Microsatellite primers in Agave utahensis (Asparagaceae), a keystone species in the Mojave Desert and Colorado Plateau

Morphological and genetic diversity of traditional varieties of agave in Hidalgo State, Mexico

The agaves are plants of cultural importance which have been used by humans for about 10,000 years and about 40 specific uses. The most culturally and economically important of those uses are for the production of fermented (pulque) and distilled beverages (mescal). Pulque continues to be produced in nearly all of Mexico, and the agaves used for this purpose have shown domestication syndrome. We carry out an ethnobotanical, morphological, and genetic analysis of the traditional varieties of pulque agave used in the production of aguamiel (agave sap) and pulque in the state of Hidalgo. We did semi-structured interviews, free listings, and tours with 11 agave managers. We analyzed morphology and studied genetic diversity and structure using nuclear microsatellites. We found wild-collected, tolerated, transplanted, and cultivated varieties of agave. This comprised 19 traditional varieties of pulque agave, 12 of them in production during the study, which corresponded to the species Agave americana, A. salmiana y A. mapisaga and five intraspecific entities. The varieties were grouped morphologically according to a management gradient; the wild-collected varieties were the smallest, with more lateral teeth and a larger terminal spine. The cultivated varieties clearly exhibited domestication syndrome, with larger plants and smaller dentition. The expected heterozygosity (He) of the varieties ranged from 0.204 to 0.721. Bayesian clustering suggested the existence of three genetic groups, both at the level of traditional varieties of pulque agaves and for management categories, a result that matches multivariate clustering. Pulque producers in the studied localities maintain high agrobiodiversity. The cultivated varieties exhibit domestication syndrome, as has been reported for other species of the genus with the same selection purposes. Our results support the hypothesis of a decrease in genetic diversity in crops compared to wild-growing agaves, which seems to be due to vegetative propagation, among other factors.

Evolutionary ecology of Agave: distribution patterns, phylogeny, and coevolution (an homage to Howard S. Gentry)

With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in many regions of Mexico and in the southwestern United States, agaves are dominant species. We describe the contributions of H. S. Gentry to the understanding of agaves and review recent advances on the study of the ecology and evolution of the genus. We analyze the present and inferred past distribution patterns of different species in the genus, describing differences in their climatic niche and adaptations to dry conditions. We interpret these patterns using molecular clock data and phylogenetic analyses and information of their coevolving pollinators and from phylogeographic, morphological, and ecological studies and discuss the prospects for their future conservation and management.

Management, morphological and genetic diversity of domesticated agaves in Michoacán, México

BACKGROUND

Pulque is a fermented beverage prepared with sap of Agave species in Mexico. Management of agaves for this purpose has motivated domestication of some species and high phenotypic variation that commonly causes uncertainty about the taxonomic identity of varieties traditionally managed by people. This study assumed that varieties of crop species continually arise from mutations, sexual reproduction and hybridization, among other processes, and some of them are favoured and maintained by humans. Identifying these varieties may be difficult and a challenging issue for botanists and evolutionary biologists studying processes of domestication. Through a case study, we analysed the traditional varieties of agaves used to produce pulque in Michoacán, Mexico. We aimed at identifying the varieties, analysing the relatedness among them and developing a methodological approach that could help solve taxonomic problems and study variation under domestication of this and other plant groups. We documented (1) the traditional varieties of agave used and their identity, (2) how these varieties are perceived, used and managed by the local people and (3) how management influences phenotypic and genetic variation among varieties.

METHODS

We interviewed pulque producers in two localities of the state of Michoacán, Mexico, where we recorded management practices of agaves, the traditional varieties used, the attributes characterizing those varieties, the varieties preferred by people, and features and mechanisms of selection. We conducted multivariate analyses of morphological features of the agave varieties, as well as genetic diversity and genetic distance studies among agave varieties through 11 nuclear microsatellites.

RESULTS

Seven traditional varieties of Agave were recorded in the study area. Multivariate analyses of morphology identified varieties belonging to the species A. salmiana, A. mapisaga and, presumably, A. americana. The preferred varieties have morphological features selected to make easier their management and produce higher sap yields. Genetic diversities (H_E = 0. 470 to 0.594) were high compared with other Agave species with similar life history traits and use. Genetic distance analyses grouped the varieties "Verde" and "Negro" (identified as A. salmiana), whereas the varieties "Tarímbaro" and "Listoncillo" (identified as A. mapisaga) formed another group. The varieties "Blanco" and "Carrizaleño" (most probably being A. americana) clustered with varieties of A. salmiana, whereas the variety "Cenizo" appeared as a distinct group. Bayesian analysis indicated that most individuals of varieties of A. salmiana form a group and those of the varieties of A. mapisaga form another, whereas individuals of the varieties putatively belonging to A. americana clustered in similar proportions with both groups.

CONCLUSIONS

The traditional pulque production in the study area is an ongoing practice. It is still an important source of products for direct consumption by households and generation of economic incomes and as part of the cultural identity of local people. The most used traditional variety exhibited a marked gigantism, and although these agaves are mainly asexually propagated, populations have high genetic diversity. The local producers promote the maintenance of different traditional varieties. Our study shows the value of an integral research approach including ethnobiological, morphological and genetic information to clarify the state of variation influenced by humans on agaves, but it would be helpful to study other organisms under domestication. In addition, such approach would help to document human and non-human mechanisms generating crop varieties managed by local people.

Phylogeography and Genetic Diversity in a Southern North American Desert: Agave kerchovei From the Tehuacán-Cuicatlán Valley, Mexico

The Tehuacán-Cuicatlán Valley, located at the southeast of the state of Puebla and the northeast of the state of Oaxaca in Central Mexico, south of the Trans-Mexican Volcanic Belt (TMVB), is of particular interest for understanding the evolutionary dynamics of arid and semi-arid environments, being one of the main reservoirs of biological diversity for the arid zones of North America, including the highest diversity of Agavaceae worldwide and high levels of endemism. Studying in detail the phylogeography, environmental history and population genetics of representative species will hopefully shed light on the evolutionary and ecological dynamics that generated the tremendous biodiversity and endemism of this important region in Mexico. We sequenced three non-coding regions of chloroplast genome of Agave kerchovei, a representative species of the Tehuacán Valley, generating 2,188 bp from 128 individuals sampled from eight populations throughout the species range. We used this data set to (i) characterize the levels of genetic diversity and genetic structure in A. kerchovei; (ii) predict the distribution of A. kerchovei for the present day, and to reconstruct the past geographical history of the species by constructing ecological niche models (ENM); and (iii) compare the levels of diversity in this species with those estimated for the widely distributed Agave lechuguilla. Agave kerchovei has high levels of total chloroplast genetic variation (Hd = 0.718), especially considering that it is a species with a very restricted distribution. However, intrapopulation diversity is low (zero in some populations), and genetic structure is high (F _ST = 0.928, G _ST = 0.824), which can be expected for endemic species with isolated populations. Our data suggest that Pleistocene glacial cycles have played an important role in the distribution of A. kerchovei, where the climatic variability of the region - likely associated with its topographic complexity - had a significant effect on the levels of genetic diversity and population dynamics, while the potential distribution of the species seems to be stable since the middle Holocene (6 kya). We conclude that in A. kerchovei there is a core group of populations in the Tehuacán Valley, and peripheric populations that appear to be evolving independently and thus the species is fundamentally an endemic species from the Tehuacán Valley while the populations outside the Valley appear to be in the process of incipient speciation.

Morphological and Genetic Variation in Monocultures, Forestry Systems and Wild Populations of Agave maximiliana of Western Mexico: Implications for Its Conservation

Forestry systems in Mexico are examples of traditional management of land and biodiversity that integrates the use, conservation and restoration of forest elements. Current in situ management practices of Agave maximiliana in western Mexico include the tolerance of many forest elements, reintroduction of young Agave plants and germination of seeds. More intense forms of management include monocultures, which are agroindustrialized systems developed in more recent times and characterized by the establishment of high densities of A. maximiliana plants in deforested areas and abandoned agricultural lands. We compared monocultures, forestry systems and wild populations (i.e., non/slightly-exploited forests) in order to evaluate whether these practices have had an effect on intraspecific morphological and genetic variation and divergence. We also tested whether divergence has a positive relationship with environmental and geographic distance. We analyzed 16 phenotypic traits in 17 populations of A. maximiliana, and 14 populations were further examined by amplifying 9 SSR loci. We employed multivariate methods and analyses of variance in phenotypic and genetic traits to test whether clusters and the percentage of variation contained in the managed and wild categories can be identified. Tests of isolation by environment (IBE) and distance (IBD) were performed to detect the magnitude of divergence explained by climatic and geographic variables. We found that forestry systems are effective as reservoirs of morphological and genetic diversity, since they maintain levels similar to those of wild populations. Moreover, the monocultures showed similar levels, reflecting their recent emergence. While the species showed high morphological diversity (IMD = 0.638, SE ± 0.07), it had low to intermediate genetic diversity (A = 2.37, H _E = 0.418). Similar morphological and genetic divergences were found among populations, but these were not correlated with each other in population pairs. Non-significant morphological differentiation was found among categories. Only IBE was significant in the genetic structure (β = 0.32, p = 0.007), while neither IBE nor IBD was detected in the morphological differentiation. We discuss the implications of these results in the context of the weaknesses and strengths of A. maximiliana in the face of the socio-ecological changes predicted for the study area in the short term.

Microsatellite markers: what they mean and why they are so useful

Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. Motivated by the importance of these sequences over the last decades this review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function. The methodologies for the development of SSR loci, genotyping and their applications as molecular markers are also reviewed. Finally, two data surveys are presented. The first was conducted using the main database of Web of Science, prospecting for articles published over the period from 2010 to 2015, resulting in approximately 930 records. The second survey was focused on papers that aimed at SSR marker development, published in the American Journal of Botany's Primer Notes and Protocols in Plant Sciences (over 2013 up to 2015), resulting in a total of 87 publications. This scenario confirms the current relevance of SSRs and indicates their continuous utilization in plant science.

Identification and characterization of microsatellite markers in Penstemon scariosus (Plantaginaceae)

PREMISE OF THE STUDY

Penstemon scariosus var. albifluvis (Plantaginaceae) has been proposed to be federally listed as threatened due to its unique, geologically oil-rich habitat. Developing simple sequence repeat (SSR) markers to study its genetic diversity would be most useful.

METHODS AND RESULTS

Using genomic reduction in combination with next-generation sequencing, we identified SSR motifs with five to 15 perfect repeats in 1067 P. scariosus contigs. After multiple qualifying tests, 16 SSRs were selected for their robust polymorphic reliability across 12 taxa with as high as 21 alleles in a given taxon. With the exception of two monomorphic loci, the observed and expected heterozygosity values ranged from 0.083 to 1.000 and 0.398 to 0.920, respectively.

CONCLUSIONS

These microsatellite markers will directly aid in studies of the genetic diversity and relatedness of P. scariosus, P. comarrhenus, P. compactus, P. cyananthus var. cyananthus, P. fremontii var. fremontii, P. fremontii var. glabrescens, P. gibbensii, P. strictus, and P. subglaber.

Genetic structure of coexisting wild and managed agave populations: implications for the evolution of plants under domestication

Domestication is a continuous evolutionary process guided by humans. This process leads to divergence in characteristics such as behaviour, morphology or genetics, between wild and managed populations. Agaves have been important resources for Mesoamerican peoples since prehistory. Some species are domesticated and others vary in degree of domestication. Agave inaequidens Koch is used in central Mexico to produce mescal, and a management gradient from gathered wild and silvicultural populations, as well as cultivated plantations, has been documented. Significant morphological differences were reported among wild and managed populations, and a high phenotypic variation in cultivated populations composed of plants from different populations. We evaluated levels of genetic diversity and structure associated with management, hypothesizing that high morphological variation would be accompanied by high genetic diversity in populations with high gene flow and low genetic structure among managed and unmanaged populations. Wild, silvicultural and cultivated populations were studied, collecting tissue of 19-30 plants per population. Through 10 nuclear microsatellite loci, we compared population genetic parameters. We analysed partition of variation associated with management categories to estimate gene flow among populations. Agave inaequidens exhibits high levels of genetic diversity (He = 0.707) and moderate genetic structure (FST = 0.112). No differences were found in levels of genetic diversity among wild (He = 0.704), silviculturally managed (He = 0.733) and cultivated (He = 0.698) populations. Bayesian analysis indicated that five genetic clusters best fit the data, with genetic groups corresponding to habitats where populations grow rather than to management. Migration rates ranged from zero between two populations to markedly high among others (M = 0.73-35.25). Natural mechanisms of gene flow and the dynamic management of agave propagules among populations favour gene flow and the maintenance of high levels of variation within all populations. The slight differentiation associated with management indicates that domestication is in an incipient stage.