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 2024 | Viewed by 3562

Special Issue Editors


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

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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

Published Papers (4 papers)

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Research

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
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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
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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
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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
Viewed by 837
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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