Forward genetics by genome sequencing reveals that rapid cyanide release deters insect herbivory of Sorghum bicolor

Cyanogenesis, a Plant Defence Strategy against Herbivores

Plants and phytophagous arthropods have coevolved in a long battle for survival. Plants respond to phytophagous feeders by producing a battery of antiherbivore chemical defences, while herbivores try to adapt to their hosts by attenuating the toxic effect of the defence compounds. Cyanogenic glucosides are a widespread group of defence chemicals that come from cyanogenic plants. Among the non-cyanogenic ones, the Brassicaceae family has evolved an alternative cyanogenic pathway to produce cyanohydrin as a way to expand defences. When a plant tissue is disrupted by an herbivore attack, cyanogenic substrates are brought into contact with degrading enzymes that cause the release of toxic hydrogen cyanide and derived carbonyl compounds. In this review, we focus our attention on the plant metabolic pathways linked to cyanogenesis to generate cyanide. It also highlights the role of cyanogenesis as a key defence mechanism of plants to fight against herbivore arthropods, and we discuss the potential of cyanogenesis-derived molecules as alternative strategies for pest control.

Species-specific dynamics of specialized metabolism in germinating sorghum grain revealed by temporal and tissue-resolved transcriptomics and metabolomics

Seed germination is crucial for plant productivity, and the biochemical changes during germination affect seedling survival, plant health and yield. While the general metabolism of germination is extensively studied, the role of specialized metabolism is less investigated. We therefore analyzed the metabolism of the defense compound dhurrin during sorghum (Sorghum bicolor) grain germination and early seedling development. Dhurrin is a cyanogenic glucoside, which is catabolized into different bioactive compounds at other stages of plant development, but its fate and role during germination is unknown. We dissected sorghum grain into three different tissues and investigated dhurrin biosynthesis and catabolism at the transcriptomic, metabolomic and biochemical level. We further analyzed transcriptional signature differences of cyanogenic glucoside metabolism between sorghum and barley (Hordeum vulgare), which produces similar specialized metabolites. We found that dhurrin is de novo biosynthesized and catabolized in the growing embryonic axis as well as the scutellum and aleurone layer, two tissues otherwise mainly acknowledged for their involvement in release and transport of general metabolites from the endosperm to the embryonic axis. In contrast, genes encoding cyanogenic glucoside biosynthesis in barley are exclusively expressed in the embryonic axis. Glutathione transferase enzymes (GSTs) are involved in dhurrin catabolism and the tissue-resolved analysis of GST expression identified new pathway candidate genes and conserved GSTs as potentially important in cereal germination. Our study demonstrates a highly dynamic tissue- and species-specific specialized metabolism during cereal grain germination, highlighting the importance of tissue-resolved analyses and identification of specific roles of specialized metabolites in fundamental plant processes.

Genetic variation in hydrogen cyanide potential of perennial sorghum evaluated by colorimetry

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

Seedling growth and fall armyworm feeding preference influenced by dhurrin production in sorghum

Cyanogenic glucosides (CGs) play a key role in host-plant defense to insect feeding; however, the metabolic tradeoffs between synthesis of CGs and plant growth are not well understood. In this study, genetic mutants coupled with nondestructive phenotyping techniques were used to study the impact of the CG dhurrin on fall armyworm [Spodoptera frugiperda (J.E. Smith)] (FAW) feeding and plant growth in sorghum [Sorghum bicolor (L.) Moench]. A genetic mutation in CYP79A1 gene that disrupts dhurrin biosynthesis was used to develop sets of near-isogenic lines (NILs) with contrasting dhurrin contents in the Tx623 bmr6 genetic background. The NILs were evaluated for differences in plant growth and FAW feeding damage in replicated greenhouse and field trials. Greenhouse studies showed that dhurrin-free Tx623 bmr6 cyp79a1 plants grew more quickly than wild-type plants but were more susceptible to insect feeding based on changes in green plant area (GPA), total leaf area, and total dry weight over time. The NILs exhibited similar patterns of growth in field trials with significant differences in leaf area and dry weight of dhurrin-free plants between the infested and non-infested treatments. Taken together, these studies reveal a significant metabolic tradeoff between CG biosynthesis and plant growth in sorghum seedlings. Disruption of dhurrin biosynthesis produces plants with higher growth rates than wild-type plants but these plants have greater susceptibility to FAW feeding.

Seedling growth and fall armyworm feeding preference influenced by dhurrin production in sorghum

Cyanogenic glucosides (CGs) play a key role in host-plant defense to insect feeding; however, the metabolic tradeoffs between synthesis of CGs and plant growth are not well understood. In this study, genetic mutants coupled with nondestructive phenotyping techniques were used to study the impact of the CG dhurrin on fall armyworm [Spodoptera frugiperda (J.E. Smith)] (FAW) feeding and plant growth in sorghum [Sorghum bicolor (L.) Moench]. A genetic mutation in CYP79A1 gene that disrupts dhurrin biosynthesis was used to develop sets of near-isogenic lines (NILs) with contrasting dhurrin contents in the Tx623 bmr6 genetic background. The NILs were evaluated for differences in plant growth and FAW feeding damage in replicated greenhouse and field trials. Greenhouse studies showed that dhurrin-free Tx623 bmr6 cyp79a1 plants grew more quickly than wild-type plants but were more susceptible to insect feeding based on changes in green plant area (GPA), total leaf area, and total dry weight over time. The NILs exhibited similar patterns of growth in field trials with significant differences in leaf area and dry weight of dhurrin-free plants between the infested and non-infested treatments. Taken together, these studies reveal a significant metabolic tradeoff between CG biosynthesis and plant growth in sorghum seedlings. Disruption of dhurrin biosynthesis produces plants with higher growth rates than wild-type plants but these plants have greater susceptibility to FAW feeding.

The Sorghum (Sorghum bicolor) Brown Midrib 30 Gene Encodes a Chalcone Isomerase Required for Cell Wall Lignification

In sorghum (Sorghum bicolor) and other C4 grasses, brown midrib (bmr) mutants have long been associated with plants impaired in their ability to synthesize lignin. The brown midrib 30 (Bmr30) gene, identified using a bulk segregant analysis and next-generation sequencing, was determined to encode a chalcone isomerase (CHI). Two independent mutations within this gene confirmed that loss of its function was responsible for the brown leaf midrib phenotype and reduced lignin concentration. Loss of the Bmr30 gene function, as shown by histochemical staining of leaf midrib and stalk sections, resulted in altered cell wall composition. In the bmr30 mutants, CHI activity was drastically reduced, and the accumulation of total flavonoids and total anthocyanins was impaired, which is consistent with its function in flavonoid biosynthesis. The level of the flavone lignin monomer tricin was reduced 20-fold in the stem relative to wild type, and to undetectable levels in the leaf tissue of the mutants. The bmr30 mutant, therefore, harbors a mutation in a phenylpropanoid biosynthetic gene that is key to the interconnection between flavonoids and monolignols, both of which are utilized for lignin synthesis in the grasses.

Regulation of dhurrin pathway gene expression during Sorghum bicolor development

Developmental and organ-specific expression of genes in dhurrin biosynthesis, bio-activation, and recycling offers dynamic metabolic responses optimizing growth and defence responses in Sorghum. Plant defence models evaluate the costs and benefits of resource investments at different stages in the life cycle. Poor understanding of the molecular regulation of defence deployment and remobilization hampers accuracy of the predictions. Cyanogenic glucosides, such as dhurrin are phytoanticipins that release hydrogen cyanide upon bio-activation. In this study, RNA-seq was used to investigate the expression of genes involved in the biosynthesis, bio-activation and recycling of dhurrin in Sorghum bicolor. Genes involved in dhurrin biosynthesis were highly expressed in all young developing vegetative tissues (leaves, leaf sheath, roots, stems), tiller buds and imbibing seeds and showed gene specific peaks of expression in leaves during diel cycles. Genes involved in dhurrin bio-activation were expressed early in organ development with organ-specific expression patterns. Genes involved in recycling were expressed at similar levels in the different organ during development, although post-floral initiation when nutrients are remobilized for grain filling, expression of GSTL1 decreased > tenfold in leaves and NITB2 increased > tenfold in stems. Results are consistent with the establishment of a pre-emptive defence in young tissues and regulated recycling related to organ senescence and increased demand for nitrogen during grain filling. This detailed characterization of the transcriptional regulation of dhurrin biosynthesis, bioactivation and remobilization genes during organ and plant development will aid elucidation of gene regulatory networks and signalling pathways that modulate gene expression and dhurrin levels. In-depth knowledge of dhurrin metabolism could improve the yield, nitrogen use efficiency and stress resilience of Sorghum.

A beta-glucosidase of an insect herbivore determines both toxicity and deterrence of a dandelion defense metabolite

Gut enzymes can metabolize plant defense compounds and thereby affect the growth and fitness of insect herbivores. Whether these enzymes also influence feeding preference is largely unknown. We studied the metabolization of taraxinic acid β-D-glucopyranosyl ester (TA-G), a sesquiterpene lactone of the common dandelion (Taraxacum officinale) that deters its major root herbivore, the common cockchafer larva (Melolontha melolontha). We have demonstrated that TA-G is rapidly deglucosylated and conjugated to glutathione in the insect gut. A broad-spectrum M. melolontha β-glucosidase, Mm_bGlc17, is sufficient and necessary for TA-G deglucosylation. Using cross-species RNA interference, we have shown that Mm_bGlc17 reduces TA-G toxicity. Furthermore, Mm_bGlc17 is required for the preference of M. melolontha larvae for TA-G-deficient plants. Thus, herbivore metabolism modulates both the toxicity and deterrence of a plant defense compound. Our work illustrates the multifaceted roles of insect digestive enzymes as mediators of plant-herbivore interactions.

Plants produce certain substances to fend off attackers like plant-feeding insects. To stop these compounds from damaging their own cells, plants often attach sugar molecules to them. When an insect tries to eat the plant, the plant removes the stabilizing sugar, ‘activating’ the compounds and making them toxic or foul-tasting. Curiously, some insects remove the sugar themselves, but it is unclear what consequences this has, especially for insect behavior.

Dandelions, Taraxacum officinale, make high concentrations of a sugar-containing defense compound in their roots called taraxinic acid β-D-glucopyranosyl ester, or TA-G for short. TA-G deters the larvae of the Maybug – a pest also known as the common cockchafer or the doodlebug – from eating dandelion roots. When Maybug larvae do eat TA-G, it is found in their systems without its sugar. However, it is unclear whether it is the plant or the larva that removes the sugar. A second open question is how the sugar removal process affects the behavior of the Maybug larvae.

Using chemical analysis and genetic manipulation, Huber et al. investigated what happens when Maybug larvae eat TA-G. This revealed that the acidity levels in the larvae’s digestive system deactivate the proteins from the dandelion that would normally remove the sugar from TA-G. However, rather than leaving the compound intact, larvae remove the sugar from TA-G themselves. They do this using a digestive enzyme, known as a beta-glucosidase, that cuts through sugar. Removing the sugar from TA-G made the compound less toxic, allowing the larvae to grow bigger, but it also increased TA-G’s deterrent effects, making the larvae less likely to eat the roots.

Any organism that eats plants, including humans, must deal with chemicals like TA-G in their food. Once inside the body, enzymes can change these chemicals, altering their effects. This happens with many medicines, too. In the future, it might be possible to design compounds that activate only in certain species, or under certain conditions. Further studies in different systems may aid the development of new methods of pest control, or new drug treatments.

Allocation of Resources to Cyanogenic Glucosides Does Not Incur a Growth Sacrifice in Sorghum bicolor (L.) Moench

In plants, the production of secondary metabolites is considered to be at the expense of primary growth. Sorghum produces a cyanogenic glycoside (dhurrin) that is believed to act as its chemical defence. Studies have shown that acyanogenic plants are smaller in size compared to the wildtype. This study aimed to investigate whether the small plant size is due to delayed germination or due to the lack of dhurrin derived nitrogen. A novel plant system consisting of totally cyanide deficient class 1 (tcd1) and adult cyanide deficient 1 (acdc1) mutant lines was employed. The data for germination, plant height and developmental stage during seedling development and final plant reproductive fitness was recorded. The possible role of phytohormones in recovering the wildtype phenotype, especially in developmentally acyanogenic acdc1 line, was also investigated. The data on plant growth have shown that the lack of dhurrin is disadvantageous to growth, but only at the early developmental stage. The tcd1 plants also took longer to mature probably due to delayed flowering. None of the tested hormones were able to recover the wildtype phenotype. We conclude that the generation of dhurrin is advantageous for plant growth, especially at critical growth stages like germinating seed by providing a ready source of reduced nitrogen.

Prediction of Dhurrin Metabolism by Transcriptome and Metabolome Analyses in Sorghum

Sorghum (Sorghum bicolor (L.)) Moench is an important food for humans and feed for livestock. Sorghum contains dhurrin which can be degraded into toxic hydrogen cyanide. Here, we report the expression patterns of 14 candidate genes related to dhurrin ((S)-4-Hydroxymandelnitrile-β-D-glucopyranoside) metabolism and the effects of the gene expression on specific metabolite content in selected sorghum accessions. Dhurrin-related metabolism is vigorous in the early stages of development of sorghum. The dhurrin contents of most accessions tested were in the range of approximately 6-22 μg mg-1 fresh leaf tissue throughout growth. The p-hydroxybenzaldehyde (pHB) contents were high at seedling stages, but almost nonexistent at adult stages. The contents of p-hydroxyphenylacetic acid (pHPAAc) were relatively low throughout growth compared to those of dhurrin or pHB. Generally, the expression of the candidate genes was higher at seedling stage than at other stages and decreased gradually as plants grew. In addition, we identified significant SNPs, and six of them were potentially associated with non-synonymous changes in CAS1. Our results may provide the basis for choosing breeding materials to regulate cyanide contents in sorghum varieties to prevent HCN toxicity of livestock or to promote drought tolerance or pathogen resistance.

Mutations in sorghum SBEIIb and SSIIa affect alkali spreading value, starch composition, thermal properties and flour viscosity

Seven novel alleles of SBEIIb and one allele of SSIIa co-segregated with the ASV phenotype and contributed to distinct starch quality traits important for food-processing applications. Sorghum is an important food crop for millions of people in Africa and Asia. Whole-genome re-sequencing of sorghum EMS mutants exhibiting an alkali spreading value (ASV) phenotype revealed candidate SNPs in Sobic.004G163700 and Sobic.010G093400. Comparative genomics identified Sobic.010G093400 as a starch synthase IIa and Sobic.004G163700 as a starch branching enzyme IIb. Segregation analyses showed that mutations in Sobic.010G093400 or Sobic.004G163700 co-segregated with the ASV phenotype. Mutants in SSIIa exhibited no change in amylose content but expressed lower final viscosity and lower starch gelatinization temperature (GT) than starches from non-mutant plants. The sbeIIb mutants exhibited significantly higher amylose levels and starch GT and lower viscosity compared to non-mutant starches and ssIIa mutants. Mutations in SBEIIb had a dosage-dependent effect on amylose content. Double mutants of sbeIIb and ssIIa resembled their sbeIIb parent in amylose content, starch thermal properties and viscosity profiles. These variants will provide opportunities to produce sorghum varieties with modified starch end-use qualities important for the beer brewing and baking industries and specialty foods for humans with diabetes.

Development of a Pedigreed Sorghum Mutant Library

Induced mutagenesis is a powerful approach to generate variations for elucidation of gene function and to create new traits for breeding. Here, we described a procedure to develop a pedigreed mutant library through chemical mutagenesis with ethylmethane sulfonate (EMS) treated seeds in sorghum and discussed its potential to generate new traits for sorghum improvement. Unlike random mutagenesis, a pedigreed mutant library, once properly established, can serve as a powerful resource to isolate and recover mutations of both agronomical and biological importance. With the development of affordable and high-throughput next-generation sequencing technologies, identification of causal mutations from a mutant library with a uniform genetic background becomes increasingly efficient and cost-effective. Fast causal gene discovery from mutant libraries combined with precise genome editing techniques will accelerate incorporation of new traits and revolutionize crop breeding.

Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum

The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS)-treated Sorghum bicolor BTx623 individuals, that using replication to detect false positive-induced variants in next-generation sequencing (NGS) data permits higher throughput variant detection with greater accuracy. We used a lower sequence coverage depth (average of 7×) from 586 independently mutagenized individuals and detected 5,399,493 homozygous single nucleotide polymorphisms (SNPs). Of these, 76% originated from only 57,872 genomic positions prone to false positive variant calling. These positions are characterized by high copy number paralogs where the error-prone SNP positions are at copies containing a variant at the SNP position. The ability of short stretches of homology to generate these error-prone positions suggests that incompletely assembled or poorly mapped repeated sequences are one driver of these error-prone positions. Removal of these false positives left 1,275,872 homozygous and 477,531 heterozygous EMS-induced SNPs, which, congruent with the mutagenic mechanism of EMS, were >98% G:C to A:T transitions. Through this analysis, we generated a collection of sequence indexed mutants of sorghum. This collection contains 4035 high-impact homozygous mutations in 3637 genes and 56,514 homozygous missense mutations in 23,227 genes. Each line contains, on average, 2177 annotated homozygous SNPs per genome, including seven likely gene knockouts and 96 missense mutations. The number of mutations in a transcript was linearly correlated with the transcript length and also the G+C count, but not with the GC/AT ratio. Analysis of the detected mutagenized positions identified CG-rich patches, and flanking sequences strongly influenced EMS-induced mutation rates. This method for detecting false positive-induced mutations is generally applicable to any organism, is independent of the choice of in silico variant-calling algorithm, and is most valuable when the true mutation rate is likely to be low, such as in laboratory-induced mutations or somatic mutation detection in medicine.

The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae)

Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.

The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae)

Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.

Comparative Transcriptome and Lipidome Analyses Reveal Molecular Chilling Responses in Chilling-Tolerant Sorghums

Chilling temperatures (0 to 15°C) are a major constraint for temperate cultivation of tropical-origin crops, including the cereal crop sorghum ( [L.] Moench). Northern Chinese sorghums have adapted to early-season chilling, but molecular mechanisms of chilling tolerance are unknown. We used RNA sequencing of seedlings to compare the chilling-responsive transcriptomes of a chilling-tolerant Chinese accession with a chilling-sensitive US reference line, and mass spectrometry to compare chilling-responsive lipidomes of four chilling-tolerant Chinese accessions with two US reference lines. Comparative transcriptomics revealed chilling-induced up-regulation of cold-response regulator C-repeat binding factor (CBF) transcription factor and genes involved in reactive oxygen detoxification, jasmonic acid (JA) biosynthesis, and lipid remodeling phospholipase Dα1 (α) gene in the chilling-tolerant Chinese line. Lipidomics revealed conserved chilling-induced increases in lipid unsaturation, as well as lipid remodeling of photosynthetic membranes that is specific to chilling-tolerant Chinese accessions. Our results point to CBF-mediated transcriptional regulation, galactolipid and phospholipid remodeling, and JA as potential molecular mechanisms underlying chilling adaptation in Chinese sorghums. These molecular systems underlying chilling response could be targeted in molecular breeding for chilling tolerance.

Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines

In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of ethyl methanesulfonate (EMS)-mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error-prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequences in wild-type siblings and heterozygous in segregating families. This region contained a single nonsynonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the Sorghum ortholog encoding the gibberellic acid (GA) biosynthetic enzyme ent-kaurene oxidase. Application of exogenous GA rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks cosegregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses

Sorghum (Sorghum bicolor) is a versatile C4 crop and a model for research in family Poaceae. High-quality genome sequence is available for the elite inbred line BTx623, but functional validation of genes remains challenging due to the limited genomic and germplasm resources available for comprehensive analysis of induced mutations. In this study, we generated 6400 pedigreed M4 mutant pools from EMS-mutagenized BTx623 seeds through single-seed descent. Whole-genome sequencing of 256 phenotyped mutant lines revealed >1.8 million canonical EMS-induced mutations, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. To demonstrate the utility of the sequenced sorghum mutant resource, we performed reverse genetics to identify eight genes potentially affecting drought tolerance, three of which had allelic mutations and two of which exhibited exact cosegregation with the phenotype of interest. Our results establish that a large-scale resource of sequenced pedigreed mutants provides an efficient platform for functional validation of genes in sorghum, thereby accelerating sorghum breeding. Moreover, findings made in sorghum could be readily translated to other members of the Poaceae via integrated genomics approaches.

TILLING in forage grasses for gene discovery and breeding improvement

Mutation breeding has a long-standing history and in some major crop species, many of the most important cultivars have their origin in germplasm generated by mutation induction. For almost two decades, methods for TILLING (Targeting Induced Local Lesions IN Genomes) have been established in model plant species such as Arabidopsis (Arabidopsis thaliana L.), enabling the functional analysis of genes. Recent advances in mutation detection by second generation sequencing technology have brought its utility to major crop species. However, it has remained difficult to apply similar approaches in forage and turf grasses, mainly due to their outbreeding nature maintained by an efficient self-incompatibility system. Starting with a description of the extent to which traditional mutagenesis methods have contributed to crop yield increase in the past, this review focuses on technological approaches to implement TILLING-based strategies for the improvement of forage grass breeding through forward and reverse genetics. We present first results from TILLING in allogamous forage grasses for traits such as stress tolerance and evaluate prospects for rapid implementation of beneficial alleles to forage grass breeding. In conclusion, large-scale induced mutation resources, used for forward genetic screens, constitute a valuable tool to increase the genetic diversity for breeding and can be generated with relatively small investments in forage grasses. Furthermore, large libraries of sequenced mutations can be readily established, providing enhanced opportunities to discover mutations in genes controlling traits of agricultural importance and to study gene functions by reverse genetics.

Metabolism, excretion and avoidance of cyanogenic glucosides in insects with different feeding specialisations

Cyanogenic glucosides (CNglcs) are widespread plant defence compounds releasing toxic hydrogen cyanide when hydrolysed by specific β-glucosidases after plant tissue damage. In contrast to specialist herbivores that have mechanisms to avoid toxicity from CNglcs, it is generally assumed that non-adapted herbivores are negatively affected by CNglcs. Recent evidence, however, implies that the defence potential of CNglcs towards herbivores may not be as effective as previously anticipated. Here, performance, metabolism and excretion products of insects not adapted to CNglcs were analysed, including species with different degrees of dietary specialisation (generalists, specialists) and different feeding modes (leaf-snipping lepidopterans, piercing-sucking aphids). Insects were reared either on cyanogenic or acyanogenic plants or on an artificial cyanogenic diet. Lepidopteran generalists (Spodoptera littoralis, Spodoptera exigua, Mamestra brassicae) were compared to lepidopteran glucosinolate-specialists (Pieris rapae, Pieris brassicae, Plutella xylostella), and a generalist aphid (Myzus persicae) was compared to an aphid glucosinolate-specialist (Lipaphis erysimi). All insects were tolerant to cyanogenic plants; in lepidopterans tolerance was mainly due to excretion of intact CNglcs. The two Pieris species furthermore metabolized aromatic CNglcs to amino acid conjugates (Cys, Gly, Ser) and derivatives of these, which is similar to the metabolism of benzylglucosinolates in these species. Aphid species avoided uptake of CNglcs during feeding. Our results imply that non-adapted insects tolerate plant CNglcs either by keeping them intact for excretion, metabolizing them, or avoiding uptake.

Molecular Breeding of Sorghum bicolor, A Novel Energy Crop

Currently, molecular breeding is regarded as an important tool for the improvement of many crop species. However, in sorghum, recently heralded as an important bioenergy crop, progress in this field has been relatively slow and limited. In this review, we present existing efforts targeted at genetic characterization of sorghum mutants. We also comprehensively review the different attempts made toward the isolation of genes involved in agronomically important traits, including the dissection of some sorghum quantitative trait loci (QTLs). We also explore the current status of the use of transgenic techniques in sorghum, which should be crucial for advancing sorghum molecular breeding. Through this report, we provide a useful benchmark to help assess how much more sorghum genomics and molecular breeding could be improved.

Natural Variation in Synthesis and Catabolism Genes Influences Dhurrin Content in Sorghum

Cyanogenic glucosides are natural compounds found in more than 1000 species of angiosperms that produce HCN and are deemed undesirable for agricultural use. However, these compounds are important components of the primary defensive mechanisms of many plant species. One of the best-studied cyanogenic glucosides is dhurrin [(S)-p-hydroxymandelonitrile-β-D-glucopyranoside], which is produced primarily in sorghum [Sorghum bicolor (L.) Moench]. The biochemical basis for dhurrin metabolism is well established; however, little information is available on its genetic control. Here, we dissect the genetic control of leaf dhurrin content through a genome-wide association study (GWAS) using a panel of 700 diverse converted sorghum lines (conversion panel) previously subjected to pre-breeding and selected for short stature (∼1 m in height) and photoperiod insensitivity. The conversion panel was grown for 2 yr in three environments. Wide variation for leaf dhurrin content was found in the sorghum conversion panel, with the Caudatum group exhibiting the highest dhurrin content and the Guinea group showing the lowest dhurrin content. A GWAS using a mixed linear model revealed significant associations (a false discovery rate [FDR] < 0.05) close to both UGT 185B1 in the canonical biosynthetic gene cluster on chromosome 1 and close to the catabolic dhurrinase loci on chromosome 8. Dhurrin content was associated consistently with biosynthetic genes in the two N-fertilized environments, while dhurrin content was associated with catabolic loci in the environment without supplemental N. These results suggest that genes for both biosynthesis and catabolism are important in determining natural variation for leaf dhurrin in sorghum in different environments.

Secondary metabolites in plant innate immunity: conserved function of divergent chemicals

Plant secondary metabolites carry out numerous functions in interactions between plants and a broad range of other organisms. Experimental evidence strongly supports the indispensable contribution of many constitutive and pathogen-inducible phytochemicals to plant innate immunity. Extensive studies on model plant species, particularly Arabidopsis thaliana, have brought significant advances in our understanding of the molecular mechanisms underpinning pathogen-triggered biosynthesis and activation of defensive secondary metabolites. However, despite the proven significance of secondary metabolites in plant response to pathogenic microorganisms, little is known about the precise mechanisms underlying their contribution to plant immunity. This insufficiency concerns information on the dynamics of cellular and subcellular localization of defensive phytochemicals during the encounters with microbial pathogens and precise knowledge on their mode of action. As many secondary metabolites are characterized by their in vitro antimicrobial activity, these compounds were commonly considered to function in plant defense as in planta antibiotics. Strikingly, recent experimental evidence suggests that at least some of these compounds alternatively may be involved in controlling several immune responses that are evolutionarily conserved in the plant kingdom, including callose deposition and programmed cell death.

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing

Background

Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced health benefits.

Results

Toward this end, we annotated a previously sequenced draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up-regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3′ end formation.

Conclusions

We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry.

Electronic supplementary material

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Rapid identification of angulata leaf mutations using next-generation sequencing

Map-based (positional) cloning has traditionally been the preferred strategy for identifying the causal genes underlying the phenotypes of mutants isolated in forward genetic screens. Massively parallel sequencing technologies are enabling the rapid cloning of genes identified in such screens. We have used a combination of linkage mapping and whole-genome re-sequencing to identify the causal mutations in four loss-of-function angulata (anu) mutants. These mutants were isolated in a screen for mutants with defects in leaf shape and leaf pigmentation. Our results show that the anu1-1, anu4-1, anu9-1 and anu12-1 mutants carry new alleles of the previously characterized SECA2, TRANSLOCON AT THE OUTER MEMBRANE OF CHLOROPLASTS 33 (TOC33), NON-INTRINSIC ABC PROTEIN 14 (NAP14) and CLP PROTEASE PROTEOLYTIC SUBUNIT 1 (CLPR1) genes. Re-sequencing the genomes of fine mapped mutants is a feasible approach that has allowed us to identify a moderate number of candidate mutations, including the one that causes the mutant phenotype, in a nonstandard genetic background. Our results indicate that anu mutations specifically affect plastid-localized proteins involved in diverse processes, such as the movement of peptides through chloroplast membranes (ANU1 and ANU4), metal homeostasis (ANU9) and protein degradation (ANU12).

Using next-generation sequencing to isolate mutant genes from forward genetic screens

The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.

The role of auxin transporters in monocots development

Auxin is a key regulator of plant growth and development, orchestrating cell division, elongation and differentiation, embryonic development, root and stem tropisms, apical dominance, and transition to flowering. Auxin levels are higher in undifferentiated cell populations and decrease following organ initiation and tissue differentiation. This differential auxin distribution is achieved by polar auxin transport (PAT) mediated by auxin transport proteins. There are four major families of auxin transporters in plants: PIN-FORMED (PIN), ATP-binding cassette family B (ABCB), AUXIN1/LIKE-AUX1s, and PIN-LIKES. These families include proteins located at the plasma membrane or at the endoplasmic reticulum (ER), which participate in auxin influx, efflux or both, from the apoplast into the cell or from the cytosol into the ER compartment. Auxin transporters have been largely studied in the dicotyledon model species Arabidopsis, but there is increasing evidence of their role in auxin regulated development in monocotyledon species. In monocots, families of auxin transporters are enlarged and often include duplicated genes and proteins with high sequence similarity. Some of these proteins underwent sub- and neo-functionalization with substantial modification to their structure and expression in organs such as adventitious roots, panicles, tassels, and ears. Most of the present information on monocot auxin transporters function derives from studies conducted in rice, maize, sorghum, and Brachypodium, using pharmacological applications (PAT inhibitors) or down-/up-regulation (over-expression and RNA interference) of candidate genes. Gene expression studies and comparison of predicted protein structures have also increased our knowledge of the role of PAT in monocots. However, knockout mutants and functional characterization of single genes are still scarce and the future availability of such resources will prove crucial to elucidate the role of auxin transporters in monocots development.