Jaime Martínez-Castillo

Diversity and structure of landraces of Agave grown for spirits under traditional agriculture: A comparison with wild populations of A. angustifolia (Agavaceae) and commercial plantations of A. tequilana

Traditional farming communities frequently maintain high levels of agrobiodiversity, so understanding their agricultural practices is a priority for biodiversity conservation. The cultural origin of agave spirits (mezcals) from west-central Mexico is in the southern part of the state of Jalisco where traditional farmers cultivate more than 20 landraces of Agave angustifolia Haw. in agroecosystems that include in situ management of wild populations. These systems, rooted in a 9000-year-old tradition of using agaves as food in Mesoamerica, are endangered by the expansion of commercial monoculture plantations of the blue agave variety (A. tequilana Weber var. Azul), the only agave certified for sale as tequila, the best-known mezcal. Using intersimple sequence repeats and Bayesian estimators of diversity and structure, we found that A. angustifolia traditional landraces had a genetic diversity (H(BT) = 0.442) similar to its wild populations (H(BT) = 0.428) and a higher genetic structure ((B) = 0.405; (B) =0. 212). In contrast, the genetic diversity in the blue agave commercial system (H(B) = 0.118) was 73% lower. Changes to agave spirits certification laws to allow the conservation of current genetic, ecological and cultural diversity can play a key role in the preservation of the traditional agroecosystems.

Intraspecific Diversity and Morpho-Phenological Variation in Phaseolus lunatus L. from the Yucatan Peninsula, Mexico

The genetic diversity ofP. lunatus in the Yucatan Peninsula was assessed on the basis of its morphological and phenological characters. Our results were then discussed in relation to ethnobotanic information obtained about the intraspecific diversity recognized by farmers, their selection criteria, agronomic management, production purpose and percentage of cultivated area. Research was undertaken in one of the cultural subareas of Mesoamerica, the Lowland Maya area, where traditional agriculture has been more persistent and where high diversity ofP. lunatus landraces has been recorded. Four of the 13 cultural-geographic zones established for the origin of this culture were included, 160 farmers from 12 localities were interviewed, and 149 seed samples ofP. lunatus germplasm were collected and analyzed using six characters. A subset of these samples was grown under ex situ uniform growth conditions and analyzed using 28 characters. Ethnobotanical and morpho-phenological data indicated 30 putative distinct landraces, two wild, and two weedy variants, suggesting gene flow among them. Richness and diversity estimates were greatest, and evenness lowest, where there was: 1) minimal agricultural intensification, 2) wild and weedy populations, and 3) greater persistence of traditional culture. Results underscored the importance of establishing in situ conservation programs in these areas.Se estimó la diversidad genética deP. lunatus en la Península de Yucatán con base en caracteres fenológicos y morfológicos, y se discute en relatión a la informatión etnobotánica obtenida acerca de la diversidad intraespecífica reconocida por los campesinos, sus criterios de selectión, su manejo agronómico, el destino de la productión y el porcentaje de área cultivada. La investigation se llevó a cabo en una de las subáreas culturales de Mesoamérica en donde la agricultura traditional ha sido más persistente y en donde se ha reportado alta diversidad de cultivares deP. lunatus: las Tierras Bajas Mayas. Cuatro de las trece zonas geográfico-culturales establecidas en el origen de esta civilizatión fueron incluídas, 160 campesinos de 12 localidades fueron entrevistados y 149 muestras de semilla del germoplasma deP. lunatus fueron analizadas con base en 6 caracteres. Un subconjunto de estas muestras se cultivó bajo condiciones homogéneas de crecimiento ex situ y se analizó usando 28 caracteres. Los datos morfólogicos y etnobotánicos indicaron 30 cultivares putativos, dos variantes silvestres y dos arvenses, y sugirió flujo génico entre ellas. La riqueza y la diversidad fue mayor, y el predominio menor, donde hubo: 1) menor intensification agrícola, 2) poblaciones silvestres y arvenses deP. lunatus, y 3) mayor persistencia de cultura traditional. Los resultados resaltan la importancia de establecer programas de conservación in situ en estas áreas.

Genetic structure within the Mesoamerican gene pool of wild Phaseolus lunatus (Fabaceae) from Mexico as revealed by microsatellite markers: Implications for conservation and the domestication of the species

UNLABELLED • PREMISE OF THE STUDY Understanding genetic structure in wild relatives of a crop is important for crop improvement and conservation. Recently, two gene pools (MI and MII) were reported in wild Lima bean (Phaseolus lunatus) from Mexico, a domestication center of Mesoamerican landraces. However, the evidence was based on limited genomic sampling. Here we sought to confirm the existence of these two gene pools by increased genome and population sampling.• METHODS We characterized 67 wild populations of P. lunatus from Mexico with 10 microsatellite loci and studied the genetic structure by means of AMOVA, cluster analyses, assignment tests, and a georeferenced map.• KEY RESULTS AMOVA indicated that most of the variation is found among populations (77%) rather than within populations (23%). Assignment tests were key to confirm not only the presence of the two gene pools (MI and MII) in Mexico, but also to propose the possible existence of two subgroups within MI (MIa and MIb). While MI and MII are mainly divergent geographically, MIa and MIb overlap in their distribution. Admixed individuals, which may represent cases of gene flow among gene pools, were detected.• CONCLUSIONS Our results show that the genetic structure of wild Lima bean in Mexico is more complex than previously thought and propose the presence of three gene pools (MIa, MIb, and MII), each one possessing relatively high levels of genetic diversity. We still need additional evidence, however, to confirm without doubt the split of the gene pool MI into subgroups MIa and MIb.

Domestication of small-seeded lima bean (Phaseolus lunatus L.) landraces in Mesoamerica: evidence from microsatellite markers

AbstractPrevious studies have suggested that the Mesoamerican small-seeded landraces of Lima bean may have been domesticated more than once in Mesoamerica, once in central-western Mexico and another one in an area between Guatemala and Costa Rica. However, these findings were based on sequencing of only one locus from nuclear DNA, and additional confirmation was needed. Here we contribute with additional data on the origin of the Mesoamerican landraces and document the founder effect due to domestication. We characterized 62 domesticated, 87 wild and six weedy Lima bean accessions with ten microsatellite loci. Genetic relationships were analyzed using genetic distances and Bayesian clustering approaches. Domestication bottlenecks were documented using inter-population comparisons and M ratios. The results support at least one domestication event in the area of distribution of gene pool MI in central-western Mexico and also show that some landraces are genetically related to wild accessions of gene pool MII. Also, our data support founder effects due to domestication in Mesoamerican Lima bean landraces. Although we could not establish more specifically the place of origin of the Mesoamerican Lima bean landraces, our results show that these are not a genetically homogeneous group, a finding that may be compatible with a scenario of more than one domestication event accompanied by gene flow. The complex genetic makeup of landraces that we found indicates that a more comprehensive geographic and genomic sampling is needed in order to establish how domestication processes and gene flow have shaped the current genetic structure of landraces.

Testing Domestication Scenarios of Lima Bean (Phaseolus lunatus L.) in Mesoamerica: Insights from Genome-Wide Genetic Markers

Plant domestication can be seen as a long-term process that involves a complex interplay among demographic processes and evolutionary forces. Previous studies have suggested two domestication scenarios for Lima bean in Mesoamerica: two separate domestication events, one from gene pool MI in central-western Mexico and another one from gene pool MII in the area Guatemala-Costa Rica, or a single domestication from gene pool MI in central-western Mexico followed by post-domestication gene flow with wild populations. In this study we evaluated the genetic structure of the wild gene pool and tested these two competing domestication scenarios of Lima bean in Mesoamerica by applying an ABC approach to a set of genome-wide SNP markers. The results confirm the existence of three gene pools in wild Lima bean, two Mesoamerican gene pools (MI and MII) and the Andean gene pool (AI), and suggest the existence of another gene pool in central Colombia. The results indicate that although both domestication scenarios may be supported by genetic data, higher statistical support was given to the single domestication scenario in central-western Mexico followed by admixture with wild populations. Domestication would have involved strong founder effects reflected in loss of genetic diversity and increased LD levels in landraces. Genomic regions affected by selection were detected and these may harbor candidate genes related to domestication.

Evaluation of molecular variability in germplasm of vanilla ( Vanilla planifolia G. Jackson in Andrews) in Southeast Mexico: implications for genetic improvement and conservation

Molecular variability of vanilla ( Vanilla planifolia ) and three wild species was assessed to explore the possible sources of variation that can be used for crop improvement. A total of 154 ISSR loci were analysed by the UPGMA, assignment tests of individuals (STRUCTURE) and indices of genetic diversity. The assignment tests were done at two levels: first considering the four species and then only the accessions of V. planifolia . The molecular analysis indicated 99.3% polymorphism among all species and 70.45% within V. planifolia . The UPGMA showed the separation of these four species into three groups and grouped V. planifolia accessions into three subgroups. The more genetically differentiated accessions were of the Rayada morphotype and a wild accession was from Oaxaca, followed by a wild accession from Quintana Roo; all the commercial accessions of V. planifolia (Mansa morphotype) were grouped together. The STRUCTURE analysis differentiated between V. planifolia and the three wild species, and among the accessions of the Mansa and Rayada morphotypes and the wild accessions. The STRUCTURE analysis also indicated the presence of mixed individuals. These results are of great importance since the accessions of V. planifolia that are genetically more differentiated are the most threatened due to the scarcity of these individuals, the destruction of habitat and replacement by the commercial morphotype. These individuals should be salvaged and used to expand the genetic background of vanilla.

Short-distance barriers affect genetic variability of Rhizophora mangle L. in the Yucatan Peninsula

Abstract The environmental variability at local scale results in different physiognomic types of mangrove forest. However, this variability has never been considered in studies of mangrove genetic variability. This study analyzed the genetic and morphological variability and structure of Rhizophora mangle at regional and local scales in the Yucatan Peninsula. Thirteen mangrove populations (eight scrub and five tall), located in seven sites, were sampled, and their morphological variability and relationship with the availability of phosphorus and salinity were analyzed. The diversity and genetic structure were estimated at different hierarchical levels with nine microsatellites, also Bayesian inference and Principal Coordinates Analysis were used. We found a great morphological variability of R. mangle that responded to local environmental variability and not to the precipitation gradient of the peninsula. The genetic diversity found in the peninsula was greater than that reported for other populations in Mexico and was grouped into two regions: the Gulf of Mexico and the Caribbean Sea. At a local scale, tall and scrub mangroves had significant genetic differentiation suggesting that ecological barriers promote genetic differentiation within sites. These results need to be considered in future population genetic studies and for mangrove management and conservation.