Landscape Genetics: From Classic Molecular Markers to Genomics

Landscape genetics combines population genetics and landscape ecology to understand processes that shape the distribution and organization of human, animal, or plant populations. This field of genetics emerged from the availability of several studies with classical molecular markers, such as isozymes, RAPD, AFLP, and microsatellites. Population genetic studies enabled the detection of population structure with those markers, but a more comprehensive analysis of natural populations was only possible with the development of statistical methods that combined both molecular data and environmental variables. Ultimately, the rapid development of sequencing technologies allowed studies at the genomic level, augmenting the resolution of association with environment factors. This chapter outlines basic concepts in landscape genetics, the main statistical methods used so far, and the perspectives of this field of knowledge into strategies for conservation of natural populations of plant and animal species. Moreover, we briefly describe the application of the field to understand historical human migration processes as well as how some diseases are spread throughout the world

Genetic similarity between Brazilian bovine breeds

A similaridade genética entre animais de duas raças bovinas brasileiras (Crioulo Lageano e Junqueira) foi estimada pela análise de polimorfismo de DNA amplificado ao acaso (RAPD), tendo como referência (outgroups) animais de raças comerciais das espécies Bos taurus e B. indicus. Estas duas raças possuem grande similaridade fenotípica, sugerindo uma origem genética comum. Uma matriz de similaridade genética baseada em polimorfismo de DNA foi obtida e representada graficamente por um dendrograma, definido após processo estatístico de reamostragem bootstrap. Ao contrário do que era previsto com base nas semelhanças morfológicas das duas raças, os animais das raças Crioulo Lageano e Junqueira não apresentaram similaridade elevada entre si quando comparados com animais de outras raças comerciais. Os dados indicam que as duas raças sofreram contribuições genéticas distintas no processo de formação racial.The genetic similarity between animals of two Brazilian bovine breeds (Crioulo Lageano e Junqueira) was estimated based on random amplified polymorphic DNA (RAPD) using animals belonging to commercial breeds of the species Bos taurus and B. indicus as reference (outgroups). A matrix of genetic similarity was obtained and displayed as a dendrogram, which was defined after bootstrap resampling statistics. Contrary to what was expected based on the mophological similarities of the two breeds, the Crioulo Lageano and Junqueira animals do not show high levels of genetic similarity when compared to animals of other commercial breeds. The data indicate that the two breeds had different genetic contributions during the process of breed development

Variabilidade genética do umbuzeiro no Semi-Árido brasileiro, por meio de marcadores AFLP

The objective of this work was to evaluate the genetic variability distribution of umbu tree (Spondias tuberosa), within Brazilian Semi-Arid region, based on AFLP markers, in order to suggest prospecting andpreservation strategies for this species. Sixty-eight umbu trees of 15 ecogeographic regions were analyzed for 141 polymorphic AFLP bands, through the UPGMA dendrogram and the multidimensional scaling (MDS),based on Jaccard’s coeffi cient . Analysis of molecular variance was accomplished by total decomposition among and within ecogeographic regions. The dendrogram presented co-phenetic value of 0.96, while theMDS presented 0.25 for the badness-of-fi t. Umbu genetic variability was estimated in 0.3138, indicating a large variance among individual groups. Specifi c clusters were observed in six ecogeographic regions, and some individual pairs were observed in the other regions, with no specifi c clustering by sampling place, which indicates that the genetic variability of umbu tree is not uniformly distributed within Brazilian Semi-Arid. Strategies are suggested to set a larger number of protection areas for in situ conservation, or a smaller number of umbu individuals sampled, in various ecoregion units, for ex situ genetic variability conservation of this species.O objetivo deste trabalho foi avaliar a distribuição da variabilidade genética do umbuzeiro (Spondias tuberosa), no Semi-Árido brasileiro, por meio de marcadores AFLP, para subsidiar estratégias de prospecçãoe conservação da espécie. Foram analisados 68 indivíduos de umbuzeiro de 15 ecorregiões, pelo dendrograma UPGMA e pela dispersão em escala multidimensional (MDS), com o coefi ciente de Jaccard de 141 bandaspolimórfi cas de AFLP. A análise da variância molecular foi realizada pela decomposição total entre e dentro das regiões ecogeográfi cas. O dendrograma apresentou valor cofenético de 0,96, e o gráfi co MDS apresentou 0,25 para a falta de ajustamento. A variabilidade genética do umbuzeiro foi estimada em 0,3138, o que indica grande variação entre os grupos de indivíduos. Agrupamentos específi cos foram observados em seis regiões ecogeográfi cas, enquanto nas demais regiões observaram-se pares entre alguns indivíduos, sem formação deagrupamentos específi cos por local de amostragem, o que indica que a variabilidade genética do umbuzeiro não está uniformemente distribuída no Semi-Árido. Sugerem-se estratégias para o estabelecimento de maiornúmero de áreas para conservação in situ ou amostragens de menor número de indivíduos, em várias unidades de paisagens, para conservação ex situ da variabilidade genética do umbuzeiro

Relation between the genetic variation of quantitative traits and the molecular markers in subpopulations (Eugenia dysenterica DC)

O objetivo do trabalho foi relacionar a diversidade genética medida a partir de três diferentes marcadores moleculares, com a variação genética quantitativa de caracteres poligênicos, estimada em ensaio de progênies, sob condições controladas. As progênies, oriundas de dez subpopulações naturais de cagaiteira do sudeste de Goiás, foram avaliadas em experimento em blocos completos casualizados, com quatro repetições e uma planta por parcela. Foram estimadas a herdabilidade ao nível de média de progênies (h mi ²) e o coeficiente de variação genética (CVgi) de cada subpopulação para a altura da planta e o diâmetro do fuste, por quatro anos, bem como para as respectivas taxas de crescimento. Estimativas da diversidade gênica (Hei) e do índice de fixação (f i) foram obtidas com dados de marcadores codominantes e dominantes. Correlação linear e regressão múltipla foram usadas para inferir sobre a associação entre a divergência quantitativa e molecular nos níveis intra e interpopulacional, A fraca correlação entre as medidas de divergência obtidas com marcadores moleculares dominantes e codominantes reduziu a expectativa de correlação positiva entre essas medidas e a diversidade quantitativa. Em geral, não foi confirmada a possibilidade de usar com segurança medidas de divergência molecular intrapopulacional para inferir a variação genética de caracteres quantitativos no nível de precisão que prevaleceu. Com o marcador baseado em maior número de locos (RAPD), verificou-se a possibilidade de uma inferência desse tipo. Em nível interpopulacional, encontrou-se associação mais pronunciada entre a divergência molecular e a quantitativa.This research aimed to measure the association between molecular diversity and the genetic variation of quantitative traits, estimated from a progeny trial, under controlled conditions. Ten natural subpopulations of cagaita tree from the southeast of Goiás State, Brazil, were investigated. The maternal families were evaluated in a trail using the randomized complete block design with four replications and a single tree per plot. Quantitative data were analyzed estimating the coefficient of heritability (h mi² ), on a progeny mean basis and the genetic coefficient of variation (CVgi) for each subpopulation. The traits considered were: plant height and the respective diameter and the corresponding annual rates of increment. Estimates of gene diversity (Hei) and fixation index (f i), available for the same subpopulations, based on isozymes, SSR and RAPD markers, were taken for comparison. Simple linear correlation and multiple regression analysis were used for measuring the association between those estimates on intra and interpopulation level. The weak correlation between gene diversity estimated with codominant and dominant markers reduced the expectation of a good correlation between those statistics and the genetic variation of the quantitative traits. In general, the possibility to infer the magnitude of quantitative variation within subpopulations, based on molecular gene diversity, was not confirmed. RAPD results were more promising, indicating the importance to have an adequate genomic coverage in this kind of research. On the other hand, the interpopulation level, a much better association was detected for all markers. The possibility of predicting quantitative variation based on molecular information was, therefore, not excluded.Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)CNP

Two Colors, One Species: The Case of Melissodes nigroaenea (Apidae: Eucerini), an Important Pollinator of Cotton Fields in Brazil

Accurate taxonomic delimitation in ecological research is absolutely critical as studies that seek to evaluate levels of biodiversity and qualify human effects on the environment are rapidly undertaken. Coloration is a widely used morphological character for species identification through dichotomous keys. However, taxonomic identification based upon coloration is often unreliable because this character can exhibit high degree of intraspecific variation. In this study, we use a DNA barcoding approach to investigate the interpretation of two color morphs (yellow or dark) in the eucerine bee Melissodes nigroaenea. Our hypothesis is that if significant genetic divergence exists between each morphotype of M. nigroaenea, coloration reflects two distinct evolutionary lineages within this species, which may require taxonomic revision. Our alternative hypothesis is that, if genetic divergence is low between each morphotype of M. nigroaenea, we can attribute this variation to color polymorphism. Our Bayesian phylogenetic reconstruction revealed that both yellow and black individuals clustered together in a highly supported phylogenetic group. Additionally, pairwise genetic distances between M. nigroaenea color morphotypes were lower than 3%. These results indicate that both mesosome color morphs correspond to intraspecific variability within the same evolutionary unit. Together, our results indicate that mesosome coloration is not a reliable character for taxonomic differentiation of these Melissodes species, and that the incorporation of DNA barcoding approaches to taxonomic classification can help resolve some of the problems that originate while relying on purely morphological taxonomy

Two Colors, One Species: The Case of Melissodes nigroaenea (Apidae: Eucerini), an Important Pollinator of Cotton Fields in Brazil

Accurate taxonomic delimitation in ecological research is absolutely critical as studies that seek to evaluate levels of biodiversity and qualify human effects on the environment are rapidly undertaken. Coloration is a widely used morphological character for species identification through dichotomous keys. However, taxonomic identification based upon coloration is often unreliable because this character can exhibit high degree of intraspecific variation. In this study, we use a DNA barcoding approach to investigate the interpretation of two color morphs (yellow or dark) in the eucerine bee Melissodes nigroaenea. Our hypothesis is that if significant genetic divergence exists between each morphotype of M. nigroaenea, coloration reflects two distinct evolutionary lineages within this species, which may require taxonomic revision. Our alternative hypothesis is that, if genetic divergence is low between each morphotype of M. nigroaenea, we can attribute this variation to color polymorphism. Our Bayesian phylogenetic reconstruction revealed that both yellow and black individuals clustered together in a highly supported phylogenetic group. Additionally, pairwise genetic distances between M. nigroaenea color morphotypes were lower than 3%. These results indicate that both mesosome color morphs correspond to intraspecific variability within the same evolutionary unit. Together, our results indicate that mesosome coloration is not a reliable character for taxonomic differentiation of these Melissodes species, and that the incorporation of DNA barcoding approaches to taxonomic classification can help resolve some of the problems that originate while relying on purely morphological taxonomy

Genetic diversity of American wild rice species

Studies on genetic diversity and genetic structure of natural populations are important in order to define strategies for in situ and ex situ conservation actions and for plant pre-breeding programs. Aiming to assess the genetic diversity and genetic structure of three wild American Oryza species with isozyme markers, 14 populations of the diploid O. glumaepatula (AglAgl), 11 populations of the tetraploid O. grandiglumis (CCDD) and five populations of the also tetraploid O. latifolia (CCDD) were studied. They were all originated from Rio Paraguay hydrographic basin and the Amazon. Four enzymes were used and they gave 40 polymorphic bands. The most polymorphic species was O. glumaepatula, followed by O. latifolia and O. grandiglumis. A cluster analysis with the Jaccard similarity coefficient separated the diploid from the two tetraploid species, and also the two tetraploid species. This separation was also evident on a scatter plot from a principal component analysis, suggesting that they should be treated as two separate species, although further studies are necessary to provide support for this affirmative. The AMOVA analyses showed a high intrapopulational variability for O. latifolia (67.6%) and O. grandiglumis (52.2%), when compared to their interpopulational variability (32.4% and 47.8%, respectively), which suggests the hypothesis of a higher degree of outcrossing events within these species. When studying the correlation between the Jaccard dissimilarity coefficient and geographic distances, a spatial genetic structure was observed for O. glumaepatula only. These results are important for defining strategies of both in situ and ex situ conservation.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Genetic diversity in soybean germplasm identified by SSR and EST-SSR markers

Os objetivos deste trabalho foram avaliar a diversidade genética de 79 acessos de soja de diferentes regiões do mundo, agrupá-los de acordo com a similaridade e testar a correlação entre os dois tipos de marcadores utilizados. Foram utilizados marcadores microssatélites genômicos (SSR) e funcionais (EST-SSR). Trinta pares de primers SSR foram selecionados (20 genômicos e 10 EST-SSR) de acordo com sua distribuição nos 20 grupos de ligação da soja, com sua unidade de repetição trinucleotídica e com seu conteúdo de informação polimórfica. Todos os lócus analisados foram polimórficos, e 259 alelos foram encontrados. O número de alelos por lócus variou entre 2–21, com média de 8,63. Os acessos possuem uma quantidade significativa de alelos raros, sendo os acessos 19, 35, 63 e 65 os que apresentaram maior número de alelos exclusivos. Os acessos 75 e 79 são os mais similares e os acessos 31 e 35, e 40 e 78 são os mais divergentes. Foi observada baixa correlação entre resultados de SSR e EST-SSR. Portanto, uma análise adequada de diversidade em soja deve ser feita utilizando-se tanto marcadores microssatélites genômicos como funcionais. A diversidade genética dos acessos selecionados é alta, tendo sido encontrados cinco grupos e vários subgrupos. Observou-se moderada relação entre divergência genética e origem geográfica dos acessos.The objectives of this work were to investigate the genetic variation in 79 soybean (Glycine max) accessions from different regions of the world, to cluster the accessions based on their similarity, and to test the correlation between the two types of markers used. Simple sequence repeat markers present in genomic (SSR) and in expressed regions (EST-SSR) were used. Thirty SSR primer-pairs were selected (20 genomic and 10 EST-SSR) based on their distribution on the 20 genetic linkage groups of soybean, on their trinucleotide repetition unit and on their polymorphism information content. All analyzed loci were polymorphic, and 259 alleles were found. The number of alleles per locus varied from 2–21, with an average of 8.63. The accessions exhibit a significant number of rare alleles, with genotypes 19, 35, 63 and 65 carrying the greater number of exclusive alleles. Accessions 75 and 79 were the most similar and accessions 31 and 35, and 40 and 78, were the most divergent ones. A low correlation between SSR and EST-SSR data was observed, thus genomic and expressed microsatellite markers are required for an appropriate analysis of genetic diversity in soybean. The genetic diversity observed was high and allowed the formation of five groups and several subgroups. A moderate relationship between genetic divergence and geographic origin of accessions was observed

Genetic diversity analysis among pigeonpea genotypes adapted to South American regions based on microsatellite markers

The pigeonpea [Cajanus cajan (L) Millspaugh] is one of the most important perennial legume crops utilized in the food, fodder, soil conservation, crop-livestock integrated systems, reclaiming of degraded pastures and symbiotic nitrogen fixation. Microsatellite markers were used to estimate the genetic diversity of 77 pigeonpea genotypes selected from the germplasm collections at Embrapa Cattle-Southeast and, to evaluate their transferability to Phaseolus vulgaris and Vigna unguiculata species. The number of alleles per locus ranged from 2 to12, with an average of 5.1 alleles. The PIC values ranged from 0.11 to 0.80 (average 0.49) and the D values from 0.23 to 0.91 (average 0.58). The averages of observed and expected heterozygosity were 0.25 and 0.47, respectively, showing a deficit in heterozygosity. A model-based Bayesian approach implemented in the software STRUCTURE was used to assign genotypes into clusters. A dendrogram was constructed based on the modified Roger's genetic distances using a neighbor-joining method (NJ). A total of four clusters were assembled by STRUCTURE and a strong tendency of correspondence between the Bayesian clusters in the NJ tree was observed. The genetic distance ranged from 0.09 to 0.62 (average 0.37), showing a low genetic diversity in the pigeonpea genotypes. Transferability of pigeonpea-specific microsatellites revealed a cross-amplification and the presence of polymorphic alleles in P. vulgaris and V. unguiculata