Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum

Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis

KEY MESSAGE

Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.

Exploring the genetic basis of anthracnose resistance in Ethiopian sorghum through a genome-wide association study

BACKGROUND

Sorghum anthracnose is a major disease that hampers the productivity of the crop globally. The disease is caused by the hemibiotrophic fungal pathogen Colletotrichum sublineola. The identification of anthracnose-resistant sorghum genotypes, defining resistance loci and the underlying genes, and their introgression into adapted cultivars are crucial for enhancing productivity. In this study, we conducted field experiments on 358 diverse accessions of Ethiopian sorghum. Quantitative resistance to anthracnose was evaluated at locations characterized by a heavy natural infestation that is suitable for disease resistance screening.

RESULTS

The field-based screening identified 53 accessions that were resistant across locations, while 213 accessions exhibited variable resistance against local pathotypes. Genome-wide association analysis (GWAS) was performed using disease response scores on 329 accessions and 83,861 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS). We identified 38 loci significantly associated with anthracnose resistance. Interestingly, a subset of these loci harbor genes encoding receptor-like kinases (RLK), nucleotide-binding leucine-rich repeats (NLRs), stress-induced antifungal tyrosine kinase that have been previously implicated in disease resistance. A SNP on chromosome 4 (S04_66140995) and two SNPs on chromosome 2 (S02_75784037, S02_2031925), localized with-in the coding region of genes that encode a putative stress-induced antifungal kinase, an F-Box protein, and Xa21-binding RLK that were strongly associated with anthracnose resistance. We also identified highly significant associations between anthracnose resistance and three SNPs linked to genes (Sobic.002G058400, Sobic.008G156600, Sobic.005G033400) encoding an orthologue of the widely known NLR protein (RPM1), Leucine Rich Repeat family protein, and Heavy Metal Associated domain-containing protein, respectively. Other SNPs linked to predicted immune response genes were also significantly associated with anthracnose resistance.

CONCLUSIONS

The sorghum germplasm collections used in the present study are genetically diverse. They harbor potentially useful, yet undiscovered, alleles for anthracnose resistance. This is supported by the identification of novel loci that are enriched for disease resistance regulators such as NLRs, LRKs, Xa21-binding LRK, and antifungal proteins. The genotypic data available for these accessions offer a valuable resource for sorghum breeders to effectively improve the crop. The genomic regions and candidate genes identified can be used to design markers for molecular breeding of sorghum diseases resistance.

Additive and Dominance Genome-Wide Association Studies Reveal the Genetic Basis of Heterosis Related to Growth Traits of Duhua Hybrid Pigs

Heterosis has been extensively used for pig genetic breeding and production, but the genetic basis of heterosis remains largely elusive. Crossbreeding between commercial and native breeds provides a good model to parse the genetic basis of heterosis. This study uses Duhua hybrid pigs, a crossbreed of Duroc and Liangguang small spotted pigs, as materials to explore the genetic basis underlying heterosis related to growth traits at the genomic level. The mid-parent heterosis (MPH) analysis showed heterosis of this Duhua offspring on growth traits. In this study, we examined the impact of additive and dominance effects on 100 AGE (age adjusted to 100 kg) and 100 BF (backfat thickness adjusted to 100 kg) of Duhua hybrid pigs. Meanwhile, we successfully identified SNPs associated with growth traits through both additive and dominance GWASs (genome-wide association studies). These findings will facilitate the subsequent in-depth studies of heterosis in the growth traits of Duhua pigs.

High-yield hybrid breeding of Camellia oleifolia based on ISSR molecular markers

BACKGROUND

C. Oleifera is among the world's largest four woody plants known for their edible oil production, yet the contribution rate of improved varieties is less than 20%. The species traditional breeding is lengthy cycle (20-30 years), occupation of land resources, high labor cost, and low accuracy and efficiency, which can be enhanced by molecular marker-assisted selection. However, the lack of high-quality molecular markers hinders the species genetic analysis and molecular breeding.

RESULTS

Through quantitative traits characterization, genetic diversity assessment, and association studies, we generated a selection population with wide genetic diversity, and identified five excellent high-yield parental combinations associated with four reliable high-yield ISSR markers. Early selection criteria were determined based on kernel fresh weight and cultivated 1-year seedling height, aided by the identification of these 4 ISSR markers. Specific assignment of selected individuals as paternal and maternal parents was made to capitalize on their unique attributes.

CONCLUSIONS

Our results indicated that molecular markers-assisted breeding can effectively shorten, enhance selection accuracy and efficiency and facilitate the development of a new breeding system for C. oleifera.

Smart reprograming of plants against salinity stress using modern biotechnological tools

Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.

The Late Embryogenesis Abundant Proteins in Soybean: Identification, Expression Analysis, and the Roles of GmLEA4_19 in Drought Stress

Late embryogenesis abundant (LEA) proteins play important roles in regulating plant growth and responses to various abiotic stresses. In this research, a genome-wide survey was conducted to recognize the LEA genes in Glycine max. A total of 74 GmLEA was identified and classified into nine subfamilies based on their conserved domains and the phylogenetic analysis. Subcellular localization, the duplication of genes, gene structure, the conserved motif, and the prediction of cis-regulatory elements and tissue expression pattern were then conducted to characterize GmLEAs. The expression profile analysis indicated that the expression of several GmLEAs was a response to drought and salt stress. The co-expression-based gene network analysis suggested that soybean LEA proteins may exert regulatory effects through the metabolic pathways. We further explored GnLEA4_19 function in Arabidopsis and the results suggests that overexpressed GmLEA4_19 in Arabidopsis increased plant height under mild or serious drought stress. Moreover, the overexpressed GmLEA4_19 soybean also showed a drought tolerance phenotype. These results indicated that GmLEA4_19 plays an important role in the tolerance to drought and will contribute to the development of the soybean transgenic with enhanced drought tolerance and better yield. Taken together, this study provided insight for better understanding the biological roles of LEA genes in soybean.

E-GWAS: an ensemble-like GWAS strategy that provides effective control over false positive rates without decreasing true positives

BACKGROUND

Genome-wide association studies (GWAS) are an effective way to explore genotype-phenotype associations in humans, animals, and plants. Various GWAS methods have been developed based on different genetic or statistical assumptions. However, no single method is optimal for all traits and, for many traits, the putative single nucleotide polymorphisms (SNPs) that are detected by the different methods do not entirely overlap due to the diversity of the genetic architecture of complex traits. Therefore, multi-tool-based GWAS strategies that combine different methods have been increasingly employed. To take this one step further, we propose an ensemble-like GWAS strategy (E-GWAS) that statistically integrates GWAS results from different single GWAS methods.

RESULTS

E-GWAS was compared with various single GWAS methods using simulated phenotype traits with different genetic architectures. E-GWAS performed stably across traits with different genetic architectures and effectively controlled the number of false positive genetic variants detected without decreasing the number of true positive variants. In addition, its performance could be further improved by using a bin-merged strategy and the addition of more distinct single GWAS methods. Our results show that the numbers of true and false positive SNPs detected by the E-GWAS strategy slightly increased and decreased, respectively, with increasing bin size and when the number and the diversity of individual GWAS methods that were integrated in E-GWAS increased, the latter being more effective than the bin-merged strategy. The E-GWAS strategy was also applied to a real dataset to study backfat thickness in a pig population, and 10 candidate genes related to this trait and expressed in adipose-associated tissues were identified.

CONCLUSIONS

Using both simulated and real datasets, we show that E-GWAS is a reliable and robust strategy that effectively integrates the GWAS results of different methods and reduces the number of false positive SNPs without decreasing that of true positive SNPs.

Distinct Genomic Loci Underlie Quantitative Resistance to Meloidogyne enterolobii Galling and Reproduction in Citrullus amarus

Meloidogyne enterolobii is a virulent species of root-knot nematode that threatens watermelon (Citrullus lanatus) production in the southeastern United States. There are no known sources of root-knot nematode resistance in cultivated C. lanatus. Specific genotypes of a wild watermelon relative, C. amarus, are resistant against M. incognita but the genetics that underly this resistance are still unknown and it is not clear that this same resistance will be effective against M. enterolobii. To identify and characterize new sources of resistance to M. enterolobii, we screened 108 diverse C. amarus lines alongside a susceptible C. lanatus cultivar (Charleston Gray) for resistance against M. enterolobii. Different C. amarus genotypes ranged from resistant to susceptible for the three resistance phenotypes measured; mean percent root system galled ranged from 10 to 73%, mean egg mass counts ranged from 0.3 to 64.5, and mean eggs per gram of root ranged from 326 to 146,160. We used each of these three resistance phenotypes combined with whole-genome resequencing data to conduct a genome-wide association scan that identified significant associations between M. enterolobii resistance and 11 single-nucleotide polymorphisms (SNPs) within the C. amarus genome. Interestingly, SNPs associated with reduced galling and egg masses were located within a single quantitative trait locus (QTL) on chromosome Ca03, while reductions in nematode eggs per gram of root were associated with separate QTL on chromosomes Ca04 and Ca08. The results of this study suggest that multiple genes are involved with M. enterolobii resistance in C. amarus and the SNPs identified will assist with efforts to breed for M. enterolobii resistance in watermelon.

Genome-Wide Association Study of Seed Morphology Traits in Senegalese Sorghum Cultivars

Sorghum is considered the fifth most important crop in the world. Despite the potential value of Senegalese germplasm for various traits, such as resistance to fungal diseases, there is limited information on the study of sorghum seed morphology. In this study, 162 Senegalese germplasms were evaluated for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness and brightness by scanning and analyzing morphology-related traits with SmartGrain software at the USDA-ARS Plant Science Research Unit. Correlations between seed morphology-related traits and traits associated with anthracnose and head smut resistance were analyzed. Lastly, genome-wide association studies were performed on phenotypic data collected from over 16,000 seeds and 193,727 publicly available single nucleotide polymorphisms (SNPs). Several significant SNPs were found and mapped to the reference sorghum genome to uncover multiple candidate genes potentially associated with seed morphology. The results indicate clear correlations among seed morphology-related traits and potential associations between seed morphology and the defense response of sorghum. GWAS analysis listed candidate genes associated with seed morphologies that can be used for sorghum breeding in the future.

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.

Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum

High-throughput genomic and phenomic data have enhanced the ability to detect genotype-to-phenotype associations that can resolve broad pleiotropic effects of mutations on plant phenotypes. As the scale of genotyping and phenotyping has advanced, rigorous methodologies have been developed to accommodate larger datasets and maintain statistical precision. However, determining the functional effects of associated genes/loci is expensive and limited due to the complexity associated with cloning and subsequent characterization. Here, we utilized phenomic imputation of a multi-year, multi-environment dataset using PHENIX which imputes missing data using kinship and correlated traits, and we screened insertions and deletions (InDels) from the recently whole-genome sequenced Sorghum Association Panel for putative loss-of-function effects. Candidate loci from genome-wide association results were screened for potential loss of function using a Bayesian Genome-Phenome Wide Association Study (BGPWAS) model across both functionally characterized and uncharacterized loci. Our approach is designed to facilitate in silico validation of associations beyond traditional candidate gene and literature-search approaches and to facilitate the identification of putative variants for functional analysis and reduce the incidence of false-positive candidates in current functional validation methods. Using this Bayesian GPWAS model, we identified associations for previously characterized genes with known loss-of-function alleles, specific genes falling within known quantitative trait loci, and genes without any previous genome-wide associations while additionally detecting putative pleiotropic effects. In particular, we were able to identify the major tannin haplotypes at the Tan1 locus and effects of InDels on the protein folding. Depending on the haplotype present, heterodimer formation with Tan2 was significantly affected. We also identified major effect InDels in Dw2 and Ma1, where proteins were truncated due to frameshift mutations that resulted in early stop codons. These truncated proteins also lost most of their functional domains, suggesting that these indels likely result in loss of function. Here, we show that the Bayesian GPWAS model is able to identify loss-of-function alleles that can have significant effects upon protein structure and folding as well as multimer formation. Our approach to characterize loss-of-function mutations and their functional repercussions will facilitate precision genomics and breeding by identifying key targets for gene editing and trait integration.

GWAS of grain color and tannin content in Chinese sorghum based on whole-genome sequencing

Seventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, and a new recessive allelic variant of TAN2 gene was discovered. Sorghum is mainly used for brewing distilled liquors in China. Since grain tannins play an important role in liquor brewing, accurately understanding the relationship between grain color and tannin content can provide basis for selection standards of tannin sorghum. We resequenced a panel of 242 Chinese sorghum accessions and performed population structure and genome-wide association study (GWAS) to identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, and tannin content. Phylogenetic analysis, principal component analysis (PCA), and admixture model were used to infer population structure. Two distinct genetic sub-populations were identified according to their corresponding northern and southern geographic origin. To investigate the genetic basis of natural variation in sorghum grain color, GWAS with 2,760,264 SNPs was conducted in four environments using multiple models (Blink, FarmCPU, GLM, and MLM). Seventy-three QTL were identified to be associated for the color of exocarp, mesocarp, testa, and tannin content on all chromosomes except chromosome 5, of which 47 might be novel QTL. Some important QTL were found to colocalize with orthologous genes in the flavonoid biosynthetic pathway from other plants, including orthologous of Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 and AT5G41220 (GST), as well as orthologous of rice (Oryza sativa) MYB61 and OsbHLH025. Our investigation of the variation in grain color and tannin content in Chinese sorghum germplasm may help guide future sorghum breeding for liquor brewing.

Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex

Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.

OMICS in Fodder Crops: Applications, Challenges, and Prospects

Biomass yield and quality are the primary targets in forage crop improvement programs worldwide. Low-quality fodder reduces the quality of dairy products and affects cattle's health. In multipurpose crops, such as maize, sorghum, cowpea, alfalfa, and oat, a plethora of morphological and biochemical/nutritional quality studies have been conducted. However, the overall growth in fodder quality improvement is not on par with cereals or major food crops. The use of advanced technologies, such as multi-omics, has increased crop improvement programs manyfold. Traits such as stay-green, the number of tillers per plant, total biomass, and tolerance to biotic and/or abiotic stresses can be targeted in fodder crop improvement programs. Omic technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, provide an efficient way to develop better cultivars. There is an abundance of scope for fodder quality improvement by improving the forage nutrition quality, edible quality, and digestibility. The present review includes a brief description of the established omics technologies for five major fodder crops, i.e., sorghum, cowpea, maize, oats, and alfalfa. Additionally, current improvements and future perspectives have been highlighted.

Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress

Sunflower is one of the most important oil crops in the world, and drought stress can severely limit its production and quality. To understand the underlying mechanism of drought tolerance, and identify candidate genes for drought tolerance breeding, we conducted a combined genome-wide association studies (GWAS) and RNA-seq analysis. A total of 226 sunflower inbred lines were collected from different regions of China and other countries. Eight phenotypic traits were evaluated under control and drought stress conditions. Genotyping was performed using a Specific-Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 934.08 M paired-end reads were generated, with an average Q30 of 91.97%. Based on the 243,291 polymorphic SLAF tags, a total of 94,162 high-quality SNPs were identified. Subsequent analysis of linkage disequilibrium (LD) and population structure in the 226 accessions was carried out based on the 94,162 high-quality SNPs. The average LD decay across the genome was 20 kb. Admixture analysis indicated that the entire population most likely originated from 11 ancestors. GWAS was performed using three methods (MLM, FarmCPU, and BLINK) simultaneously. A total of 80 SNPs showed significant associations with the 8 traits (p < 1.062 × 10-6). Next, a total of 118 candidate genes were found. To obtain more reliable candidate genes, RNA-seq analysis was subsequently performed. An inbred line with the highest drought tolerance was selected according to phenotypic traits. RNA was extracted from leaves at 0, 7, and 14 days of drought treatment. A total of 18,922 differentially expressed genes were obtained. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed up-regulated genes were mainly enriched in the branched-chain amino acid catabolic process, while the down-regulated genes were mainly enriched in the photosynthesis-related process. Six DEGs were randomly selected from all DEGs for validation; these genes showed similar patterns in RNA-seq and RT-qPCR analysis, with a correlation coefficient of 0.8167. Through the integration of the genome-wide association study and the RNA-sequencing, 14 candidate genes were identified. Four of them (LOC110885273, LOC110872899, LOC110891369, LOC110920644) were abscisic acid related protein kinases and transcription factors. These genes may play an important role in sunflower drought response and will be used for further study. Our findings provide new insights into the response mechanisms of sunflowers against drought stress and contribute to further genetic breeding.

Sorghum polyphenols: plant stress, human health benefits, and industrial applications

MAIN CONCLUSION

Various phenolic compounds of sorghum are effective in the management of abiotic stress (salt, nutrients) and biotic stress (caused by birds, fungi and aphids). The health and industrial application of phenolics is mainly contributed by inherent antioxidant and nutraceutical potential. In a natural environment, plant growth is affected by various biotic and abiotic stresses. In every ecosystem, the presence of a wide range of harmful biological agents (bacteria, fungi, nematodes, mites, and insects) and undesirable environmental factors (drought, salinity, heat, excessive or low rainfall, etc.) may cause a heavy loss in crop productivity. Being sessile during evolution, plants have evolved multiple defense mechanisms against various types of microbial pathogens and environmental stresses. A plant's natural defense system produces some compounds named secondary metabolites, which include phenolics, terpenes, and nitrogen. The phenolic profile of grain sorghum, the least utilized staple crop, is unique, more diverse, and more abundant than in any other common cereal grain. It mainly contains phenolic acids, 3-deoxyanthocyanidins and condensed tannins. Sorghum polyphenols play a major role in plant defense against biotic and abiotic stresses and have many additional health benefits along with various industrial applications. The objective of this review is to discuss the phenolic compounds derived from grain sorghum and describe their role in plant defense, human health, and industrial applications.

The Sorghum Grain Mold Disease Complex: Pathogens, Host Responses, and the Bioactive Metabolites at Play

Grain mold is a major concern in sorghum [Sorghum bicolor (L.) Moench] production systems, threatening grain quality, safety, and nutritional value as both human food and livestock feed. The crop's nutritional value, environmental resilience, and economic promise poise sorghum for increased acreage, especially in light of the growing pressures of climate change on global food systems. In order to fully take advantage of this potential, sorghum improvement efforts and production systems must be proactive in managing the sorghum grain mold disease complex, which not only jeopardizes agricultural productivity and profitability, but is also the culprit of harmful mycotoxins that warrant substantial public health concern. The robust scholarly literature from the 1980s to the early 2000s yielded valuable insights and key comprehensive reviews of the grain mold disease complex. Nevertheless, there remains a substantial gap in understanding the complex multi-organismal dynamics that underpin the plant-pathogen interactions involved - a gap that must be filled in order to deliver improved germplasm that is not only capable of withstanding the pressures of climate change, but also wields robust resistance to disease and mycotoxin accumulation. The present review seeks to provide an updated perspective of the sorghum grain mold disease complex, bolstered by recent advances in the understanding of the genetic and the biochemical interactions among the fungal pathogens, their corresponding mycotoxins, and the sorghum host. Critical components of the sorghum grain mold disease complex are summarized in narrative format to consolidate a collection of important concepts: (1) the current state of sorghum grain mold in research and production systems; (2) overview of the individual pathogens that contribute to the grain mold complex; (3) the mycotoxin-producing potential of these pathogens on sorghum and other substrates; and (4) a systems biology approach to the understanding of host responses.

Transcriptome analysis of early stages of sorghum grain mold disease reveals defense regulators and metabolic pathways associated with resistance

Background

Sorghum grain mold is the most important disease of the crop. The disease results from simultaneous infection of the grain by multiple fungal species. Host responses to these fungi and the underlying molecular and cellular processes are poorly understood. To understand the genetic, molecular and biochemical components of grain mold resistance, transcriptome profiles of the developing grain of resistant and susceptible sorghum genotypes were studied.

Results

The developing kernels of grain mold resistant RTx2911 and susceptible RTx430 sorghum genotypes were inoculated with a mixture of fungal pathogens mimicking the species complexity of the disease under natural infestation. Global transcriptome changes corresponding to multiple molecular and cellular processes, and biological functions including defense, secondary metabolism, and flavonoid biosynthesis were observed with differential regulation in the two genotypes. Genes encoding pattern recognition receptors (PRRs), regulators of growth and defense homeostasis, antimicrobial peptides, pathogenesis-related proteins, zein seed storage proteins, and phytoalexins showed increased expression correlating with resistance. Notably, SbLYK5 gene encoding an orthologue of chitin PRR, defensin genes SbDFN7.1 and SbDFN7.2 exhibited higher expression in the resistant genotype. The SbDFN7.1 and SbDFN7.2 genes are tightly linked and transcribed in opposite orientation with a likely common bidirectional promoter. Interestingly, increased expression of JAZ and other transcriptional repressors were observed that suggested the tight regulation of plant defense and growth. The data suggest a pathogen inducible defense system in the developing grain of sorghum that involves the chitin PRR, MAPKs, key transcription factors, downstream components regulating immune gene expression and accumulation of defense molecules. We propose a model through which the biosynthesis of 3-deoxyanthocynidin phytoalexins, defensins, PR proteins, other antimicrobial peptides, and defense suppressing proteins are regulated by a pathogen inducible defense system in the developing grain.

Conclusions

The transcriptome data from a rarely studied tissue shed light into genetic, molecular, and biochemical components of disease resistance and suggested that the developing grain shares conserved immune response mechanisms but also components uniquely enriched in the grain. Resistance was associated with increased expression of genes encoding regulatory factors, novel grain specific antimicrobial peptides including defensins and storage proteins that are potential targets for crop improvement.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07609-y.