The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement

Genetic and Environmental Patterns Underlying Phenotypic Plasticity in Flowering Time and Plant Height in Sorghum

Phenotypic plasticity is the property of a genotype to produce different phenotypes under different environmental conditions. Understanding genetic and environmental factors behind phenotypic plasticity helps answer some longstanding biology questions and improve phenotype prediction. In this study, we investigated the phenotypic plasticity of flowering time and plant height with a set of diverse sorghum lines evaluated across 14 natural field environments. An environmental index was identified to quantitatively connect the environments. Reaction norms were then obtained with the identified indices for genetic dissection of phenotypic plasticity and performance prediction. Genome-wide association studies (GWAS) detected different sets of loci for reaction-norm parameters (intercept and slope), including 10 new genomic regions in addition to known maturity (Ma1) and dwarfing genes (Dw1, Dw2, Dw3, Dw4 and qHT7.1). Cross-validations under multiple scenarios showed promising results in predicting diverse germplasm in dynamic environments. Additional experiments conducted at four new environments, including one from a site outside of the geographical region of the initial environments, further validated the predictions. Our findings indicate that identifying the environmental index enriches our understanding of gene-environmental interplay underlying phenotypic plasticity, and that genomic prediction with the environmental dimension facilitates prediction-guided breeding for future environments.

Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits

Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.

Association mapping identifies stable loci containing novel genes for developmental and reproductive traits in sorghum

Key message We mapped 11 sorghum traits, identified 33 candidate genes, and found a grain yield gene (GID1) that regulates seed development and a grass-specific tillering gene (DUF1618) transferred to Striga hermonthica.

Genomic resources, opportunities, and prospects for accelerated improvement of millets

KEY MESSAGE

Genomic resources, alongside the tools and expertise required to leverage them, are essential for the effective improvement of globally significant millet crop species. Millets are essential for global food security and nutrition, particularly in sub-Saharan Africa and South Asia. They are crucial in promoting nutrition, climate resilience, economic development, and cultural heritage. Despite their critical role, millets have historically received less investment in developing genomic resources than major cereals like wheat, maize, and rice. However, recent advancements in genomics, particularly next-generation sequencing technologies, offer unprecedented opportunities for rapid improvement in millet crops. This review paper provides an overview of the status of genomic resources in millets and in harnessing the recent opportunities in artificial intelligence to address challenges in millet crop improvement to boost productivity, nutrition, and end quality. It emphasizes the significance of genomics in tackling global food security issues and underscores the necessity for innovative breeding strategies to translate genomics and AI into effective breeding strategies for millets.

High water use efficiency due to maintenance of photosynthetic capacity in sorghum under water stress

Environmental change requires more crop production per water use to meet the rising global food demands. However, improving crop intrinsic water use efficiency (iWUE) usually comes at the expense of carbon assimilation. Sorghum is a key crop in many vulnerable agricultural systems with higher tolerance to water stress (WS) than most widely planted crops. To investigate physiological controls on iWUE and its inheritance in sorghum, we screened 89 genotypes selected based on inherited haplotypes from an elite line or five exotics lines, containing a mix of geographical origins and dry versus milder climates, which included different aquaporin (AQP) alleles. We found significant variation among key highly heritable gas exchange and hydraulic traits, with some being significantly affected by variation in haplotypes among parental lines. Plants with a higher proportion of the non-stomatal component of iWUE still maintained iWUE under WS by maintaining photosynthetic capacity, independently of reduction in leaf hydraulic conductance. Haplotypes associated with two AQPs (SbPIP1.1 and SbTIP3.2) influenced iWUE and related traits. These findings expand the range of traits that bridge the trade-off between iWUE and productivity in C4 crops, and provide possible genetic regions that can be targeted for breeding.

Identifying genetic determinants of forage sorghum [Sorghum bicolor (Moench)] adaptation through GWAS

BACKGROUND

Forage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker - trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS).

RESULTS

Using 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length.

CONCLUSION

FarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security.

Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects

Sorghum, renowned for its substantial biomass production and remarkable tolerance to various stresses, possesses extensive gene resources and phenotypic variations. A comprehensive understanding of the genetic basis underlying complex agronomic traits is essential for unlocking the potential of sorghum in addressing food and feed security and utilizing marginal lands. In this context, we provide an overview of the major trends in genomic resource studies focusing on key agronomic traits over the past decade, accompanied by a summary of functional genomic platforms. We also delve into the molecular functions and regulatory networks of impactful genes for important agricultural traits. Lastly, we discuss and synthesize the current challenges and prospects for advancing molecular design breeding by gene-editing and polymerization of the excellent alleles, with the aim of accelerating the development of desired sorghum varieties.

Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping

Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.

Crop-GPA: an integrated platform of crop gene-phenotype associations

With the increasing availability of large-scale biology data in crop plants, there is an urgent demand for a versatile platform that fully mines and utilizes the data for modern molecular breeding. We present Crop-GPA ( https://crop-gpa.aielab.net ), a comprehensive and functional open-source platform for crop gene-phenotype association data. The current Crop-GPA provides well-curated information on genes, phenotypes, and their associations (GPAs) to researchers through an intuitive interface, dynamic graphical visualizations, and efficient online tools. Two computational tools, GPA-BERT and GPA-GCN, are specifically developed and integrated into Crop-GPA, facilitating the automatic extraction of gene-phenotype associations from bio-crop literature and predicting unknown relations based on known associations. Through usage examples, we demonstrate how our platform enables the exploration of complex correlations between genes and phenotypes in crop plants. In summary, Crop-GPA serves as a valuable multi-functional resource, empowering the crop research community to gain deeper insights into the biological mechanisms of interest.

Precise colocalization of sorghum's major chilling tolerance locus with Tannin1 due to tight linkage drag rather than antagonistic pleiotropy

Chilling tolerance in crops can increase resilience through longer growing seasons, drought escape, and nitrogen use efficiency. In sorghum (Sorghum bicolor [L.] Moench), breeding for chilling tolerance has been stymied by coinheritance of the largest-effect chilling tolerance locus, qSbCT04.62, with the major gene underlying undesirable grain proanthocyanidins, WD40 transcriptional regulator Tannin1. To test if this coinheritance is due to antagonistic pleiotropy of Tannin1, we developed and studied near-isogenic lines (NILs) carrying chilling tolerant haplotypes at qCT04.62. Whole-genome sequencing of the NILs revealed introgressions spanning part of the qCT04.62 confidence interval, including the Tannin1 gene and an ortholog of Arabidopsis cold regulator CBF/DREB1G. Segregation pattern of grain tannin in NILs confirmed the presence of wildtype Tannin1 and the reconstitution of a functional MYB-bHLH-WD40 regulatory complex. Low-temperature germination did not differ between NILs, suggesting that Tannin1 does not modulate this component of chilling tolerance. Similarly, NILs did not differ in seedling growth rate under either of two contrasting controlled environment chilling scenarios. Finally, while the chilling tolerant parent line had notably different photosynthetic responses from the susceptible parent line - including greater non-photochemical quenching before, during, and after chilling - the NIL responses match the susceptible parent. Thus, our findings suggest that tight linkage drag, not pleiotropy, underlies the precise colocalization of Tan1 with qCT04.62 and the qCT04.62 quantitative trait nucleotide lies outside the NIL introgressions. Breaking linkage at this locus should advance chilling tolerance breeding in sorghum and the identification of a novel chilling tolerance regulator.

Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology

The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and automated curation and sourced from more than 40 partner databases and resources. Here, we report on updates to the Planteome reference ontologies, namely, the Plant Ontology (PO), Trait Ontology (TO), the Plant Experimental Conditions Ontology (PECO), and integration of species/crop-specific vocabularies from our partners, the Crop Ontology (CO) into the TO ontology graph. Currently, 11 CO vocabularies are integrated into the Planteome with the addition of yam, sorghum, and potato since 2018. In addition, the size of the annotation database has increased by 34%, and the number of bioentities (genes, proteins, etc.) from 125 plant taxa has increased by 72%. We developed new tools to facilitate user requests and improvements to the CO vocabularies, and to allow fast searching and browsing of PO terms and definitions. These enhancements and future changes to automate the TO-CO mappings and knowledge discovery tools ensure that the Planteome will continue to be a valuable resource for plant biology.

Pilot-scale genome-wide association mapping in diverse sorghum germplasms identified novel genetic loci linked to major agronomic, root and stomatal traits

This genome-wide association studies (GWAS) used a subset of 96 diverse sorghum accessions, constructed from a large collection of 219 accessions for mining novel genetic loci linked to major agronomic, root morphological and physiological traits. The subset yielded 43,452 high quality single nucleotide polymorphic (SNP) markers exhibiting high allelic diversity. Population stratification showed distinct separation between caudatum and durra races. Linkage disequilibrium (LD) decay was rapidly declining with increasing physical distance across all chromosomes. The initial 50% LD decay was ~ 5 Kb and background level was within ~ 80 Kb. This study detected 42 significant quantitative trait nucleotide (QTNs) for different traits evaluated using FarmCPU, SUPER and 3VmrMLM which were in proximity with candidate genes related and were co-localized in already reported quantitative trait loci (QTL) and phenotypic variance (R2) of these QTNs ranged from 3 to 20%. Haplotype validation of the candidate genes from this study resulted nine genes showing significant phenotypic difference between different haplotypes. Three novel candidate genes associated with agronomic traits were validated including Sobic.001G499000, a potassium channel tetramerization domain protein for plant height, Sobic.010G186600, a nucleoporin-related gene for dry biomass, and Sobic.002G022600 encoding AP2-like ethylene-responsive transcription factor for plant yield. Several other candidate genes were validated and associated with different root and physiological traits including Sobic.005G104100, peroxidase 13-related gene with root length, Sobic.010G043300, homologous to Traes_5BL_8D494D60C, encoding inhibitor of apoptosis with iWUE, and Sobic.010G125500, encoding zinc finger, C3HC4 type domain with Abaxial stomatal density. In this study, 3VmrMLM was more powerful than FarmCPU and SUPER for detecting QTNs and having more breeding value indicating its reliable output for validation. This study justified that the constructed subset of diverse sorghums can be used as a panel for mapping other key traits to accelerate molecular breeding in sorghum.

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.

Discovering useful genetic variation in the seed parent gene pool for sorghum improvement

Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.

Genetic dissection of root architecture in Ethiopian sorghum landraces

KEY MESSAGE

This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.

Genomics and phenomics enabled prebreeding improved early-season chilling tolerance in Sorghum

In temperate climates, earlier planting of tropical-origin crops can provide longer growing seasons, reduce water loss, suppress weeds, and escape post-flowering drought stress. However, chilling sensitivity of sorghum, a tropical-origin cereal crop, limits early planting, and over 50 years of conventional breeding has been stymied by coinheritance of chilling tolerance (CT) loci with undesirable tannin and dwarfing alleles. In this study, phenomics and genomics-enabled approaches were used for prebreeding of sorghum early-season CT. Uncrewed aircraft systems (UAS) high-throughput phenotyping platform tested for improving scalability showed moderate correlation between manual and UAS phenotyping. UAS normalized difference vegetation index values from the chilling nested association mapping population detected CT quantitative trait locus (QTL) that colocalized with manual phenotyping CT QTL. Two of the 4 first-generation Kompetitive Allele Specific PCR (KASP) molecular markers, generated using the peak QTL single nucleotide polymorphisms (SNPs), failed to function in an independent breeding program as the CT allele was common in diverse breeding lines. Population genomic fixation index analysis identified SNP CT alleles that were globally rare but common to the CT donors. Second-generation markers, generated using population genomics, were successful in tracking the donor CT allele in diverse breeding lines from 2 independent sorghum breeding programs. Marker-assisted breeding, effective in introgressing CT allele from Chinese sorghums into chilling-sensitive US elite sorghums, improved early-planted seedling performance ratings in lines with CT alleles by up to 13-24% compared to the negative control under natural chilling stress. These findings directly demonstrate the effectiveness of high-throughput phenotyping and population genomics in molecular breeding of complex adaptive traits.

Integrating stay-green and PIN-FORMED genes: PIN-FORMED genes as potential targets for designing climate-resilient cereal ideotypes

Plant architecture modification (e.g. short-stature crops) is one of the key outcomes of modern crop breeding for high-yielding crop varieties. In cereals, delayed senescence, or stay-green, is an important trait that enables post-anthesis drought stress adaptation. Stay-green crops can prolong photosynthetic capacity during grain-filling period under post-anthesis drought stress, which is essential to ensure grain yield is not impacted under drought stress conditions. Although various stay-green quantitative trait loci have been identified in cereals, the underlying molecular mechanisms regulating stay-green remain elusive. Recent advances in various gene-editing technologies have provided avenues to fast-track crop improvement, such as the breeding of climate-resilient crops in the face of climate change. We present in this viewpoint the focus on using sorghum as the model cereal crop, to study PIN-FORMED (PIN) auxin efflux carriers as means to modulate plant architecture, and the potential to employ it as an adaptive strategy to address the environmental challenges posed by climate uncertainties.

Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [Sorghum bicolor (L.) Moench]

Sorghum is an important but arguably undervalued cereal crop, grown in large areas in Asia and Africa due to its natural resilience to drought and heat. There is growing demand for sweet sorghum as a source of bioethanol as well as food and feed. The improvement of bioenergy-related traits directly affects bioethanol production from sweet sorghum; therefore, understanding the genetic basis of these traits would enable new cultivars to be developed for bioenergy production. In order to reveal the genetic architecture behind bioenergy-related traits, we generated an F₂ population from a cross between sweet sorghum cv. 'Erdurmus' and grain sorghum cv. 'Ogretmenoglu'. This was used to construct a genetic map from SNPs discovered by double-digest restriction-site associated DNA sequencing (ddRAD-seq). F₃ lines derived from each F₂ individual were phenotyped for bioenergy-related traits in two different locations and their genotypes were analyzed with the SNPs to identify QTL regions. On chromosomes 1, 7, and 9, three major plant height (PH) QTLs (qPH1.1, qPH7.1, and qPH9.1) were identified, with phenotypic variation explained (PVE) ranging from 10.8 to 34.8%. One major QTL (qPJ6.1) on chromosome 6 was associated with the plant juice trait (PJ) and explained 35.2% of its phenotypic variation. For fresh biomass weight (FBW), four major QTLs (qFBW1.1, qFBW6.1, qFBW7.1, and qFBW9.1) were determined on chromosomes 1, 6, 7, and 9, which explained 12.3, 14.5, 10.6, and 11.9% of the phenotypic variation, respectively. Moreover, two minor QTLs (qBX3.1 and qBX7.1) of Brix (BX) were mapped on chromosomes 3 and 7, explaining 8.6 and 9.7% of the phenotypic variation, respectively. The QTLs in two clusters (qPH7.1/qBX7.1 and qPH7.1/qFBW7.1) overlapped for PH, FBW and BX. The QTL, qFBW6.1, has not been previously reported. In addition, eight SNPs were converted into cleaved amplified polymorphic sequences (CAPS) markers, which can be easily detected by agarose gel electrophoresis. These QTLs and molecular markers can be used for pyramiding and marker-assisted selection studies in sorghum, to develop advanced lines that include desirable bioenergy-related traits.

Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding

Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.

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.

Genetic modification of PIN genes induces causal mechanisms of stay-green drought adaptation phenotype

The stay-green trait is recognized as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging, and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, the contributing genes that regulate functional stay-green are not known. Here we show that the PIN FORMED family of auxin efflux carrier genes induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that nine of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2), and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture, and panicle growth in sorghum, with SbPIN1, SbPIN2, and SbPIN4 differentially expressed in various organs relative to the non-stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview

Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.

Natural variation further increases resilience of sorghum bred for chronically drought-prone environments

Drought stress is one of the major constraints for crop production in the Sahel region of Africa. Here, we explore the potential to use natural genetic variation to build on the inherent drought tolerance of an elite sorghum cultivar, Teshale, that has been bred for Ethiopian conditions including chronic drought. We evaluated a backcross nested-association mapping population using 12 diverse founder lines crossed with Teshale under three drought-prone environments in Ethiopia. All 12 populations averaged higher head exsertion and lower leaf senescence than the recurrent parent in the two most stressful environments, reflecting new drought resilience mechanisms from the donors. A total of 154 quantitative trait loci (QTLs) were detected for eight drought-responsive traits, and their validity was supported by the fact that 113 (73.4%) overlapped with QTLs previously detected for the same traits, concentrated in regions previously associated with 'stay-green' traits. Allele effects showed that some favourable alleles are already present in the Ethiopian cultivar; however, the exotic donors offer rich scope for increasing drought resilience. Using model-selected SNPs associated with the eight traits identified in this study and three in a companion study, phenotypic prediction accuracies for grain yield were equivalent to genome-wide SNPs and were significantly better than random SNPs, indicating that the selected traits are predictive of sorghum grain yield.

Genetic basis of sorghum leaf width and its potential as a surrogate for transpiration efficiency

Leaf width was correlated with plant-level transpiration efficiency and associated with 19 QTL in sorghum, suggesting it could be a surrogate for transpiration efficiency in large breeding program. Enhancing plant transpiration efficiency (TE) by reducing transpiration without compromising photosynthesis and yield is a desirable selection target in crop improvement programs. While narrow individual leaf width has been correlated with greater intrinsic water use efficiency in C₄ species, the extent to which this translates to greater plant TE has not been investigated. The aims of this study were to evaluate the correlation of leaf width with TE at the whole-plant scale and investigate the genetic control of leaf width in sorghum. Two lysimetry experiments using 16 genotypes varying for stomatal conductance and three field trials using a large sorghum diversity panel (n = 701 lines) were conducted. Negative associations of leaf width with plant TE were found in the lysimetry experiments, suggesting narrow leaves may result in reduced plant transpiration without trade-offs in biomass accumulation. A wide range in width of the largest leaf was found in the sorghum diversity panel with consistent ranking among sorghum races, suggesting that environmental adaptation may have a role in modifying leaf width. Nineteen QTL were identified by genome-wide association studies on leaf width adjusted for flowering time. The QTL identified showed high levels of correspondence with those in maize and rice, suggesting similarities in the genetic control of leaf width across cereals. Three a priori candidate genes for leaf width, previously found to regulate dorsoventrality, were identified based on a 1-cM threshold. This study provides useful physiological and genetic insights for potential manipulation of leaf width to improve plant adaptation to diverse environments.

Genome-wide screening of lectin putative genes from Sorghum bicolor L., distribution in QTLs and a probable implications of lectins in abiotic stress tolerance

BACKGROUND

Sorghum bicolor is one of the most important crops worldwide with the potential to provide resilience when other economic staples might fail against the continuous environmental changes. Many physiological, developmental and tolerance traits in plants are either controlled or influenced by lectins; carbohydrate binding proteins. Hence, we aimed at providing a comprehensive in silico account on sorghum's lectins and study their possible implication on various desired agronomical traits.

RESULTS

We have searched sorghum's genome from grain and sweet types for lectins putative genes that encode proteins with domains capable of differentially binding carbohydrate moieties and trigger various physiological responses. Of the 12 known plant lectin families, 8 were identified regarding their domain architectures, evolutionary relationships, physiochemical characteristics, and gene expansion mechanisms, and they were thoroughly addressed. Variations between grain and sweet sorghum lectin homologs in term of the presence/absence of certain other joint domains like dirigent and nucleotide-binding adaptor shared by APAF-1, R-proteins, and CED-4 (NB-ARC) indicate a possible neofunctionalization. Lectin sequences were found to be preferentially overrepresented in certain quantitative trait loci (QTLs) related to various traits under several subcategories such as cold, drought, salinity, panicle/grain composition, and leaf morphology. The co-localization and distribution of lectins among multiple QTLs provide insights into the pleiotropic effects that could be played by one lectin gene in numerous traits.

CONCLUSION

Our study offers a first-time inclusive details on sorghum lectins and their possible role in conferring tolerance against abiotic stresses and other economically important traits that can be informative for future functional analysis and breeding studies.

Genetic and genomic diversity in the sorghum gene bank collection of Uganda

BACKGROUND

The Plant Genetic Resources Centre at the Uganda National Gene Bank houses has over 3000 genetically diverse landraces and wild relatives of Sorghum bicolor accessions. This genetic diversity resource is untapped, under-utilized, and has not been systematically incorporated into sorghum breeding programs. In this study, we characterized the germplasm collection using whole-genome SNP markers (DArTseq). Discriminant analysis of principal components (DAPC) was implemented to study the racial ancestry of the accessions in comparison to a global sorghum diversity set and characterize the sub-groups present in the Ugandan (UG) germplasm.

RESULTS

Population structure and phylogenetic analysis revealed the presence of five subgroups among the Ugandan accessions. The samples from the highlands of the southwestern region were genetically distinct as compared to the rest of the population. This subset was predominated by the caudatum race and unique in comparison to the other sub-populations. In this study, we detected QTL for juvenile cold tolerance by genome-wide association studies (GWAS) resulting in the identification of 4 markers associated (-log10p > 3) to survival under cold stress under both field and climate chamber conditions, located on 3 chromosomes (02, 06, 09). To our best knowledge, the QTL on Sb09 with the strongest association was discovered for the first time.

CONCLUSION

This study demonstrates how genebank genomics can potentially facilitate effective and efficient usage of valuable, untapped germplasm collections for agronomic trait evaluation and subsequent allele mining. In face of adverse climate change, identification of genomic regions potentially involved in the adaptation of Ugandan sorghum accessions to cooler climatic conditions would be of interest for the expansion of sorghum production into temperate latitudes.

DOMINANT AWN INHIBITOR Encodes the ALOG Protein Originating from Gene Duplication and Inhibits AWN Elongation by Suppressing Cell Proliferation and Elongation in Sorghum

The awn, a needle-like structure extending from the tip of the lemma in grass species, plays a role in environmental adaptation and fitness. In some crops, awns appear to have been eliminated during domestication. Although numerous genes involved in awn development have been identified, several dominant genes that eliminate awns are also known to exist. For example, in sorghum (Sorghum bicolor), the dominant awn-inhibiting gene has been known since 1921; however, its molecular features remain uncharacterized. In this study, we conducted quantitative trait locus analysis and a genome-wide association study of awn-related traits in sorghum and identified DOMINANT AWN INHIBITOR (DAI), which encodes the ALOG family protein on chromosome 3. DAI appeared to be present in most awnless sorghum cultivars, likely because of its effectiveness. Detailed analysis of the ALOG protein family in cereals revealed that DAI originated from a duplication of its twin paralog (DAIori) on chromosome 10. Observations of immature awns in near-isogenic lines revealed that DAI inhibits awn elongation by suppressing both cell proliferation and elongation. We also found that only DAI gained a novel function to inhibit awn elongation through an awn-specific expression pattern distinct from that of DAIori. Interestingly, heterologous expression of DAI with its own promoter in rice inhibited awn elongation in the awned cultivar Kasalath. We found that DAI originated from gene duplication, providing an interesting example of gain-of-function that occurs only in sorghum but shares its functionality with rice and sorghum.

Selection Signatures in Chinese Sorghum Reveals Its Unique Liquor-Making Properties

Chinese sorghum (S. bicolor) has been a historically critical ingredient for brewing famous distilled liquors ever since Yuan Dynasty (749 ∼ 652 years BP). Incomplete understanding of the population genetics and domestication history limits its broad applications, especially that the lack of genetics knowledge underlying liquor-brewing properties makes it difficult to establish scientific standards for sorghum breeding. To unravel the domestic history of Chinese sorghum, we re-sequenced 244 Chinese sorghum lines selected from 16 provinces. We found that Chinese sorghums formed three distinct genetic sub-structures, referred as the Northern, the Southern, and the Chishui groups, following an obviously geographic pattern. These sorghum accessions were further characterized in liquor brewing traits and identified selection footprints associated with liquor brewing efficiency. An importantly selective sweep region identified includes several homologous genes involving in grain size, pericarp thickness, and architecture of inflorescence. Our result also demonstrated that pericarp strength rather than grain size determines the ability of the grains to resist repeated cooking during brewing process. New insight into the traits beneficial to the liquor-brewing process provides both a better understanding on Chinese sorghum domestication and a guidance on breeding sorghum as a multiple use crop in China.

Genome-wide association mapping identifies an SNF4 ortholog that impacts biomass and sugar yield in sorghum and sugarcane

Sorghum is a feed/industrial crop in developed countries and a staple food elsewhere in the world. This study evaluated the sorghum mini core collection for days to 50% flowering (DF), biomass, plant height (PH), soluble solid content (SSC), and juice weight (JW), and the sorghum reference set for DF and PH, in 7-12 testing environments. We also performed genome-wide association mapping with 6 094 317 and 265 500 single nucleotide polymorphism markers in the mini core collection and the reference set, respectively. In the mini core panel we identified three quantitative trait loci for DF, two for JW, one for PH, and one for biomass. In the reference set panel we identified another quantitative trait locus for PH on chromosome 6 that was also associated with biomass, DF, JW, and SSC in the mini core panel. Transgenic studies of three genes selected from the locus revealed that Sobic.006G061100 (SbSNF4-2) increased biomass, SSC, JW, and PH when overexpressed in both sorghum and sugarcane, and delayed flowering in transgenic sorghum. SbSNF4-2 encodes a γ subunit of the evolutionarily conserved AMPK/SNF1/SnRK1 heterotrimeric complexes. SbSNF4-2 and its orthologs will be valuable in genetic enhancement of biomass and sugar yield in plants.

Genome-wide association studies identify putative pleiotropic locus mediating drought tolerance in sorghum

Drought is a key constraint on plant productivity and threat to food security. Sorghum (Sorghum bicolor L. Moench), a global staple food and forage crop, is among the most drought-adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large-tube lysimeter system under well-watered (WW) versus a preflowering drought water-stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerant check genotypes and genome-wide association studies (GWAS) that mapped the major height locus at QHT7.1 and Dw3. GWAS further identified marker trait associations (MTAs) for drought-related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7-70% of phenotypic variance. Most MTAs for drought-related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co-localized with staygreen post-flowering drought tolerance loci (Stg3a and Stg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS revealed oligogenic variants for drought tolerance in sorghum landraces, which could be used as trait predictive markers for improved drought adaptation.

Dissecting the genetic control of natural variation in sorghum photosynthetic response to drought stress

Drought stress causes crop yield losses worldwide. Sorghum is a C4 species tolerant to moderate drought stress, and its extensive natural variation for photosynthetic traits under water-limiting conditions can be exploited for developing cultivars with enhanced stress tolerance. The objective of this study was to discover genes/genomic regions that control the sorghum photosynthetic capacity under pre-anthesis water-limiting conditions. We performed a genome-wide association study for seven photosynthetic gas exchange and chlorophyll fluorescence traits during three periods of contrasting soil volumetric water content (VWC): control (30% VWC), drought (15% VWC), and recovery (30% VWC). Water stress was imposed with an automated irrigation system that generated a controlled dry-down period for all plants, to perform an unbiased genotypic comparison. A total of 60 genomic regions were associated with natural variation in one or more photosynthetic traits in a particular treatment or with derived variables. We identified 33 promising candidate genes with predicted functions related to stress signaling, oxidative stress protection, hormonal response to stress, and dehydration protection. Our results provide new knowledge about the natural variation and genetic control of sorghum photosynthetic response to drought with the ultimate goal of improving its adaptation and productivity under water stress scenarios.

Does Plant Breeding for Antioxidant-Rich Foods Have an Impact on Human Health?

Given the general beneficial effects of antioxidants-rich foods on human health and disease prevention, there is a continuous interest in plant secondary metabolites conferring attractive colors to fruits and grains and responsible, together with others, for nutraceutical properties. Cereals and Solanaceae are important components of the human diet, thus, they are the main targets for functional food development by exploitation of genetic resources and metabolic engineering. In this review, we focus on the impact of antioxidants-rich cereal and Solanaceae derived foods on human health by analyzing natural biodiversity and biotechnological strategies aiming at increasing the antioxidant level of grains and fruits, the impact of agronomic practices and food processing on antioxidant properties combined with a focus on the current state of pre-clinical and clinical studies. Despite the strong evidence in in vitro and animal studies supporting the beneficial effects of antioxidants-rich diets in preventing diseases, clinical studies are still not sufficient to prove the impact of antioxidant rich cereal and Solanaceae derived foods on human

Quantitative and population genomics suggest a broad role of stay-green loci in the drought adaptation of sorghum

Drought is a major constraint on plant productivity globally. Sorghum [Sorghum bicolor (L.) Moench] landraces have evolved in drought-prone regions, but the genetics of their adaptation is poorly understood. Here we sought to identify novel drought-tolerance loci and test hypotheses on the role of known loci including those underlying stay-green (Stg) postflowering drought tolerance. We phenotyped 590 diverse sorghum accessions from West Africa in 10 environments, under field-based managed drought stress [preflowering water stress (WS1), postflowering water stress (WS2), and well-watered (WW)] and rainfed (RF) conditions over 4 yr. Days to 50% flowering (DFLo), aboveground dry biomass (DBM), plant height (PH), and plant grain yield components (including grain weight [GrW], panicle weight [PW] and grain number [GrN] per plant, and 1000-grain weight [TGrW]) were measured, and genome-wide association studies (GWAS) was conducted. Broad-sense heritability for biomass and plant grain yield was high (33-92%) across environments. There was a significant correlation between stress tolerance index (STI) for GrW per plant across WS1 and WS2. Genome-wide association studies revealed that SbZfl1 and SbCN12, orthologs of maize (Zea mays L.) flowering genes, likely underlie flowering time variation under these conditions. Genome-wide association studies further identified associations (n = 134; common between two GWAS models) for STI and drought effects on plant yield components including 16 putative pleiotropic associations. Thirty of the associations colocalized with Stg1, Stg2, Stg3, and Stg4 loci and had large effects. Seven lead associations, including some within Stg1, overlapped with positive selection outliers. Our findings reveal previously undescribed natural genetic variation for drought-tolerance-related traits and suggest a broad role of Stg loci in drought adaptation of sorghum.

Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize

Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.

Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes

Livestock provides an additional source of income for marginal cropping farmers, but crop residues that are used as a main source of animal feed are characteristically low in digestibility and protein content. This reduces the potential livestock product yield and quality. The key trait, which influences the quality and the cost of animal feed, is digestibility. In this study, we demonstrate that sorghum breeding can be directed to achieve genetic gains for both fodder biomass and digestibility without any trade-offs. The genotypic variance has shown significant differences for biomass across years (13,035 in 2016 and 3,395 in 2017) while in vitro organic matter digestibility (IVOMD) showed significant genotypic variation in 2016 (0.253) under drought. A range of agronomic and fodder quality traits was found to vary significantly in the population within both the control and drought conditions and across both years of the study. There was significant genotypic variance (σg2) and genotypic × treatment variance (σgxt2) in dry matter production in a recombinant inbred line (RIL) population in both study years, while there was only significant σg2 and σgxt2 in IVOMD under the control conditions. There was no significant correlation identified between biomass and digestibility traits under the control conditions, but there was a positive correlation under drought. However, a negative relation was observed between digestibility and grain yield under the control conditions, while there was no significant correlation under drought population, which was genotyped using the genotyping-by-sequencing (GBS) technique, and 1,141 informative single nucleotide polymorphism (SNP) markers were identified. A linkage map was constructed, and a total of 294 quantitative trait loci (QTLs) were detected, with 534 epistatic interactions, across all of the traits under study. QTL for the agronomic traits fresh and dry weight, together with plant height, mapped on to the linkage group (LG) 7, while QTL for IVOMD mapped on to LG1, 2, and 8. A number of genes previously reported to play a role in nitrogen metabolism and cell wall-related functions were found to be associated with these QTL.

Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing

BACKGROUND

Leaf angle is an important plant architecture trait, affecting plant density, light interception efficiency, photosynthetic rate, and yield. The "smart canopy" model proposes more vertical leaves in the top plant layers and more horizontal leaves in the lower canopy, maximizing conversion efficiency and photosynthesis. Sorghum leaf arrangement is opposite to that proposed in the "smart canopy" model, indicating the need for improvement. Although leaf angle quantitative trait loci (QTL) have been previously reported, only the Dwarf3 (Dw3) auxin transporter gene, colocalizing with a major-effect QTL on chromosome 7, has been validated. Additionally, the genetic architecture of leaf angle across canopy layers remains to be elucidated.

RESULTS

This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. A set of 284 differentially expressed genes for at least one layer comparison (FDR < 0.05) co-localized with 69 leaf angle QTL and were consistently identified across genotypes. These genes are involved in transmembrane transport, hormone regulation, oxidation-reduction process, response to stimuli, lipid metabolism, and photosynthesis. The most relevant eleven candidate genes for layer-specific angle modification include those homologous to genes controlling leaf angle in rice and maize or genes associated with cell size/expansion, shape, and cell number.

CONCLUSIONS

Considering the predicted functions of candidate genes, their potential undesirable pleiotropic effects should be further investigated across tissues and developmental stages. Future validation of proposed candidates and exploitation through genetic engineering or gene editing strategies targeted to collar cells will bring researchers closer to the realization of a "smart canopy" sorghum.

Genetic control of leaf angle in sorghum and its effect on light interception

Developing sorghum genotypes adapted to different light environments requires understanding of a plant's ability to capture light, determined through leaf angle specifically. This study dissected the genetic basis of leaf angle in 3 year field trials at two sites, using a sorghum diversity panel (729 accessions). A wide range of variation in leaf angle with medium heritability was observed. Leaf angle explained 36% variation in canopy light extinction coefficient, highlighting the extent to which variation in leaf angle influences light interception at the whole-canopy level. This study also found that the sorghum races of Guinea and Durra consistently having the largest and smallest leaf angle, respectively, highlighting the potential role of leaf angle in adaptation to distinct environments. The genome-wide association study detected 33 quantitative trait loci (QTLs) associated with leaf angle. Strong synteny was observed with previously detected leaf angle QTLs in maize (70%) and rice (40%) within 10 cM, among which the overlap was significantly enriched according to χ2 tests, suggesting a highly consistent genetic control in grasses. A priori leaf angle candidate genes identified in maize and rice were found to be enriched within a 1-cM window around the sorghum leaf angle QTLs. Additionally, protein domain analysis identified the WD40 protein domain as being enriched within a 1-cM window around the QTLs. These outcomes show that there is sufficient heritability and natural variation in the angle of upper leaves in sorghum which may be exploited to change light interception and optimize crop canopies for different contexts.

Genetic control of source-sink relationships in grain sorghum

QTL hotspots identified for selected source-sink-related traits provide the opportunity for pyramiding favorable alleles for improving sorghum productivity under diverse environments. A sorghum bi-parental mapping population was evaluated under six different environments at Hays and Manhattan, Kansas, USA, in 2016 and 2017, to identify genomic regions controlling source-sink relationships. The population consisted of 210 recombinant inbred lines developed from US elite post-flowering drought susceptible (RTx430) and a known post-flowering drought tolerant cultivar (SC35). Selected physiological traits related to source (effective quantum yield of photosystem II and chlorophyll index), sink (grain yield per panicle) and panicle neck diameter were recorded during grain filling. The results showed strong phenotypic and genotypic association between panicle neck diameter and grain yield per panicle during mid-grain filling and at maturity. Multiple QTL model revealed 5-12 including 2-5 major QTL for each trait. Among them 3, 7 and 8 QTL for quantum yield, panicle neck diameter and chlorophyll index, respectively, have not been identified previously in sorghum. Phenotypic variation explained by QTL identified across target traits ranged between 5.5 and 25.4%. Panicle neck diameter and grain yield per panicle were positively associated, indicating the possibility of targeting common co-localized QTL to improve both traits simultaneously through marker-assisted selection. Three major QTL hotspots, controlling multiple traits were identified on chromosome 1 (52.23-61.18 Mb), 2 (2.52-11.43 Mb) and 3 (1.32-3.95 Mb). The identified genomic regions and underlying candidate genes can be utilized in pyramiding favorable alleles for improving source-sink relationships in sorghum under diverse environments.

A sorghum genome-wide association study (GWAS) identifies a WRKY transcription factor as a candidate gene underlying sugarcane aphid (Melanaphis sacchari) resistance

A WRKY transcription factor identified through forward genetics is associated with sorghum resistance to the sugarcane aphid and through heterologous expression reduces aphid populations in multiple plant species. Crop plant resistance to insect pests is based on genetically encoded traits which often display variability across diverse germplasm. In a comparatively recent event, a predominant sugarcane aphid (SCA: Melanaphis sacchari) biotype has become a significant agronomic pest of grain sorghum (Sorghum bicolor). To uncover candidate genes underlying SCA resistance, we used a forward genetics approach combining the genetic diversity present in the Sorghum Association Panel (SAP) and the Bioenergy Association Panel (BAP) for a genome-wide association study, employing an established SCA damage rating. One major association was found on Chromosome 9 within the WRKY transcription factor 86 (SbWRKY86). Transcripts encoding SbWRKY86 were previously identified as upregulated in SCA-resistant germplasm and the syntenic ortholog in maize accumulates following Rhopalosiphum maidis infestation. Analyses of SbWRKY86 transcripts displayed patterns of increased SCA-elicited accumulation in additional SCA-resistant sorghum lines. Heterologous expression of SbWRKY86 in both tobacco (Nicotiana benthamiana) and Arabidopsis resulted in reduced population growth of green peach aphid (Myzus persicae). Comparative RNA-Seq analyses of Arabidopsis lines expressing 35S:SbWRKY86-YFP identified changes in expression for a small network of genes associated with carbon-nitrogen metabolism and callose deposition, both contributing factors to defense against aphids. As a test of altered plant responses, 35S:SbWRKY86-YFP Arabidopsis lines were activated using the flagellin epitope elicitor, flg22, and displayed significant increases in callose deposition. Our findings indicate that both heterologous and increased native expression of the transcription factor SbWRKY86 contributes to reduced aphid levels in diverse plant models.

Identification of Candidate Forage Yield Genes in Sorghum (Sorghum bicolor L.) Using Integrated Genome-Wide Association Studies and RNA-Seq

Genetic dissection of forage yield traits is critical to the development of sorghum as a forage crop. In the present study, association mapping was performed with 85,585 SNP markers on four forage yield traits, namely plant height (PH), tiller number (TN), stem diameter (SD), and fresh weight per plant (FW) among 245 sorghum accessions evaluated in four environments. A total of 338 SNPs or quantitative trait nucleotides (QTNs) were associated with the four traits, and 21 of these QTNs were detected in at least two environments, including four QTNs for PH, ten for TN, six for SD, and one for FW. To identify candidate genes, dynamic transcriptome expression profiling was performed at four stages of sorghum development. One hundred and six differentially expressed genes (DEGs) that were enriched in hormone signal transduction pathways were found in all stages. Weighted gene correlation network analysis for PH and SD indicated that eight modules were significantly correlated with PH and that three modules were significantly correlated with SD. The blue module had the highest positive correlation with PH and SD, and the turquoise module had the highest negative correlation with PH and SD. Eight candidate genes were identified through the integration of genome-wide association studies (GWAS) and RNA sequencing. Sobic.004G143900, an indole-3-glycerol phosphate synthase gene that is involved in indoleacetic acid biosynthesis, was down-regulated as sorghum plants grew in height and was identified in the blue module, and Sobic.003G375100, an SD candidate gene, encoded a DNA repair RAD52-like protein 1 that plays a critical role in DNA repair-linked cell cycle progression. These findings demonstrate that the integrative analysis of omics data is a promising approach to identify candidate genes for complex traits.

SorghumBase: a web-based portal for sorghum genetic information and community advancement

SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal ( https://www.sorghumbase.org ), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.

Genetic Architecture of Novel Sources for Reproductive Cold Tolerance in Sorghum

Enhancements in reproductive cold tolerance of sorghum are essential to expand growing areas into both high-latitude temperate areas and tropical high-altitude environments. Here we present first insights into the genetic architecture of this trait via genome-wide association studies in a broad genetic diversity set (n = 330) phenotyped in multi-location field trials including high-altitude tropical (Mexico) and high-latitude temperate (Germany) environments. We observed a high degree of phenotypic variation and identified several novel, temperate-adapted accessions with superior and environmentally stable cold tolerance. Good heritability indicates strong potential for implementation of reproductive cold tolerance in breeding. Although the trait was found to be strongly quantitative, promising genomic regions with multiple-trait associations were found, including hotspots on chromosomes 3 and 10 which contain candidate genes implicated in different developmental and survival processes under abiotic stress conditions.

QTL mapping for bioenergy traits in sweet sorghum recombinant inbred lines

During the past decade, sweet sorghum (Sorghum bicolor Moench L.) has shown great potential for bioenergy production, especially biofuels. In this study, 223 recombinant inbred lines (RILs) derived from a cross between two sweet sorghum lines (Brandes × Wray) were evaluated in three trials. Single-nucleotide polymorphisms (SNPs) derived from genotyping by sequencing of 272 RILs were used to build a high-density genetic map comprising 3,767 SNPs spanning 1,368.83 cM. Multitrait multiple interval mapping (MT-MIM) was carried out to map quantitative trait loci (QTL) for eight bioenergy traits. A total of 33 QTLs were identified for flowering time, plant height, total soluble solids and sucrose (five QTLs each), fibers (four QTLs), and fresh biomass yield, juice extraction yield, and reducing sugars (three QTLs each). QTL hotspots were found on chromosomes 1, 3, 6, 9, and 10, in addition to other QTLs detected on chromosomes 4 and 8. We observed that 14 out of the 33 mapped QTLs were found in all three trials. Upon further development and validation in other crosses, the results provided by the present study have a great potential to be used in marker-assisted selection in sorghum breeding programs for biofuel production.

Genome-Wide Association Mapping Identifies Novel Panicle Morphology Loci and Candidate Genes in Sorghum

Panicle morphology is an important trait in racial classification and can determine grain yield and other agronomic traits in sorghum. In this study, we performed association mapping of panicle length, panicle width, panicle compactness, and peduncle recurving in the sorghum mini core panel measured in multiple environments with 6,094,317 single nucleotide polymorphism (SNP) markers. We mapped one locus each on chromosomes 7 and 9 to recurving peduncles and eight loci for panicle length, panicle width, and panicle compactness. Because panicle length was positively correlated with panicle width, all loci for panicle length and width were colocalized. Among the eight loci, two each were on chromosomes 1, 2, and 6, and one each on chromosomes 8 and 10. The two loci on chromosome 2, i.e., Pm 2-1 and Pm 2-2, were detected in 7 and 5 out of 11 testing environments, respectively. Pm 2-2 colocalized with panicle compactness. Candidate genes were identified from both loci. The rice Erect Panicle2 (EP2) ortholog was among the candidate genes in Pm 2-2. EP2 regulates panicle erectness and panicle length in rice and encodes a novel plant-specific protein with unknown functions. The results of this study may facilitate the molecular identification of panicle morphology-related genes and the enhancement of yield and adaptation in sorghum.

Manipulating assimilate availability provides insight into the genes controlling grain size in sorghum

Variation in grain size, a major determinant of grain yield and quality in cereal crops, is determined by both the plant's genetic potential and the available assimilate to fill the grain in the absence of stress. This study investigated grain size variation in response to variation in assimilate supply in sorghum using a diversity panel (n = 837) and a backcross-nested association mapping population (n = 1421) across four experiments. To explore the effects of genetic potential and assimilate availability on grain size, the top half of selected panicles was removed at anthesis. Results showed substantial variation in five grain size parameters with high heritability. Artificial reduction in grain number resulted in a general increase in grain weight, with the extent of the increase varying across genotypes. Genome-wide association studies identified 44 grain size quantitative trait locus (QTL) that were likely to act on assimilate availability and 50 QTL that were likely to act on genetic potential. This finding was further supported by functional enrichment analysis and co-location analysis with known grain number QTL and candidate genes. RNA interference and overexpression experiments were conducted to validate the function of one of the identified gene, SbDEP1, showing that SbDEP1 positively regulates grain number and negatively regulates grain size by controlling primary branching in sorghum. Haplotype analysis of SbDEP1 suggested a possible role in racial differentiation. The enhanced understanding of grain size variation in relation to assimilate availability presented in this study will benefit sorghum improvement and have implications for other cereal crops.

SorGSD: updating and expanding the sorghum genome science database with new contents and tools

BACKGROUND

As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C4 model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has been accumulated for sorghum. Integrating this information may accelerate genetic research and improve molecular breeding for sorghum agronomic traits.

RESULTS

We updated the Sorghum Genome SNP Database (SorGSD) by adding new data, new features and renamed it to Sorghum Genome Science Database (SorGSD). In comparison with the original version SorGSD, which contains SNPs from 48 sorghum accessions mapped to the reference genome BTx623 (v2.1), the new version was expanded to 289 sorghum lines with both single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs), which were aligned to the newly assembled and annotated sorghum genome BTx623 (v3.1). Moreover, phenotypic data and panicle pictures of critical accessions were provided in the new version. We implemented new tools including ID Conversion, Homologue Search and Genome Browser for analysis and updated the general information related to sorghum research, such as online sorghum resources and literature references. In addition, we deployed a new database infrastructure and redesigned a new user interface as one of the Genome Variation Map databases. The new version SorGSD is freely accessible online at http://ngdc.cncb.ac.cn/sorgsd/ .

CONCLUSIONS

SorGSD is a comprehensive integration with large-scale genomic variation, phenotypic information and incorporates online data analysis tools for data mining, genome navigation and analysis. We hope that SorGSD could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis.

Genetic characterization of a Sorghum bicolor multiparent mapping population emphasizing carbon-partitioning dynamics

Sorghum bicolor, a photosynthetically efficient C₄ grass, represents an important source of grain, forage, fermentable sugars, and cellulosic fibers that can be utilized in myriad applications ranging from bioenergy to bioindustrial feedstocks. Sorghum’s efficient fixation of carbon per unit time per unit area per unit input has led to its classification as a preferred biomass crop highlighted by its designation as an advanced biofuel by the U.S. Department of Energy. Due to its extensive genetic diversity and worldwide colonization, sorghum has considerable diversity for a range of phenotypes influencing productivity, composition, and sink/source dynamics. To dissect the genetic basis of these key traits, we present a sorghum carbon-partitioning nested association mapping (NAM) population generated by crossing 11 diverse founder lines with Grassl as the single recurrent female. By exploiting existing variation among cellulosic, forage, sweet, and grain sorghum carbon partitioning regimes, the sorghum carbon-partitioning NAM population will allow the identification of important biomass-associated traits, elucidate the genetic architecture underlying carbon partitioning and improve our understanding of the genetic determinants affecting unique phenotypes within Poaceae. We contrast this NAM population with an existing grain population generated using Tx430 as the recurrent female. Genotypic data are assessed for quality by examining variant density, nucleotide diversity, linkage decay, and are validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family NAM population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbon-partitioning regimes.

Classical phenotyping and deep learning concur on genetic control of stomatal density and area in sorghum

Stomatal density (SD) and stomatal complex area (SCA) are important traits that regulate gas exchange and abiotic stress response in plants. Despite sorghum (Sorghum bicolor) adaptation to arid conditions, the genetic potential of stomata-related traits remains unexplored due to challenges in available phenotyping methods. Hence, identifying loci that control stomatal traits is fundamental to designing strategies to breed sorghum with optimized stomatal regulation. We implemented both classical and deep learning methods to characterize genetic diversity in 311 grain sorghum accessions for stomatal traits at two different field environments. Nearly 12,000 images collected from abaxial (Ab) and adaxial (Ad) leaf surfaces revealed substantial variation in stomatal traits. Our study demonstrated significant accuracy between manual and deep learning methods in predicting SD and SCA. In sorghum, SD was 32%-39% greater on the Ab versus the Ad surface, while SCA on the Ab surface was 2%-5% smaller than on the Ad surface. Genome-Wide Association Study identified 71 genetic loci (38 were environment-specific) with significant genotype to phenotype associations for stomatal traits. Putative causal genes underlying the phenotypic variation were identified. Accessions with similar SCA but carrying contrasting haplotypes for SD were tested for stomatal conductance and carbon assimilation under field conditions. Our findings provide a foundation for further studies on the genetic and molecular mechanisms controlling stomata patterning and regulation in sorghum. An integrated physiological, deep learning, and genomic approach allowed us to unravel the genetic control of natural variation in stomata traits in sorghum, which can be applied to other plants.

A genomics resource for genetics, physiology, and breeding of West African sorghum

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in western Africa (WA) has diversified across a mosaic of cultures and end uses and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing (GBS) was used to generate 159,101 high-quality biallelic single nucleotide polymorphisms (SNPs), with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = .00045), only slightly less than in a global diversity panel (GDP) (π = .00055). Linkage disequilibrium (LD) decayed to background level (r² < .1) by ∼50 kb in the WASAP. Genome-wide diversity was structured both by botanical type and by populations within botanical type with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies (GWAS) of days to flowering (DFLo) and plant height (PH) revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height loci Dw3 and SbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in U.S. germplasm (Ma6 and SbCN8) suggests that photoperiodic flowering in West African sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in WA.

Sorghum breeding in the genomic era: opportunities and challenges

The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.