Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content

Genome-wide association studies unveils the genetic basis of cell wall composition and saccharification of cassava pulp

Cassava (Manihot esculenta Crantz) is a key crop for starch and biofuels production. This study focuses on the polysaccharide composition and saccharification efficiency in cassava pulp through genome-wide association studies (GWAS), targeting the improvement of root characteristics for industrial use. We analyzed 135 partially inbred lines population, performing monosaccharide composition and saccharification analyses to reveal substantial variability in storage root biomass. Among 33 traits examined, 128 significant SNPs were associated with 23 biomass traits, highlighting a complex genetic architecture. Saccharification potential varied from 39 to 95 nmol Glu mg-1 h-1, with high broad-sense heritability for saccharification and several monosaccharide traits, indicating a strong genetic control. Our findings revealed that cassava pulp comprises similar proportions of pectin, hemicellulose, and cellulose in all genotypes. Correlation analysis showed significant associations between cellulose content and saccharification, suggesting that enhancing these traits can improve bioconversion efficiency. Negative correlations with glucose and glucuronic acid in hemicellulose and pectin fractions imply these components may inhibit saccharification. We identified 118 candidate genes associated with 21 traits, with many involved in stress responses affecting cell wall composition. This study verified 12 key candidate genes through sequence and expression analysis, including MANES_07G081200, a YTH domain-containing protein associated with saccharification. Several stress-response genes, such as MANES_04G118600 and MANES_09G174600, were linked to monosaccharide traits, suggesting that adaptive stress pathways influence biomass characteristics. This study provides insights into the genetic determinants of cassava pulp's saccharification and polysaccharide composition, aiding breeding efforts to develop cassava varieties optimized for industrial applications.

Genetic diversity and population structure of Uganda cassava germplasm

Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.

Carotenoid-carbohydrate crosstalk: evidence for genetic and physiological interactions in storage tissues across crop species

Carotenoids play essential roles in photosynthesis, photoprotection, and human health. Efforts to increase carotenoid content in several staple crops have been successful through both conventional selection and genetic engineering methods. Interestingly, in some cases, altering carotenoid content has had unexpected effects on other aspects of plant metabolism, impacting traits like sugar content, dry matter percentage, fatty acid content, stress tolerance, and phytohormone concentrations. Studies across several diverse crop species have identified negative correlations between carotenoid and starch contents, as well as positive correlations between carotenoids and soluble sugars. Collectively, these reports suggest a metabolic interaction between carotenoids and carbohydrates. We synthesize evidence pointing to four hypothesized mechanisms: (1) direct competition for precursors; (2) physical interactions in plastids; (3) influences of sugar or apocarotenoid signaling networks; and (4) nonmechanistic population or statistical sources of correlations. Though the carotenoid biosynthesis pathway is well understood, the regulation and interactions of carotenoids, especially in nonphotosynthetic tissues, remain unclear. This topic represents an underexplored interplay between primary and secondary metabolism where further research is needed.

Carbon usage in yellow-fleshed Manihot esculenta storage roots shifts from starch biosynthesis to cell wall and raffinose biosynthesis via the myo-inositol pathway

Cassava is a crucial staple crop for smallholder farmers in tropical Asia and Sub-Saharan Africa. Although high yield remains the top priority for farmers, the significance of nutritional values has increased in cassava breeding programs. A notable negative correlation between provitamin A and starch accumulation poses a significant challenge for breeding efforts. The negative correlation between starch and carotenoid levels in conventional and genetically modified cassava plants implies the absence of a direct genomic connection between the two traits. The competition among various carbon pathways seems to account for this relationship. In this study, we conducted a thorough analysis of 49 African cassava genotypes with varying levels of starch and provitamin A. Our goal was to identify factors contributing to differential starch accumulation. Considering carotenoid levels as a confounding factor in starch production, we found that yellow- and white-fleshed storage roots did not differ significantly in most measured components of starch or de novo fatty acid biosynthesis. However, genes and metabolites associated with myo-inositol synthesis and cell wall polymer production were substantially enriched in high provitamin A genotypes. These results indicate that yellow-fleshed cultivars, in comparison to their white-fleshed counterparts, direct more carbon toward the synthesis of raffinose and cell wall components. This finding is underlined by a significant rise in cell wall components measured within the 20 most contrasting genotypes for carotenoid levels. Our findings enhance the comprehension of the biosynthesis of starch and carotenoids in the storage roots of cassava.

Genome-wide association study for yield and quality of granulated cassava processed product

The starchy storage roots of cassava are commonly processed into a variety of products, including cassava granulated processed products (gari). The commercial value of cassava roots depends on the yield and quality of processed products, directly influencing the acceptance of new varieties by farmers, processors, and consumers. This study aims to estimate genetic advance through phenotypic selection and identify genomic regions associated and candidate genes linked with gari yield and quality. Higher single nucleotide polymorphism (SNP)-based heritability estimates compared to broad-sense heritability estimates were observed for most traits highlighting the influence of genetic factors on observed variation. Using genome-wide association analysis of 188 clones, genotyped using 53,150 genome-wide SNPs, nine SNPs located on seven chromosomes were significantly associated with peel loss, gari yield, color parameters for gari and eba, bulk density, swelling index, and textural properties of eba. Future research will focus on validating and understanding the functions of identified genes and their influence on gari yield and quality traits.

Exploring genetic variability, heritability, and trait correlations in gari and eba quality from diverse cassava varieties in Nigeria

BACKGROUND

Gari (especially in Nigeria) is an important West African food product made from cassava. It is an affordable, precooked, dry, easy to prepare and store food product. Eba is a stiff dough produced by reconstituting gari in hot water. Gari and eba quality is an important driver of varietal acceptance by farmers, processors, and consumers.

RESULTS

This study characterized the genetic variability, heritability, and correlations among quality-related traits of fresh roots, gari, and eba. Thirty-three diverse genotypes, including landraces and released and advanced breeding genotypes, were used in this study. In total, 40 traits categorized into fresh root quality, colour, functional, and texture properties trait groups were assessed. We observed broad phenotypic variability among the genotypes used in this study. Dry matter content had a positive (P < 0.05) correlation with gari%, bulk density and a negative correlation with eba hardness and gumminess. Broad-sense heritability across all environments varied considerably among the different trait groups: 62% to 79% for fresh root quality, 0% to 96% for colour, 0% to 79% for functional and 0% to 57% for texture properties.

CONCLUSIONS

The stable broad-sense heritability found for gari%, gari and eba colour, bulk density, swelling index, and hardness measured using instrumental texture profile analysis coupled with sufficient variability in the population indicate good potential for genetic improvement of these traits through recurrent selection. Also, it is possible to genetically improve gari%, bulk density, and swelling power by simultaneously improving the dry matter content of fresh roots. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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.

Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz)

Flowering in cassava (Manihot esculenta Crantz) is crucial for the generation of botanical seed for breeding. However, genotypes preferred by most farmers are erect and poor at flowering or never flower. To elucidate the genetic basis of flowering, 293 diverse cassava accessions were evaluated for flowering-associated traits at two locations and seasons in Uganda. Genotyping using the Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on the 18 cassava chromosomes. Population structure analysis using principal components (PCs) and kinships showed three clusters; the first five PCs accounted for 49.2% of the observed genetic variation. Linkage disequilibrium (LD) estimation averaged 0.32 at a distance of ~2850 kb (kilo base pairs). Polymorphism information content (PIC) and minor allele frequency (MAF) were 0.25 and 0.23, respectively. A genome-wide association study (GWAS) analysis uncovered 53 significant marker-trait associations (MTAs) with flowering-associated traits involving 27 loci. Two loci, SNPs S5_29309724 and S15_11747301, were associated with all the traits. Using five of the 27 SNPs with a Phenotype_Variance_Explained (PVE) ≥ 5%, 44 candidate genes were identified in the peak SNP sites located within 50 kb upstream or downstream, with most associated with branching traits. Eight of the genes, orthologous to Arabidopsis and other plant species, had known functional annotations related to flowering, e.g., eukaryotic translation initiation factor and myb family transcription factor. This study identified genomic regions associated with flowering-associated traits in cassava, and the identified SNPs can be useful in marker-assisted selection to overcome hybridization challenges, like unsynchronized flowering, and candidate gene validation.

Transcriptome and metabolome profiling identify factors potentially involved in pro-vitamin A accumulation in cassava landraces

Cassava (Manihot esculenta Crantz) is a predominant food security crop in several developing countries. Its storage roots, rich in carbohydrate, are deficient in essential micronutrients, including provitamin A carotenoids. Increasing carotenoid content in cassava storage roots is important to reduce the incidence of vitamin A deficiency, a public health problem in sub-Saharan Africa. However, cassava improvement advances slowly, mainly due to limited information on the molecular factors influencing β-carotene accumulation in cassava. To address this problem, we performed comparative transcriptomic and untargeted metabolic analyses of roots and leaves of eleven African cassava landraces ranging from white to deep yellow colour, to uncover regulators of carotenoid biosynthesis and accumulation with conserved function in yellow cassava roots. Sequence analysis confirmed the presence of a mutation, known to influence β-carotene content, in PSY transcripts of deep yellow but not of pale yellow genotypes. We identified genes and metabolites with expression and accumulation levels significantly associated with β-carotene content. Particularly an increased activity of the abscisic acid catabolism pathway together with a reduced amount of L-carnitine, may be related to the carotenoid pathway flux, higher in yellow than in white storage roots. In fact, NCED_3.1 was specifically expressed at a lower level in all yellow genotypes suggesting that it could be a potential target for increasing carotenoid accumulation in cassava. These results expand the knowledge on metabolite compositions and molecular mechanisms influencing carotenoid biosynthesis and accumulation in cassava and provide novel information for biotechnological applications and genetic improvement of cassava with high nutritional values.

Biofortification to avoid malnutrition in humans in a changing climate: Enhancing micronutrient bioavailability in seed, tuber, and storage roots

Malnutrition results in enormous socio-economic costs to the individual, their community, and the nation's economy. The evidence suggests an overall negative impact of climate change on the agricultural productivity and nutritional quality of food crops. Producing more food with better nutritional quality, which is feasible, should be prioritized in crop improvement programs. Biofortification refers to developing micronutrient -dense cultivars through crossbreeding or genetic engineering. This review provides updates on nutrient acquisition, transport, and storage in plant organs; the cross-talk between macro- and micronutrients transport and signaling; nutrient profiling and spatial and temporal distribution; the putative and functionally characterized genes/single-nucleotide polymorphisms associated with Fe, Zn, and β-carotene; and global efforts to breed nutrient-dense crops and map adoption of such crops globally. This article also includes an overview on the bioavailability, bioaccessibility, and bioactivity of nutrients as well as the molecular basis of nutrient transport and absorption in human. Over 400 minerals (Fe, Zn) and provitamin A-rich cultivars have been released in the Global South. Approximately 4.6 million households currently cultivate Zn-rich rice and wheat, while ~3 million households in sub-Saharan Africa and Latin America benefit from Fe-rich beans, and 2.6 million people in sub-Saharan Africa and Brazil eat provitamin A-rich cassava. Furthermore, nutrient profiles can be improved through genetic engineering in an agronomically acceptable genetic background. The development of "Golden Rice" and provitamin A-rich dessert bananas and subsequent transfer of this trait into locally adapted cultivars are evident, with no significant change in nutritional profile, except for the trait incorporated. A greater understanding of nutrient transport and absorption may lead to the development of diet therapy for the betterment of human health.

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 markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm

INTRODUCTION

The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection.

METHODS

We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda.

RESULTS

Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes.

DISCUSSION

The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.

Phenotypic diversity and selection in biofortified cassava germplasm for yield and quality root traits

Increasing carotenoid content and improving other root quality traits has been the focus of cassava biofortification. This study aimed to (i) evaluate the genetic variability for total carotenoid content (TCC), as well as for root yield and root quality attributes; (ii) estimate potentially useful correlations for selection; and (iii) select parents for breeding and estimate the genetic gain. Data from 2011 to 2020 of 265 cassava genotypes with cream and yellow roots were analyzed for dry matter content (DMC), shoot yield, fresh root yield (FRY), dry root yield (DRY), harvest index, average number of roots per plant, starch content, root pulp color, cyanogenic compounds, and TCC. The best linear unbiased predictions showed great phenotypic variation for all traits. Six distinct groups were formed for productive characteristics of root quality, mainly TCC, DMC and FRY. Only TCC showed high broad-sense heritability ( h 2 = 0.72), while the other traits had low to medium magnitude (0.21 ≤ h 2 ≤ 0.60). TCC was strongly correlated with pulp color (r = 0.70), but null significance for DMC. The network analysis identified a clear separation between the agronomic and quality attributes of cassava roots. The selection of the 30 genotypes for recombination in the breeding program has the potential to raise TCC by 27.05% and reduce the cyanogenic compounds content by 23.03%, in addition to increasing FRY and DRY by 22.72% and 22.95%, respectively. This is the first consolidated study on the potential of germplasm for the development biofortified cassava cultivars in Brazil.

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.

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.

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.

Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava

More than 40 QTLs associated with 14 stress-related, quality and agro-morphological traits were identified. A catalogue of favourable SNP markers for MAS and a list of candidate genes are provided. Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture-Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.

Orphan Crops: A Best Fit for Dietary Enrichment and Diversification in Highly Deteriorated Marginal Environments

Orphan crops are indigenous and invariably grown by small and marginal farmers under subsistence farming systems. These crops, which are common and widely accepted by local farmers, are highly rich in nutritional profile, good for medicinal purposes, and well adapted to suboptimal growing conditions. However, these crops have suffered neglect and abandonment from the scientific community because of very low or no investments in research and genetic improvement. A plausible reason for this is that these crops are not traded internationally at a rate comparable to that of the major food crops such as wheat, rice, and maize. Furthermore, marginal environments have poor soils and are characterized by extreme weather conditions such as heat, erratic rainfall, water deficit, and soil and water salinity, among others. With more frequent extreme climatic events and continued land degradation, orphan crops are beginning to receive renewed attention as alternative crops for dietary diversification in marginal environments and, by extension, across the globe. Increased awareness of good health is also a major contributor to the revived attention accorded to orphan crops. Thus, the introduction, evaluation, and adaptation of outstanding varieties of orphan crops for dietary diversification will contribute not only to sustained food production but also to improved nutrition in marginal environments. In this review article, the concept of orphan crops vis-à-vis marginality and food and nutritional security is defined for a few orphan crops. We also examined recent advances in research involving orphan crops and the potential of these crops for dietary diversification within the context of harsh marginal environments. Recent advances in genomics coupled with molecular breeding will play a pivotal role in improving the genetic potential of orphan crops and help in developing sustainable food systems. We concluded by presenting a potential roadmap to future research engagement and a policy framework with recommendations aimed at facilitating and enhancing the adoption and sustainable production of orphan crops under agriculturally marginal conditions.

Genome-wide association study of cassava starch paste properties

An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h²) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r² <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.

Characterization of cassava ORANGE proteins and their capability to increase provitamin A carotenoids accumulation

Cassava (Manihot esculenta Crantz) biofortification with provitamin A carotenoids is an ongoing process that aims to alleviate vitamin A deficiency. The moderate content of provitamin A carotenoids achieved so far limits the contribution to providing adequate dietary vitamin A levels. Strategies to increase carotenoid content focused on genes from the carotenoids biosynthesis pathway. In recent years, special emphasis was given to ORANGE protein (OR), which promotes the accumulation of carotenoids and their stability in several plants. The aim of this work was to identify, characterize and investigate the role of OR in the biosynthesis and stabilization of carotenoids in cassava and its relationship with phytoene synthase (PSY), the rate-limiting enzyme of the carotenoids biosynthesis pathway. Gene and protein characterization of OR, expression levels, protein amounts and carotenoids levels were evaluated in roots of one white (60444) and two yellow cassava cultivars (GM5309-57 and GM3736-37). Four OR variants were found in yellow cassava roots. Although comparable expression was found for three variants, significantly higher OR protein amounts were observed in the yellow varieties. In contrast, cassava PSY1 expression was significantly higher in the yellow cultivars, but PSY protein amount did not vary. Furthermore, we evaluated whether expression of one of the variants, MeOR_X1, affected carotenoid accumulation in cassava Friable Embryogenic Callus (FEC). Overexpression of maize PSY1 alone resulted in carotenoids accumulation and induced crystal formation. Co-expression with MeOR_X1 led to greatly increase of carotenoids although PSY1 expression was high in the co-expressed FEC. Our data suggest that posttranslational mechanisms controlling OR and PSY protein stability contribute to higher carotenoid levels in yellow cassava. Moreover, we showed that cassava FEC can be used to study the efficiency of single and combinatorial gene expression in increasing the carotenoid content prior to its application for the generation of biofortified cassava with enhanced carotenoids levels.

Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm

Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing data and a validated multigenerational pedigree from the International Institute of Tropical Agriculture cassava breeding germplasm consisting of 7020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium. We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.

Genome-wide association mapping and genomic prediction of yield-related traits and starch pasting properties in cassava

KEY MESSAGE

GWAS identified eight yield-related, peak starch type of waxy and wild-type starch and 21 starch pasting property-related traits (QTLs). Prediction ability of eight GS models resulted in low to high predictability, depending on trait, heritability, and genetic architecture. Cassava is both a food and an industrial crop in Africa, South America, and Asia, but knowledge of the genes that control yield and starch pasting properties remains limited. We carried out a genome-wide association study to clarify the molecular mechanisms underlying these traits and to explore marker-based breeding approaches. We estimated the predictive ability of genomic selection (GS) using parametric, semi-parametric, and nonparametric GS models with a panel of 276 cassava genotypes from Thai Tapioca Development Institute, International Center for Tropical Agriculture, International Institute of Tropical Agriculture, and other breeding programs. The cassava panel was genotyped via genotyping-by-sequencing, and 89,934 single-nucleotide polymorphism (SNP) markers were identified. A total of 31 SNPs associated with yield, starch type, and starch properties traits were detected by the fixed and random model circulating probability unification (FarmCPU), Bayesian-information and linkage-disequilibrium iteratively nested keyway and compressed mixed linear model, respectively. GS models were developed, and forward predictabilities using all the prediction methods resulted in values of - 0.001-0.71 for the four yield-related traits and 0.33-0.82 for the seven starch pasting property traits. This study provides additional insight into the genetic architecture of these important traits for the development of markers that could be used in cassava breeding programs.

Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

Can Cross-Country Genomic Predictions Be a Reasonable Strategy to Support Germplasm Exchange? - A Case Study With Hydrogen Cyanide in Cassava

Genomic prediction (GP) offers great opportunities for accelerated genetic gains by optimizing the breeding pipeline. One of the key factors to be considered is how the training populations (TP) are composed in terms of genetic improvement, kinship/origin, and their impacts on GP. Hydrogen cyanide content (HCN) is a determinant trait to guide cassava's products usage and processing. This work aimed to achieve the following objectives: (i) evaluate the feasibility of using cross-country (CC) GP between germplasm's of Embrapa Mandioca e Fruticultura (Embrapa, Brazil) and The International Institute of Tropical Agriculture (IITA, Nigeria) for HCN; (ii) provide an assessment of population structure for the joint dataset; (iii) estimate the genetic parameters based on single nucleotide polymorphisms (SNPs) and a haplotype-approach. Datasets of HCN from Embrapa and IITA breeding programs were analyzed, separately and jointly, with 1,230, 590, and 1,820 clones, respectively. After quality control, ∼14K SNPs were used for GP. The genomic estimated breeding values (GEBVs) were predicted based on SNP effects from analyses with TP composed of the following: (i) Embrapa genotypic and phenotypic data, (ii) IITA genotypic and phenotypic data, and (iii) the joint datasets. Comparisons on GEBVs' estimation were made considering the hypothetical situation of not having the phenotypic characterization for a set of clones for a certain research institute/country and might need to use the markers' effects that were trained with data from other research institutes/country's germplasm to estimate their clones' GEBV. Fixation index (FST) among the genetic groups identified within the joint dataset ranged from 0.002 to 0.091. The joint dataset provided an improved accuracy (0.8-0.85) compared to the prediction accuracy of either germplasm's sources individually (0.51-0.67). CC GP proved to have potential use under the present study's scenario, the correlation between GEBVs predicted with TP from Embrapa and IITA was 0.55 for Embrapa's germplasm, whereas for IITA's it was 0.1. This seems to be among the first attempts to evaluate the CC GP in plants. As such, a lot of useful new information was provided on the subject, which can guide new research on this very important and emerging field.

Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Background

Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome.

Results

We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB.

Conclusions

This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-021-02524-7.

Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).

Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security

Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz)

Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower's genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.

Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

KEY MESSAGE

Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.

Integrating multi-omics data for crop improvement

Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.

Technological Innovations for Improving Cassava Production in Sub-Saharan Africa

Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.

Orphan Crops and their Wild Relatives in the Genomic Era

More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.

The Cassava Source-Sink project: opportunities and challenges for crop improvement by metabolic engineering

Cassava (Manihot esculenta Crantz) is one of the important staple foods in Sub-Saharan Africa. It produces starchy storage roots that provide food and income for several hundred million people, mainly in tropical agriculture zones. Increasing cassava storage root and starch yield is one of the major breeding targets with respect to securing the future food supply for the growing population of Sub-Saharan Africa. The Cassava Source-Sink (CASS) project aims to increase cassava storage root and starch yield by strategically integrating approaches from different disciplines. We present our perspective and progress on cassava as an applied research organism and provide insight into the CASS strategy, which can serve as a blueprint for the improvement of other root and tuber crops. Extensive profiling of different field-grown cassava genotypes generates information for leaf, phloem, and root metabolic and physiological processes that are relevant for biotechnological improvements. A multi-national pipeline for genetic engineering of cassava plants covers all steps from gene discovery, cloning, transformation, molecular and biochemical characterization, confined field trials, and phenotyping of the seasonal dynamics of shoot traits under field conditions. Together, the CASS project generates comprehensive data to facilitate conventional breeding strategies for high-yielding cassava genotypes. It also builds the foundation for genome-scale metabolic modelling aiming to predict targets and bottlenecks in metabolic pathways. This information is used to engineer cassava genotypes with improved source-sink relations and increased yield potential.

Genome-Wide Association Analysis for Tuber Dry Matter and Oxidative Browning in Water Yam (Dioscorea alata L.)

Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker-trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam.

Improving root characterisation for genomic prediction in cassava

Cassava is cultivated due to its drought tolerance and high carbohydrate-containing storage roots. The lack of uniformity and irregular shape of storage roots poses constraints on harvesting and post-harvest processing. Here, we phenotyped the Genetic gain and offspring (C1) populations from the International Institute of Tropical Agriculture (IITA) breeding program using image analysis of storage root photographs taken in the field. In the genome-wide association analysis (GWAS), we detected for most shape and size-related traits, QTL on chromosomes 1 and 12. In a previous study, we found the QTL on chromosome 12 to be associated with cassava mosaic disease (CMD) resistance. Because the root uniformity is important for breeding, we calculated the standard deviation (SD) of individual root measurements per clone. With SD measurements we identified new significant QTL for Perimeter, Feret and Aspect Ratio on chromosomes 6, 9 and 16. Predictive accuracies of root size and shape image-extracted traits were mostly higher than yield trait prediction accuracies. This study aimed to evaluate the feasibility of the image phenotyping protocol and assess GWAS and genomic prediction for size and shape image-extracted traits. The methodology described and the results are promising and open up the opportunity to apply high-throughput methods in cassava.

Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]

KEY MESSAGE

β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.

Toward the 'golden' era: The status in uncovering the regulatory control of carotenoid accumulation in plants

Carotenoids are essential pigments to plants and important natural products to humans. Carotenoids as both primary and specialized metabolites fulfill multifaceted functions in plants. As such, carotenoid accumulation (a net process of biosynthesis, degradation and sequestration) is subjected to complicated regulation throughout plant life cycle in response to developmental and environmental signals. Investigation of transcriptional regulation of carotenoid metabolic genes remains the focus in understanding the regulatory control of carotenoid accumulation. While discovery of bona fide carotenoid metabolic regulators is still challenging, the recent progress of identification of various transcription factors and regulators helps us to construct hierarchical regulatory network of carotenoid accumulation. The elucidation of carotenoid regulatory mechanisms at protein level and in chromoplast provides some insights into post-translational regulation of carotenogenic enzymes and carotenoid sequestration in plastid sink. This review briefly describes the pathways and main flux-controlling steps for carotenoid accumulation in plants. It highlights our recent understanding of the regulatory mechanisms underlying carotenoid accumulation at both transcriptional and post-translational levels. It also discusses the opportunities to expand toolbox for further shedding light upon the intrinsic regulation of carotenoid accumulation in plants.

Genetic Correlation, Genome-Wide Association and Genomic Prediction of Portable NIRS Predicted Carotenoids in Cassava Roots

Random forests (RF) was used to correlate spectral responses to known wet chemistry carotenoid concentrations including total carotenoid content (TCC), all-trans β-carotene (ATBC), violaxanthin (VIO), lutein (LUT), 15-cis beta-carotene (15CBC), 13-cis beta-carotene (13CBC), alpha-carotene (AC), 9-cis beta-carotene (9CBC), and phytoene (PHY) from laboratory analysis of 173 cassava root samples in Columbia. The cross-validated correlations between the actual and estimated carotenoid values using RF ranged from 0.62 in PHY to 0.97 in ATBC. The developed models were used to evaluate the carotenoids of 594 cassava clones with spectral information collected across three locations in a national breeding program (NRCRI, Umudike), Nigeria. Both populations contained cassava clones characterized as white and yellow. The NRCRI evaluated phenotypes were used to assess the genetic correlations, conduct genome-wide association studies (GWAS), and genomic predictions. Estimates of genetic correlation showed various levels of the relationship among the carotenoids. The associations between TCC and the individual carotenoids were all significant (P < 0.001) with high positive values (r > 0.75, except in LUT and PHY where r < 0.3). The GWAS revealed significant genomic regions on chromosomes 1, 2, 4, 13, 14, and 15 associated with variation in at least one of the carotenoids. One of the identified candidate genes, phytoene synthase (PSY) has been widely reported for variation in TCC in cassava. On average, genomic prediction accuracies from the single-trait genomic best linear unbiased prediction (GBLUP) and RF as well as from a multiple-trait GBLUP model ranged from ∼0.2 in LUT and PHY to 0.52 in TCC. The multiple-trait GBLUP model gave slightly higher accuracies than the single trait GBLUP and RF models. This study is one of the initial attempts in understanding the genetic basis of individual carotenoids and demonstrates the usefulness of NIRS in cassava improvement.

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection

Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.

Variability of carotenoids in a Musa germplasm collection and implications for provitamin A biofortification

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Banana genotypes, a good source of provitamin A was screened for carotenoid content.

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Carotenoid in fruit pulp were quantified using high performance liquid chromatography.

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Total carotenoid content in the fruit varied from 1.45 to 36.21 µg/g fresh weight.

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78% of carotenoids isolated were provitamin A carotenoids β-carotene and α-carotene.

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Data generated are useful for provitamin A biofortification strategies.

Bananas are important staples in tropical and sub-tropical regions and their potential as a source of provitamin A has recently attracted attention for biofortification. A collection of 189 banana genotypes (AAB-plantains, M. acuminata cultivars and bred hybrids) was screened to determine variability in fruit pulp provitamin A carotenoid (pVAC) content using high performance liquid chromatography. Total carotenoid content in tested genotypes varied from 1.45 µg/g for hybrid 25447-S7 R2P8 to 36.21 µg/g for M. acuminata cultivar ITC.0601 Hung Tu with a mean of 8.00 µg/g fresh weight. Predominant carotenoids identified were α-carotene (38.67%), trans-β-carotene (22.08%), lutein (22.08%), 13-cis-β-carotene (14.45%) and 9-cis-β-carotene (2.92%), indicating that about 78% of the carotenoids in bananas are pVAC. High pVAC genotypes were identified for integration into biofortification strategies to combat vitamin A deficiency in developing countries.

Using Genomic Sequence Information to Increase Conservation and Sustainable Use of Crop Diversity and Benefit-Sharing

This article describes how CGIAR centers and partners are using genomic sequence information to promote the conservation and sustainable use of crop genetic diversity, and to generate and share benefits derived from those uses. The article highlights combined institutional, and benefit-sharing-related challenges that need to be addressed to support expanded use of digital sequence information in agricultural research and development.

Validation of QTLs for plant ideotype, earliness and growth habit traits in pigeonpea (Cajanus cajan Millsp.)

Pigeonpea productivity is greatly constrained by poor plant ideotype of existing Indian cultivars. Enhancing pigeonpea yield demands a renewed focus on restructuring the ideal plant type by using more efficient approaches like genomic tools. Therefore, the present study aims to identify and validate a set of QTLs/gene(s) presumably associated with various plant ideotype traits in pigeonpea. A total of 133 pigeonpea germplasms were evaluated along with four checks in the augmented design for various ideotype traits i.e. initiation of flowering (IF), days to 50% flowering (DFF), days to maturity (DM), plant height (PH), primary branches (PB), seeds per pod (SP) and pod length (PL). We observed significant genetic diversity in the germplasm lines for these traits. The genetic control of IF, DFF, DM and PH renders these traits suitable for detection of marker trait associations. By using residual maximum likelihood algorithm, we obtained appropriate variance-covariance structures for modeling heterogeneity, correlation of genetic effects and non-genetic residual effects. The estimates of genetic correlations indicated a strong association among earliness traits. The best linear unbiased prediction values were calculated for individual traits, and association analysis was performed in a panel of 95 diverse genotypes with 19 genic SSRs. Out of five QTL-flanking SSRs used here for validation, only ASSR295 could show significant association with FDR and Bonferroni corrections, and accounted for 15.4% IF, 14.2% DFF and 16.2% DM of phenotypic variance (PV). Remaining SSR markers (ASSR1486, ASSR206 and ASSR408) could not qualify false discovery rate (FDR) and Bonferroni criteria, hence declared as false positives. Additionally, we identified two highly significant SSR markers, ASSR8 and ASSR390 on LG 1 and LG 2, respectively. The SSR marker ASSR8 explained up to 22 and 11% PV for earliness traits and PB respectively, whereas ASSR390 controlled up to 17% PV for earliness traits. The validation and identification of new QTLs in pigeonpea across diverse genetic backgrounds brightens the prospects for marker-assisted selection to improve yield gains in pigeonpea.

Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda. Our GWAS study found two regions associated to CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. Predictive accuracy values varied between CBSD foliar severity traits at 3 months after planting (MAP) (0.27-0.32), 6 MAP (0.40-0.42) and root severity (0.31-0.42). For all traits, Random Forest and reproducing kernel Hilbert spaces regression showed the highest predictive accuracies. Our results provide an insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding.