Genetic Improvement of Cassava

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 9411

Special Issue Editors


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Guest Editor
Empresa Brasileira de Pesquisa Agropecuária - Embrapa, Brasilia, Brazil
Interests: cassava; breeding; crop system; geonomics

E-Mail Website
Guest Editor
Consultative Group on International Agricultural Research, Malaga, Spain
Interests: cassava; plant genetics; starch; plant breeding

Special Issue Information

Dear Colleagues,

Cassava (Manihot esculenta Crantz) holds a significant position as one of the most vital energy sources in the diets of numerous tropical and subtropical countries. It plays an essential role in ensuring food security for millions of people, particularly in Sub-Saharan Africa. Recently, it has also emerged as the second most important starch source worldwide, solidifying its significance in various agro-industrial processes and as a crucial source of income for countless farmers.

Previously regarded as an "orphan crop", cassava has witnessed remarkable progress in genetic improvement, comparable to advancements made in other major crops. The application of cutting-edge technologies, such as genome sequencing, deep genome diagnostics, genetic transformation, genomic selection programs, and gene editing, has facilitated scientific breakthroughs. These advancements have provided valuable insights and technologies to address the challenges related to root quality and disease resistance. However, there is still considerable work ahead to fully integrate cassava into the transformation of the global food system.

In this Special Issue topic (Genetic Improvement of Cassava) of the journal Plants, we cordially invite the scientific community to share their research findings focused on cassava improvement. We encourage contributions that explore diverse research approaches, aiming to resolve the current bottlenecks and maximize the effectiveness of cassava genetic improvement.

Dr. Eder Jorge De Oliveira
Dr. Hernan Ceballos
Guest Editors

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Keywords

  • Manihot esculenta Crantz
  • breeding
  • genomics
  • genetics
  • phenotyping
  • rapid cycling

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Published Papers (6 papers)

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Research

23 pages, 3131 KiB  
Article
High-Throughput Phenotyping for Agronomic Traits in Cassava Using Aerial Imaging
by José Henrique Bernardino Nascimento, Diego Fernando Marmolejo Cortes, Luciano Rogerio Braatz de Andrade, Rodrigo Bezerra de Araújo Gallis, Ricardo Luis Barbosa and Eder Jorge de Oliveira
Plants 2025, 14(1), 32; https://doi.org/10.3390/plants14010032 - 25 Dec 2024
Viewed by 629
Abstract
Large-scale phenotyping using unmanned aerial vehicles (UAVs) has been considered an important tool for plant selection. This study aimed to estimate the correlations between agronomic data and vegetation indices (VIs) obtained at different flight heights and to select prediction models to evaluate the [...] Read more.
Large-scale phenotyping using unmanned aerial vehicles (UAVs) has been considered an important tool for plant selection. This study aimed to estimate the correlations between agronomic data and vegetation indices (VIs) obtained at different flight heights and to select prediction models to evaluate the potential use of aerial imaging in cassava breeding programs. Various VIs were obtained and analyzed using mixed models to derive the best linear unbiased predictors, heritability parameters, and correlations with various agronomic traits. The VIs were also used to build prediction models for agronomic traits. Aerial imaging showed high potential for estimating plant height, regardless of flight height (r = 0.99), although lower-altitude flights (20 m) resulted in less biased estimates of this trait. Multispectral sensors showed higher correlations compared to RGB, especially for vigor, shoot yield, and fresh root yield (−0.40 ≤ r ≤ 0.50). The heritability of VIs at different flight heights ranged from moderate to high (0.51 ≤ HCullis2 ≤ 0.94), regardless of the sensor used. The best prediction models were observed for the traits of plant vigor and dry matter content, using the Generalized Linear Model with Stepwise Feature Selection (GLMSS) and the K-Nearest Neighbor (KNN) model. The predictive ability for dry matter content increased with flight height for the GLMSS model (R2 = 0.26 at 20 m and R2 = 0.44 at 60 m), while plant vigor ranged from R2 = 0.50 at 20 m to R2 = 0.47 at 40 m in the KNN model. Our results indicate the practical potential of implementing high-throughput phenotyping via aerial imaging for rapid and efficient selection in breeding programs. Full article
(This article belongs to the Special Issue Genetic Improvement of Cassava)
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21 pages, 3716 KiB  
Article
Validation of SNP Markers for Diversity Analysis, Quality Control, and Trait Selection in a Biofortified Cassava Population
by Edwige Gaby Nkouaya Mbanjo, Adebukola Ogungbesan, Afolabi Agbona, Patrick Akpotuzor, Seyi Toyinbo, Peter Iluebbey, Ismail Yusuf Rabbi, Prasad Peteti, Sharon A. Wages, Joanna Norton, Xiaofei Zhang, Adriana Bohórquez-Chaux, Hapson Mushoriwa, Chiedozie Egesi, Peter Kulakow and Elizabeth Parkes
Plants 2024, 13(16), 2328; https://doi.org/10.3390/plants13162328 - 21 Aug 2024
Cited by 2 | Viewed by 1558
Abstract
A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials [...] Read more.
A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future. Full article
(This article belongs to the Special Issue Genetic Improvement of Cassava)
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17 pages, 1662 KiB  
Article
Genetic Variation and Heritability for Hydrogen Cyanide in Fresh Cassava Roots: Implications for Low-Cyanide Cassava Breeding
by Michael Kanaabi, Mukasa B. Settumba, Ephraim Nuwamanya, Nicholas Muhumuza, Paula Iragaba, Alfred Ozimati, Fatumah B. Namakula, Ismail S. Kayondo, Julius K. Baguma, Ann Ritah Nanyonjo, Williams Esuma and Robert S. Kawuki
Plants 2024, 13(9), 1186; https://doi.org/10.3390/plants13091186 - 24 Apr 2024
Cited by 1 | Viewed by 1410
Abstract
Breeding for low-hydrogen-cyanide (HCN) varieties is a major objective of programs targeting boiled cassava food products. To enhance the breeding of low-HCN varieties, knowledge of genetic variation and trait heritability is essential. In this study, 64 cassava clones were established across four locations [...] Read more.
Breeding for low-hydrogen-cyanide (HCN) varieties is a major objective of programs targeting boiled cassava food products. To enhance the breeding of low-HCN varieties, knowledge of genetic variation and trait heritability is essential. In this study, 64 cassava clones were established across four locations and evaluated for HCN using three HCN assessment methods: one with a 1 to 9 scale, on with a 0 ppm to 800 ppm scale, and a quantitative assay based on spectrophotometer readings (HCN_Spec). Data were also collected on the weather variables precipitation, relative humidity, and temperature. Highly significant differences were observed among clones (p < 0.001) and locations (p < 0.001). There was also significant clone–environment interactions, varying from p < 0.05 to p < 0.001. Locations Arua and Serere showed higher HCN scores among clones and were associated with significantly higher (p < 0.001) mean daily temperatures (K) and lower relative humidity values (%) across 12 h and 18 h intervals. Within locations, HCN broad sense heritability estimates ranged from 0.22 to 0.64, while combined location heritability estimates ranged from 0.14 to 0.32. Relationships between the methods were positive and strong (r = 0.75–0.92). The 1 to 9 scale is more accurate and more reproducible than either the 0 to 800 ppm scale or spectrophotometric methods. It is expected that the information herein will accelerate efforts towards breeding for low-HCN cassava varieties. Full article
(This article belongs to the Special Issue Genetic Improvement of Cassava)
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22 pages, 3804 KiB  
Article
Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz)
by Julius K. Baguma, Settumba B. Mukasa, Ephraim Nuwamanya, Titus Alicai, Christopher Abu Omongo, Mildred Ochwo-Ssemakula, Alfred Ozimati, Williams Esuma, Michael Kanaabi, Enoch Wembabazi, Yona Baguma and Robert S. Kawuki
Plants 2024, 13(6), 796; https://doi.org/10.3390/plants13060796 - 12 Mar 2024
Cited by 2 | Viewed by 1820
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Genetic Improvement of Cassava)
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13 pages, 1355 KiB  
Article
Development of Methods for Improving Flowering and Seed Set of Diverse Germplasm in Cassava Breeding
by Peter T. Hyde, Olayemisi Esan, Elohor Mercy Diebiru-Ojo, Peter Iluebbey, Peter A. Kulakow, Prasad Peteti and Tim L. Setter
Plants 2024, 13(3), 382; https://doi.org/10.3390/plants13030382 - 27 Jan 2024
Viewed by 1401
Abstract
Cassava breeding faces obstacles due to late flowering and poor flower and seed set. The acceleration of breeding processes and the reduction in each cycle’s duration hinge upon efficiently conducting crosses to yield ample progeny for subsequent cycles. Our primary objective was to [...] Read more.
Cassava breeding faces obstacles due to late flowering and poor flower and seed set. The acceleration of breeding processes and the reduction in each cycle’s duration hinge upon efficiently conducting crosses to yield ample progeny for subsequent cycles. Our primary objective was to identify methods that provide tools for cassava breeding programs, enabling them to consistently and rapidly generate offspring from a wide array of genotypes. In greenhouse trials, we examined the effects of the anti-ethylene silver thiosulfate (STS) and the cytokinin benzyladenine (BA). STS, administered via petiole infusion, and BA, applied as an apical spray, combined with the pruning of young branches, significantly augmented the number of flowers. Controls produced no flowers, whereas treatments with pruning plus either BA or STS alone produced an average maximum of 86 flowers per plant, and the combination of pruning, BA and STS yielded 168 flowers per plant. While STS had its primary effect on flower numbers, BA increased the fraction of female flowers from less than 20% to ≥87%, thus increasing the number of progeny from desired parents. Through field studies, we devised an optimal protocol that maintained acceptable levels of phytodamage ratings while substantially increasing seed production per plant compared to untreated plants. This protocol involves adjusting the dosage and timing of treatments to accommodate genotypic variations. As a result, cassava breeding programs can effectively leverage a diverse range of germplasm to develop cultivars with the desired traits. Full article
(This article belongs to the Special Issue Genetic Improvement of Cassava)
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23 pages, 3387 KiB  
Article
The Development of Thematic Core Collections in Cassava Based on Yield, Disease Resistance, and Root Quality Traits
by Caroline Cardoso dos Santos, Luciano Rogerio Braatz de Andrade, Cátia Dias do Carmo and Eder Jorge de Oliveira
Plants 2023, 12(19), 3474; https://doi.org/10.3390/plants12193474 - 4 Oct 2023
Cited by 1 | Viewed by 1493
Abstract
Thematic collections (TCs), which are composed of genotypes with superior agronomic traits and reduced size, offer valuable opportunities for parental selection in plant breeding programs. Three TCs were created to focus on crucial attributes: root yield (CC_Yield), pest and disease resistance (CC_Disease), and [...] Read more.
Thematic collections (TCs), which are composed of genotypes with superior agronomic traits and reduced size, offer valuable opportunities for parental selection in plant breeding programs. Three TCs were created to focus on crucial attributes: root yield (CC_Yield), pest and disease resistance (CC_Disease), and root quality traits (CC_Root_quality). The genotypes were ranked using the best linear unbiased predictors (BLUP) method, and a truncated selection was implemented for each collection based on specific traits. The TCs exhibited minimal overlap, with each collection comprising 72 genotypes (CC_Disease), 63 genotypes (CC_Root_quality), and 64 genotypes (CC_Yield), representing 4%, 3.5%, and 3.5% of the total individuals in the entire collection, respectively. The Shannon–Weaver Diversity Index values generally varied but remained below 10% when compared to the entire collection. Most TCs exhibited observed heterozygosity, genetic diversity, and the inbreeding coefficient that closely resembled those of the entire collection, effectively retaining 90.76%, 88.10%, and 88.99% of the alleles present in the entire collection (CC_Disease, CC_Root_quality, and CC_Disease, respectively). A PCA of molecular and agro-morphological data revealed well-distributed and dispersed genotypes, while a discriminant analysis of principal components (DAPC) displayed a high discrimination capacity among the accessions within each collection. The strategies employed in this study hold significant potential for advancing crop improvement efforts. Full article
(This article belongs to the Special Issue Genetic Improvement of Cassava)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1. The Role of Genetic Resources and Genebanks in Cassava Breeding: Past Achievements and Future Prospects:

Authors: Clair H. Hershey and Alfredo Alves

2. Identification of immune response genes of cassava during early phases of cassava brown streak virus infection

Author: Samar Sheat

 

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