Cassava Germplasm Collection Research Articles

Collection, genotyping and virus elimination of cassava landraces from Tanzania and documentation of farmer knowledge.

Cassava (Manihot esculenta Crantz.) has been a vital staple and food security crop in Tanzania for several centuries, and it is likely that its resilience will play a key role in mitigating livelihood insecurities arising from climate change. The sector is dominated by smallholder farmers growing traditional landrace varieties. A recent surge in virus diseases and awareness in the commercial potential of cassava has prompted a drive to disseminate improved varieties in the country. These factors however also threaten the existence of landraces and associated farmer knowledge. It is important that the landraces are conserved and utilized as the adaptive gene complexes they harbor can drive breeding for improved varieties that meet agro-ecological adaptation as well as farmer and consumer needs, thereby improving adoption rates. Here we report on cassava germplasm collection missions and documentation of farmer knowledge in seven zones of Tanzania. A total of 277 unique landraces are identified through high-density genotyping. The large number of landraces is attributable to a mixed clonal/sexual reproductive system in which the soil seed bank and incorporation of seedlings plays an important role. A striking divergence in genetic relationships between the coastal regions and western regions is evident and explained by (i) independent introductions of cassava into the country, (ii) adaptation to prevailing agro-ecological conditions and (iii) farmer selections according to the intended use or market demands. The main uses of cassava with different product profiles are evident, including fresh consumption, flour production, dual purpose incorporating both these uses and longer-term food security. Each of these products have different trait requirements. Individual landraces were not widely distributed across the country with limited farmer-to-farmer diffusion with implications for seed systems.

Postharvest physiological deterioration in cassava: potential problems, possible inhibition, and resistant level identification

Cassava roots can only be utilized quickly because the roots suffer physiological damage in only 1–3 days after harvest because of postharvest physiological deterioration (PPD). Once the cassava roots are physiologically damaged, they cannot either be consumed or marketed. Indonesia is the second-largest cassava producer in Southeast Asia that is most used for food and feeds. Unless there is a solution, the PPD problem may become the main obstacle in cassava production. Therefore, finding solutions to the PPD problem in cassava is necessary, may be approached either by treatment to inhibit PPD occurrences, identification of tolerance accessions among cassava germplasm, and development of PPD tolerance cassava through breeding programs. In our research, the identification method was done by applying various staining methods to detect color changes associated with PPD symptoms during the cassava storage period and then compared to the conventional observation of PPD symptoms. Subsequently, the effective staining approaches are used to evaluate various genotypes’ responses in the cassava germplasm collections. Finally, the breeding approaches to develop PPD tolerance cassava varieties are outlined. Hopefully, with these research results, the solution for PPD problems associated with cassava production in Indonesia will be available.

Cyanogenic, carotenoids and protein composition in leaves and roots across seven diverse population found in the world cassava germplasm collection at CIAT, Colombia

SummaryThe objective of this study was to characterise the nutritional potential of leaves and identify a diversity centre with low cyanide and high nutrient content among 178 Latin American cassava genotypes. This field‐based collection represents the seven diversity centres, held at The International Center for Tropical Agriculture (CIAT Palmira, Colombia) by the Cassava Program. The cyanide, all‐trans‐β‐carotene and lutein concentrations in cassava leaves ranged from 346 to 7484 ppm dry basis (db), from 174–547 μg g−1db and 15–181 μg g−1db, respectively. Cassava leaves also showed significant levels of essential amino acids leucine, lysine, phenylalanine, valine and threonine, and average total protein content of 26.24 g 100 g−1db. Among seven diversity centres, South American rainforest group showed low cyanide and high carotene content in leaves. In addition, VEN77 and PAN51 genotypes stood out for having low cyanide in leaves and roots and high carotene in leaves. This genetic diversity can be used to select high potential progenitors for breeding purposes.

Exploring the chemotypes underlying important agronomic and consumer traits in cassava (Manihot esculenta crantz)

A broad diversity of phenotypes are available within the cassava germplasm collections. The phenotypes include improved nutritional, starch or culinary root quality as well as abiotic and biotic resistance properties. Some of these traits can be found naturally occurring in cassava landraces, whereas others are the result of targeted breeding efforts. For future breeding programmes it is important to know the underlying mechanisms of these desirable traits. Metabolomics can assist in the elucidation of these mechanisms by measuring the end products of the cellular processes conferring the traits of interest. The present study focused on the comparison of two or more variants of the same trait such as high and low culinary quality or resistance and susceptibility to thrips. Overall, eight different traits were assessed.Results showed that amino acids and umami compounds were associated with superior culinary attributes and the phenylpropanoid superpathway plays an important role in pest resistance. Furthermore, the data highlighted a low chemodiversity in African cassavas and that the source-sink relation was still active at the harvest stage.

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis

Cassava is one of the most important food security crops in tropical countries, and a competitive resource for the starch, food, feed and ethanol industries. However, genomics research in this crop is much less developed compared to other economically important crops such as rice or maize. The International Center for Tropical Agriculture (CIAT) maintains the largest cassava germplasm collection in the world. Unfortunately, the genetic potential of this diversity for breeding programs remains underexploited due to the difficulties in phenotypic screening and lack of deep genomic information about the different accessions. A chromosome-level assembly of the cassava reference genome was released this year and only a handful of studies have been made, mainly to find quantitative trait loci (QTL) on breeding populations with limited variability. This work presents the results of pooled targeted resequencing of more than 1500 cassava accessions from the CIAT germplasm collection to obtain a dataset of more than 2000 variants within genes related to starch functional properties and herbicide tolerance. Results of twelve bioinformatic pipelines for variant detection in pooled samples were compared to ensure the quality of the variant calling process. Predictions of functional impact were performed using two separate methods to prioritize interesting variation for genotyping and cultivar selection. Targeted resequencing, either by pooled samples or by similar approaches such as Ecotilling or capture, emerges as a cost effective alternative to whole genome sequencing to identify interesting alleles of genes related to relevant traits within large germplasm collections.

Genetic diversity of farmer-preferred cassava landraces in Tanzania based on morphological descriptors and single nucleotide polymorphisms

Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.

Molecular differentiation and diversity of cassava (Manihot esculenta) taken from 162 locations across Puerto Rico and assessed with microsatellite markers

Background and aims Knowledge of germplasm diversity and its genetic characterization is an invaluable asset in crop improvement as well as conservation strategies. Although an important crop and present in the Caribbean since the 15th century, the origins of today’s cassava in the Caribbean are poorly understood. Genetic variability and long growing cycles provide a unique set of challenges when researching cassava, and it is in part due to these challenges that little knowledge regarding the genetic diversity of cassava in Puerto Rico exists. Methodology In order to evaluate the genetic diversity of cassava in Puerto Rico, 162 samples with unknown genetic background were collected from different townships of the island and were analysed by 33 single sequence repeat markers. For comparative purposes, 23 accessions of the Puerto Rican cassava germplasm collection were also evaluated. Principal results Our results show that the genetic diversity (HE) of unknown cassava samples (0.7174) is slightly higher than in the current Puerto Rican cassava collection (0.6996). The observed proportion of heterozygotes (HO) was higher in the Puerto Rican cassava collection compared with the unknown samples. An unweighted pair-group method with arithmetic averaging analysis showed that most of the samples clustered with the accessions of the Puerto Rican cassava collection. However, there was one cluster of only unknown cassava samples and no accessions of the Puerto Rican collection. Members of this cluster most likely share alleles which are not represented by the accessions in the collection. Conclusion This broad study shows the presence of high levels of genetic diversity in the unknown samples. Traditional practices, especially intercropping and incorporation of volunteer seedlings, have led to the contribution of recombinant genotypes to cultivated stocks. This study revealed a high potential for local Puerto Rican cassava to be a useful part of future genetic improvement programmes.

A Multiplex Microsatellite Marker Kit for Diversity Assessment of Large Cassava (Manihot esculenta Crantz) Germplasm Collections

Current methods for molecular fingerprinting of cassava (Manihot esculenta Crantz) have limited throughput or are costly, thus preventing the characterization of large germplasm collections such as those held by the International Agricultural Research Centers or National Research Institutions, which comprise hundreds to thousands of accessions. Here, we report the development of a fluorescence-based multiplex simple sequence repeat (SSR) marker kit that enables accurate and cost-effective cassava fingerprinting. The kit comprises 16 SSR markers assembled into five multiplex panels and was tested on 21 cassava cultivars alongside one accession of Manihot epruinosa, a wild relative. A total of 68 alleles were detected with, on average, 4.25 alleles per locus and a polymorphism information content of 0.53. The marker kit reported here is comparable to previously published amplified fragment length polymorphism and SSR marker systems in terms of discriminating power and informativeness while offering significant advantages in speed and cost of marker analysis. Previous molecular genetic diversity studies have suggested that cassava germplasm collections contain duplicate entries based on the occurrence of identical genetic profiles. Using the newly developed microsatellite kit, three out of six putative duplicate accessions could be readily differentiated, showing that these are distinct genotypes. The relevance of these findings with respect to the characterization and management of large cassava germplasm collections is discussed.

Screening of Starch Quality Traits in Cassava (Manihot esculenta Crantz)

AbstractCassava (Manihot esculenta Crantz) is one of the most important sources of starch in the tropics. There is limited and contradictory information regarding cassava starch characteristics. The International Center for Tropical Agriculture (CIAT) holds in trust FAO's cassava germplasm collection. Starches from 3272 landraces (including 12 wild relatives) and 772 improved clones were extracted and analyzed over a period of several years. In most cases only one starch sample per genotype was analyzed. Average cyanogenic potential was 327 ppm but considerably higher in the landraces (340 ppm) than in improved clones (267 ppm). Average total and reducing sugars were slightly higher in improved clones (4.06 and 1.56%, respectively) than in landraces (3.68 and 1.25%, respectively). Amylose content was similar in both types of germplasm with an average of 20.7%. Average pasting temperature was 65.3°C. Maximum viscosity was 777.5 mPa s, breakdown was 298.1 mPa s, consistency was 155.8 mPa s and setback was ‐144.5 mPa s. The large sample of starches analyzed provides very robust information regarding the actual characteristics of cassava starch.

Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz)

Several molecular marker systems have been developed for assessing genetic diversity in crop germplasm collections. A trade-off often exists between the number of loci that can feasibly be sampled by a marker system and the amount of information provided by each locus. We compared the usefulness of two marker systems for revealing genetic diversity and population structure in cassava (Manihot esculenta Crantz): simple sequence repeats (SSRs) and diversity array technology (DArT) markers. DArTs survey many more loci per reaction than do SSRs; however, as bi-allelic, dominant markers, DArTs provide less polymorphism information per locus. Genetic differentiation was assessed in a randomly selected set of 436 cassava accessions, consisting of 155 African and 281 Latin American accessions. A genome-wide set of 36 SSR markers and a DArT array of approximately 1000 polymorphic clones were used to assess genetic diversity and differentiation. Cluster analyses were performed using principal coordinate analysis (PCoA). Results were compared with a priori expectations of genetic differentiation based on previous genetic analyses. Analyses of the two datasets generated broadly similar clustering patterns. However, SSRs revealed greater differentiation than DArTs, and more effectively recovered patterns of genetic differentiation observed in previous analyses (differentiation between Latin American and African accessions, and some geographical differentiation within each of these groups). These results suggest that SSR markers, while low throughput in comparison with DArTs, are relatively better at detecting genetic differentiation in cassava germplasm collections. Nonetheless, DArTs will likely prove useful in ‘orphan crop’ species, where alternative molecular markers have not been developed.

Expression and structure of an elongation factor-1α gene (MeEF1) from cassava (Manihot esculenta Crantz)

In order to isolate an elongation factor-1α (EF-1α)gene from cassava, a lambda EMBL3 genomic library, made from a single cassava genotype (MBRA 534, from the CIAT cassava germplasm collection), was screened with a full length EF-1α cDNA clone(blt63) from barley. Six positive clones were isolated from an amplified library and 4866 bp from one clone (MeEF1) were subcloned into pGEM3zf(-) and pGEM5zf(-). The sequence has 2709 bp5' of the translation start site, 1347 bp of coding sequence split into two exons by an intron (374 bp) and 435 bp 3' of the stop codon. A 657 bpintron was also found 5' of the translation start site. The coding sequence is very similar, with 86% DNA sequence identity and 95% deduced amino acid sequence identity, to an EF-1α gene from Arabidopsis thaliana. The promoter region of MeEF1 contains 3putative control elements that are located upstream of the transcription start site. These control elements include a TEF1 box, a TELO box and two TATA boxes. The gene is expressed in early stages of development and in young tissue. Transient expression using particle bombardment shows that the promoter drives uidA gene expression in leaves of cassava and Arabidopsis. An interesting feature of the MeEF1 gene is that the presence of the 5'UTR intron affects the level of expression.

Diversity within American cassava germ plasm based on RAPD markers

This work focuses on the genetic diversity of American cassava through RAPD molecular markers. The 126 genotypes studied were distributed on four geographical levels ranging from local to continental. Samples included ethnocultivars from the Santa Isabel community in the Brazilian Amazon, local cultivars collected in the State of São Paulo, native accessions from very diverse Brazilian regions, and representative accessions from the Centro Internacional de Agricultura Tropical (CIAT) core collection. Eighty-eight polymorphic bands were analyzed. Results revealed the weak genetic structure of the cassava analyzed. The pattern formed by the first two axes of the principal coordinates analysis (PCoA) revealed an overlapping of the São Paulo State genotype, the Brazilian group and the core collection accessions. The Santa Isabel ethnocultures formed a separate group. The weak genetic structure of cassava can be explained by the common practice of exchanging botanical material among small producers as well as by recombinations among genotypes. When the genotypes were analyzed using climatic data, the sample sites were found to be structured according to temperature and precipitation. RAPD markers proved very useful in the genetic diversity study, resulting in important implications for cassava germ plasm collections and genetic breeding.

Evaluation of a cassava germplasm collection for reaction to three major diseases and the effect on yield.

Thirty-five cassava (Manihot esculenta Crantz) genotypes from the International Institute of Tropical Agriculture (IITA), germplasm collection were planted in May 1992 under natural disease infection conditions, at the IITA field plots at Ibadan, Nigeria. The genotypes were evaluated at monthly intervals for six months, for incidence and severity of cassava anthracnose disease (CAD), cassava bacterial blight (CBB) and African cassava mosaic virus (ACMV). The effect of the pathogens on yield was also evaluated twelve months after planting (MAP). CAD, CBB and ACMV incidence and severity were significantly different (P<0.05) among the cassava genotypes at 3 and 6 months after planting. ACMV incidence and severity reached the maximum levels at 3 MAP while CAD and CBB had a low incidence and severity at that period but exhibited a high disease symptom expression at 6 MAP. Yield parameters (plant stand, tuber number, tuber weight and tuber dry matter) differed significantly (P<0.05) between the cassava genotypes. ACMV and CBB severity was negatively correlated with tuber number (r = −0.54 and r = −0.62 respectively). CAD severity was negatively correlated with tuber number (r = −0.46) and tuber weight (r = −0.63). Percentage dry matter was significantly correlated with ACMV severity (r = 0.71), CBB severity (r = 0.63) and CAD severity (r = 0.42). There was also a significant correlation between CBB and ACMD severity (r=0.46) and CBB and CAD severity (r=0.62). Tuber number and yield were significantly correlated (r=0.60), while% dry matter content and root rot showed a significant negative correlation (−0.42).

Genetic potential and stability of carotene content in cassava roots

People in vast areas of the tropics suffer from vitamin A deficiency, resulting in progressive eye damage and eventually leading to blindness. Improving the content of vitamin A precursors in staple crops could alleviate or solve such a problem. The objective of this work was to study the range of variability for carotene content in a sub-set of the global cassava germplasm collection, and to determine the inheritance of carotenes, as well as their stability in response to different processing methodologies. Genotypes with more than 2 mg carotenes/100 g of fresh roots have been selected as parental material for population development. Although root colour is highly correlated with carotene content, a quantitative evaluation of genotypes selected by colour is required in order to increase the efficiency of selection. Relatively few major genes are involved in the determination of carotene accumulation in cassava roots. Stability of carotenes in response to different processing methods is genotypically dependant, representing a trait to be evaluated after selecting for high carotene concentration in fresh roots. The results from this work have provided the basis for defining future strategies for the improvement of the nutritional quality of cassava.