Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy

Screening for genetic variability in photosynthetic regulation provides insights into salt performance traits in forage sorghum under salt stress

BACKGROUND

Sorghum (Sorghum bicolor) is a promising opportunity crop for arid regions of Africa due to its high tolerance to drought and heat stresses. Screening for genetic variability in photosynthetic regulation under salt stress can help to identify target trait combinations essential for sorghum genetic improvement. The primary objective of this study was to identify reliable indicators of photosynthetic performance under salt stress for forage yield within a panel of 18 sorghum varieties from stage 1 (leaf 3) to stage 7 (late flowering to early silage maturity). We dissected the genetic diversity and variability in five stress-sensitive photosynthetic parameters: nonphotochemical chlorophyll fluorescence quenching (NPQ), the electron transport rate (ETR), the maximum potential quantum efficiency of photosystem II (FV/FM), the CO2 assimilation rate (A), and the photosynthetic performance based on absorption (PIABS). Further, we investigated potential genes for target phenotypes using a combined approach of bioinformatics, transcriptional analysis, and homologous overexpression.

RESULTS

The panel revealed polymorphism, two admixed subpopulations, and significant molecular variability between and within population. During the investigated development stages, the PIABS varied dramatically and consistently amongst varieties. Under higher saline conditions, PIABS also showed a significant positive connection with A and dry matter gain. Because PIABS is a measure of plants' overall photosynthetic performance, it was applied to predict the salinity performance index (SPI). The SPI correlated positively with dry matter gain, demonstrating that PIABS could be used as a reliable salt stress performance marker for forage sorghum. Eight rubisco large subunit genes were identified in-silico and validated using qPCR with variable expression across the varieties under saline conditions. Overexpression of Rubisco Large Subunit 8 increased PIABS, altered the OJIP, and growth with an insignificant effect on A.

CONCLUSIONS

These findings provide insights into strategies for enhancing the photosynthetic performance of sorghum under saline conditions for improved photosynthetic performance and potential dry matter yield. The integration of molecular approaches, guided by the identified genetic variability, holds promise for genetically breeding sorghum tailored to thrive in arid and saline environments, contributing to sustainable agricultural practices.

Biostimulant and Arbuscular Mycorrhizae Application on Four Major Biomass Crops as the Base of Phytomanagement Strategies in Metal-Contaminated Soils

Using contaminated land to grow lignocellulosic crops can deliver biomass and, in the long term, improve soil quality. Biostimulants and microorganisms are nowadays an innovative approach to define appropriate phytomanagement strategies to promote plant growth and metal uptake. This study evaluated biostimulants and mycorrhizae application on biomass production and phytoextraction potential of four lignocellulosic crops grown under two metal-contaminated soils. Two greenhouse pot trials were setup to evaluate two annual species (sorghum, hemp) in Italy and two perennial ones (miscanthus, switchgrass) in China, under mycorrhizae (M), root (B2) and foliar (B1) biostimulants treatments, based on humic substances and protein hydrolysates, respectively, applied both alone and in combination (MB1, MB2). MB2 increased the shoot dry weight (DW) yield in hemp (1.9 times more), sorghum (3.6 times more) and miscanthus (tripled) with additional positive effects on sorghum and miscanthus Zn and Cd accumulation, respectively, but no effects on hemp metal accumulation. No treatment promoted switchgrass shoot DW, but M enhanced Cd and Cr shoot concentrations (+84%, 1.6 times more, respectively) and the phytoextraction efficiency. Root biostimulants and mycorrhizae were demonstrated to be more efficient inputs than foliar biostimulants to enhance plant development and productivity in order to design effective phytomanagement strategies in metal-contaminated soil.

Effects of soaking glutinous sorghum grains on physicochemical properties of starch

Glutinous sorghum grains were soaked (60-80 °C, 2-8 h) to explore the effects of soaking, an essential step in industrial processing of brewing, on starch. As the soaking temperature increased, the peak viscosity and crystallinity of starch gradually decreased, while the enzymatic hydrolysis rate and storage modulus first increased and then decreased. At 70 °C, the content of amylose, the enzymatic hydrolysis rate of starch, and the final viscosity first increase and then decrease with the increase of soaking time, reaching their maximum at 6 h, increased by 53.1 %, 11.0 %, and 10.4 %, respectively, as compared with the non-soaked sample. At 80 °C (4 h), the laser confocal microscopy images showed a network structure formed between the denatured protein chains and the leached-out amylose chains. The molecular weights of starch before and after soaking were all in the range of 3.82-8.98 × 107 g/mol. Since 70 °C is lower than that of starch gelatinization and protein denaturation, when soaking for 6 h, the enzymatic hydrolysis rate of starch is the highest, and the growth of miscellaneous bacteria is inhibited, which is beneficial for subsequent processing technology. The result provides a theoretical basis for the intelligent control of glutinous sorghum brewing.

Xylan-directed cell wall assembly in grasses

Xylan is the most abundant hemicellulosic polysaccharide in the cell walls of grasses and is pivotal for the assembly of distinct cell wall structures that govern various cellular functions. Xylan also plays a crucial role in regulating biomass recalcitrance, ultimately affecting the utilization potential of lignocellulosic materials. Over the past decades, our understanding of the xylan biosynthetic machinery and cell wall organization has substantially improved due to the innovative application of multiple state-of-the-art techniques. Notably, novel xylan-based nanostructures have been revealed in the cell walls of xylem vessels, promoting a more extensive exploration of the role of xylan in the formation of cell wall structures. This Update summarizes recent achievements in understanding xylan biosynthesis, modification, modeling, and compartmentalization in grasses, providing a brief overview of cell wall assembly regarding xylan. We also discuss the potential for tailoring xylan to facilitate the breeding of elite energy and feed crops.

Novel allelic variations in Tannin1 and Tannin2 contribute to tannin absence in sorghum

Sorghum is an important food crop commonly used for brewing, feed, and bioenergy. Certain genotypes of sorghum contain high concentrations of condensed tannins in seeds, which are beneficial, such as protecting grains from herbivore bird pests, but also impair grain quality and digestibility. Previously, we identified Tannin1 and Tannin2, each with three recessive causal alleles, regulate tannin absence in sorghum. In this study, via characterizing 421 sorghum accessions, we further identified three novel recessive alleles from these two genes. The tan1-d allele contains a 12-bp deletion at position 659 nt and the tan1-e allele contains a 10-bp deletion at position 771 nt in Tannin1. The tan2-d allele contains a C-to-T transition, which results in a premature stop codon before the bHLH domain in Tannin2, and was predominantly selected in China. We further developed KASP assays targeting these identified recessive alleles to efficiently genotype large populations. These studies provide new insights in sorghum domestication and convenient tools for breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01463-y.

Mapping and Screening of Candidate Gene Regulating the Biomass Yield of Sorghum (Sorghum bicolor L.)

Biomass yield is one of the important traits of sorghum, which is greatly affected by leaf morphology. In this study, a lobed-leaf mutant (sblob) was screened and identified, and its F2 inbred segregating line was constructed. Subsequently, MutMap and whole-genome sequencing were employed to identify the candidate gene (sblob1), the locus of which is Sobic.003G010300. Pfam and homologous analysis indicated that sblob1 encodes a Cytochrome P450 protein and plays a crucial role in the plant serotonin/melatonin biosynthesis pathway. Structural and functional changes in the sblob1 protein were elucidated. Hormone measurements revealed that sblob1 regulates both leaf morphology and sorghum biomass through regulation of the melatonin metabolic pathway. These findings provide valuable insights for further research and the enhancement of breeding programs, emphasizing the potential to optimize biomass yield in sorghum cultivation.

Sorghum: A Multipurpose Crop

Sorghum (Sorghum bicolor L.) is one of the top five cereal crops in the world in terms of production and planting area and is widely grown in areas with severe abiotic stresses such as drought and saline-alkali land due to its excellent stress resistance. Moreover, sorghum is a rare multipurpose crop that can be classified into grain sorghum, energy sorghum, and silage sorghum according to its domestication direction and utilization traits, endowing it with broad breeding and economic value. In this review, we mainly discuss the latest research progress and regulatory genes of agronomic traits of sorghum as a grain, energy, and silage crop, as well as the future improvement direction of multipurpose sorghum. We also emphasize the feasibility of cultivating multipurpose sorghum through genetic engineering methods by exploring potential targets using wild sorghum germplasm and genetic resources, as well as genomic resources.

Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications

The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.

Metabolic pathways engineering for drought or/and heat tolerance in cereals

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

Ethylene-responsive SbWRKY50 suppresses leaf senescence by inhibition of chlorophyll degradation in sorghum

The onset of leaf de-greening and senescence is governed by a complex regulatory network including environmental cues and internal factors such as transcription factors (TFs) and phytohormones, in which ethylene (ET) is one key inducer. However, the detailed mechanism of ET signalling for senescence regulation is still largely unknown. Here, we found that the WRKY TF SbWRKY50 from Sorghum bicolor L., a direct target of the key component ETHYLENE INSENSITIVE 3 in ET signalling, functioned for leaf senescence repression. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein9-edited SbWRKY50 mutant (SbWRKY5O-KO) of sorghum displayed precocious senescent phenotypes, while SbWRKY50 overexpression delayed age-dependent and dark-induced senescence in sorghum. SbWRKY50 negatively regulated chlorophyll degradation through direct binding to the promoters of several chlorophyll catabolic genes. In addition, SbWRKY50 recruited the Polycomb repressive complex 1 through direct interaction with SbBMI1A, to induce histone 2A mono-ubiquitination accumulation on the chlorophyll catabolic genes for epigenetic silencing and thus delayed leaf senescence. Especially, SbWRKY50 can suppress early steps of chlorophyll catabolic pathway via directly repressing SbNYC1 (NON-YELLOW COLORING 1). Other senescence-related hormones could also influence leaf senescence through repression of SbWRKY50. Hence, our work shows that SbWRKY50 is an essential regulator downstream of ET and SbWRKY50 also responds to other phytohormones for senescence regulation in sorghum.

Global Decrease in H3K9 Acetylation in Sorghum Seed Postgermination Stages

Sorghum seed germination is accompanied by increases in nutrient contents and reduced levels of antinutrients and is therefore being applied to food processing. However, the characterization of acetylated histone H3 at lysine residue 9 (H3K9ac) in sorghum postgermination has lagged. In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to identify H3K9ac enrichment and obtained transcriptome in postgermination stages. More than 10,000 hypoacetylated genes gained H3K9ac marks in the postgermination stages. In addition, we observed that the expression of the main histone deacetylase (HDAC) genes was elevated. The application of the HDAC inhibitor trichostatin A (TSA) resulted in seed growth arrest, suggesting that the repression of the H3K9ac modification is critical for postgermination. Additionally, we obtained a comprehensive view of abundant genomic changes in H3K9ac-marked regions and transcription between the mock and TSA treatment groups, which suggested that H3K9ac was required in the late stage of autotrophic seedling establishment. Metabolic profiling, transcriptome analyses, and ChIP-seq revealed that H3K9ac is enriched at genes involved in phenylpropanoid, including lignin and flavonoid, biosynthesis. Our results suggest important roles of H3K9ac in sorghum seed postgermination stages.

Genetic architecture and molecular regulation of sorghum domestication

Over time, wild crops have been domesticated by humans, and the knowledge gained from parallel selection and convergent domestication-related studies in cereals has contributed to current techniques used in molecular plant breeding. Sorghum (Sorghum bicolor (L.) Moench) is the world's fifth-most popular cereal crop and was one of the first crops cultivated by ancient farmers. In recent years, genetic and genomic studies have provided a better understanding of sorghum domestication and improvements. Here, we discuss the origin, diversification, and domestication processes of sorghum based on archeological discoveries and genomic analyses. This review also comprehensively summarized the genetic basis of key genes related to sorghum domestication and outlined their molecular mechanisms. It highlights that the absence of a domestication bottleneck in sorghum is the result of both evolution and human selection. Additionally, understanding beneficial alleles and their molecular interactions will allow us to quickly design new varieties by further de novo domestication.

Genetic control of morphological traits useful for improving sorghum

Global climate change and global warming, coupled with the growing population, have raised concerns about sustainable food supply and bioenergy demand. Sorghum [Sorghum bicolor (L.) Moench] ranks fifth among cereals produced worldwide; it is a C₄ crop with a higher stress tolerance than other major cereals and has a wide range of uses, such as grains, forage, and biomass. Therefore, sorghum has attracted attention as a promising crop for achieving sustainable development goals (SDGs). In addition, sorghum is a suitable genetic model for C₄ grasses because of its high morphological diversity and relatively small genome size compared to other C₄ grasses. Although sorghum breeding and genetic studies have lagged compared to other crops such as rice and maize, recent advances in research have identified several genes and many quantitative trait loci (QTLs) that control important agronomic traits in sorghum. This review outlines traits and genetic information with a focus on morphogenetic aspects that may be useful in sorghum breeding for grain and biomass utilization.

Identification and analysis of proline-rich proteins and hybrid proline-rich proteins super family genes from Sorghum bicolor and their expression patterns to abiotic stress and zinc stimuli

Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and development-specific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants.

Reproductive-Stage Heat Stress in Cereals: Impact, Plant Responses and Strategies for Tolerance Improvement

Reproductive-stage heat stress (RSHS) poses a major constraint to cereal crop production by damaging main plant reproductive structures and hampering reproductive processes, including pollen and stigma viability, pollination, fertilization, grain setting and grain filling. Despite this well-recognized fact, research on crop heat stress (HS) is relatively recent compared to other abiotic stresses, such as drought and salinity, and in particular, RSHS studies in cereals are considerably few in comparison with seedling-stage and vegetative-stage-centered studies. Meanwhile, climate change-exacerbated HS, independently or synergistically with drought, will have huge implications on crop performance and future global food security. Fortunately, due to their sedentary nature, crop plants have evolved complex and diverse transient and long-term mechanisms to perceive, transduce, respond and adapt to HS at the molecular, cell, physiological and whole plant levels. Therefore, uncovering the molecular and physiological mechanisms governing plant response and tolerance to RSHS facilitates the designing of effective strategies to improve HS tolerance in cereal crops. In this review, we update our understanding of several aspects of RSHS in cereals, particularly impacts on physiological processes and yield; HS signal perception and transduction; and transcriptional regulation by heat shock factors and heat stress-responsive genes. We also discuss the epigenetic, post-translational modification and HS memory mechanisms modulating plant HS tolerance. Moreover, we offer a critical set of strategies (encompassing genomics and plant breeding, transgenesis, omics and agronomy) that could accelerate the development of RSHS-resilient cereal crop cultivars. We underline that a judicious combination of all of these strategies offers the best foot forward in RSHS tolerance improvement in cereals. Further, we highlight critical shortcomings to RSHS tolerance investigations in cereals and propositions for their circumvention, as well as some knowledge gaps, which should guide future research priorities. Overall, our review furthers our understanding of HS tolerance in plants and supports the rational designing of RSHS-tolerant cereal crop cultivars for the warming climate.

Identification of Tartary Buckwheat Varieties Suitable for Forage via Nutrient Value Analysis at Different Growth Stages

It is important to select buckwheat varieties suitable for foraging and determining their best harvest time as increasing attention was paid to the forage value of buckwheat. Here, eight tartary buckwheat varieties were identified as suitable for forage based on their potential forage value through assaying the contents of ash, crude protein, crude fiber, crude fat, acid detergent fiber, neutral detergent fiber, nitrogen free extract, calcium, phosphorus, total flavonoids, and rutin in these tartary buckwheat varieties at flowering, pustulation, and mature stages, respectively. In addition, analysis of relative feed value (RFV), relative forage quality (RFQ), and principal component analysis (PCA) based on the assayed contents was applied for comprehensive evaluation of these tartary buckwheat varieties. Results showed that all the eight tartary buckwheat varieties possessed potential high forage value as their RFV is from 121.31% to 217.39% and RFQ from 117.26% to 224.54% at all three stages. In particular, both RFV and RFQ values of PS-07 reached the highest at the flowering stage among the eight tartary buckwheat varieties, followed by CQ-3 and EWPS. Accordingly, the comprehensive scoring of principal component values of PS-07 and CQ-3 are relatively higher at the flowering stage. Our research thus revealed that the eight tartary buckwheat varieties are all suitable for forage, and also provided an experimental basis for selecting the eight tartary buckwheat varieties harvested at different growth stages for livestock forage.