Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Molecular characterization of cassava zinc finger-homeodomain (ZF-HD) transcription factors reveals their role in disease resistance

The production of cassava (Manihot esculenta Crantz) is constantly threatened by cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm). Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes widely implicated in various developmental and physiological processes in plants. Despite their importance, a comprehensive analysis of ZF-HD genes, particularly those involved in disease resistance, has not been performed for cassava. In the present study, we utilized bioinformatics methods to identify 21 ZF-HD genes distributed across 11 chromosomes of cassava genome, with the majority exhibiting gene structure without introns. Phylogenetic analysis categorized these genes into two major groups (MIF and ZHD) with five subgroups. We observed fourteen pairs of duplicated genes, suggesting that segmental duplication has likely facilitated the expansion of the cassava ZF-HD gene family. Comparative orthologous analyses between cassava and other plant species shed light on the evolutionary trajectory of this gene family. Promoter analyses revealed multiple hormone- and stress-related elements, indicative of a functional role in stress responses. Expression profiling through RNA-seq and quantitative real-time PCR (qRT-PCR) demonstrated that certain cassava ZF-HD genes are up-regulated in response to Xpm infection, suggesting their involvement in defense mechanisms. Notably, MeZHD7 gene was identified via virus induced gene silencing (VIGS) as potentially crucial in conferring resistance against CBB. Results from subcellular localization experiments indicated that MeZHD7 was localized in the nucleus. The Luciferase reporter assay demonstrated an interaction between MeZHD7 and MeMIF5. These findings may lay the foundation for further cloning and functional analyses of cassava ZF-HD genes, particularly those associated with pathogen resistance.

Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America

Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world's largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.

Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton

Interspecific genomic introgression is an important evolutionary process with respect to the generation of novel phenotypic diversity and adaptation. A key question is how gene flow perturbs gene expression networks and regulatory interactions. Here, an introgression population of two species of allopolyploid cotton (Gossypium) to delineate the regulatory perturbations of gene expression regarding fiber development accompanying fiber quality change is utilized. De novo assembly of the recipient parent (G. hirsutum Emian22) genome allowed the identification of genomic variation and introgression segments (ISs) in 323 introgression lines (ILs) from the donor parent (G. barbadense 3-79). It documented gene expression dynamics by sequencing 1,284 transcriptomes of developing fibers and characterized genetic regulatory perturbations mediated by genomic introgression using a multi-locus model. Introgression of individual homoeologous genes exhibiting extreme low or high expression bias can lead to a parallel expression bias in their non-introgressed duplicates, implying a shared yet divergent regulatory fate of duplicated genes following allopolyploidy. Additionally, the IL N182 with improved fiber quality is characterized, and the candidate gene GhFLAP1 related to fiber length is validated. This study outlines a framework for understanding introgression-mediated regulatory perturbations in polyploids, and provides insights for targeted breeding of superior upland cotton fiber.

RNA splicing modulates the postharvest physiological deterioration of cassava storage root

Rapid postharvest physiological deterioration (PPD) of cassava (Manihot esculenta Crantz) storage roots is a major constraint that limits the potential of this plant as a food and industrial crop. Extensive studies have been performed to explore the regulatory mechanisms underlying the PPD processes in cassava to understand their molecular and physiological responses. However, the exceptional functional versatility of alternative splicing (AS) remains to be explored during the PPD process in cassava. Here, we identified several aberrantly spliced genes during the early PPD stage. An in-depth analysis of AS revealed that the abscisic acid (ABA) biosynthesis pathway might serve as an additional molecular layer in attenuating the onset of PPD. Exogenous ABA application alleviated PPD symptoms through maintaining ROS generation and scavenging. Interestingly, the intron retention transcript of MeABA1 (ABA DEFICIENT 1) was highly correlated with PPD symptoms in cassava storage roots. RNA yeast 3-hybrid and RNA immunoprecipitation (RIP) assays showed that the serine/arginine-rich protein MeSCL33 (SC35-like splicing factor 33) binds to the precursor mRNA of MeABA1. Importantly, overexpressing MeSCL33 in cassava conferred improved PPD resistance by manipulating the AS and expression levels of MeABA1 and then modulating the endogenous ABA levels in cassava storage roots. Our results uncovered the pivotal role of the ABA biosynthesis pathway and RNA splicing in regulating cassava PPD resistance and proposed the essential roles of MeSCL33 for conferring PPD resistance, broadening our understanding of SR proteins in cassava development and stress responses.

Dhurrin in Sorghum: Biosynthesis, Regulation, Biological Function and Challenges for Animal Production

Sorghum (Sorghum bicolor) holds a significant position as the fifth most vital cereal crop globally. Its drought resistance and robust biomass production, coupled with commendable nutritional value, make sorghum a promising choice for animal feed. Nevertheless, the utilization of sorghum in animal production faces hurdles of dhurrin (a cyanogenic glycoside) poisoning. While dhurrin serves as a protective secondary metabolite during sorghum growth, the resulting highly toxic hydrogen cyanide poses a significant threat to animal safety. This review extensively examines the biometabolic processes of dhurrin, the pivotal genes involved in the regulation of dhurrin biosynthesis, and the factors influencing dhurrin content in sorghum. It delves into the impact of dhurrin on animal production and explores measures to mitigate its content, aiming to provide insights for advancing research on dhurrin metabolism regulation in sorghum and its rational utilization in animal production.

The coevolutionary consequences of biodiversity change

Coevolutionary selection is a powerful process shaping species interactions and biodiversity. Anthropogenic global environmental change is reshaping planetary biodiversity, including by altering the structure and intensity of interspecific interactions. However, remarkably little is understood of how coevolutionary selection is changing in the process. Here, we outline three interrelated pathways - change in evolutionary potential, change in community composition, and shifts in interaction trait distributions - that are expected to redirect coevolutionary selection under biodiversity change. Assessing how both ecological and evolutionary rules governing species interactions are disrupted under anthropogenic global change is of paramount importance to understand the past, present, and future of Earth's biodiversity.

Deepening genomic sequences of 1081 Gossypium hirsutum accessions reveals novel SNPs and haplotypes relevant for practical breeding utility

Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090, GhM_D05G1692, GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.

Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance

Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.

Phenotypic Variability in Resistance to Anthracnose, White, Brown, and Blight Leaf Spot in Cassava Germplasm

Despite fungal diseases affecting the aerial parts of cassava (Manihot esculenta Crantz) and causing significant yield losses, there is a lack of comprehensive studies assessing resistance in the species' germplasm. This study aimed to evaluate the phenotypic diversity for resistance to anthracnose disease (CAD), blight leaf spot (BliLS), brown leaf spot (BLS), and white leaf spot (WLS) in cassava germplasm and to identify genotypes suitable for breeding purposes. A total of 837 genotypes were evaluated under field conditions across two production cycles (2021 and 2022). Artificial inoculations were carried out in the field, and data on yield and disease severity were collected using a standardized rating scale. The top 25 cassava genotypes were selected based on a selection index for disease resistance and agronomic traits. High environmental variability resulted in low heritabilities (h2) for CAD, WLS, and BLS (h2 = 0.42, 0.34, 0.29, respectively) and moderate heritability for BliLS (h2 = 0.51). While the range of data for disease resistance was narrow, it was considerably wider for yield traits. Cluster analysis revealed that increased yield traits and disease severity were associated with higher scores of the first and second discriminant functions, respectively. Thus, most clusters comprised genotypes with hybrid characteristics for both traits. Overall, there was a strong correlation among aerial diseases, particularly between BLS and BliLS (r = 0.96), while the correlation between CAD and other diseases ranged from r = 0.53 to 0.58. Yield traits showed no significant correlations with disease resistance. Although the mean selection differential for disease resistance was modest (between -2.31% and -3.61%), selection based on yield traits showed promising results, particularly for fresh root yield (82%), dry root yield (39%), shoot yield (49%), and plant vigor (26%). This study contributes to enhancing genetic gains for resistance to major aerial part diseases and improving yield traits in cassava breeding programs.

Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer

The accumulation of proline in response to the most diverse types of stress is a widespread defense mechanism. In prokaryotes, fungi, and certain unicellular eukaryotes (green algae), the first two reactions of proline biosynthesis occur through two distinct enzymes, γ-glutamyl kinase (GK E.C. 2.7.2.11) and γ-glutamyl phosphate reductase (GPR E.C. 1.2.1.41), encoded by two different genes, ProB and ProA, respectively. Plants, animals, and a few unicellular eukaryotes carry out these reactions through a single bifunctional enzyme, the Δ1-pyrroline-5-carboxylate synthase (P5CS), which has the GK and GPR domains fused. To better understand the origin and diversification of the P5CS gene, we use a robust phylogenetic approach with a broad sampling of the P5CS, ProB and ProA genes, including species from all three domains of life. Our results suggest that the collected P5CS genes have arisen from a single fusion event between the ProA and ProB gene paralogs. A peculiar fusion event occurred in an ancestral eukaryotic lineage and was spread to other lineages through horizontal gene transfer. As for the diversification of this gene family, the phylogeny of the P5CS gene in plants shows that there have been multiple independent processes of duplication and loss of this gene, with the duplications being related to old polyploidy events.

Identifying genetically redundant accessions in the world's largest cassava collection

Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava (Manihot esculenta) plays a vital role in providing carbohydrates to approximately 500 million people in Africa and other continents. The International Center for Tropical Agriculture (CIAT) conserves the largest global cassava collection, housing 5,963 accessions of cultivated cassava and wild relatives within its genebank. Efficient genebank management requires identifying and eliminating genetic redundancy within collections. In this study, we optimized the identification of genetic redundancy in CIAT's cassava genebank, applying empirical distance thresholds, and using two types of molecular markers (single-nucleotide polymorphism (SNP) and SilicoDArT) on 5,302 Manihot esculenta accessions. A series of quality filters were applied to select the most informative and high-quality markers and to exclude low-quality DNA samples. The analysis identified a total of 2,518 and 2,526 (47 percent) distinct genotypes represented by 1 to 87 accessions each, using SNP or SilicoDArT markers, respectively. A total of 2,776 (SNP) and 2,785 (SilicoDArT) accessions were part of accession clusters with up to 87 accessions. Comparing passport and historical characterization data, such as pulp color and leaf characteristic, we reviewed clusters of genetically redundant accessions. This study provides valuable guidance to genebank curators in defining minimum genetic-distance thresholds to assess redundancy within collections. It aids in identifying a subset of genetically distinct accessions, prioritizing collection management activities such as cryopreservation and provides insights for follow-up studies in the field, potentially leading to removal of duplicate accessions.

Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales

Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization of lipid droplets (LDs) in seeds of oil crops. Despite the proposal of five oleosin clades (i.e., U, SL, SH, T, and M) in angiosperms, their evolution in eudicots has not been well-established. In this study, we employed Brassicales, an economically important order of flowering plants possessing the lineage-specific T clade, as an example to address this issue. Three to 10 members were identified from 10 species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, and Cleomaceae. Evolutionary and reciprocal best hit-based homologous analyses assigned 98 oleosin genes into six clades (i.e., U, SL, SH, M, N, and T) and nine orthogroups (i.e., U1, U2, SL, SH1, SH2, SH3, M, N, and T). The newly identified N clade represents an ancient group that has already appeared in the basal angiosperm Amborella trichopoda, which are constitutively expressed in the tree fruit crop Carica papaya, including pulp and seeds of the fruit. Moreover, similar to Clade N, the previously defined M clade is actually not Lauraceae-specific but an ancient and widely distributed group that diverged before the radiation of angiosperm. Compared with A. trichopoda, lineage-specific expansion of the family in Brassicales was largely contributed by recent whole-genome duplications (WGDs) as well as the ancient γ event shared by all core eudicots. In contrast to the flower-preferential expression of Clade T, transcript profiling revealed an apparent seed/embryo/endosperm-predominant expression pattern of most oleosin genes in Arabidopsis thaliana and C. papaya. Moreover, the structure and expression divergence of paralogous pairs was frequently observed, and a good example is the lineage-specific gain of an intron. These findings provide insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in nonmodel plants such as C. papaya.

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root

BACKGROUND

Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient quality and domestication of root and tuber crops remain largely unknown.

RESULTS

We report a comprehensive study combining metabolic and phenotypic genome-wide association studies to dissect the genetic basis of metabolites in the storage root (SR) of cassava. We quantify 2,980 metabolic features in 299 cultivated cassava accessions. We detect 18,218 significant marker-metabolite associations via metabolic genome-wide association mapping and identify 12 candidate genes responsible for the levels of metabolites that are of potential nutritional importance. Me3GT, MeMYB4, and UGT85K4/UGT85K5, which are involved in flavone, anthocyanin, and cyanogenic glucoside metabolism, respectively, are functionally validated through in vitro enzyme assays and in vivo gene silencing analyses. We identify a cluster of cyanogenic glucoside biosynthesis genes, among which CYP79D1, CYP71E7b, and UGT85K5 are highly co-expressed and their allelic combination contributes to low linamarin content. We find MeMYB4 is responsible for variations in cyanidin 3-O-glucoside and delphinidin 3-O-rutinoside contents, thus controlling SR endothelium color. We find human selection affects quercetin 3-O-glucoside content and SR weight per plant. The candidate gene MeFLS1 is subject to selection during cassava domestication, leading to decreased quercetin 3-O-glucoside content and thus increased SR weight per plant.

CONCLUSIONS

These findings reveal the genetic basis of cassava SR metabolome variation, establish a linkage between metabolites and agronomic traits, and offer useful resources for genetically improving the nutrition of cassava and other root crops.

Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.

Microbiome and plant cell transformation trigger insect gall induction in cassava

Several specialised insects can manipulate normal plant development to induce a highly organised structure known as a gall, which represents one of the most complex interactions between insects and plants. Thus far, the mechanism for insect-induced plant galls has remained elusive. To study the induction mechanism of insect galls, we selected the gall induced by Iatrophobia brasiliensis (Diptera: Cecidomyiidae) in cassava (Euphorbiaceae: Manihot esculenta Crantz) as our model. PCR-based molecular markers and deep metagenomic sequencing data were employed to analyse the gall microbiome and to test the hypothesis that gall cells are genetically transformed by insect vectored bacteria. A shotgun sequencing discrimination approach was implemented to selectively discriminate between foreign DNA and the reference host plant genome. Several known candidate insertion sequences were identified, the most significant being DNA sequences found in bacterial genes related to the transcription regulatory factor CadR, cadmium-transporting ATPase encoded by the cadA gene, nitrate transport permease protein (nrtB gene), and arsenical pump ATPase (arsA gene). In addition, a DNA fragment associated with ubiquitin-like gene E2 was identified as a potential accessory genetic element involved in gall induction mechanism. Furthermore, our results suggest that the increased quality and rapid development of gall tissue are mostly driven by microbiome enrichment and the acquisition of critical endophytes. An initial gall-like structure was experimentally obtained in M. esculenta cultured tissues through inoculation assays using a Rhodococcus bacterial strain that originated from the inducing insect, which we related to the gall induction process. We provide evidence that the modification of the endophytic microbiome and the genetic transformation of plant cells in M. esculenta are two essential requirements for insect-induced gall formation. Based on these findings and having observed the same potential DNA marker in galls from other plant species (ubiquitin-like gene E2), we speculate that bacterially mediated genetic transformation of plant cells may represent a more widespread gall induction mechanism found in nature.

Analysis of Carica papaya Informs Lineage-Specific Evolution of the Aquaporin (AQP) Family in Brassicales

Aquaporins (AQPs), a type of intrinsic membrane proteins that transport water and small solutes across biological membranes, play crucial roles in plant growth and development. This study presents a first genome-wide identification and comparative analysis of the AQP gene family in papaya (Carica papaya L.), an economically and nutritionally important fruit tree of tropical and subtropical regions. A total of 29 CpAQP genes were identified, which represent five subfamilies, i.e., nine plasma intrinsic membrane proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). Although the family is smaller than the 35 members reported in Arabidopsis, it is highly diverse, and the presence of CpXIP genes as well as orthologs in Moringa oleifera and Bretschneidera sinensis implies that the complete loss of the XIP subfamily in Arabidopsis is lineage-specific, sometime after its split with papaya but before Brassicaceae-Cleomaceae divergence. Reciprocal best hit-based sequence comparison of 530 AQPs and synteny analyses revealed that CpAQP genes belong to 29 out of 61 identified orthogroups, and lineage-specific evolution was frequently observed in Brassicales. Significantly, the well-characterized NIP3 group was completely lost; lineage-specific loss of the NIP8 group in Brassicaceae occurred sometime before the divergence with Cleomaceae, and lineage-specific loss of NIP2 and SIP3 groups in Brassicaceae occurred sometime after the split with Cleomaceae. In contrast to a predominant role of recent whole-genome duplications (WGDs) on the family expansion in B. sinensis, Tarenaya hassleriana, and Brassicaceae plants, no recent AQP repeats were identified in papaya, and ancient WGD repeats are mainly confined to the PIP subfamily. Subfamily even group-specific evolution was uncovered via comparing exon-intron structures, conserved motifs, the aromatic/arginine selectivity filter, and gene expression profiles. Moreover, down-regulation during fruit ripening and expression divergence of duplicated CpAQP genes were frequently observed in papaya. These findings will not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further studies of AQP genes in papaya and species beyond.

Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources

Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope® in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions.

Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression

Cassava is a crucial crop that makes a significant contribution to ensuring human food security. However, high-quality telomere-to-telomere cassava genomes have not been available up to now, which has restricted the progress of haploid molecular breeding for cassava. In this study, we constructed two nearly complete haploid resolved genomes and an integrated, telomere-to-telomere gap-free reference genome of an excellent cassava variety, 'Xinxuan 048', thereby providing a new high-quality genomic resource. Furthermore, the evolutionary history of several species within the Euphorbiaceae family was revealed. Through comparative analysis of haploid genomes, it was found that two haploid genomes had extensive differences in linear structure, transcriptome features, and epigenetic characteristics. Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway. The high heterozygosity of cassava 'Xinxuan 048' leads to rapid trait segregation in the first selfed generation. This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.

The role of orphan crops in the transition to nutritional quality-oriented crop improvement

Micronutrient malnutrition is a persisting problem threatening global human health. Biofortification via metabolic engineering has been proposed as a cost-effective and short-term means to alleviate this burden. There has been a recent rise in the recognition of potential that underutilized, orphan crops can hold in decreasing malnutrition concerns. Here, we illustrate how orphan crops can serve as a medium to provide micronutrients to populations in need, whilst promoting and maintaining dietary diversity. We provide a roadmap, illustrating which aspects to be taken into consideration when evaluating orphan crops. Recent developments have shown successful biofortification via metabolic engineering in staple crops. This review provides guidance in the implementation of these successes to relevant orphan crop species, with a specific focus on the relevant micronutrients iron, zinc, provitamin A and folates.

Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis

Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays a vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, and 2 MSODs) in cassava. Bioinformatics analyses provided insights into chromosomal location, phylogenetic relationships, gene structure, conserved motifs, and gene ontology annotations. MeSOD genes were classified into two groups through phylogenetic analysis, revealing evolutionary connections. Promoters of these genes harbored stress-related cis-elements. Duplication analysis indicated the functional significance of MeCSOD2/MeCSOD4 and MeMSOD1/MeMSOD2. Through qRT-PCR, MeCSOD2 responded to salt stress, MeMSOD2 to drought, and cassava bacterial blight. Silencing MeMSOD2 increased XpmCHN11 virulence, indicating MeMSOD2 is essential for cassava's defense against XpmCHN11 infection. These findings enhance our understanding of the SOD gene family's role in cassava and contribute to strategies for stress tolerance improvement.

Genome-wide identification and expression analysis of Hsp70 family genes in Cassava (Manihot esculenta Crantz)

Hsp70 proteins function as molecular chaperones, regulating various cellular processes in plants. In this study, a genome-wide analysis led to the identification of 22 Hsp70 (MeHsp70) genes in cassava. Phylogenetic relationship studies with other Malpighiales genomes (Populus trichocarpa, Ricinus communis and Salix purpurea) classified MeHsp70 proteins into eight groups (Ia, Ib, Ic, Id, Ie, If, IIa and IIb). Promoter analysis of MeHsp70 genes revealed the presence of tissue-specific, light, biotic and abiotic stress-responsive cis-regulatory elements showing their functional importance in cassava. Meta-analysis of publically available RNA-seq transcriptome datasets showed constitutive, tissue-specific, biotic and abiotic stress-specific expression patterns among MeHsp70s in cassava. Among 22 Hsp70, six MeHsp70s viz., MecHsp70-3, MecHsp70-6, MeBiP-1, MeBiP-2, MeBiP-3 and MecpHsp70-2 displayed constitutive expression, while three MecHsp70s were induced under both drought and cold stress conditions. Five MeHsp70s, MecHsp70-7, MecHsp70-11, MecHsp70-12, MecHsp70-13, and MecHsp70-14 were induced under drought stress conditions. We predicted that 19 MeHsp70 genes are under the regulation of 24 miRNAs. This comprehensive genome-wide analysis of the Hsp70 gene family in cassava provided valuable insights into their functional roles and identified various potential Hsp70 genes associated with stress tolerance and adaptation to environmental stimuli.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03760-3.

Development of cassava core collections based on morphological and agronomic traits and SNPS markers

Cassava (Manihot esculenta Crantz) holds significant importance as one of the world's key starchy crop species. This study aimed to develop core collections by utilizing both phenotypic data (15 quantitative and 33 qualitative descriptors) and genotypic data (20,023 single-nucleotide polymorphisms) obtained from 1,486 cassava accessions. Six core collections were derived through two optimization strategies based on genetic distances: Average accession-to-nearest-entry and Average entry-to-nearest-entry, along with combinations of phenotypic and genotypic data. The quality of the core collections was evaluated by assessing genetic parameters such as genetic diversity Shannon-Weaver Index, inbreeding (Fis), observed (Ho), and expected (Hs) heterozygosity. While the selection of accessions varied among the six core collections, a seventh collection (consolidated collection) was developed, comprising accessions selected by at least two core collections. Most collections exhibited genetic parameters similar to the complete collection, except for those developed by the Average accession-to-nearest-entry algorithm. However, the variations in the maximum and minimum values of Ho, Hs, and Fis parameters closely resembled the complete collection. The consolidated collection and the collection constructed using genotypic data and the Average entry-to-nearest-entry algorithm (GenEN) retained the highest number of alleles (>97%). Although the differences were not statistically significant (above 5%), the consolidated collection demonstrated a distribution profile and mean trait values most similar to the complete collection, with a few exceptions. The Shannon-Weaver Index of qualitative traits exhibited variations exceeding ±10% when compared to the complete collection. Principal component analysis revealed that the consolidated collection selected cassava accessions with a more uniform dispersion in all four quadrants compared to the other core collections. These findings highlight the development of optimized and valuable core collections for efficient breeding programs and genomic association studies.

Integrated Characterization of Cassava (Manihot esculenta) Pectin Methylesterase (MePME) Genes to Filter Candidate Gene Responses to Multiple Abiotic Stresses

Plant pectin methylesterases (PMEs) play crucial roles in regulating cell wall modification and response to various stresses. Members of the PME family have been found in several crops, but there is a lack of research into their presence in cassava (Manihot esculent), which is an important crop for world food security. In this research, 89 MePME genes were identified in cassava that were separated into two types (type-Ⅰ and type-Ⅱ) according to the existence or absence of a pro-region (PMEI domain). The MePME gene members were unevenly located on 17 chromosomes, with 19 gene pairs being identified that most likely arose via duplication events. The MePMEs could be divided into ten sub-groups in type-Ⅰ and five sub-groups in type-Ⅱ. The motif analysis revealed 11 conserved motifs in type-Ⅰ and 8 in type-Ⅱ MePMEs. The number of introns in the CDS region of type-Ⅰ MePMEs ranged between one and two, and the number of introns in type-Ⅱ MePMEs ranged between one and nine. There were 21 type-Ⅰ and 31 type-Ⅱ MePMEs that contained signal peptides. Most of the type-Ⅰ MePMEs had two conserved "RK/RLL" and one "FPSWVS" domain between the pro-region and the PME domain. Multiple stress-, hormone- and tissue-specific-related cis-acting regulatory elements were identified in the promoter regions of MePME genes. A total of five co-expressed genes (MePME1, MePME2, MePME27, MePME65 and MePME82) were filtered from different abiotic stresses via the use of UpSet Venn diagrams. The gene expression pattern analysis revealed that the expression of MePME1 was positively correlated with the degree of cassava postharvest physiological deterioration (PPD). The expression of this gene was also significantly upregulated by 7% PEG and 14 °C low-temperature stress, but slightly downregulated by ABA treatment. The tissue-specific expression analysis revealed that MePME1 and MePME65 generally displayed higher expression levels in most tissues than the other co-expressed genes. In this study, we obtain an in-depth understanding of the cassava PME gene family, suggesting that MePME1 could be a candidate gene associated with multiple abiotic tolerance.

CRISPRi in Xanthomonas demonstrates functional convergence of transcription activator-like effectors in two divergent pathogens

Functional analysis of large gene families in plant pathogens can be cumbersome using classical insertional mutagenesis. Additionally, Cas9 toxicity has limited the application of CRISPR-Cas9 for directed mutagenesis in bacteria. Here, we successfully applied a CRISPR interference strategy to investigate the cryptic role of the transcription activator-like effector (tale) multigene family in several plant-pathogenic Xanthomonas bacterial species, owing to their contribution to pathogen virulence. Single guide RNAs (sgRNAs) designed against Xanthomonas phaseoli pv manihotis tale conserved gene sequences efficiently silenced expression of all tales, with concomitant decrease in virulence and TALE-induced host gene expression. The system is readily translatable to other Xanthomonas species infecting rice, citrus, Brassica, and cassava, silencing up to 16 tales in a given strain using a single sgRNA. Complementation with plasmid-borne designer tales lacking the sgRNA-targeted sequence restored molecular and virulence phenotypes in all pathosystems. Our results evidenced that X. campestris pv campestris CN08 tales are relevant for symptom development in cauliflower. They also show that the MeSWEET10a sugar transporter is surprisingly targeted by the nonvascular cassava pathogen X. cassavae, highlighting a new example of TALE functional convergence between phylogenetically distant Xanthomonas. Overall, this novel technology provides a platform for discovery and rapid functional understanding of highly conserved gene families.

DNA methylation signatures of duplicate gene evolution in angiosperms

Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.

A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus

A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.

CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production

Cassava (Manihot esculenta) is a starchy root crop that supports over a billion people in tropical and subtropical regions of the world. This staple, however, produces the neurotoxin cyanide and requires processing for safe consumption. Excessive consumption of insufficiently processed cassava, in combination with protein-poor diets, can have neurodegenerative impacts. This problem is further exacerbated by drought conditions which increase this toxin in the plant. To reduce cyanide levels in cassava, we used CRISPR-mediated mutagenesis to disrupt the cytochrome P450 genes CYP79D1 and CYP79D2 whose protein products catalyze the first step in cyanogenic glucoside biosynthesis. Knockout of both genes eliminated cyanide in leaves and storage roots of cassava accession 60444; the West African, farmer-preferred cultivar TME 419; and the improved variety TMS 91/02324. Although knockout of CYP79D2 alone resulted in significant reduction of cyanide, mutagenesis of CYP79D1 did not, indicating these paralogs have diverged in their function. The congruence of results across accessions indicates that our approach could readily be extended to other preferred or improved cultivars. This work demonstrates cassava genome editing for enhanced food safety and reduced processing burden, against the backdrop of a changing climate.

Analysis of the molecular and biochemical mechanisms involved in the symbiotic relationship between Arbuscular mycorrhiza fungi and Manihot esculenta Crantz

INTRODUCTION

Plants and arbuscular mycorrhizal fungi (AMF) mutualistic interactions are essential for sustainable agriculture production. Although it is shown that AMF inoculation improves cassava physiological performances and yield traits, the molecular mechanisms involved in AM symbiosis remain largely unknown. Herein, we integrated metabolomics and transcriptomics analyses of symbiotic (Ri) and asymbiotic (CK) cassava roots and explored AM-induced biochemical and transcriptional changes.

RESULTS

Three weeks (3w) after AMF inoculations, proliferating fungal hyphae were observable, and plant height and root length were significantly increased. In total, we identified 1,016 metabolites, of which 25 were differentially accumulated (DAMs) at 3w. The most highly induced metabolites were 5-aminolevulinic acid, L-glutamic acid, and lysoPC 18:2. Transcriptome analysis identified 693 and 6,481 differentially expressed genes (DEGs) in the comparison between CK (3w) against Ri at 3w and 6w, respectively. Functional enrichment analyses of DAMs and DEGs unveiled transport, amino acids and sugar metabolisms, biosynthesis of secondary metabolites, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions as the most differentially regulated pathways. Potential candidate genes, including nitrogen and phosphate transporters, transcription factors, phytohormone, sugar metabolism-related, and SYM (symbiosis) signaling pathway-related, were identified for future functional studies.

DISCUSSION

Our results provide molecular insights into AM symbiosis and valuable resources for improving cassava production.

High throughput sRNA sequencing revealed gene regulatory role mediated by pathogen-derived small RNAs during Sri Lankan Cassava Mosaic Virus infection in Cassava

Small RNA (sRNA) mediated gene regulation during Sri Lankan Cassava Mosaic Virus (SLCMV) infection was studied from the Indian Cassava Cultivar H226. Our study generated high throughput sRNA dataset of 23.64 million reads from the control and SLCMV infected H226 leaf libraries. mes-miR9386 was detected as the most prominent miRNA expressed in control and infected leaf. Among the differentially expressed miRNAs, mes-miR156, mes- miR395 and mes-miR535a/b showed significant down regulation in the infected leaf. Genome-wide analysis of the three small RNA profiles revealed critical role of virus-derived small RNAs (vsRNAs) from the infected leaf tissues of H226. The vsRNAs were mapped to the bipartite SLCMV genome and high expression of siRNAs generated from the virus genomic region encoding AV1/AV2 genes in the infected leaf pointed towards the susceptibility of H226 cultivars to SLCMV. Furthermore, the sRNA reads mapped to the antisense strand of the SLCMV ORFs was higher than the sense strand. These vsRNAs were potential to target key host genes involved in virus interaction such as aldehyde dehydrogenase, ADP-ribosylation factor1 and ARF1-like GTP-binding proteins. The sRNAome-assisted analysis also revealed the origin of virus-encoded miRNAs from the SLCMV genome in the infected leaf. These virus-derived miRNAs were predicted to have hair-pin like secondary structures, and have different isoforms. Moreover, our study revealed that the pathogen sRNAs play a critical role in the infection process in H226 plants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03494-2.

Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet

Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.

The rubber tree kinome: Genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, with the aim of providing novel inferences about the mechanisms associated with the stress response developed by PKs and retained throughout evolution, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species Manihot esculenta and Ricinus communis. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.

Genome-wide association studies reveal genetic basis of ionomic variation in cassava

As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome-wide association studies were performed to reveal the specific single nucleotide polymorphisms (SNPs) that affect the ionomic variation in cassava. We identified 164 SNPs with P-values lower than the threshold located in 88 loci associated with divergent ionomic variations. Among them, 13 SNPs are related to both calcium (Ca) and magnesium (Mg), and many loci for different ionomic traits seem to be clustered on specific chromosome regions. Moreover, we identified the peak SNPs in the promoter regions of Sc10g003170 (encoding methionyl-tRNA synthetase [MetRS]) and Sc18g015190 (encoding the transcriptional regulatory protein AlgP) for nitrogen (N) and phosphorus (P) accumulation, respectively. Notably, these two SNPs (chr10_32807962 and chr18_31343738) were directly correlated with the transcript levels of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively modulated N accumulation and P concentration in cassava, respectively. Taken together, this study provides important insight into the genetic basis of cassava natural ionomic variation, which will promote genetic breeding to improve nutrient use and accumulation of elements in cassava.

Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers' performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers' effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.

CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects

Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.

Insights to the superoxide dismutase genes and its roles in Hevea brasiliensis under abiotic stress

The superoxide dismutase (SOD) protein significantly influences the development and growth of plants and their reaction to abiotic stresses. However, little is known about the characteristics of rubber tree SOD genes and their expression changes under abiotic stresses. The present study recognized 11 SOD genes in the rubber tree genome, including 7 Cu/ZnSODs, 2 MnSODs, and 2 FeSODs. Except for HbFSD1, SODs were scattered on five chromosomes. The phylogenetic analysis of SOD proteins in rubber trees and a few other plants demonstrated that the SOD proteins contained three major subgroups. Moreover, the genes belonging to the same clade contained similar gene structures, which confirmed their classification further. The extension of the SOD gene family in the rubber tree was mainly induced by the segmental duplication events. The cis-acting components analysis showed that HbSODs were utilized in many biological procedures. The transcriptomics data indicated that the phosphorylation of the C-terminal domain of RNA polymerase II might control the cold response genes through the CBF pathway and activate the SOD system to respond to cold stress. The qRT-PCR results showed that the expression of HbCSD1 was significantly downregulated under drought and salt stresses, which might dominate the adaption capability to different stresses. Additionally, salt promoted the expression levels of HbMSD1 and HbMSD2, exhibiting their indispensable role in the salinity reaction. The study results will provide a theoretical basis for deep research on HbSODs in rubber trees.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03328-7.

Long-day photoperiod and cool temperature induce flowering in cassava: Expression of signaling genes

Cassava is a staple food crop in the tropics, and is of particular importance in Africa. Recent development of genomic selection technology have improved the speed of cassava breeding; however, cassava flower initiation and development remains a bottleneck. The objectives of the current studies were to elucidate the effect of photoperiod, temperature and their interactions on the time of flowering and flower development in controlled environments, and to use RNA-sequencing to identify transcriptome expression underlying these environmental responses. Compared to a normal tropical day-length of 12 h, increasing the photoperiod by 4 h or decreasing the air temperature from 34/31 to 22°/19°C (day/night) substantially hastened the time to flowering. For both photoperiod and temperature, the environment most favorable for flowering was opposite the one for storage root harvest index. There was a pronounced treatment interaction: at warm day-time temperatures, percent flowering was low, and photoperiod had little effect. In contrast, at cooler temperatures, percent flowering increased, and long-day (LD) photoperiod had a strong effect in hastening flowering. In response to temperature, many differentially expressed genes in the sugar, phase-change, and flowering-time-integrator pathways had expression/flowering patterns in the same direction as in Arabidopsis (positive or negative) even though the effect of temperature on flowering operates in the reverse direction in cassava compared to Arabidopsis. Three trehalose-6-phosphate-synthase-1 (TPS1) genes and four members of the SPL gene family had significantly increased expression at cool temperature, suggesting sugar signaling roles in flower induction. In response to LD photoperiod, regulatory genes were expressed as in Arabidopsis and other LD flowering plants. Several hormone-related genes were expressed in response to both photoperiod and temperature. In summary, these findings provide insight on photoperiod and temperature responses and underlying gene expression that may assist breeding programs to manipulate flowering for more rapid crop improvement.

Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in Jatropha curcas and Related Species

Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play important roles in organ development and stress response. However, the function of LBD genes has not been reported in Euphorbiaceae. In this paper, we used Jatropha curcas as the main study object and added rubber tree (Hevea brasiliensis), cassava (Manihot esculenta Crantz) and castor (Ricinus communis L.) to take a phylogenetic analysis of LBD genes. Of LBD, 33, 58, 54 and 30 members were identified in J. curcas, rubber tree, cassava and castor, respectively. The phylogenetic analysis showed that LBD members of Euphorbiaceae could be classified into two major classes and seven subclasses (Ia-Ie,IIa-IIb), and LBD genes of Euphorbiaceae tended to cluster in the same branch. Further analysis showed that the LBD genes of Euphorbiaceae in the same clade usually had similar protein motifs and gene structures, and tissue expression patterns showed that they also have similar expression profiles. JcLBDs in class Ia and Ie are mainly expressed in male and female flowers, and there are multiple duplication genes with similar expression profiles in these clades. It was speculated that they are likely to play important regulatory roles in flower development. Our study provided a solid foundation for further investigation of the role of LBD genes in the sexual differentiaion of J. curcas.

Genome sequence of Gossypium anomalum facilitates interspecific introgression breeding

Crop wild relatives are an important reservoir of natural biodiversity. However, incorporating wild genetic diversity into breeding programs is often hampered by reproductive barriers and a lack of accurate genomic information. We assembled a high-quality, accurately centromere-anchored genome of Gossypium anomalum, a stress-tolerant wild cotton species. We provided a strategy to discover and transfer agronomically valuable genes from wild diploid species to tetraploid cotton cultivars. With a (Gossypium hirsutum × G. anomalum)2 hexaploid as a bridge parent, we developed a set of 74 diploid chromosome segment substitution lines (CSSLs) of the wild cotton species G. anomalum in the G. hirsutum background. This set of CSSLs included 70 homozygous substitutions and four heterozygous substitutions, and it collectively contained about 72.22% of the G. anomalum genome. Twenty-four quantitative trait loci associated with plant height, yield, and fiber qualities were detected on 15 substitution segments. Integrating the reference genome with agronomic trait evaluation of the CSSLs enabled location and cloning of two G. anomalum genes that encode peroxiredoxin and putative callose synthase 8, respectively, conferring drought tolerance and improving fiber strength. We have demonstrated the power of a high-quality wild-species reference genome for identifying agronomically valuable alleles to facilitate interspecific introgression breeding in crops.

Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.

Evolution and function of ubiquitin-specific proteases (UBPs): Insight into seed development roles in tung tree (Vernicia fordii)

The tung oil produced by the tung tree (Vernicia fordii) provides resources for the manufacture of biodiesel. Ubiquitin-specific proteases (UBPs) are the largest group of deubiquitinases and play key roles in regulating development and stress responses. Here, 21 UBPs were identified in V. fordii, roughly one-half the number found in Manihot esculenta and Hevea brasiliensis. Most UBP duplications are produced from whole-genome duplication (WGD), and significant differences in gene retention existed among Euphorbiaceae. The great majority of UBP-containing blocks in V. fordii, V. montana, Ricinus communis, and Jatropha curcas exhibited extensive conservation with the duplicated regions of M. esculenta and H. brasiliensis. These blocks formed 14 orthologous groups, indicating they shared WGD with UBPs in M. esculenta and H. brasiliensis, but most of these UBPs copies were lost. The UBP orthologs contained significant functional divergence which explained the susceptibility of V. fordii to Fusarium wilt and the resistance of V. montana to Fusarium wilt. The expression patterns and experiments suggested that Vf03G1417 could affect the seed-related traits and positively regulate the seed oil accumulation. This study provided important insights into the evolution of UBPs in Euphorbiaceae and identified important candidate VfUBPs for marker-assisted breeding in V. fordii.

A Ca2+-sensor switch for tolerance to elevated salt stress in Arabidopsis

Excessive Na⁺ in soils inhibits plant growth. Here, we report that Na⁺ stress triggers primary calcium signals specifically in a cell group within the root differentiation zone, thus forming a "sodium-sensing niche" in Arabidopsis. The amplitude of this primary calcium signal and the speed of the resulting Ca²⁺ wave dose-dependently increase with rising Na⁺ concentrations, thus providing quantitative information about the stress intensity encountered. We also delineate a Ca²⁺-sensing mechanism that measures the stress intensity in order to mount appropriate salt detoxification responses. This is mediated by a Ca²⁺-sensor-switch mechanism, in which the sensors SOS3/CBL4 and CBL8 are activated by distinct Ca²⁺-signal amplitudes. Although the SOS3/CBL4-SOS2/CIPK24-SOS1 axis confers basal salt tolerance, the CBL8-SOS2/CIPK24-SOS1 module becomes additionally activated only in response to severe salt stress. Thus, Ca²⁺-mediated translation of Na⁺ stress intensity into SOS1 Na⁺/H⁺ antiporter activity facilitates fine tuning of the sodium extrusion capacity for optimized salt-stress tolerance.

PP2C1 fine-tunes melatonin biosynthesis and phytomelatonin receptor PMTR1 binding to melatonin in cassava

Melatonin is an important molecule in both animals and plants, regulating circadian rhythms and stress responses. Therefore, the improvement of melatonin accumulation not only strengthens the function of melatonin but also improves stress resistance in crops. Although melatonin biosynthetic enzymes have been identified through reverse genetics previously, an investigation of melatonin level-related genes through forward genetics in plants has yet to be performed. In this study, a genome-wide association study using cassava natural population of 298 genetic resources identified melatonin accumulation 1 (MA1), which regulates the natural variation of melatonin levels in cassava. We found that MA1 encodes type 2C protein phosphatase 1 (PP2C1), which serves as a negative regulator of melatonin levels in cassava. MePP2C1 physically interacts with MeRAV1/2 and MeWRKY20 and dephosphorylates them at serine (S) 35 residue, S34 residue, and S176 residue, respectively, thereby hindering their transcriptional activation on downstream melatonin biosynthetic genes. Notably, MePP2C1 interacts with phytomelatonin receptor MePMTR1 and dephosphorylates it at S11 residue, repressing its binding to melatonin. In summary, this study demonstrates that MePP2C1 as MA1 plays dual roles in negatively regulating both melatonin accumulation and signaling, extending the understanding of the molecular mechanism underlying melatonin accumulation and signaling through forward genetics in plants.

The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.)

The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.

Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses

Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for this loss of resistance, whole genome sequencing and genetic variant analysis was performed and the CMD2 locus was fine-mapped to a 190 kilobase interval. Collectively, these data indicate that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase δ subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a CMD-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional candidate resistance alleles within MePOLD1. Genetic variation of MePOLD1, therefore, could represent an important genetic resource for resistance breeding and/or genome editing, and elucidating mechanisms of resistance to geminiviruses.

Natural variation MeMYB108 associated with tolerance to stress-induced leaf abscission linked to enhanced protection against reactive oxygen species in cassava

Natural variation of the MeMYB108 exon was associated with reactive oxygen scavengers led to alleviate leaf abscission under drought in cassava. The reactive oxygen scavengers play important roles in regulating the cassava (Manihot esculenta Crantz) leaf abscission induced by stresses. To date, the relationship between natural variations of MYB genes and reactive oxygen scavengers under drought in cassava genotypes remains unclear. Here, we reported the transcription factor MeMYB108 played an important role in regulating leaf abscission exposed to drought in cassava. The expression levels of MeMYB108 in abscission zones of cassava leaf pulvinus were higher in cassava genotype SC124, which were less easy to shed leaves under stress than cassava genotype SC8 when the leaf abscission induced by the same drought condition. Compared with wild type and interference expression plants, overexpression of MeMYB108 significantly reduced the drought-induced leaf abscission rate under drought. The consecutively 2-year analysis of reactive oxygen scavengers showed significant differences among different cassava genotypes under drought-induced leaf abscission, indicating the relevance between reactive oxygen scavengers and leaf abscission. Correlation analysis revealed the natural variation of the MeMYB108 exon was associated with reactive oxygen scavengers during drought-induced leaf abscission. Association analysis between pairwise LD of DNA polymorphism indicated the MeMYB108 allele enhanced the tolerance of cassava to drought-induced leaf abscission. Complementation transgenic lines containing the elite allele of MeMYB108 ^SC124 decreased the leaf abscission rate induced by drought conditions, demonstrating natural variation in MeMYB108 contributed to leaf abscission tolerance induced by drought in cassava. Further studies showed MeMYB108 played an active role in the tolerance of cassava to drought-induced leaf abscission by inducing scavenging of reactive oxygen species.

Advances in Genetic Analysis and Breeding of Cassava (Manihot esculenta Crantz): A Review

Cassava (Manihot esculenta Crantz) is the sixth most important food crop and consumed by 800 million people worldwide. In Africa, cassava is the second most important food crop after maize and Africa is the worlds' largest producer. Though cassava is not one of the main commodity crops in South Africa, it is becoming a popular crop among farming communities in frost-free areas, due to its climate-resilient nature. This necessitated the establishment of a multi-disciplinary research program at the Agricultural Research Council of South Africa. The objective of this review is to highlight progress made in cassava breeding and genetic analysis. This review highlights the progress of cassava research worldwide and discusses research findings on yield, quality, and adaptability traits in cassava. It also discusses the limitations and the prospects of the cassava R&D program towards development of the cassava industry in South Africa.

Genome-wide association study and selection for field resistance to cassava root rot disease and productive traits

Cassava root rot disease is caused by a complex of soil-borne pathogens and has high economic impacts because it directly affects the tuberous roots, which are the main commercial product. This study aimed to evaluate cassava genotypes for resistance to root rot disease in a field with a previous history of high disease incidence. It also aimed to identify possible genomic regions associated with field resistance based on genome-wide association studies. A total of 148 genotypes from Embrapa Mandioca and Fruticultura were evaluated over two years, including improved materials and curated germplasms. Analysis of phenotypic data was conducted, as well as a genomic association analysis, based on the general linear model, mixed linear model, and fixed and random model circulating probability unification. The observed high disease index (ω) was directly correlated with genotype survival, affecting plant height, shoot yield, and fresh root yield. The genotypes were grouped into five clusters, which were classified according to level of root rot resistance (i.e., extremely susceptible, susceptible, moderately susceptible, moderately resistant, and resistant). The 10 genotypes with the best performance in the field were selected as potential progenitors for the development of segregating progenies. Estimates of genomic kinship between these genotypes ranged from -0.183 to 0.671. The genotypes BGM-1171 and BGM-1190 showed the lowest degree of kinship with the other selected sources of resistance. The genotypes BGM-0209, BGM-0398, and BGM-0659 showed negative kinship values with most elite varieties, while BGM-0659 presented negative kinship with all landraces. A genome-wide association analysis detected five significant single nucleotide polymorphisms related to defense mechanisms against biotic and abiotic stresses, with putative association with fresh root yield in soil infested with root rot pathogens. These findings can be utilized to develop molecular selection for root rot resistance in cassava.

NMR-Based Metabolomic Approach for Evaluation of the Harvesting Time and Cooking Characteristics of Different Cassava Genotypes

Cassava is an important staple food for low-income countries. However, its cooking characteristics are especially affected by genotype. In this study, two groups of genotypes, namely hard to cook (HTC) and easy to cook (ETC), were harvested at different times (9 and 15 months), and evaluated by NMR coupled to chemometrics. Additionally, lignin of these materials was studied by ¹H-¹³C HSQC NMR. The carbohydrates were the most important class of compounds to differentiate the cassava genotypes. The correlation of NMR with cooking time and starch content showed that the higher content of primary metabolites, mostly glucose, can be associated with longer cooking times and reduction of starch, corroborating the metabolic pathways analysis. Furthermore, it was observed that the lignin from cell walls did not differentiate the cooking performance of the genotypes.

Current status and impending progress for cassava structural genomics

KEY MESSAGE

We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.