Lúcia Vieira Hoffmann

In situ conservation and genetic diversity of three populations of Gossypium mustelinum Miers ex Watt

Gossypium mustelinum Miers ex Watt is a native from Northeastern Brazil and belongs to the primary gene pool of the cultivated cotton. The unique places where the species was known to occur were visited to plan ex situ and in situ preservation. Two populations at Caicó became extinct, and only eleven individuals were found. At Jaguarari, although one population became extinct, a new one was localized with approximately 500 adult plants, where a fence avoided cattle feeding. The population from Macururé consisted of 28 plants protected from animals by thorns of Bromelia laciniosa Mart. ex Schult. f. Thirteen SSR primer pairs amplified 40 alleles, among which 30% were exclusive of one of the populations. The genetic differences between populations represented 58.3% of the total genetic variation observed. The high genetic distances are likely to be caused by geographical isolation as well as by the small number of individuals which contribute to new generations, and consequential genetic drift.

In situ and genetic characterization of Gossypium barbadense populations from the states of Pará and Amapá, Brazil

The objective of this work was to characterize the populations of Gossypium barbadense in the states of Amapa and Para, Brazil. In situ characterization was conducted through interviews with the owners of the plants and environmental observations. Leaf or petal tissue as well as seed samples were collected for genetic characterization by single sequence repeats markers and for storage in germplasm banks, respectively. The plants were maintained in dooryards and used mainly for medical purposes. The genetic analysis showed no heterozygous plants at the loci tested ( f = 1), indicating that reproduction occurs mainly through selfi ng. The total genetic diversity was high (H e = 0.39); and a high level of differentiation was observed between cotton plants from the two states (F ST = 0.36). Conventional methods of in situ maintenance of G. barbadense populations are not applicable. The conservation of the genetic variability of populations present in the two states could be achieved through germplasm collection and establishing of ex situ seed banks. Index term: cotton, genetic diversity, germplasm, SSR markers.

Distância genética entre linhagens avançadas de germoplasma de algodão com uso de marcadores de RAPD e microssatélites

The objective of this work was to select similarity coefficients to be used among sets of cotton genotypes with low genetic diversity. Sixty-five lineages and four cotton cultivars were analyzed by RAPD and SSR markers; and the genetic similarity was estimated by seven similarity coefficients: Simple Matching, Rogers & Tanimoto, Ochiai, Hamman, Jaccard, Dice and Russel & Rao. The adequacy of the use of each coefficient to the collected data was verified by correlation between the distance matrices, the consensus index between the dendrograms and the Tochers optimization method. The coefficient of Russel & Rao was the most divergent, and its use is not recommended. Among the parameters used to estimate the quality of information provided by each coefficient, differences were observed only by the consensus index, which established two groups: one in which simultaneous absence of bands are taken into account, and other in which it is excluded. Considering the presence of only two microsatellite alleles per polymorphic locus and the higher consensus index coefficients, the Simple Matching, Hamman and Rogers & Tanimoto coefficients should be preferred when analyzing cotton elite genotypes with low genetic similarity.

A SSR marker linked to the B 12 gene that confers resistance to race 18 of Xanthomonas axonopodis pv. malvacearum in cotton is also associated with other bacterial blight resistance gene complexes

The SSR marker CIR246, which is linked to the B12 gene that confers resistance to race 18 of Xanthomonas axonopodis pv. malvacearum (Xam), was used to evaluate a series of cotton germplasms that were also tested for their response to inoculation with race 18 of Xam (S-295, Delta Opal, 101-102B, Guazuncho-2, Acala 44, Mebane B1, and Stoneville 2B-S9). The allele associated with resistance was amplified in genotypes that carry the B12 gene (S-295 and Delta Opal) as well as in those that carry B2B3 (101-102B) and B9LB10L (Guazuncho-2), indicating that the molecular marker is able to identify genotypes resistant to the Xam races up to race 18, with resistance genes other than B12.

Marcadores SSR para detecção de fluxo gênico de algodoeiro herbáceo para algodoeiro mocó

O algodoeiro moco foi a planta cultivada mais importante do Nordeste do Brasil. Variedades locais desenvolvidas anteriormente aos programas de melhoramento governamentais devem ser identificadas e preservadas como recurso genetico. O objetivo deste trabalho foi selecionar marcadores SSR para monitorar o fluxo de genes do algodoeiro herbaceo para o moco, usando plantas de algodoeiro herbaceo nao transgenicas como fonte de polen. Populacoes ferais de algodoeiro moco raras foram identificadas no estado Rio Grande do Norte, e plantas maes e suas sementes foram coletadas. As frequencias alelicas foram estudadas nas plantas mae utilizando 64 marcadores SSR. Dez marcadores SSR com alelos exclusivos dos algodoeiros mocos ou dos algodoeiros herbaceos foram usados para monitorar o fluxo genico pela analise de paternidade (BNL3627; 2960; 2572; 3261; 3398; 3948; 3502; 3646 and CIR 094; 097). As sementes coletadas nao possuiam nenhum alelo de algodoeiro herbaceo. A ausencia de alelos exclusivos de algodoeiro herbaceo na progenie mostrou que o fluxo genico para o algodoeiro moco era ausente ou menor do que a analise pode detectar. Entre as plantas mae, o numero de individuos homozigotos em quatro locos polimorficos era maior que o esperado, mostrando que a reproducao ocorre preferencialmente por autofecundacao ou cruzamento entre individuos aparentados. O teste de paternidade mede com acuracia o fluxo de genes, e pode ser utilizada para monitorar esta ou outras populacoes. A preservacao das populacoes e ameacada principalmente pela seca.

Validação de métodos laboratoriais aplicadas a análises com marcadores microssatélites

Resumo - A troca de informacao sobre biodiversidade e a utilizacao de recursos geneticos podem ser melhor realizadas se os laboratorios que geram as informacoes puderem demonstrar que seus resultados sao confiaveis atraves de metodologias adequadas de validacao. Para definir criterios que sirvam para demonstrar a confiabilidade de resultados em laboratorios onde sao realizadas pesquisas com marcadores de DNA, foram analisados erros associados a quantificacao de DNA em gel de agarose e a repetitividade e robustez da reacao da polimerase em cadeia (PCR) utilizando primers baseados em marcadores microssatelites (SSR). O erro associado a quantificacao de DNA foi menor quando 100 ng foram quantificadas, e aumentou para quantidades de DNA maiores, com a tendencia de subestimar sua quantidade. O limite de quantificacao , entendido como as menores diferencas de quantidade de DNA que o metodo detecta, variou expressivamente com pequena variacao da quantidade de DNA. A incerteza associada ao PCR foi estimada por sua repetitividade, que mostrou-se sensivel a quantidade de DNA da reacao. A baixa robustez da PCR quanto a quantidade de DNA demonstra a necessidade prioritaria de avaliacao deste parâmetro. As consideracoes feitas podem ser auxiliares para que laboratorios de marcadores moleculares utilizem procedimentos de validacao. Palavras-chave - Genetica Vegetal. Microssatelites. Laboratorios biologicos - controle de qualidade.

Genetic diversity of Gossypium barbadense from the central Brazilian Amazon

The Amazon Basin is a center of diversity of Gossypium barbadense and the strategy for conservation of this genetic resource depends on the knowledge of the diversity maintained in Amazonas State. During two expeditions, in 2012 and 2014, plants were collected in ten municipalities in the state of Amazonas, in the central Brazilian Amazon region. The molecular diversity was estimated by SSR markers for 50 samples collected in 2012. The morphological diversity of 24 plants collected in 2014 was assessed ex situ and compared to that of 50 plants of the same and other cotton varieties from other Brazilian states. Most of plants evaluated in situ in Amazonas had purple petioles and veins (82%), associated to medicinal use, and kidney seeds (78%). The ex situ morphological analysies showed that G. barbadense plants from the Amazonas state: i) presented higher similarity to cotton plants from other northern Brazilian states, and ii) were grouped separately from those of other northern Brazilian states by descriptor analysis. Both the molecular (H=0.41) and morphological (H=0.38±0.02) diversity among the collected plants was considered intermediary. Our study indicates the distinctiveness of Amazon cottons, and contributes to demonstrate the discrimination power of multicategorical traits.

Genetic diversity of high performance cultivars of upland and irrigated Brazilian rice.

The objective of this study was to analyze the diversity and discrimination of high-performance Brazilian rice cultivars using microsatellite markers. Twenty-nine rice cultivars belonging to EMBRAPA Arroz e Feijão germplasm bank in Brazil were genotyped by 24 SSR markers to establish their structure and genetic discrimination. It was demonstrated that the analyzed germplasm of rice presents an expressive and significant genetic diversity with low heterogeneity among the cultivars. All 29 cultivars were differentiated genetically, and were organized into two groups related to their upland and irrigated cultivation systems. These groups showed a high genetic differentiation, with greater diversity within the group that includes the cultivars for irrigated system. The genotyping data of these cultivars, with the morphological e phenotypical data, are valuable information to be used by rice breeding programs to develop new improved cultivars.

Genetic diversity of arboreal cotton populations of the Brazilian semiarid: a remnant primary gene pool for cotton cultivars.

Mocó cotton belong to the same species as the cultivated species, Gossypium hirsutum, and cultivated forms were mainly landraces but also developed as cultivars, bearing good fiber quality and drought tolerant when cropped as a perennial species. The northeast Brazil crop system based on this cotton type is finished, with a few small area planted in the three main States, where it was previously cultivated (Ceará, Paraíba, and Rio Grande do Norte), but in others, maintenance is accomplished by single dooryard plants. Plants were found in all visited Northeast Brazil municipalities, sometimes in the North of the country, and were collected for ex situ preservation and evaluation. Most of seeds had no fuzz (62.2%) and 94.6% of the genotypes presented spot in flowers. Seventy-one alleles were revealed in 12 loci. The genetic structure of the population evaluated by microsatellite markers shows two main groups, one comprising the Seridó region where landraces were originated and other comprising the state of Ceará, where a specific breeding program was developed. Genotypes collected in North Brazil States as well as those collected in Bahia, Alagoas, and Sergipe grouped with those collected in Ceará. The Mantel correlogram indicates a significant (P < 0.05) correlation between genetic and geographical distances up to 77 km. The ex situ maintenance and agronomical evaluation are the main concerns for mocó, as the use of the agricultural interesting traits, possibly introgressed to other genotypes, is predicted. The in situ preservation is still of interest since there is more diversity there than in the collected plants and some should be continued due to use as medicinal plant.

Genetic Diversity, Erosion, and Population Structure in Cotton Genetic Resources

It is strongly believed that the wide genetic variability within the cotton (Gossypium spp.,) increases their chance for adaptation to changing harmful environments, and thus upsurge the likelihood of long-term survival of such unusual and important cash crop in the world. Given, the importance of cotton in the world economy and its usefulness to the human, cotton genetic resources should be conserved effectively and managed wisely, since such cotton genetic resources are used as the raw material for breeding new cultivars and act as a reservoir, and/or buffer against ecological and economic changes. However, the trend is reverse as there has been significant loss of genetic diversity during the past couple of decades, and the process of genetic erosion continues. Although, the narrow genetic diversity that exists in cotton has been noticed for more than two decades, there is little data on its amount and extent. Besides the threatening genetic base of future cotton breeding programs, erosion of cotton genetic resources could pose a severe threat to the world’s natural fiber production in the long-term, since loss of genetic variation may decrease the potential for a species to persist in the face of abiotic and biotic environmental changes. Future progress in the improvement of cotton largely depends on discovery, collection, and immediate conservation of genetic resources such as wild progenitors and landraces of Gossypium for their effective and sustainable utilization in the cotton breeding program. This chapter describes the challenges to cotton genetic diversity, presents the strategies that are being implemented to reverse the erosion of that diversity, outlines several gaps in our knowledge, and describes strategies that must be addressed to make such approaches more effective. Deployment of biotechnological tools in the study and conservation of cotton genetic resources are also highlighted in this chapter. Integration of the knowledge about evolution and natural population structure of domesticated Gossypium species combined with emerging sequence and functional genomics information will lead to the better management of cotton germplasm resources and more efficient utilization of natural variation for cotton genetic improvement.