Genome-wide association studies for waxy starch in cassava

Carmo, Cátia Dias do; Sousa, Massáine Bandeira e; Brito, Ana Carla; Oliveira, E. J. de

doi:10.1007/s10681-020-02615-9

Cited by 16 publications

(14 citation statements)

References 78 publications

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“…Similar conclusion about the number of distinct groups has been drawn in cassava (do Carmo et al, 2020). The LD decay over physical distance is crucial in determining the number and density of markers required for genomic analyses such as GWAS (Flint-Garcia et al, 2003;do Carmo et al, 2020). We observed LD decay in the population composed of white and yellow accessions at approximately 30 kb, which is higher than that in Brazilian cassava germplasm (~20 kb; Albuquerque et al, 2018) and elite IITA cassava breeding lines (10 kb; Rabbi et al, 2020), but lower compared to East-West African breeding lines (~50 kb; Wolfe et al, 2016).…”

Section: Discussionsupporting

confidence: 81%

“…The three complementary approaches employed in this study, namely DAPC, NJ phylogenetic tree, and admixture ancestry to define the optimal number of subgroups all revealed the presence of four genetic subgroups among the 142 cassava accessions. Similar conclusion about the number of distinct groups has been drawn in cassava (do Carmo et al, 2020). The LD decay over physical distance is crucial in determining the number and density of markers required for genomic analyses such as GWAS (Flint-Garcia et al, 2003;do Carmo et al, 2020).…”

Section: Discussionsupporting

confidence: 60%

“…The alpha-amylase gene performs important functions and roles in carbohydrate metabolism. The importance of this protein in initiating starch degradation has been reported in different starchy crops, including cassava (Oyewole and Odunfa, 1992;do Carmo et al, 2020). Lengbamroung et al (2005) found a high expression of the gene encoding alpha-amylase protein in cassava storage roots.…”

Section: Discussionmentioning

confidence: 99%

“…Lengbamroung et al (2005) found a high expression of the gene encoding alpha-amylase protein in cassava storage roots. In cassava, the genes for alpha-amylase and beta-amylase were co-located with significant polymorphisms identified for waxy starch (do Carmo et al, 2020). Thus, the alpha-amylase gene may be a waxy gene (Wx) involved in the expression of waxy phenotype in cassava.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Discussionsupporting

confidence: 81%

Section: Discussionsupporting

confidence: 60%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…The percentage of phenotypic variance explained by the QTLs ranged from 11.3 to 27.3% of the phenotypic variation ( Sraphet et al, 2017 ; Table 2 ). Using GWAS, 10 SNP associated with waxy phenotypes were identified on chromosome 2 that co-located in genic regions that included five known genes and five genes of unknown function ( do Carmo et al, 2020 ; Table 3 ).…”

Section: Connecting Genotypic and Phenotypic Information And Discovermentioning

confidence: 99%

Technological Innovations for Improving Cassava Production in Sub-Saharan Africa

et al. 2021

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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.

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Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations

Hyten

2022

Methods in Molecular Biology

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Genome-wide association studies for waxy starch in cassava

Cited by 16 publications

References 78 publications

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

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

Technological Innovations for Improving Cassava Production in Sub-Saharan Africa

Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations

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