Dataset Information

Morphological Diversity and Genetic Relationships in Pulque Production Agaves in Tlaxcala, Mexico, by Means of Unsupervised Learning and Gene Sequencing Analysis.

ABSTRACT: Pulque is one of the oldest fermented beverages, with its origins dating back to pre-Hispanic Mexico. Recently, public consumption has increased. However, the majority of Agave plantations for pulque production have disappeared or been abandoned in recent decades. To create strategies for the conservation and production of pulque agaves, it is necessary to first determine their taxonomic identities and to better understand their genetic and morphological diversity. Despite the historical importance of pulque in Mexico, little attention has been placed on the study of Agave plants used for its production. Therefore, we analyzed the morphological diversity of vegetative characters of nine landraces of two Agave species (A. salmiana and A. mapisaga) which are widely cultivated for pulque production in Tlaxcala, Mexico. The analysis of morphological characters showed that the landraces largely clustered based on classic taxonomic relationships. One cluster of landraces associated with Agave mapisaga var. mapisaga and another with A. salmiana subsp. salmiana, but with the exception of A. salmiana subsp. salmiana "Ayoteco", which is more closely related with A. mapisaga var. mapisaga. Additionally, we analyzed the genetic relationships between 14 landraces and wild individuals using molecular markers (trnL and ITS). The identified genetic variants or haplotypes and genetic pools mainly corresponded with the species. In the case of "Ayoteco", incongruence between markers was observed. Low selection intensity, genetic flow events, and the plasticity of morphological traits may explain the high number of landraces without clear differences in their morphological diversity (vegetative characters) or genetic pools. The use of reproductive traits and massive sequencing might be useful for identifying possible morphological and genetic changes in the Agave landraces used for pulque production.

SUBMITTER: Trejo L

PROVIDER: S-EPMC7505951 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Morphological Diversity and Genetic Relationships in Pulque Production Agaves in Tlaxcala, Mexico, by Means of Unsupervised Learning and Gene Sequencing Analysis.

Trejo Laura L Reyes Miguel M Cortés-Toto Daniela D Romano-Grande Elvira E Muñoz-Camacho Lizbeth L LL

Frontiers in plant science 20200908

Pulque is one of the oldest fermented beverages, with its origins dating back to pre-Hispanic Mexico. Recently, public consumption has increased. However, the majority of <i>Agave</i> plantations for pulque production have disappeared or been abandoned in recent decades. To create strategies for the conservation and production of pulque agaves, it is necessary to first determine their taxonomic identities and to better understand their genetic and morphological diversity. Despite the historical ...[more]

PMID: 33013957

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Project description: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.

Project description:BackgroundHuanglongbing (HLB, yellow shoot disease) is a highly destructive citrus disease associated with a nonculturable bacterium, "Candidatus Liberibacter asiaticus" (CLas), which is transmitted by Asian citrus psyllid (ACP, Diaphorina citri). In Mexico, HLB was first reported in Tizimin, Yucatán, in 2009 and is now endemic in 351 municipalities of 25 states. Understanding the population diversity of CLas is critical for HLB management. Current CLas diversity research is exclusively based on analysis of the bacterial genome, which composed two regions, chromosome (> 1,000 genes) and prophage (about 40 genes).Methods and resultsIn this study, 40 CLas-infected ACP samples from 20 states in Mexico were collected. CLas was detected and confirmed by PCR assays. A prophage gene(terL)-based typing system (TTS) divided the Mexican CLas strains into two groups: Term-G including four strains from Yucatán and Chiapas, as well as strain psy62 from Florida, USA, and Term-A included all other 36 Mexican strains, as well as strain AHCA1 from California, USA. CLas diversity was further evaluated to include all chromosomal and prophage genes assisted by using machine learning (ML) tools to resolve multidimensional data handling issues. A Term-G strain (YTMX) and a Term-A strain (BCSMX) were sequenced and analyzed. The two Mexican genome sequences along with the CLas genome sequences available in GenBank were studied. An unsupervised ML was implemented through principal component analysis (PCA) on average nucleotide identities (ANIs) of CLas whole genome sequences; And a supervised ML was implemented through sparse partial least squares discriminant analysis (sPLS-DA) on single nucleotide polymorphisms (SNPs) of coding genes of CLas guided by the TTS. Two CLas Geno-groups, Geno-group 1 that extended Term-A and Geno-group 2 that extended Term-G, were established.ConclusionsThis study concluded that: 1) there were at least two different introductions of CLas into Mexico; 2) CLas strains between Mexico and USA are closely related; and 3) The two Geno-groups provide the basis for future CLas subspecies research.

Dataset Information

Morphological Diversity and Genetic Relationships in Pulque Production Agaves in Tlaxcala, Mexico, by Means of Unsupervised Learning and Gene Sequencing Analysis.

Publications

Morphological Diversity and Genetic Relationships in Pulque Production Agaves in Tlaxcala, Mexico, by Means of Unsupervised Learning and Gene Sequencing Analysis.

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