Identification of duplicates in cassava germplasm banks based on single-nucleotide polymorphisms (SNPs)

Albuquerque, Hilçana Ylka Gonçalves de; Oliveira, E. J. de; Brito, Ana Carla; Andrade, Luciano Rogério Braatz de; Carmo, Cátia Dias do; Morgante, Carolina Vianna; Vieira, Eduardo Alano; Cunha, E. F. M.; Faleiro, Fábio Gelape

doi:10.1590/1678-992x-2017-0389

Cited by 19 publications

(8 citation statements)

References 23 publications

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“…However, the phenotypic classification dealt with a small number of traits while the genotypic classification dealt with more than 18 000 SNPs, hence the genotypic classification showed a lot of differences between accessions. Comparable results have been reported by [55, 56] while identifying duplicate accessions based on multi-locus analysis, and concluded that accessions presenting similar SNP profiles were assumed to be putative duplicates as each multi locus genotype corresponded to a single genotype.…”

Section: Discussionsupporting

confidence: 79%

Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

Pierre

Wamalwa

Muiru

et al. 2021

Preprint

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In Burundi, most of small-scale farmers still grow traditional cassava landraces that are adapted to local conditions and have been selected for consumer preferred attributes. They tend to be susceptible, in varying degrees, to devastating cassava viral diseases such as Cassava Brown Steak Disease (CBSD) and Cassava Mosaic Disease (CMD) with production annual losses of US$1 billion annually. For long term resistance to the disease, several breeding strategies have been proposed. A sound basis for a breeding program is to understand the genetic diversity of both landraces and elite introduced breeding cultivars. This will also assist in efforts to conserve landraces ahead of the broad distribution of improved varieties which have the possibility of replacing landraces. Our study aimed at determining the genetic diversity and relationships of local landraces and introduced elite germplasm using morphological and simple nucleotide polymorphism (SNP) markers as well as identifying a core set of germplasm from the local varieties to be used in the cassava breeding program. A total of 118 cultivars were characterized for morphological trait variation based on leaf, stem and root traits, and genetic variation using SNP markers. Results of morphological characterization based on Ward’s Method revealed three main clusters and five accessions sharing similar characteristics. Molecular characterization identified over 18,000 SNPs and six main clusters and three pairs of duplicates which should be pooled together as one cultivar to avoid redundancy. Results of population genetic analysis showed low genetic distance between populations and between local landraces and elite germplasm. Accessions that shared similar morphological traits were divergent at the molecular level indicating that clustering using morphological traits was inconsistent. Despite the variabilities found within the collection, it was observed that cassava germplasm in Burundi have a narrow genetic base.

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Section: Discussionsupporting

confidence: 79%

Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

Pierre

Wamalwa

Muiru

et al. 2021

Preprint

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“…Errors in classification according to the level of ploidy and taxonomy and the presence of duplicate genotypes in germplasm banks and genetic breeding collections can be detrimental at an economic level in conservation strategies and for the selection of promising genotypes because they can identify materials with full genetic identity. Therefore, these materials must be identified and excluded for the estimation and identification of duplicates with molecular markers rather than conserving and using a duplicate accession as a different accession in a germplasm bank [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis of a potato (Solanum tuberosum L.) breeding collection for southern Colombia using Single Nucleotide Polymorphism (SNP) markers

2021

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Detailed knowledge on genetic parameters such as diversity, structure, and linkage disequilibrium (LD) and identification of duplicates in a germplasm bank and/or breeding collection are essential to conservation and breeding strategies in any crop. Therefore, the potato genetic breeding collection at the Universidad de Nariño in Colombia, which is made up of diploid and tetraploid genotypes in two of the more diverse genebanks in the world, was analyzed with 8303 single nucleotide polymorphisms (SNP) from SolCAP version 1. In total, 144 genotypes from this collection were analyzed identifying an 57.2% of the polymorphic markers that allowed establishing two and three subpopulations that differentiated the diploid genotypes from the tetraploids. These subpopulations had high levels of heterozygosity and linkage disequilibrium. The diversity levels were higher in the tetraploid genotypes, while the LD levels were higher in the diploid genotypes. For the tetraploids, the genotypes from Peru had greater diversity and lower linkage disequilibrium than those from Colombia, which had slightly lower diversity and higher degrees of LD. The genetic analysis identified, adjusted and/or selected diploid and tetraploid genotypes under the following characteristics: 1) errors in classification associated with the level of ploidy; 2) presence of duplicates; and 3) genotypes with broad genetic distances and potential use in controlled hybridization processes. These analyses suggested that the potato genetic breeding collection at the Universidad de Nariño has a genetic base with a potential use in breeding programs for this crop in the Department of Nariño, in southern Colombia.

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“…C. moschata is allogamous, therefore analysing the variability of its germplasm can assist in the orientation of crossings between more diverse genotypes, thereby aiding the exploration of hybrid vigour [62, 5]. Regarding the assistance in the management of plant germplasm, variability analysis allows the identification of duplicates in the germplasm collections [63, 64, 65], which correspond to pairs or groups of accessions with high similarity. In fact, it is estimated that less than 30% of the accessions maintained in the collections worldwide are distinct, which hinders their maintenance [28].…”

Section: Discussionmentioning

confidence: 99%

Germplasm of Brazilian winter squash (Cucurbita moschataD.) displays vast genetic variability, allowing identification of promising genotypes for agro-morphological traits

Gomes

Júnior

Almeida

et al. 2020

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13Winter squash fruits (Cucurbita moschata D.) are among the best sources of vitamin A 14 precursors and constitute sources of bioactive components such as phenolic compounds and 15 flavonoids. Approximately 70% of C. moschata seed oil is made up of unsaturated fatty acids, 16 with high levels of monounsaturated fatty acids and components such as vitamin E and 17 carotenoids, which represent a promising nutritional aspect in the production of this vegetable. 18C. moschata germplasm expresses high genetic variability, especially in Brazil. We assessed 91 19 C. moschata accessions, from different regions of Brazil, and maintained at the UFV Vegetable 20 Germplasm Bank, to identify early-flowering accessions with high levels of carotenoids in the 21 fruit pulp and high yields of seed and seed oil. Results showed that the accessions have high 22 variability in the number and mass of seeds per fruit, number of accumulated degree-days for 23 flowering, total carotenoid content, and fruit productivity, which allowed selection for 24 considerable gains in these characteristics. Analysis of the correlation between these 25 characteristics provided information that will assist in selection to improve this crop. Cluster 26 analysis resulted in the formation of 16 groups, confirming the variability of the accessions. Per 27 se analysis identified accessions BGH-6749, BGH-5639, and BGH-219 as those with the earliest 28flowering. Accessions BGH-5455A and BGH-5598A had the highest carotenoid content, with 29 averages greater than 170.00 μg g -1 of fresh mass. With a productivity of 0.13 t ha -1 , accessions 30 BGH-5485A, BGH-4610A, and BGH-5472A were the most promising for seed oil production. 31These last two accessions corresponded to those with higher seed productivity, averaging 0.58 2 32 and 0.54 t ha -1 , respectively. This study confirms the high potential of this germplasm for use in 33 breeding for promotion of earlier flowering and increase in total carotenoid content of the fruit 34 pulp and in seed and seed oil productivity. 35 36 38 39 3 65 making this crop fundamental for ensuring healthier diets and promoting food security in the 66 regions where it is grown, particularly in less developed regions and in the context of family-67 based farming. 68 Associated with its socio-economic importance, C. moschata germplasm commonly expresses 69 high genetic variability in all regions where it occurs [15, 16, 17], especially in Brazil [18, 19, 70 20]. Archaeological evidence indicates that this species was present in Latin America prior to 71 colonisation, and appears to have already been an important component in the diet of the native 72 peoples living there [21, 22, 23]. Currently, the variability of this vegetable in Brazil is closely 73 tied to the human populations involved in its cultivation, who are predominantly family-based 74 farmers. The selection practised over time by these populations, associated with the exchange of 75 seeds between them, and the natural occurrence of hybridization in the germplasm of th...

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Identification of duplicates in cassava germplasm banks based on single-nucleotide polymorphisms (SNPs)

Cited by 19 publications

References 23 publications

Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

Genetic analysis of a potato (Solanum tuberosum L.) breeding collection for southern Colombia using Single Nucleotide Polymorphism (SNP) markers

Germplasm of Brazilian winter squash (Cucurbita moschataD.) displays vast genetic variability, allowing identification of promising genotypes for agro-morphological traits

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