Potential of SNP markers for the characterization of Brazilian cassava germplasm

Oliveira, Eder Jorge de; Ferreira, Cláudia Fortes; Santos, V. da S.; Jesus, O. N. de; Oliveira, Gilmara Alvarenga Fachardo; Silva, Maiane Suzarte da

doi:10.1007/s00122-014-2309-8

Cited by 35 publications

(35 citation statements)

References 38 publications

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“…The average observed heterozygosity across the 160 genotypes was 0.39, similar to heterozygosity reported for samples from Brazil [31]. Using SNP genotyping to discriminate samples genetically, 22 duplicates of genotypes were obtained among 173 samples.…”

Section: Manioc Diversity and Manioc Classification In Indigenous Comsupporting

confidence: 73%

Differences in Manioc Diversity Among Five Ethnic Groups of the Colombian Amazon

et al. 2014

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Abstract:Manioc is an important root crop in the tropics and the most important staple food in the Amazon. Manioc is diverse but its diversity has not yet been clearly associated with environmental or social factors. Our study evaluates how variation in edaphic environments and in social factors influences manioc diversity among five ethnic groups of the Amazon region of Colombia. Inventories of landraces, genetic analysis of manioc diversity, visits to farmers' swiddens and interviews with farmers were carried out during two years of field work. Morphotypic and genotypic diversity of manioc were large. The different ethnic groups of our study cultivate different sweet and bitter manioc landraces which they select and maintain in accordance with their ancestral rules and norms. Differences in available environments among indigenous communities (such as the presence of different soils) did not markedly affect manioc morphotypic or genotypic diversity, while social factors considerably influenced observed manioc diversity. Manioc diversity was explained by two parallel processes of manioc diversification: volunteer seedling selection and manioc seed OPEN ACCESS Diversity 2014, 6 793 exchange. We argue that, for a full understanding of manioc diversity, indigenous knowledge, as well as morphological and genetic variation should be taken into account.

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Section: Manioc Diversity and Manioc Classification In Indigenous Comsupporting

confidence: 73%

Differences in Manioc Diversity Among Five Ethnic Groups of the Colombian Amazon

et al. 2014

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“…The accessions of germplasm-containing alleles that were associated with CMD resistance, as identified when using MAS, along with two elite hybrids (9624-09 and 98150-06), nine improved varieties (BRS Aipim Brazil, BRS Caipira, BRS Formosa, BRS Guaíra, BRS Kiriris, BRS Mulatinha, BRS Tapioqueira, BRS Verdinha and Equador 72) and six local varieties (Baianinha, Cidade Rica, Irará, Lagoa, Mani Branca and Sergipe), were analyzed with data from a previous genotyping of 402 SNP-like markers (Single Nucleotide polymorphism) that were obtained by Oliveira et al (2014).…”

Section: Identification Of Contrasts To Generate Segregating Populationsmentioning

confidence: 99%

“…The DAPC has been used for large data volumes, particularly generated by SNP markers. Recently, the DAPC was used to structure the germplasm of Carica papaya L. with microsatellite markers (Matos et al, 2013) and cassava with SNPs markers (Oliveira et al, 2014).…”

Section: Analysis Of Parental Diversity Available For Breedingmentioning

confidence: 99%

“…This need is especially true for long-cycled crops (> 12 months), such as cassava, which require 8 to 12 years for the development of a variety using conventional procedures (Okogbenin et al, 2007;Oliveira et al, 2014). In the specific case of breeding cassava for CMD resistance, MAS was used for the initial identification of resistance sources, while SNP markers were used to estimate the relatedness of individuals seeking to guide the crossings.…”

Section: Prospects For Cassava Breeding Aiming To Improve Cmd Resistancementioning

confidence: 99%

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Molecular-assisted selection for resistance to cassava mosaic disease in Manihot esculenta Crantz

Carmo

Silva

Oliveira

et al. 2015

Sci. agric. (Piracicaba, Braz.)

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The geminivirus complex known as cassava mosaic disease (CMD) is one of the most devastating viruses for cassava (Manihot esculenta Crantz). The aim of this study was to use molecular-assisted selection (MAS) to identify CMD-resistant accessions and ascertain promising crosses with elite Brazilian varieties. One thousand two hundred twenty-four accessions were genotyped using five molecular markers (NS169, NS158, SSRY028, SSRY040 and RME1) that were associated with resistance to CMD, along with 402 SNPs (single-nucleotide polymorphism). The promising crosses were identified using a discriminant analysis of main component (DAPC), and the matrix of genomic relationship was estimated with SNP markers. The CMD1 gene, previously described in M. glaziovii, was not found in M. esculenta. In contrast, the CMD2 gene was found in 5, 4 and 5 % of cassava accessions, with flanking markers NS169+RME1, NS158+RME1 and SSRY28+RME1, respectively. Only seven accessions presented all markers linked to the CMD resistance. The DAPC of the seven accessions along with 17 elite cassava varieties led to the formation of three divergent clusters. Potential sources of resistance to CMD were divided into two groups, while the elite varieties were distributed into three groups. The low estimates of the genomic relationship (ranging from -0.167 to 0.681 with an average of 0.076) contributed to the success in identifying contrasting genotypes. The use of MAS in countries where CMD is a quarantine disease constitutes a successful strategy not only for identifying the resistant accessions but also for determining the promising crosses.

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“…Therefore, the maintenance of cassava genetic diversity ensures the conservation of useful alleles that are related to resistance to pests and diseases, conferring better root quality and differential starch characteristics (Raji et al, 2007;Oliveira et al, 2014). The availability of a wide genetic variability is essential for cassava breeding programs that are aimed at developing new varieties with levels of adaptation to cultivation in different environments and industrial adjustments.…”

Section: Introductionmentioning

confidence: 99%

Selection of the most informative morphoagronomic descriptors for cassava germplasm

Oliveira

Filho

Santos

2014

Pesq. agropec. bras.

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-The objective of this work was to select the most informative morphoagronomic descriptors for cassava (Manihot esculenta) germplasm and to evaluate the ability of different methods to select the descriptors. Ninety-five accessions were characterized using 51 morphoagronomic descriptors. Data were subjected to a multiple correspondence analysis (MCA), whose information was used in the following four methods of descriptor selection: reverse order of the descriptor for the pth factorial axis of the MCA (Jolliffe); sequential, multiple correspondence analysis (SMCA); mean of the contribution orders of the descriptor in the first three factorial axes (C3PA); and C3PA method weighted by the respective eigenvalues of the full analysis (C3PAWeig). The correlations between the dissimilarity matrix with all descriptors and the most informative descriptors were high and significant (0.75, 0.77, 0.83, and 0.84 for C3PAWeig, C3PA, SMCA, and Jolliffe, respectively). The less informative descriptors were discarded, considering those common among the selection methods and relevant for the breeding interests. Therefore, 32 morphoagronomic descriptors with correlation between the dissimilarity matrices (r=0.81) were selected, due to their high capacity to discriminate cassava germplasm and to their ability to maintain some preliminary agronomic traits, useful for the initial characterization of the germplasm. Index terms: Manihot esculenta, descriptor selection, genetic resources, multiple correspondence analysis. Seleção dos descritores morfoagronômicos mais informativos para germoplasma de mandiocaResumo -O objetivo deste trabalho foi selecionar os descritores morfoagronômicos mais informativos para o germoplasma de mandioca (Manihot esculenta), e avaliar a capacidade de diferentes métodos em selecionar os descritores. Foram caracterizados 95 acessos com uso de 51 descritores morfoagronômicos. Os dados foram submetidos à análise de correspondência múltipla (ACM), cujas informações foram utilizadas nos seguintes quatro métodos de seleção de descritores: ordem inversa do descritor para o eixo fatorial pth da ACM (Jolliffe); análise de correspondência múltipla sequencial (ACMS); média das ordens de contribuição do descritor nos três primeiros eixos fatoriais (C3PE); e método C3PE ponderado pelos pesos dos respectivos autovalores da análise completa (C3PEPond). As correlações entre a matriz de dissimilaridade com todos os descritores e os descritores mais informativos foram altas e significativas (0,75, 0,77, 0,83 e 0,84 para C3PEPond, C3PE, ACMS e Jolliffe, respectivamente). Os descritores menos informativos foram descartados, tendo-se considerado apenas aqueles comuns entre os métodos de seleção e relevantes para os interesses do melhoramento. Assim, foram selecionados 32 descritores morfoagronômicos com correlação entre as matrizes de dissimilaridade (r=0,81), em razão de sua alta capacidade para discriminar o germoplasma de mandioca e de sua habilidade de manter alguns caracteres agronômicos preliminares, úteis para a...

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Potential of SNP markers for the characterization of Brazilian cassava germplasm

Cited by 35 publications

References 38 publications

Differences in Manioc Diversity Among Five Ethnic Groups of the Colombian Amazon

Differences in Manioc Diversity Among Five Ethnic Groups of the Colombian Amazon

Molecular-assisted selection for resistance to cassava mosaic disease in Manihot esculenta Crantz

Selection of the most informative morphoagronomic descriptors for cassava germplasm

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