the production of reactive oxygen species (ROS), death acids, cell wall modifications, callose synthesis, and defense-related phytohormones in SCA-resistant perennial sorghum line. Increased expression of various transcription factors (TFs) such as bHLH, NAC, and MYB were also observed uniquely in the SCA-resistant genotype. In summary, our results suggest that the SCA-resistant sorghum perennial plants were better adapted to activate defense signaling mechanisms to curb SCA infestation. By identifying novel sources of perennial sorghum resistance to SCA, our findings contribute to advancing sorghum breeding programs, ultimately enhancing crop resilience and productivity.

Polyploidy has repeatedly shaped grass evolution, yet direct observations of how polyploid-derived chromosomes behave when returned to diploidy remain rare. Interspecific crosses between diploid Sorghum bicolor and tetraploid hybrids derived from Sorghum halepense generate mixed-ploidy progeny, providing an opportunity to examine chromosome transmission during the early stages of diploidization. Using genome-wide SNP markers, we characterized chromosomal inheritance patterns in 2 diploid and 2 tetraploid families derived from these crosses. Genotype-dosage profiles alone distinguished diploids from tetraploids with complete accuracy, reflecting strong ploidy-dependent differences in dosage-class distributions. Although diploid progeny retained much of the halepense-derived genomic background, several genomic intervals exhibited extended, nonrandom runs of S. bicolor homozygosity that remained polymorphic in corresponding tetraploid populations. These patterns, together with recurrent segregation distortion across independent families, suggest that the transition from tetraploidy to diploidy can expose allelic combinations that differ in transmission or viability. Analyses of flowering time further indicated that diploid and tetraploid derivatives possess distinct genomic architectures, with major association peaks occurring in different chromosomal regions across ploidy levels. Collectively, these results indicate that early diploidization involves nonrandom retention and loss of parental haplotypes shaped by both selective and structural constraints. The diploid extractions characterized here provide a rare empirical system for investigating the early stages of diploidization and a practical framework for studying and eventually mobilizing polyploid-derived variation for sorghum germplasm development. However, broader integration into elite breeding programs will require additional evaluation of cross-fertility, meiotic behavior, and chromosomal stability across diverse breeding backgrounds.

With growing concerns over the sustainability of conventional farming systems, perennial crops offer an environmentally friendly and resilient alternative for long-term agricultural production. Perennial grain crops provide numerous benefits, such as low input investment, reduced tillage, soil conservation, better carbon sequestration, sustainable yields, and enhanced biodiversity support. Sorghum (Sorghum bicolor) is the fifth most-grown cereal crop grown for food, fuel, and food grain in the world. The development of perennial sorghum offers a substitute for traditional annual sorghum crops by providing long-term environmental, economic, and agronomic benefits. Sugarcane aphid (SCA; Melanaphis sacchari), a phloem-feeder, is considered a major threat to sorghum production. Since its first report in 2013, it caused $40.95 million in losses in South Texas alone by 2015, accounting for about 19% of the total value of sorghum production in the region. In this study, we screened diverse perennial sorghum genotypes using no-choice and choice assays to determine their innate antibiosis and antixenosis resistance levels to SCAs. Based on aphid reproduction and plant damage rating, no-choice bioassay classified the 43 perennial sorghum genotypes into four clusters: highly susceptible, moderately susceptible, moderately resistant, and highly resistant. To further investigate the resistance mechanisms, we selected two genotypes, X999 > R485 (SCA-resistant) and PR376 ~ Tift241 (SCA-susceptible) that showed the greatest variation in resistance to SCA, for subsequent experiments. Choice bioassay results indicated that aphids chose PR376 ~ Tift241 for settlement, whereas no significant preference was observed for X999 > R485 compared to the control genotype. Electrical penetration graph (EPG) results demonstrated that aphids feeding on the SCA-resistant genotype spent significantly less time in the phloem phase than the susceptible genotype and control plants. The identification of SCA-resistant perennial sorghum genotypes will be valuable for future sorghum breeding programs in managing this economically important pest.

Due to the reality of a rapidly shrinking carbon budget, managing a just transition from fossil fuels requires the democratization of decision-making processes for the use of remaining fossil fuel supplies. Through collective and enduring modes of participatory governance, decisions around carbon emissions and societal needs can be made in a way that allows impacted workers and communities to respond appropriately to inevitable trade-offs and unforeseen consequences. This chapter explores non-market decision-making processes and institutions organized around community and labor needs that can be leveraged to ensure a managed decline of fossil fuels. Through a review of historical, contemporary, and conceptual examples, including participatory budgeting, worker cooperatives, public utilities, and rationing boards, this chapter envisions what participative and democratic fossil fuel energy governance might look like. By recognizing the injustices of market-based allocation of fossil fuel stocks and the viability of democratic models of governance, society can improve its capacity to re-imagine, experiment, and implement necessary alternatives for an energy transition that is just, equitable, reparative, and sustainable.

Social Impact StatementAlthough tremendously successful at feeding humanity, row crop agriculture based on annuals contributes to numerous ecosystem dis‐services, ranging from soil degradation and aquatic eutrophication to greenhouse gas production. In contrast, perennial grain crops (which produce harvests for multiple seasons from single plantings) have the potential to provide valuable regulating and supporting ecosystem services in addition to food production. In particular, losses of ecological capital that threaten permanent food insecurity such as ~1% of global soil per year are expected to be mitigated or even reversed by crops that combine the high yield realized by scientific breeding via multiple cropping cycles from single plantings.Summary Perennial herbaceous may provide food and biomass while preserving ecological capital and reducing energy inputs. Sorghum has two perennial relatives and rich morphological diversity being used to breed for perenniality. We elucidate genetic determinants of rhizomatousness and survival, in two BC1F2 populations totaling 246 genotypes derived from backcrossing different annual Sorghum bicolor X perennial S. halepense F1 plants to a tetraploidized S. bicolor. RNA‐seq assisted in identifying candidate genes for rhizomatousness. Correspondence of rhizomatousness quantitative trait loci (QTLs) with those from two populations derived from crosses between S. halepense progenitors S. bicolor X S. propinquum suggests either the preservation of interspecific polymorphism or the formation of novel alleles following polyploid S. halepense formation. Correspondence of tillering and branching QTLs further supports their developmental. Identification of genes from RNA‐seq study within QTL intervals provides insight toward discovery of causal rhizomatous genes. An unexpected finding from both S. halepense‐ and S. propinquum‐derived populations is that alleles contributing to late flowering are related to reduced rhizomatousness. Twelve of 16 QTL regions conferring rhizomatousness fall in paleo‐duplicated regions tracing to single ancestral regions 96 million years ago, indicating that corresponding genes in these regions have retained similar functions since the duplication event.

Both annual and perennial sorghum biomass serve as important forage for ruminant animals around the world. Unfortunately, sorghum can produce hydrogen cyanide (HCN), which, if occurring in high enough concentrations, can be toxic or lethal to animals that consume it. The objectives of this study were to develop a fast and inexpensive colorimetric assay to measure the hydrogen cyanide potential (HCN-P) as well as to compare this with existing visual assays while assessing the range of variation for HCN-P among perennial and annual sorghum biomass. The HCN-P of 100 sorghum lines derived from an interspecific hybridization program was determined over 2 years (establishment and regrowth) using both visual and colorimetric assays. Visual assessment underestimated the HCN-P and was less accurate than colorimetry. Repeatability for HCN-P across all sampling dates was functionally zero in the visual assessment and low for the colorimetric assay. This was mostly explained by the significant pedigree × year interaction effects and growth stage. Growth stage substantially influenced HCN-P, which should be considered when feeding animals on fresh forage.

Perennial grain sorghum [Sorghum bicolor (L.) Moench] has potential to produce grain and forage while improving soil health, ecosystem services, and carbon soil sequestration but requires further genetic improvement. Unoccupied aerial systems (UAS, also known as drones and unmanned aerial systems) provide opportunities to quickly evaluate plant traits on a large scale with precision. Unoccupied aerial system flights were used to evaluate biomass yield and rhizome characteristics of 100 diverse sorghum hybrids, most being from an interspecific hybridization program, in the establishment year and first year of regrowth. Twenty-one vegetation indices (VIs) with canopy height measurements (CHMs) were processed from seven UAS flights made temporally during each growing season. Regression of the temporal data (VI and CHM) and phenotypic traits, including rhizome characteristics based on plant stand count (PSC), rhizome-derived shoots (RDS), and fresh and dry biomass yields, showed useful predictions when combining temporal VI with CHM and machine learning. Blue chromatic coordinate index (BCC) best predicted all measured traits. If predictions could be generalized, UAS would reduce field evaluation time for perennial sorghum or breeding perennial grasses in general and allow breeders to evaluate additional genotypes. In this study, we found that optimizing flights to specific dates after planting could minimize resource requirements and costs in prediction of regrowth and biomass yield of perennial sorghum.

Tillering and secondary branching are two plastic traits with high agronomic importance, especially in terms of the ability of plants to adapt to changing environments. We describe a quantitative trait analysis of tillering and secondary branching in two novel BC1F2 populations totaling 246 genotypes derived from backcrossing two Sorghum bicolor x S. halepense F1 plants to a tetraploidized S. bicolor. A two-year, two-environment phenotypic evaluation in Bogart, GA and Salina, KS permitted us to identify major effect and environment specific QTLs. Significant correlation between tillering and secondary branching followed by discovery of overlapping sets of QTLs continue to support the developmental relationship between these two organs and suggest the possibility of pleiotropy. Comparisons with two other populations sharing S. bicolor BTx623 as a common parent but sampling the breadth of the Sorghum genus, increase confidence in QTL detected for these two plastic traits and provide insight into the evolution of morphological diversity in the Eusorghum clade. Correspondence between flowering time and vegetative branching supports other evidence in suggesting a pleiotropic effect of flowering genes. We propose a model to predict biomass weight from plant architecture related traits, quantifying contribution of each trait to biomass and providing guidance for future breeding experiments.

From noble beginnings as a prospective forage, polyploid Sorghum halepense (‘Johnsongrass’) is both an invasive species and one of the world’s worst agricultural weeds. Formed by S. bicolor x S. propinquum hybridization, we show S. halepense to have S. bicolor-enriched allele composition and striking mutations in 5,957 genes that differentiate it from representatives of its progenitor species and an outgroup. The spread of S. halepense may have been facilitated by introgression from closely-related cultivated sorghum near genetic loci affecting rhizome development, seed size, and levels of lutein, a photochemical protectant and abscisic acid precursor. Rhizomes, subterranean stems that store carbohydrates and spawn clonal propagules, have growth correlated with reproductive rather than other vegetative tissues, and increase survival of both temperate cold seasons and tropical dry seasons. Rhizomes of S. halepense are more extensive than those of its rhizomatous progenitor S. propinquum, with gene expression including many alleles from its non-rhizomatous S. bicolor progenitor. The first surviving polyploid in its lineage in ∼96 million years, its post-Columbian spread across six continents carried rich genetic diversity that in the United States has facilitated transition from agricultural to non-agricultural niches. Projected to spread another 200–600 km northward in the coming century, despite its drawbacks S. halepense may offer novel alleles and traits of value to improvement of sorghum.

Despite a "ploidy barrier," interspecific crosses to wild and/or cultivated sorghum (Sorghum bicolor, 2n = 2x = 20) may have aided the spread across six continents of Sorghum halepense, also exemplifying risks of "transgene escape" from crops that could make weeds more difficult to control. Genetic maps of two BC1F1 populations derived from crosses of S. bicolor (sorghum) and S. halepense with totals of 722 and 795 single nucleotide polymorphism (SNP) markers span 37 and 35 linkage groups, with 2-6 for each of the 10 basic sorghum chromosomes due to fragments covering different chromosomal portions or independent segregation from different S. halepense homologs. Segregation distortion favored S. halepense alleles on chromosomes 2 (1.06-4.68 Mb, near a fertility restoration gene), 7 (1.20-6.16 Mb), 8 (1.81-5.33 Mb, associated with gene conversion), and 9 (47.5-50.1 Mb); and S. bicolor alleles on chromosome 6 (0-40 Mb), which contains both a large heterochromatin block and the Ma1 gene. Regions of the S. halepense genome that are recalcitrant to gene flow from sorghum might be exploited as part a multi-component system to reduce the likelihood of spread of transgenes or other modified genes. Its SNP profile suggests that chromosome segments from its respective progenitors S. bicolor and Sorghum propinquum have extensively recombined in S. halepense. This study reveals genomic regions that might discourage crop-to-weed gene escape, and provides a foundation for marker-trait association analysis to determine the genetic control of traits contributing to weediness, invasiveness, and perenniality of S. halepense.

A perennial version of grain sorghum [S. bicolor (L.) Moench] would create opportunities for greatly reducing tillage and preventing soil degradation. Efforts to select for perenniality and grain production among progeny of hybrids between S. bicolor (2n = 20) and the weedy tetraploid perennial S. halepense (L.) Pers. (2n = 40) are complicated in that F1 hybrids produced by diploid × tetraploid sorghum crosses are usually tetraploid. In 2013, a set of random pollinations between 19 diploid cytoplasmic male-sterile inbred lines and 43 tetraploid perennial plants produced 165 F1 hybrid plants, more than 75% of which had highly atypical plant, panicle, and seed phenotypes. Phenotypic segregation in F2 populations derived from atypical hybrids was also anomalous. Examination of mitotic metaphase cells in F1 or F2 root tips revealed that 129 of the 165 hybrids were diploid. Parentage of the diploid progenies was confirmed using simple-sequence repeat analysis. The mechanism by which diploid hybrids arise from diploid × tetraploid crosses is unknown, but it may involve either production of monohaploid (n = 10) pollen by the tetraploid parent or chromosome elimination during early cell divisions following formation of the triploid zygote. The ability to produce diploid germplasm segregating for S. bicolor and S. halepense alleles could have great utility, both for the development of perennial sorghum and for the improvement of conventional grain sorghum.

The purpose of this work was to assess biomass and grain yields, path modelling of yield components, and perenniality in 97 Sorghum bicolor x S. halepense (SB x SH) lines, and compare their biomass production to a series of 38 historic (1987-2015) biomass SB trials. Perenniality was evaluated as rhizome overwintering, while other traits were scored using standard procedures. Contrary to SB, several SB x SH lines developed rhizomes and overwintered, depending mostly upon increased dosage of SH genome in SB background. A few backcross-derived SB x SH lines overwintered, indicating that perenniality can be introgressed in sorghum using backcrossing approach. SB x SH lines were competitive in terms of grain and aboveground dry biomass yields compared to SB. SB x SH selections outperformed or were comparable to the best commercial biomass SB hybrid checks, and ranked among the best selections from the historic trials. Grain yield in SB x SH lines depended mainly on number of culms, whereas biomass yields depended mainly on plant height, dry mass and fiber mass fractions of dry material, and number of culms. We identified superior dual purpose SB x SH genotypes producing 5-11 and 38-45 t ha(-1) of grain and aboveground biomass, respectively, most of which displayed satisfactory overwintering rates (56-100%) and high levels of fiber (61-69%) mass fraction. These lines represent high energy sorghums suitable for biofuel and food production. The best SB x SH crosses for developing perennial biomass and grain sorghums were represented by perennial/perennial, annual/perennial/perennial, and annual/ perennial combinations. (c) 2017 Elsevier Ltd. All rights reserved.

Many landraces and improved cultivars of sorghum (Sorghum bicolor) grown in Uganda have late maturity and are susceptible to several biotic and abiotic stresses. Introgression of the rhizomatous trait from perennial sorghum (Sorghum halepense) could improve stress tolerance. However, phenotypic characterization of exotic perennial sorghum germplasm under Ugandan environmental conditions is essential to select desirable genotypes. Rhizome-forming capacity of 192 S. bicolor × S. halepense backcross tetraploid families developed in a temperate North American environment was evaluated at two locations in Uganda over two consecutive growing seasons. Numbers of rhizomes and emerging shoots as well as mean distances from shoot to crown were evaluated. Forty-seven percent of families were moderately to strongly rhizomatous in the first season of growth and this value rose to 91% in the second season. Developing perennial grain sorghum for East Africa will require hybridization between exotic perennial and locally adapted germplasm. Screening for emerging rhizome-derived shoots in early generations is simple, rapid, and effective; however, more detailed selection based on both aboveground and belowground rhizome traits is recommended for later generations. Researchers and farmers should work together to find suitable ways in which perennial sorghum might fit into new types of crop and livestock systems. Key words: Rhizome, perennial sorghum, rhizome buds, ramets.

Perennial germplasm derived from crosses between Sorghum bicolor and either S. halepense or S. propinquum is being developed with the goal of preventing and reversing soil degradation in the world’s grain sorghum-growing regions. Perennial grain sorghum plants produce subterranean stems known as rhizomes that sprout to form the next season’s crop. In Kansas, breeding perennial sorghum involves crossing S. bicolor cultivars or breeding lines to S. halepense or perennial S. bicolorn × S. halepense breeding lines, selecting perennial plants from F2 or subsequent populations, crossing those plants with S. bicolor, and repeating the cycle. A retrospective field trial in Kansas showed that selection and backcrossing during 2002–2009 had improved grain yields and seed weights of breeding lines. Second-season grain yields of sorghum lines regrowing from rhizomes were similar to yields in the first season. Further selection cycles have been completed since 2009. Many rhizomatous lines that cannot survive winters in Kansas are perennial at subtropical or tropical locations in North America and Africa. Grain yield in Kansas was not correlated with rhizomatousness in either Kansas or Uganda. Genomic regions affecting rhizome growth and development have been mapped, providing new breeding tools. The S. halepense gene pool may harbor many alleles useful for improving sorghum for a broad range of traits in addition to perenniality.

Johnsongrass (Sorghum halepense) is a striking example of a post-Columbian founder event. This natural experiment within ecological time-scales provides a unique opportunity for understanding patterns of continent-wide genetic diversity following range expansion. Microsatellite markers were used for population genetic analyses including leaf-optimized Neighbor-Joining tree, pairwise FST, mismatch analysis, principle coordinate analysis, Tajima's D, Fu's F and Bayesian clusterings of population structure. Evidence indicates two geographically distant introductions of divergent genotypes, which spread across much of the US in <200 years. Based on geophylogeny, gene flow patterns can be inferred to have involved five phases. Centers of genetic diversity have shifted from two introduction sites separated by ~2000 miles toward the middle of the range, consistent with admixture between genotypes from the respective introductions. Genotyping provides evidence for a 'habitat switch' from agricultural to non-agricultural systems and may contribute to both Johnsongrass ubiquity and aggressiveness. Despite lower and more structured diversity at the invasion front, Johnsongrass continues to advance northward into cooler and drier habitats. Association genetic approaches may permit identification of alleles contributing to the habitat switch or other traits important to weed/invasive management and/or crop improvement.

Perennial crops offer an avenue by which marginal lands might be brought into sustainable production while arresting or even reversing losses of ecological capital. The natural adaptation of sorghum to its native Sahelian region makes it essential to some of the poorest and most food-insecure G E N E T I C S A N D B R E E D I N G : S TAT E O F T H E A R T , G A P S A N D O P P O R T U N I T I E S 90 P E R E N N I A L C R O P S F O R F O O D S E C U R I T Y P R O C E E D I N G S O F T H E F A O E X P E R T W O R K S H O P

Agriculture's impact on the Earth has been amplified by industrial farming, but the fundamental problem has its origins 10,000 years ago, in the domestication of those annual crops that are still the staples of the global food supply. Annual crops, with ephemeral, often low-density root systems, have a lower capacity than do perennials to foster microbial ecosystems in the soil or micro-manage nutrients and water. Some of the more striking results of annual cropping have been the emergence of marine hypoxic zones at the mouths of major rivers and soil salinisation in parts of Australia. The means that modern agriculture relies upon to overcome the weaknesses of annual crops cannot simultaneously resolve all of the key problems. For example, no-till methods curtail erosion in the top layer of soil but, done consistently on a large scale, they require heavier use of chemical inputs and leave the lower soil profile unimproved. Conversely, organic methods eliminate toxic pesticides but not the soil erosion and water deterioration that occur as consequences of tillage. In an effort to resolve the dilemma, plant breeders in the US, Australia, and other countries are now breeding perennial counterparts of annual grain and legume crops, including wheat, wheatgrasses, sorghum, sunflower, and others. With their longer growing seasons and the greater opportunity for carbon fixation that results, diverse systems of such crops are aimed for both grazing and grain production. Perennial grains, combined with established and novel sustainable-agriculture practices, could help end the 10,000-year-old conflict between food production and ecological health.

The Wheat Genetics Resource Center, a pioneering center without walls, has served the wheat genetics community for 25 years. The Wheat Genetics Resource Center (WGRC) assembled a working collection of over 11,000 wild wheat relatives and cytogenctic stocks for conservation and use in wheat genome analysis and crop improvement. Over 30,000 samples from the WGRC collection of wheat wild relatives, cytogenetic stocks, and improved germplasm have been distributed to scientists in 45 countries and 39 states in the United States. The WGRC and collaborators have developed standard karyotypes of 26 species of the Triticum/Aegilops complex, rye, and some perennial genera of the Triticeae. They have developed over 800 cytogenetic stocks including addition, substitution, and deletion lines. The anchor karyotypes, technical innovations, and associated cytogenetic stocks are a part of the basic tool kit of every wheat geneticist. They have cytogenetically characterized over six-dozen wheat-alien introgression lines. The WGRC has released 47 improved germplasm lines incorporating over 50 novel genes against pathogens and pests; some genes have been deployed in agriculture. The WGRC hosted over three-dozen scientists especially from developing countries for advanced training. The WGRC was engaged in international agriculture through several collaborating projects. Particularly noteworthy was the collaborative project with Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT) on the production of synthetic wheats. It is estimated that "by the year 2003-2004, 26% of all new advanced lines made available through CIMMYT screening nurseries to cooperators for either irrigated or semi-arid conditions were synthetic derivatives." The WGRC is applying genomics tools to further expedite the use of exotic germplasm in wheat crop improvement. (c) 2006, Elsevier Inc.