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.

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

10.21203/rs.3.rs-143808/v1 ◽

2021 ◽

Author(s):

Carmen Julia Figueredo-Urbina ◽

Gonzalo D. Álvarez-Ríos ◽

Mario Adolfo García-Montes ◽

Pablo Octavio-Aguilar

Keyword(s):

Genetic Diversity ◽

Morphological Characteristics ◽

Plant Size ◽

Structured Interviews ◽

Main Method ◽

Domestication Syndrome ◽

Cultural Importance ◽

Genetic Groups ◽

Expected Heterozygosity ◽

Distilled Beverages

Abstract Background: The agaves are plants of cultural importance that have been used by humans for about 10,000 years for about 40 specific uses, of which the most culturally and economically important are fermented (Pulque) and distilled beverages (Mescal). Pulque continues to be produced in nearly all of Mexico, and the agaves used for this propose have shown domestication syndrome and selected morphological characteristics, such as larger plant size (since size is positively related to sap production) and less dentition of the leaves.Methods: In this study, 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 two localities of the state of Hidalgo. We did semi-structured interviews and tours with crop owners, tlachiqueros (sap harvesters), and people related to the production system. We analyzed the morphology of 111 plants, and we studied the diversity and genetic structure of 130 individuals using 16 nuclear microsatellites.Results: We found wild, tolerated, transplanted, and cultivated varieties of agave. Asexual reproduction was the main method of propagation. We recorded 19 traditional varieties of pulque agave, 12 of them in production during the study, which correspond to the species Agave americana, A. salmiana y A. mapisaga with five intraspecific entities. The varieties were grouped according to a management gradient; the wild 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 between 0.204 to 0.721. Bayesian clustering suggested the existence of three genetic groups (K = 3), both at the level of traditional varieties of pulque agaves and for management categories, a result that matches multivariate clustering.Conclusions: 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 agaves, which seems to be due to vegetative propagation, among other factors.

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Genetic diversity and structure of Dorstenia elata (Moraceae) in an Atlantic Forest remnant

Rodriguésia ◽

10.1590/2175-7860202172081 ◽

2021 ◽

Vol 72 ◽

Author(s):

Liliana Aparecida Ribeiro Martins ◽

Rodrigo Monte Lorenzoni ◽

Ronald Martins Pereira Júnior ◽

Fábio Demolinari de Miranda ◽

Milene Miranda Praça Fontes ◽

...

Keyword(s):

Genetic Diversity ◽

Atlantic Forest ◽

Shannon Index ◽

The Road ◽

Expected Heterozygosity ◽

Forest Remnant ◽

Genetic Diversity And Structure ◽

Native Populations ◽

The Matrix ◽

Issr Primers

Abstract Plant species that show gregarious spatial distribution and endemism to the Atlantic Forest, such as Dorstenia elata, are particularly sensitive to the effects of genetic diversity loss. In the present study, we aimed to quantify the genetic diversity in native populations of this species in an Atlantic Forest remnant. The sample included three aggregates of individuals, and molecular characterization was performed with twelve ISSR primers. Intrapopulation analyses were based on the calculation of the Shannon index; total expected heterozygosity and the matrix of distances between pairs of individuals were also calculated. The obtained grouping dendrogram evinced the formation of two groups. Interpopulation investigations were based on the analysis of molecular variance and the estimate of historical gene flow. The results demonstrate that one group comprised the genotypes from two subpopulations, and the other contained exclusively the genotypes of a third subpopulation. The greatest genetic variability was observed within rather than among populations, indicating that the geographical distance and the road that divides the studied populations are not causing loss of genetic diversity.

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Genetic diversity and structure of native maize races from Northwestern Mexico

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2017001100008 ◽

2017 ◽

Vol 52 (11) ◽

pp. 1023-1032 ◽

Cited By ~ 4

Author(s):

Isrrael Vega-Alvarez ◽

Amalio Santacruz-Varela ◽

Mario Rocandio-Rodríguez ◽

Leobigildo Córdova-Téllez ◽

Higinio López-Sánchez ◽

...

Keyword(s):

Genetic Diversity ◽

Zea Mays ◽

Bayesian Model ◽

Population Distribution ◽

Principal Coordinate Analysis ◽

Expected Heterozygosity ◽

Genetic Diversity And Structure ◽

Broad Variation ◽

Northwestern Mexico ◽

Probabilistic Value

Abstract: The objective of this work was to evaluate the genetic diversity of nine maize races (Zea mays ssp. mays) from Northwestern Mexico and one population of teosinte of the Balsas race (Zea mays ssp. parviglumis). A total of 649 alleles were identified, with an average of 20.9 alleles per locus using 31 microsatellite loci; 84.3% of them were polymorphic loci with a 0.49 expected heterozygosity. Graphic representation of principal coordinate analysis (PCoA) showed broad variation and population distribution. The highest probabilistic value obtained with the ΔK criterion confirmed the existence of five population groups clustered by the Bayesian model. This grouping coincided with the population distribution observed in the PCoA graph. Maize races examined retain broad genetic diversity among and within the evaluated populations.

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Historical migration and taxonomic entity of Korean endemic shrub Lespedeza maritima (Fabaceae) based on microsatellite loci

AoB Plants ◽

10.1093/aobpla/plab009 ◽

2021 ◽

Vol 13 (2) ◽

Author(s):

Dong-Pil Jin ◽

Jong-Soo Park ◽

Byoung-Hee Choi

Keyword(s):

Genetic Diversity ◽

Microsatellite Loci ◽

Clustering Analysis ◽

Internal Transcribed Spacers ◽

Bayesian Clustering ◽

Evolutionary Divergence ◽

Niche Modelling ◽

Land Bridge ◽

Bayesian Tree ◽

Genetic Diversity And Structure

Abstract Various plant species are endemic to the Korean Peninsula, but their evolutionary divergence and establishment are poorly understood. One of these, Lespedeza maritima, has been proposed as either a hybrid (L. cyrtobotrya × L. maximowiczii) or a synonym of L. thunbergii. A distinct taxon, L. uekii, has been proposed for inland populations. We investigated genetic diversity and structure in L. maritima and related taxa to resolve this. Genotypes of L. maritima (n = 244, including L. uekii) were determined using 12 microsatellite loci, then compared with those of related species. Genetic diversity within L. maritima was estimated, and Bayesian clustering analysis was used to represent its genetic structure and that of related taxa. Its distribution during the last glacial maximum (LGM) was predicted using ecological niche modelling (ENM). Neighbour-joining (NJ) analysis and principal coordinate analysis (PCoA) were used to investigate relationships among species. Bayesian tree based on nuclear ribosomal internal transcribed spacers (nrITS) was also reconstructed to show relationships and divergence time among species. Morphological features were examined using flower characteristics. In result, expected heterozygosity (HE) and allelic richness (AR) within L. maritima were higher in southern than northern populations. Bayesian clustering analysis largely assigned populations to two clusters (K = 2) (south vs. north). The ENM showed that L. maritima occurred around the East China Sea and Korean Strait land bridge during the LGM. Compared with other Lespedeza species, L. maritima was assigned to an independent cluster (K = 2–5), supported by the NJ, PCoA, Bayesian tree and morphological examination results. Lespedeza maritima and L. uekii were clustered to one clade on Bayesian tree. Given results, current L. maritima populations derive from post-LGM colonization away from southern refugia. The type L. uekii, which grows inland, is thought synonym of L. maritima. In addition, L. maritima is considered a distinct species, compared with related taxa.

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Assessing Genetic Diversity Cocoa (Theobroma cacaoL.) Collection Resistant to Cocoa Pod Borer Using Simple Sequence Repeat Markers

Pelita Perkebunan (a Coffee and Cocoa Research Journal) ◽

10.22302/iccri.jur.pelitaperkebunan.v29i1.186 ◽

2013 ◽

Vol 29 (1) ◽

Cited By ~ 1

Author(s):

Agung Wahyu Susilo ◽

Dapeng Zhang ◽

Lambert Motilal

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Perennial Crop ◽

High Genetic Diversity ◽

Genetic Groups ◽

Expected Heterozygosity ◽

Pod Borer ◽

Cocoa Farm ◽

Simple Sequence

Breeding for cocoa pod borer (CPB) resistance on cocoa was initiated by selecting the resistant genotypes through cocoa farm in the endemic area. For breeding purpose the collected genotypes should be assessed for their diversity in constructing appropriate mating design. This research has objective to assess genetic diversity of the exploratory collection using DNA fingerprinting. The tested clones were 25 exploratory collections compared to the references of seven international clones from International Cocoa Genebanks, Trinidad and12 national clones. DNA of the tested clones was sequenced using 15 SSR markers at Sustainable Perennial Crop Laboratory of Beltsville Agriculture Research Center.Data of fingerprinting were analyzed using GenAlEx program to perform number of alleles, observed heterozygosity (Ho), expected heterozygosity (He) and genetic distance. The tested clones performed high genetic diversity with the number of alleles was 98 (6.53 per locus) compared to the national clones andinternational clones were 95 (6.33 per locus) and 86 (5.73 per locus), respectively. The observed heterozygosity of the tested clones (Ho = 0.63) was higher thannational clones (Ho = 0.60) and international clones (Ho = 0.49) then supported by the expected heterozygosity (He) of the tested clones (He = 0.71) also highin equal value with international clones (He = 0.74). Cluster analysis grouped the tested clones to three main genetic groups, namely Trinitario, Forastero and unidentified group. The CPB-resistant clones of ARDACIAR 10 and KW 397 were clustered in different group that indicate a far distance of their genetic background.Key words:Genetic diversity, cocoa, CPB resistance, simple sequence repeat marker.

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Genetic Diversity and Structure of Local Pear Cultivars from Mountainous Areas from Aragon (Northeastern Spain)

Agronomy ◽

10.3390/agronomy11091778 ◽

2021 ◽

Vol 11 (9) ◽

pp. 1778

Author(s):

Francisco Javier Bielsa ◽

Patricia Irisarri ◽

Pilar Errea ◽

Ana Pina

Keyword(s):

Genetic Diversity ◽

Genetic Relatedness ◽

Mountainous Areas ◽

Bayesian Procedure ◽

Breeding Programs ◽

Local Varieties ◽

Expected Heterozygosity ◽

Genetic Diversity And Structure ◽

Genetic Stratification ◽

Shed Light

The genetic diversity of pear local varieties prospected in mountainous areas from Northeastern Spain (Pyrenees and Iberian Cordillera) is not well known so far. In this study, an overall set of 252 accessions (178 prospected in mountainous areas from Aragon and a diverse set of 74 reference cultivars) was analyzed using 14 SSRs in order to estimate its genetic diversity and to identify the genetic structure and relationships among the pear germplasm studied. A total of 251 distinct alleles were successfully amplified with an average of 17.9 alleles per locus and with a wide genetic diversity (mean expected heterozygosity of 0.82). In total, 228 unique genotypes were identified and 210 genotypes were represented by a single accession indicating a situation of extreme vulnerability of these pear genetic resources held in the CITA collection. An amount of 32.9% of accessions were considered triploids displaying three alleles at least into two loci. Genetic analyses performed by a model-based Bayesian procedure, principal coordinate analysis and analysis of molecular variance supported the presence of a genetic stratification with the existence of four sub-groups among the accessions, with a highly significant differentiation (FST = 0.132; p < 0.001). These results shed light on the characterization and genetic relatedness between these local accessions and currently cultivated pear cultivars and highlight the importance to safeguarding this diversity that might be essential for new breeding programs.

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Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Animals ◽

10.3390/ani11041067 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1067

Author(s):

Emel Özkan Ünal ◽

Raziye Işık ◽

Ayşe Şen ◽

Elif Geyik Kuş ◽

Mehmet İhsan Soysal

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Water Buffalo ◽

Polymorphic Information Content ◽

Breeding Strategy ◽

Weinberg Equilibrium ◽

Expected Heterozygosity ◽

Genetic Diversity And Structure ◽

Hardy Weinberg Equilibrium ◽

The Mean

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy–Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy–Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.

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Genetic diversity and structure in natural populations of Cajui from Brazilian Cerrado

Bioscience Journal ◽

10.14393/bj-v37n0a2021-53974 ◽

2021 ◽

Vol 37 ◽

pp. e37080

Author(s):

Maria Fernanda Da Costa Gomes ◽

Artemisa Nazaré Costa Borges ◽

Giovana Sarah Sales Batista ◽

Gizele De Andrade Luz ◽

Maria Edileide Alencar Oliveira ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Small Animal ◽

Floral Biology ◽

Diversity Indices ◽

Conservation Strategies ◽

Brazilian Cerrado ◽

Genetic Groups ◽

Genetic Diversity And Structure ◽

High Gene

Cajui (Anacardium spp.) is a native fruit tree (small cashew) of the Brazilian Cerrado and possesses the potential for commercialization. However, cajui exploitation occurs exclusively through extractivism in the absence of conservation strategies. The lack of conservation strategies may lead to a decrease in genetic diversity of Anacardium. In this work, the genetic diversity and population structure of three natural populations in Sete Cidades National Park (PNSC; PI, Brazil) were assessed using ISSR analysis of 56 cajui accessions and two A. occidentale accessions (outgroup) from Pacajus (CE, Brazil). A total of 112 markers were obtained, 93 (83.04%) of which were polymorphic. The diversity indices of these populations indicated moderate levels of genetic diversity. According to AMOVA, 96.17% of the genetic variability lay within populations, with low genetic differentiation among populations (ΦST = 0.03828). Furthermore, STRUCTURE analysis indicated the existence of four connected genetic groups. The findings show that the individuals from the three collection sites did not represent different subpopulations, likely due to the high gene flow (Nm = 6.7) favored by the floral biology of Anacardium, pollinators and small-animal seed dispersers. This research identifies genetically divergent individuals (C-03, C-05, C-22, C-26, C-34 and C-39), which should be considered priority individuals for conservation and can inform conservation programs for Anacardium spp.

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AFLP analyses on genetic diversity and structure of Eupatorium adenophorum populations in China

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236208002076 ◽

2008 ◽

Vol 5 (1) ◽

pp. 33-41 ◽

Cited By ~ 3

Author(s):

Huang Wen-Kun ◽

Guo Jian-Ying ◽

Wan Fang-Hao ◽

Gao Bi-Da ◽

Xie Bing-Yan

Keyword(s):

Genetic Diversity ◽

Regional Differences ◽

Shannon Index ◽

Group Method ◽

Eupatorium Adenophorum ◽

Data Set ◽

Pair Group ◽

Expected Heterozygosity ◽

Crofton Weed ◽

Genetic Diversity And Structure

AbstractEupatorium adenophorum (crofton weed) is one of the most widespread invasive species in China. Its genetic diversity and population structure in China were analysed by amplified fragment length polymorphism (AFLP). Three primer pairs were selected for the analysis and 490 bands were produced from 62 E. adenophorum populations selected from five major geographic areas. A total of 328 of the bands showed polymorphism [percentage of polymorphic bands (PPB)=59.4%]. Diversity levels of populations were relatively high (mean expected heterozygosity=0.154, mean Shannon index=0.241). At the regional level, the AMOVA indicated that about 70.25% of variation in the data set was from genotypic variations within populations, whereas 8.04% of the variation was due to regional differences, and the remaining 21.71% to differences among populations within the provincial regions. Cluster analysis based on the unweighted pair-group method using the method of arithmetic averages (UPGMA) grouped the majority of E. adenophorum populations into four main clusters, which correspond to their geographic regions. It is concluded that E. adenophorum spread mainly by wind or water and its genetic diversity level in newly invaded areas was lower than that in formerly colonized areas.

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Diversity and Genetic Structure Inferred with Microsatellites in Natural Populations of Pseudotsuga menziesii (Mirb.) Franco (Pinaceae) in the Central Region of Mexico

Forests ◽

10.3390/f10020101 ◽

2019 ◽

Vol 10 (2) ◽

pp. 101 ◽

Cited By ~ 2

Author(s):

Paulina Montiel Castelán ◽

Moisés Cortés-Cruz ◽

Ma. Mendoza-Castillo ◽

Serafín Cruz-Izquierdo ◽

Javier López-Upton ◽

...

Keyword(s):

Genetic Diversity ◽

Pseudotsuga Menziesii ◽

Central Region ◽

Natural Populations ◽

The United States ◽

Effective Number ◽

Genetic Studies ◽

Genetic Groups ◽

Expected Heterozygosity ◽

Mexican Populations

The amount and structure of the genetic diversity in Mexican populations of Pseudotsuga menziesii (Mirb.) Franco, is almost unknown, since most genetic studies have been carried out on populations from Canada and the United States. Here, we applied a set of 12 microsatellite markers to 12 populations (234 trees) from the central region of Mexico in order to determine values of genetic diversity and differentiation. Seventy-three different alleles were identified: an average number of alleles per locus (Na) of 6.083, effective number of alleles (Ne) of 2.039, observed heterozygosity (Ho) of 0.229, and expected heterozygosity (Ht) of 0.417. Genetic differentiation was high: the coefficient of differentiation (θ) was 0.270, while the coefficient of structure (Φst) was 0.278. Bayesian analysis identified two genetic groups in central Mexico. The PCoA and the dendrogram were in concordance with the two genetic groups. The results of the analysis of molecular variance (AMOVA) indicate that genetic variation exists mainly within populations (72.149%). Therefore, conservation efforts should focus on as many individuals within populations as possible, to maintain this variation.

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